From b9a8c8fca4ab3a2c8436265981b240a3f3f431df Mon Sep 17 00:00:00 2001 From: April Shen Date: Wed, 28 Jun 2023 14:52:31 +0100 Subject: [PATCH 01/13] add counts --- opentargets_pharmgkb/counts.py | 20 ++++++++++++++++++++ opentargets_pharmgkb/evidence_generation.py | 19 ++++++++++++++++--- 2 files changed, 36 insertions(+), 3 deletions(-) create mode 100644 opentargets_pharmgkb/counts.py diff --git a/opentargets_pharmgkb/counts.py b/opentargets_pharmgkb/counts.py new file mode 100644 index 0000000..7f61938 --- /dev/null +++ b/opentargets_pharmgkb/counts.py @@ -0,0 +1,20 @@ +class ClinicalAnnotationCounts: + """Simple class to hold counts for generating clinical annotation evidence.""" + + def __init__(self): + # Input counts (before exploding by allele, etc.) + self.clinical_annotations = 0 + self.with_rs = 0 + # Output counts (after exploding) + self.evidence_strings = 0 + self.with_chebi = 0 + self.with_efo = 0 + + def report(self): + report_str = f'\nTotal clinical annotations: {self.clinical_annotations}\n' + report_str += f'\tWith RS: {self.with_rs}\n' + report_str += f'Total evidence strings: {self.evidence_strings}\n' + report_str += f'\tWith CHEBI: {self.with_chebi}\n' + report_str += f'\tWith EFO phenotype: {self.with_efo}\n' + print(report_str) + return report_str diff --git a/opentargets_pharmgkb/evidence_generation.py b/opentargets_pharmgkb/evidence_generation.py index d169854..2b6a5e2 100644 --- a/opentargets_pharmgkb/evidence_generation.py +++ b/opentargets_pharmgkb/evidence_generation.py @@ -6,6 +6,7 @@ from cmat.consequence_prediction.common.biomart import query_biomart from cmat.consequence_prediction.snp_indel_variants.pipeline import process_variants +from opentargets_pharmgkb.counts import ClinicalAnnotationCounts from opentargets_pharmgkb.ontology_apis import get_chebi_iri, get_efo_iri from opentargets_pharmgkb.pandas_utils import none_to_nan, explode_column from opentargets_pharmgkb.variant_coordinates import get_coordinates_for_clinical_annotation @@ -19,11 +20,17 @@ def pipeline(clinical_annot_path, clinical_alleles_path, clinical_evidence_path, clinical_evidence_table = read_tsv_to_df(clinical_evidence_path) drugs_table = read_tsv_to_df(drugs_path) - merged_table = pd.merge(clinical_annot_table, clinical_alleles_table, on=ID_COL_NAME, how='left') # Restrict to variants with rsIDs - rs_only_table = merged_table[merged_table['Variant/Haplotypes'].str.contains('rs')] + rs_only_table = clinical_annot_table[clinical_annot_table['Variant/Haplotypes'].str.contains('rs')] - coordinates_table = get_vcf_coordinates(rs_only_table) + # Gather input counts + counts = ClinicalAnnotationCounts() + counts.clinical_annotations = len(clinical_annot_table) + counts.with_rs = len(rs_only_table) + + # Main processing + merged_with_alleles_table = pd.merge(rs_only_table, clinical_alleles_table, on=ID_COL_NAME, how='left') + coordinates_table = get_vcf_coordinates(merged_with_alleles_table) consequences_table = get_functional_consequences(coordinates_table) mapped_genes = explode_and_map_genes(consequences_table) mapped_drugs = explode_and_map_drugs(mapped_genes, drugs_table) @@ -34,6 +41,12 @@ def pipeline(clinical_annot_path, clinical_alleles_path, clinical_evidence_path, evidence_table = pd.merge(mapped_phenotypes, pmid_evidence.groupby(by=ID_COL_NAME).aggregate( publications=('PMID', list)), on=ID_COL_NAME) + # Gather output counts + counts.evidence_strings = len(evidence_table) + counts.with_chebi = evidence_table['chebi'].count() + counts.with_efo = evidence_table['efo'].count() + counts.report() + # Generate evidence evidence = [generate_clinical_annotation_evidence(created_date, row) for _, row in evidence_table.iterrows()] with open(output_path, 'w+') as output: From 47e67b279700b0501adfaa903567e7d04121b68a Mon Sep 17 00:00:00 2001 From: April Shen Date: Thu, 29 Jun 2023 16:37:47 +0100 Subject: [PATCH 02/13] add counts for genes and consequences --- opentargets_pharmgkb/counts.py | 8 ++++++++ opentargets_pharmgkb/evidence_generation.py | 9 +++++++++ 2 files changed, 17 insertions(+) diff --git a/opentargets_pharmgkb/counts.py b/opentargets_pharmgkb/counts.py index 7f61938..5867aa4 100644 --- a/opentargets_pharmgkb/counts.py +++ b/opentargets_pharmgkb/counts.py @@ -9,6 +9,10 @@ def __init__(self): self.evidence_strings = 0 self.with_chebi = 0 self.with_efo = 0 + self.with_consequence = 0 + self.with_pgkb_gene = 0 + self.with_vep_gene = 0 + self.pgkb_vep_gene_diff = 0 def report(self): report_str = f'\nTotal clinical annotations: {self.clinical_annotations}\n' @@ -16,5 +20,9 @@ def report(self): report_str += f'Total evidence strings: {self.evidence_strings}\n' report_str += f'\tWith CHEBI: {self.with_chebi}\n' report_str += f'\tWith EFO phenotype: {self.with_efo}\n' + report_str += f'\tWith functional consequence: {self.with_consequence}\n' + report_str += f'\tWith PGKB gene: {self.with_pgkb_gene}\n' + report_str += f'\tWith VEP gene: {self.with_vep_gene}\n' + report_str += f'\t\tPGKB gene != VEP gene: {self.pgkb_vep_gene_diff}\n' print(report_str) return report_str diff --git a/opentargets_pharmgkb/evidence_generation.py b/opentargets_pharmgkb/evidence_generation.py index 2b6a5e2..2a4b96e 100644 --- a/opentargets_pharmgkb/evidence_generation.py +++ b/opentargets_pharmgkb/evidence_generation.py @@ -45,6 +45,13 @@ def pipeline(clinical_annot_path, clinical_alleles_path, clinical_evidence_path, counts.evidence_strings = len(evidence_table) counts.with_chebi = evidence_table['chebi'].count() counts.with_efo = evidence_table['efo'].count() + counts.with_consequence = evidence_table['consequence_term'].count() + counts.with_pgkb_gene = evidence_table['gene_from_pgkb'].count() + counts.with_vep_gene = evidence_table['overlapping_gene'].count() + counts.pgkb_vep_gene_diff = len(evidence_table[ + evidence_table['gene_from_pgkb'].notna() & evidence_table['overlapping_gene'].notna() & + (evidence_table['gene_from_pgkb'] != evidence_table['overlapping_gene']) + ]) counts.report() # Generate evidence @@ -98,6 +105,8 @@ def get_functional_consequences(df): for batch in all_consequences for variant_id, gene_id, gene_symbol, consequence_term in batch ]) + # TODO does this explode by gene/conseq correctly? + # How do we match with the appropriate PGKB gene if there are multiple? return pd.merge(df, mapped_consequences, on='vcf_coords', how='left') From e83124cb4a59afe5d632a8da4187df64b4808eed Mon Sep 17 00:00:00 2001 From: April Shen Date: Wed, 5 Jul 2023 09:26:28 +0100 Subject: [PATCH 03/13] fix bugs and add tests --- opentargets_pharmgkb/evidence_generation.py | 6 +-- tests/resources/expected_output.json | 48 ++++++++++----------- tests/test_evidence_generation.py | 22 ++++++++++ 3 files changed, 49 insertions(+), 27 deletions(-) diff --git a/opentargets_pharmgkb/evidence_generation.py b/opentargets_pharmgkb/evidence_generation.py index 2a4b96e..3586ec0 100644 --- a/opentargets_pharmgkb/evidence_generation.py +++ b/opentargets_pharmgkb/evidence_generation.py @@ -105,8 +105,6 @@ def get_functional_consequences(df): for batch in all_consequences for variant_id, gene_id, gene_symbol, consequence_term in batch ]) - # TODO does this explode by gene/conseq correctly? - # How do we match with the appropriate PGKB gene if there are multiple? return pd.merge(df, mapped_consequences, on='vcf_coords', how='left') @@ -175,7 +173,9 @@ def explode_and_map_drugs(df, drugs_table): def chebi_id_to_iri(id_): - return f'http://purl.obolibrary.org/obo/CHEBI_{id_}' + if pd.notna(id_): + return f'http://purl.obolibrary.org/obo/CHEBI_{id_}' + return None def explode_and_map_phenotypes(df): diff --git a/tests/resources/expected_output.json b/tests/resources/expected_output.json index 9c31e8e..54488b8 100644 --- a/tests/resources/expected_output.json +++ b/tests/resources/expected_output.json @@ -16,18 +16,18 @@ {"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "targetFromSourceId": "ENSG00000272395", "variantFunctionalConsequenceId": "upstream_gene_variant", "variantOverlappingGeneId": "ENSG00000197110", "genotype": "CC", "genotypeAnnotationText": "Patients with the rs12979860 CC genotype and hepatitis C infection may have increased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CT or TT genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugText": "boceprevir", "drugId": "http://purl.obolibrary.org/obo/CHEBI_68621", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} {"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "targetFromSourceId": "ENSG00000272395", "variantFunctionalConsequenceId": "upstream_gene_variant", "variantOverlappingGeneId": "ENSG00000197110", "genotype": "CT", "genotypeAnnotationText": "Patients with the rs12979860 CT genotype and hepatitis C infection may have decreased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CC genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugText": "boceprevir", "drugId": "http://purl.obolibrary.org/obo/CHEBI_68621", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} {"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "targetFromSourceId": "ENSG00000272395", "variantFunctionalConsequenceId": "upstream_gene_variant", "variantOverlappingGeneId": "ENSG00000197110", "genotype": "TT", "genotypeAnnotationText": "Patients with the rs12979860 TT genotype and hepatitis C infection may have decreased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CC genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugText": "boceprevir", "drugId": "http://purl.obolibrary.org/obo/CHEBI_68621", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "targetFromSourceId": "ENSG00000197110", "variantFunctionalConsequenceId": "upstream_gene_variant", "variantOverlappingGeneId": "ENSG00000197110", "genotype": "CC", "genotypeAnnotationText": "Patients with the rs12979860 CC genotype and hepatitis C infection may have increased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CT or TT genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugText": "peginterferon alfa-2a", "drugId": "http://purl.obolibrary.org/obo/CHEBI_nan", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "targetFromSourceId": "ENSG00000197110", "variantFunctionalConsequenceId": "upstream_gene_variant", "variantOverlappingGeneId": "ENSG00000197110", "genotype": "CT", "genotypeAnnotationText": "Patients with the rs12979860 CT genotype and hepatitis C infection may have decreased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CC genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugText": "peginterferon alfa-2a", "drugId": "http://purl.obolibrary.org/obo/CHEBI_nan", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "targetFromSourceId": "ENSG00000197110", "variantFunctionalConsequenceId": "upstream_gene_variant", "variantOverlappingGeneId": "ENSG00000197110", "genotype": "TT", "genotypeAnnotationText": "Patients with the rs12979860 TT genotype and hepatitis C infection may have decreased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CC genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugText": "peginterferon alfa-2a", "drugId": "http://purl.obolibrary.org/obo/CHEBI_nan", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "targetFromSourceId": "ENSG00000272395", "variantFunctionalConsequenceId": "upstream_gene_variant", "variantOverlappingGeneId": "ENSG00000197110", "genotype": "CC", "genotypeAnnotationText": "Patients with the rs12979860 CC genotype and hepatitis C infection may have increased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CT or TT genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugText": "peginterferon alfa-2a", "drugId": "http://purl.obolibrary.org/obo/CHEBI_nan", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "targetFromSourceId": "ENSG00000272395", "variantFunctionalConsequenceId": "upstream_gene_variant", "variantOverlappingGeneId": "ENSG00000197110", "genotype": "CT", "genotypeAnnotationText": "Patients with the rs12979860 CT genotype and hepatitis C infection may have decreased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CC genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugText": "peginterferon alfa-2a", "drugId": "http://purl.obolibrary.org/obo/CHEBI_nan", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "targetFromSourceId": "ENSG00000272395", "variantFunctionalConsequenceId": "upstream_gene_variant", "variantOverlappingGeneId": "ENSG00000197110", "genotype": "TT", "genotypeAnnotationText": "Patients with the rs12979860 TT genotype and hepatitis C infection may have decreased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CC genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugText": "peginterferon alfa-2a", "drugId": "http://purl.obolibrary.org/obo/CHEBI_nan", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "targetFromSourceId": "ENSG00000197110", "variantFunctionalConsequenceId": "upstream_gene_variant", "variantOverlappingGeneId": "ENSG00000197110", "genotype": "CC", "genotypeAnnotationText": "Patients with the rs12979860 CC genotype and hepatitis C infection may have increased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CT or TT genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugText": "peginterferon alfa-2b", "drugId": "http://purl.obolibrary.org/obo/CHEBI_nan", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "targetFromSourceId": "ENSG00000197110", "variantFunctionalConsequenceId": "upstream_gene_variant", "variantOverlappingGeneId": "ENSG00000197110", "genotype": "CT", "genotypeAnnotationText": "Patients with the rs12979860 CT genotype and hepatitis C infection may have decreased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CC genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugText": "peginterferon alfa-2b", "drugId": "http://purl.obolibrary.org/obo/CHEBI_nan", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "targetFromSourceId": "ENSG00000197110", "variantFunctionalConsequenceId": "upstream_gene_variant", "variantOverlappingGeneId": "ENSG00000197110", "genotype": "TT", "genotypeAnnotationText": "Patients with the rs12979860 TT genotype and hepatitis C infection may have decreased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CC genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugText": "peginterferon alfa-2b", "drugId": "http://purl.obolibrary.org/obo/CHEBI_nan", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "targetFromSourceId": "ENSG00000272395", "variantFunctionalConsequenceId": "upstream_gene_variant", "variantOverlappingGeneId": "ENSG00000197110", "genotype": "CC", "genotypeAnnotationText": "Patients with the rs12979860 CC genotype and hepatitis C infection may have increased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CT or TT genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugText": "peginterferon alfa-2b", "drugId": "http://purl.obolibrary.org/obo/CHEBI_nan", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "targetFromSourceId": "ENSG00000272395", "variantFunctionalConsequenceId": "upstream_gene_variant", "variantOverlappingGeneId": "ENSG00000197110", "genotype": "CT", "genotypeAnnotationText": "Patients with the rs12979860 CT genotype and hepatitis C infection may have decreased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CC genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugText": "peginterferon alfa-2b", "drugId": "http://purl.obolibrary.org/obo/CHEBI_nan", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "targetFromSourceId": "ENSG00000272395", "variantFunctionalConsequenceId": "upstream_gene_variant", "variantOverlappingGeneId": "ENSG00000197110", "genotype": "TT", "genotypeAnnotationText": "Patients with the rs12979860 TT genotype and hepatitis C infection may have decreased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CC genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugText": "peginterferon alfa-2b", "drugId": "http://purl.obolibrary.org/obo/CHEBI_nan", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "targetFromSourceId": "ENSG00000197110", "variantFunctionalConsequenceId": "upstream_gene_variant", "variantOverlappingGeneId": "ENSG00000197110", "genotype": "CC", "genotypeAnnotationText": "Patients with the rs12979860 CC genotype and hepatitis C infection may have increased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CT or TT genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugText": "peginterferon alfa-2a", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "targetFromSourceId": "ENSG00000197110", "variantFunctionalConsequenceId": "upstream_gene_variant", "variantOverlappingGeneId": "ENSG00000197110", "genotype": "CT", "genotypeAnnotationText": "Patients with the rs12979860 CT genotype and hepatitis C infection may have decreased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CC genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugText": "peginterferon alfa-2a", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "targetFromSourceId": "ENSG00000197110", "variantFunctionalConsequenceId": "upstream_gene_variant", "variantOverlappingGeneId": "ENSG00000197110", "genotype": "TT", "genotypeAnnotationText": "Patients with the rs12979860 TT genotype and hepatitis C infection may have decreased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CC genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugText": "peginterferon alfa-2a", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "targetFromSourceId": "ENSG00000272395", "variantFunctionalConsequenceId": "upstream_gene_variant", "variantOverlappingGeneId": "ENSG00000197110", "genotype": "CC", "genotypeAnnotationText": "Patients with the rs12979860 CC genotype and hepatitis C infection may have increased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CT or TT genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugText": "peginterferon alfa-2a", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "targetFromSourceId": "ENSG00000272395", "variantFunctionalConsequenceId": "upstream_gene_variant", "variantOverlappingGeneId": "ENSG00000197110", "genotype": "CT", "genotypeAnnotationText": "Patients with the rs12979860 CT genotype and hepatitis C infection may have decreased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CC genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugText": "peginterferon alfa-2a", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "targetFromSourceId": "ENSG00000272395", "variantFunctionalConsequenceId": "upstream_gene_variant", "variantOverlappingGeneId": "ENSG00000197110", "genotype": "TT", "genotypeAnnotationText": "Patients with the rs12979860 TT genotype and hepatitis C infection may have decreased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CC genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugText": "peginterferon alfa-2a", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "targetFromSourceId": "ENSG00000197110", "variantFunctionalConsequenceId": "upstream_gene_variant", "variantOverlappingGeneId": "ENSG00000197110", "genotype": "CC", "genotypeAnnotationText": "Patients with the rs12979860 CC genotype and hepatitis C infection may have increased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CT or TT genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugText": "peginterferon alfa-2b", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "targetFromSourceId": "ENSG00000197110", "variantFunctionalConsequenceId": "upstream_gene_variant", "variantOverlappingGeneId": "ENSG00000197110", "genotype": "CT", "genotypeAnnotationText": "Patients with the rs12979860 CT genotype and hepatitis C infection may have decreased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CC genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugText": "peginterferon alfa-2b", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "targetFromSourceId": "ENSG00000197110", "variantFunctionalConsequenceId": "upstream_gene_variant", "variantOverlappingGeneId": "ENSG00000197110", "genotype": "TT", "genotypeAnnotationText": "Patients with the rs12979860 TT genotype and hepatitis C infection may have decreased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CC genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugText": "peginterferon alfa-2b", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "targetFromSourceId": "ENSG00000272395", "variantFunctionalConsequenceId": "upstream_gene_variant", "variantOverlappingGeneId": "ENSG00000197110", "genotype": "CC", "genotypeAnnotationText": "Patients with the rs12979860 CC genotype and hepatitis C infection may have increased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CT or TT genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugText": "peginterferon alfa-2b", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "targetFromSourceId": "ENSG00000272395", "variantFunctionalConsequenceId": "upstream_gene_variant", "variantOverlappingGeneId": "ENSG00000197110", "genotype": "CT", "genotypeAnnotationText": "Patients with the rs12979860 CT genotype and hepatitis C infection may have decreased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CC genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugText": "peginterferon alfa-2b", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "targetFromSourceId": "ENSG00000272395", "variantFunctionalConsequenceId": "upstream_gene_variant", "variantOverlappingGeneId": "ENSG00000197110", "genotype": "TT", "genotypeAnnotationText": "Patients with the rs12979860 TT genotype and hepatitis C infection may have decreased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CC genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugText": "peginterferon alfa-2b", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} {"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "targetFromSourceId": "ENSG00000197110", "variantFunctionalConsequenceId": "upstream_gene_variant", "variantOverlappingGeneId": "ENSG00000197110", "genotype": "CC", "genotypeAnnotationText": "Patients with the rs12979860 CC genotype and hepatitis C infection may have increased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CT or TT genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugText": "ribavirin", "drugId": "http://purl.obolibrary.org/obo/CHEBI_63580", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} {"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "targetFromSourceId": "ENSG00000197110", "variantFunctionalConsequenceId": "upstream_gene_variant", "variantOverlappingGeneId": "ENSG00000197110", "genotype": "CT", "genotypeAnnotationText": "Patients with the rs12979860 CT genotype and hepatitis C infection may have decreased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CC genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugText": "ribavirin", "drugId": "http://purl.obolibrary.org/obo/CHEBI_63580", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} {"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "targetFromSourceId": "ENSG00000197110", "variantFunctionalConsequenceId": "upstream_gene_variant", "variantOverlappingGeneId": "ENSG00000197110", "genotype": "TT", "genotypeAnnotationText": "Patients with the rs12979860 TT genotype and hepatitis C infection may have decreased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CC genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugText": "ribavirin", "drugId": "http://purl.obolibrary.org/obo/CHEBI_63580", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} @@ -106,21 +106,21 @@ {"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "targetFromSourceId": "ENSG00000176890", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2 or 2R/2R genotype may have an increased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 2R/3R or 3R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugText": "fluorouracil", "drugId": "http://purl.obolibrary.org/obo/CHEBI_46345", "pgxCategory": "Efficacy", "phenotypeText": "overall survival"} {"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "targetFromSourceId": "ENSG00000176890", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3 or 2R/3R genotype may have an increased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 3R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugText": "fluorouracil", "drugId": "http://purl.obolibrary.org/obo/CHEBI_46345", "pgxCategory": "Efficacy", "phenotypeText": "overall survival"} {"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "targetFromSourceId": "ENSG00000176890", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)3/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3 or 3R/3R genotype may have a decreased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 2R/2R or 2R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugText": "fluorouracil", "drugId": "http://purl.obolibrary.org/obo/CHEBI_46345", "pgxCategory": "Efficacy", "phenotypeText": "overall survival"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "targetFromSourceId": "ENSG00000176890", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2 or 2R/2R genotype may have an increased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 2R/3R or 3R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugText": "FOLFIRI", "drugId": "http://purl.obolibrary.org/obo/CHEBI_nan", "pgxCategory": "Efficacy", "phenotypeText": "overall survival"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "targetFromSourceId": "ENSG00000176890", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3 or 2R/3R genotype may have an increased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 3R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugText": "FOLFIRI", "drugId": "http://purl.obolibrary.org/obo/CHEBI_nan", "pgxCategory": "Efficacy", "phenotypeText": "overall survival"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "targetFromSourceId": "ENSG00000176890", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)3/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3 or 3R/3R genotype may have a decreased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 2R/2R or 2R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugText": "FOLFIRI", "drugId": "http://purl.obolibrary.org/obo/CHEBI_nan", "pgxCategory": "Efficacy", "phenotypeText": "overall survival"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "targetFromSourceId": "ENSG00000176890", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2 or 2R/2R genotype may have an increased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 2R/3R or 3R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugText": "FOLFOX", "drugId": "http://purl.obolibrary.org/obo/CHEBI_nan", "pgxCategory": "Efficacy", "phenotypeText": "overall survival"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "targetFromSourceId": "ENSG00000176890", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3 or 2R/3R genotype may have an increased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 3R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugText": "FOLFOX", "drugId": "http://purl.obolibrary.org/obo/CHEBI_nan", "pgxCategory": "Efficacy", "phenotypeText": "overall survival"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "targetFromSourceId": "ENSG00000176890", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)3/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3 or 3R/3R genotype may have a decreased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 2R/2R or 2R/3R genotype. 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However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugText": "FOLFIRI", "pgxCategory": "Efficacy", "phenotypeText": "overall survival"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "targetFromSourceId": "ENSG00000176890", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3 or 2R/3R genotype may have an increased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 3R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugText": "FOLFIRI", "pgxCategory": "Efficacy", "phenotypeText": "overall survival"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "targetFromSourceId": "ENSG00000176890", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)3/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3 or 3R/3R genotype may have a decreased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 2R/2R or 2R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugText": "FOLFIRI", "pgxCategory": "Efficacy", "phenotypeText": "overall survival"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "targetFromSourceId": "ENSG00000176890", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2 or 2R/2R genotype may have an increased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 2R/3R or 3R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugText": "FOLFOX", "pgxCategory": "Efficacy", "phenotypeText": "overall survival"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "targetFromSourceId": "ENSG00000176890", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3 or 2R/3R genotype may have an increased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 3R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugText": "FOLFOX", "pgxCategory": "Efficacy", "phenotypeText": "overall survival"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "targetFromSourceId": "ENSG00000176890", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)3/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3 or 3R/3R genotype may have a decreased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 2R/2R or 2R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugText": "FOLFOX", "pgxCategory": "Efficacy", "phenotypeText": "overall survival"} {"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "targetFromSourceId": "ENSG00000176890", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2 or 2R/2R genotype may have an increased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 2R/3R or 3R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugText": "fluorouracil", "drugId": "http://purl.obolibrary.org/obo/CHEBI_46345", "pgxCategory": "Efficacy", "phenotypeText": "progression-free survival"} {"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "targetFromSourceId": "ENSG00000176890", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3 or 2R/3R genotype may have an increased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 3R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugText": "fluorouracil", "drugId": "http://purl.obolibrary.org/obo/CHEBI_46345", "pgxCategory": "Efficacy", "phenotypeText": "progression-free survival"} {"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "targetFromSourceId": "ENSG00000176890", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)3/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3 or 3R/3R genotype may have a decreased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 2R/2R or 2R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugText": "fluorouracil", "drugId": "http://purl.obolibrary.org/obo/CHEBI_46345", "pgxCategory": "Efficacy", "phenotypeText": "progression-free survival"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "targetFromSourceId": "ENSG00000176890", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2 or 2R/2R genotype may have an increased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 2R/3R or 3R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugText": "FOLFIRI", "drugId": "http://purl.obolibrary.org/obo/CHEBI_nan", "pgxCategory": "Efficacy", "phenotypeText": "progression-free survival"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "targetFromSourceId": "ENSG00000176890", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3 or 2R/3R genotype may have an increased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 3R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugText": "FOLFIRI", "drugId": "http://purl.obolibrary.org/obo/CHEBI_nan", "pgxCategory": "Efficacy", "phenotypeText": "progression-free survival"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "targetFromSourceId": "ENSG00000176890", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)3/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3 or 3R/3R genotype may have a decreased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 2R/2R or 2R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugText": "FOLFIRI", "drugId": "http://purl.obolibrary.org/obo/CHEBI_nan", "pgxCategory": "Efficacy", "phenotypeText": "progression-free survival"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "targetFromSourceId": "ENSG00000176890", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2 or 2R/2R genotype may have an increased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 2R/3R or 3R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugText": "FOLFOX", "drugId": "http://purl.obolibrary.org/obo/CHEBI_nan", "pgxCategory": "Efficacy", "phenotypeText": "progression-free survival"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "targetFromSourceId": "ENSG00000176890", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3 or 2R/3R genotype may have an increased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 3R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugText": "FOLFOX", "drugId": "http://purl.obolibrary.org/obo/CHEBI_nan", "pgxCategory": "Efficacy", "phenotypeText": "progression-free survival"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "targetFromSourceId": "ENSG00000176890", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)3/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3 or 3R/3R genotype may have a decreased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 2R/2R or 2R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugText": "FOLFOX", "drugId": "http://purl.obolibrary.org/obo/CHEBI_nan", "pgxCategory": "Efficacy", "phenotypeText": "progression-free survival"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "targetFromSourceId": "ENSG00000176890", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2 or 2R/2R genotype may have an increased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 2R/3R or 3R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugText": "FOLFIRI", "pgxCategory": "Efficacy", "phenotypeText": "progression-free survival"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "targetFromSourceId": "ENSG00000176890", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3 or 2R/3R genotype may have an increased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 3R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugText": "FOLFIRI", "pgxCategory": "Efficacy", "phenotypeText": "progression-free survival"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "targetFromSourceId": "ENSG00000176890", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)3/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3 or 3R/3R genotype may have a decreased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 2R/2R or 2R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugText": "FOLFIRI", "pgxCategory": "Efficacy", "phenotypeText": "progression-free survival"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "targetFromSourceId": "ENSG00000176890", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2 or 2R/2R genotype may have an increased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 2R/3R or 3R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugText": "FOLFOX", "pgxCategory": "Efficacy", "phenotypeText": "progression-free survival"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "targetFromSourceId": "ENSG00000176890", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3 or 2R/3R genotype may have an increased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 3R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugText": "FOLFOX", "pgxCategory": "Efficacy", "phenotypeText": "progression-free survival"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "targetFromSourceId": "ENSG00000176890", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)3/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3 or 3R/3R genotype may have a decreased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 2R/2R or 2R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugText": "FOLFOX", "pgxCategory": "Efficacy", "phenotypeText": "progression-free survival"} {"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1444668808", "evidenceLevel": "3", "literature": ["11593098", "11910301"], "variantId": "17_63488530_ATACAGTCACTTTT_ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCATACAGTCACTTTT", "variantRsId": "rs1799752", "targetFromSourceId": "ENSG00000159640", "variantFunctionalConsequenceId": "intron_variant", "variantOverlappingGeneId": "ENSG00000159640", "genotype": "ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC", "genotypeAnnotationText": "Hypertensive patients with the rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC genotype may have an increased response to irbesartan as compared to patients with the ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/del or del/del genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to irbesartan.", "drugText": "irbesartan", "drugId": "http://purl.obolibrary.org/obo/CHEBI_5959", "pgxCategory": "Efficacy", "phenotypeText": "Hypertension", "phenotypeFromSourceId": "http://www.ebi.ac.uk/efo/EFO_0000537"} {"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1444668808", "evidenceLevel": "3", "literature": ["11593098", "11910301"], "variantId": "17_63488530_ATACAGTCACTTTT_ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCATACAGTCACTTTT", "variantRsId": "rs1799752", "targetFromSourceId": "ENSG00000159640", "variantFunctionalConsequenceId": "intron_variant", "variantOverlappingGeneId": "ENSG00000159640", "genotype": "ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/del", "genotypeAnnotationText": "Hypertensive patients with the rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/del genotype may have a decreased response to irbesartan as compared to patients with the ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to irbesartan.", "drugText": "irbesartan", "drugId": "http://purl.obolibrary.org/obo/CHEBI_5959", "pgxCategory": "Efficacy", "phenotypeText": "Hypertension", "phenotypeFromSourceId": "http://www.ebi.ac.uk/efo/EFO_0000537"} {"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1444668808", "evidenceLevel": "3", "literature": ["11593098", "11910301"], "variantId": "17_63488530_ATACAGTCACTTTT_ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCATACAGTCACTTTT", "variantRsId": "rs1799752", "targetFromSourceId": "ENSG00000159640", "variantFunctionalConsequenceId": "intron_variant", "variantOverlappingGeneId": "ENSG00000159640", "genotype": "del/del", "genotypeAnnotationText": "Hypertensive patients with the rs1799752 del/del genotype may have a decreased response to irbesartan as compared to patients with the ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to irbesartan.", "drugText": "irbesartan", "drugId": "http://purl.obolibrary.org/obo/CHEBI_5959", "pgxCategory": "Efficacy", "phenotypeText": "Hypertension", "phenotypeFromSourceId": "http://www.ebi.ac.uk/efo/EFO_0000537"} diff --git a/tests/test_evidence_generation.py b/tests/test_evidence_generation.py index 35685a6..4e2e032 100644 --- a/tests/test_evidence_generation.py +++ b/tests/test_evidence_generation.py @@ -1,10 +1,32 @@ import os +import pandas as pd + from opentargets_pharmgkb import evidence_generation +from opentargets_pharmgkb.evidence_generation import get_functional_consequences, explode_and_map_drugs, read_tsv_to_df resources_dir = os.path.join(os.path.dirname(__file__), 'resources') +def test_get_functional_consequences(): + df = pd.DataFrame(columns=['vcf_coords'], data=[['10_100980986_C_T']]) + annotated_df = get_functional_consequences(df) + assert annotated_df.shape == (2, 3) + assert 'ENSG00000095539' in annotated_df['overlapping_gene'].values + assert 'intron_variant' in annotated_df['consequence_term'].values + + +def test_explode_and_map_drugs(): + drugs_table = read_tsv_to_df(os.path.join(resources_dir, 'drugs.tsv')) + df = pd.DataFrame(columns=['Drug(s)'], data=[['tamoxifen; fluorouracil'], ['peginterferon alfa-2a']]) + annotated_df = explode_and_map_drugs(df, drugs_table) + assert annotated_df.shape[0] == 3 + annotated_df = annotated_df.set_index('split_drug') + assert annotated_df.loc['tamoxifen']['chebi'] == 'http://purl.obolibrary.org/obo/CHEBI_41774' + assert annotated_df.loc['fluorouracil']['chebi'] == 'http://purl.obolibrary.org/obo/CHEBI_46345' + assert annotated_df.loc['peginterferon alfa-2a']['chebi'] is None + + def test_pipeline(): output_path = os.path.join(resources_dir, 'test_output.json') expected_path = os.path.join(resources_dir, 'expected_output.json') From c27f00fcb7f322f760ad9520b29220a4936dba84 Mon Sep 17 00:00:00 2001 From: April Shen Date: Wed, 5 Jul 2023 15:04:49 +0100 Subject: [PATCH 04/13] remove PGKB gene from main processing, add counts for gene comparisons --- opentargets_pharmgkb/counts.py | 6 +- opentargets_pharmgkb/evidence_generation.py | 33 ++-- tests/resources/expected_output.json | 204 +++++++------------- 3 files changed, 100 insertions(+), 143 deletions(-) diff --git a/opentargets_pharmgkb/counts.py b/opentargets_pharmgkb/counts.py index 5867aa4..ad5d331 100644 --- a/opentargets_pharmgkb/counts.py +++ b/opentargets_pharmgkb/counts.py @@ -10,7 +10,7 @@ def __init__(self): self.with_chebi = 0 self.with_efo = 0 self.with_consequence = 0 - self.with_pgkb_gene = 0 + # self.with_pgkb_gene = 0 self.with_vep_gene = 0 self.pgkb_vep_gene_diff = 0 @@ -21,8 +21,8 @@ def report(self): report_str += f'\tWith CHEBI: {self.with_chebi}\n' report_str += f'\tWith EFO phenotype: {self.with_efo}\n' report_str += f'\tWith functional consequence: {self.with_consequence}\n' - report_str += f'\tWith PGKB gene: {self.with_pgkb_gene}\n' + # report_str += f'\tWith PGKB gene: {self.with_pgkb_gene}\n' report_str += f'\tWith VEP gene: {self.with_vep_gene}\n' - report_str += f'\t\tPGKB gene != VEP gene: {self.pgkb_vep_gene_diff}\n' + report_str += f'Annotations where PGKB genes != VEP genes: {self.pgkb_vep_gene_diff}\n' print(report_str) return report_str diff --git a/opentargets_pharmgkb/evidence_generation.py b/opentargets_pharmgkb/evidence_generation.py index 3586ec0..302db12 100644 --- a/opentargets_pharmgkb/evidence_generation.py +++ b/opentargets_pharmgkb/evidence_generation.py @@ -32,8 +32,8 @@ def pipeline(clinical_annot_path, clinical_alleles_path, clinical_evidence_path, merged_with_alleles_table = pd.merge(rs_only_table, clinical_alleles_table, on=ID_COL_NAME, how='left') coordinates_table = get_vcf_coordinates(merged_with_alleles_table) consequences_table = get_functional_consequences(coordinates_table) - mapped_genes = explode_and_map_genes(consequences_table) - mapped_drugs = explode_and_map_drugs(mapped_genes, drugs_table) + # mapped_genes = explode_and_map_genes(consequences_table) + mapped_drugs = explode_and_map_drugs(consequences_table, drugs_table) mapped_phenotypes = explode_and_map_phenotypes(mapped_drugs) # Add clinical evidence with PMIDs @@ -46,19 +46,18 @@ def pipeline(clinical_annot_path, clinical_alleles_path, clinical_evidence_path, counts.with_chebi = evidence_table['chebi'].count() counts.with_efo = evidence_table['efo'].count() counts.with_consequence = evidence_table['consequence_term'].count() - counts.with_pgkb_gene = evidence_table['gene_from_pgkb'].count() + # counts.with_pgkb_gene = evidence_table['gene_from_pgkb'].count() counts.with_vep_gene = evidence_table['overlapping_gene'].count() - counts.pgkb_vep_gene_diff = len(evidence_table[ - evidence_table['gene_from_pgkb'].notna() & evidence_table['overlapping_gene'].notna() & - (evidence_table['gene_from_pgkb'] != evidence_table['overlapping_gene']) - ]) - counts.report() # Generate evidence evidence = [generate_clinical_annotation_evidence(created_date, row) for _, row in evidence_table.iterrows()] with open(output_path, 'w+') as output: output.write('\n'.join(json.dumps(ev) for ev in evidence)) + # Final count report + gene_comparison_counts(evidence_table, counts) + counts.report() + def read_tsv_to_df(path): return pd.read_csv(path, sep='\t', dtype=str) @@ -215,16 +214,16 @@ def generate_clinical_annotation_evidence(created_date, row): # VARIANT ATTRIBUTES 'variantId': row['vcf_coords'], 'variantRsId': row['Variant/Haplotypes'], - 'targetFromSourceId': row['gene_from_pgkb'], + # 'originalSourceGeneId': row['gene_from_pgkb'], 'variantFunctionalConsequenceId': row['consequence_term'], - 'variantOverlappingGeneId': row['overlapping_gene'], + 'targetFromSourceId': row['overlapping_gene'], # GENOTYPE ATTRIBUTES 'genotype': row['Genotype/Allele'], 'genotypeAnnotationText': row['Annotation Text'], # PHENOTYPE ATTRIBUTES - 'drugText': row['split_drug'], + 'drugFromSource': row['split_drug'], 'drugId': row['chebi'], 'pgxCategory': row['Phenotype Category'], 'phenotypeText': row['split_phenotype'], @@ -234,3 +233,15 @@ def generate_clinical_annotation_evidence(created_date, row): evidence_string = {key: value for key, value in evidence_string.items() if value and (isinstance(value, list) or pd.notna(value))} return evidence_string + + +def gene_comparison_counts(df, counts): + # Map PGKB genes + mapped_genes = explode_and_map_genes(df) + # Re-group by ID column + genes_table = mapped_genes.groupby(by=ID_COL_NAME).aggregate( + all_pgkb_genes=('gene_from_pgkb', set), + all_vep_genes=('overlapping_gene', set) + ) + # Compare sets of genes + counts.pgkb_vep_gene_diff = len(genes_table[genes_table['all_pgkb_genes'] != genes_table['all_vep_genes']]) diff --git a/tests/resources/expected_output.json b/tests/resources/expected_output.json index 54488b8..0b5b5b5 100644 --- a/tests/resources/expected_output.json +++ b/tests/resources/expected_output.json @@ -1,129 +1,75 @@ -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1450375701", "evidenceLevel": "3", "literature": ["30924126"], "variantRsId": "rs4659982", "targetFromSourceId": "ENSG00000180875", "genotype": "AA", "genotypeAnnotationText": "Patients with the AA genotype may have a decreased response to allopurinol as compared to patients with the AC, CC or CT genotypes. Other genetic and clinical factors may also affect a patient's response to allopurinol.", "drugText": "allopurinol", "drugId": "http://purl.obolibrary.org/obo/CHEBI_40279", "pgxCategory": "Efficacy"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1450375701", "evidenceLevel": "3", "literature": ["30924126"], "variantRsId": "rs4659982", "targetFromSourceId": "ENSG00000180875", "genotype": "AC", "genotypeAnnotationText": "Patients with the AC genotype may have an increased response to allopurinol as compared to patients with the AA, AT or TT genotypes. Other genetic and clinical factors may also affect a patient's response to allopurinol.", "drugText": "allopurinol", "drugId": "http://purl.obolibrary.org/obo/CHEBI_40279", "pgxCategory": "Efficacy"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1450375701", "evidenceLevel": "3", "literature": ["30924126"], "variantRsId": "rs4659982", "targetFromSourceId": "ENSG00000180875", "genotype": "AT", "genotypeAnnotationText": "Patients with the AT genotype may have a decreased response to allopurinol as compared to patients with the AC, CC or CT genotypes. Other genetic and clinical factors may also affect a patient's response to allopurinol.", "drugText": "allopurinol", "drugId": "http://purl.obolibrary.org/obo/CHEBI_40279", "pgxCategory": "Efficacy"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1450375701", "evidenceLevel": "3", "literature": ["30924126"], "variantRsId": "rs4659982", "targetFromSourceId": "ENSG00000180875", "genotype": "CC", "genotypeAnnotationText": "Patients with the CC genotype may have an increased response to allopurinol as compared to patients with the AA, AT or TT genotypes. Other genetic and clinical factors may also affect a patient's response to allopurinol.", "drugText": "allopurinol", "drugId": "http://purl.obolibrary.org/obo/CHEBI_40279", "pgxCategory": "Efficacy"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1450375701", "evidenceLevel": "3", "literature": ["30924126"], "variantRsId": "rs4659982", "targetFromSourceId": "ENSG00000180875", "genotype": "CT", "genotypeAnnotationText": "Patients with the CT genotype may have an increased response to allopurinol as compared to patients with the AA, AT or TT genotypes. Other genetic and clinical factors may also affect a patient's response to allopurinol.", "drugText": "allopurinol", "drugId": "http://purl.obolibrary.org/obo/CHEBI_40279", "pgxCategory": "Efficacy"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1450375701", "evidenceLevel": "3", "literature": ["30924126"], "variantRsId": "rs4659982", "targetFromSourceId": "ENSG00000180875", "genotype": "TT", "genotypeAnnotationText": "Patients with the TT genotype may have a decreased response to allopurinol as compared to patients with the AC, CC or CT genotypes. Other genetic and clinical factors may also affect a patient's response to allopurinol.", "drugText": "allopurinol", "drugId": "http://purl.obolibrary.org/obo/CHEBI_40279", "pgxCategory": "Efficacy"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1448603303", "evidenceLevel": "3", "literature": ["25558980"], "variantId": "1_46399999_A_G", "variantRsId": "rs3766246", "targetFromSourceId": "ENSG00000117480", "variantFunctionalConsequenceId": "intron_variant", "variantOverlappingGeneId": "ENSG00000117480", "genotype": "AA", "genotypeAnnotationText": "Children with the AA genotype who are undergoing a tonsillectomy may have an increased risk for post-operative nausea and vomiting (PONV) when treated with morphine as compared to patients with the GG genotype. Other genetic and clinical factors may also influence risk of PONV.", "drugText": "morphine", "drugId": "http://purl.obolibrary.org/obo/CHEBI_17303", "pgxCategory": "Toxicity"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1448603303", "evidenceLevel": "3", "literature": ["25558980"], "variantId": "1_46399999_A_G", "variantRsId": "rs3766246", "targetFromSourceId": "ENSG00000117480", "variantFunctionalConsequenceId": "intron_variant", "variantOverlappingGeneId": "ENSG00000117480", "genotype": "AG", "genotypeAnnotationText": "Children with the AG genotype who are undergoing a tonsillectomy may have an increased risk for post-operative nausea and vomiting (PONV) when treated with morphine as compared to patients with the GG genotype. Other genetic and clinical factors may also influence risk of PONV.", "drugText": "morphine", "drugId": "http://purl.obolibrary.org/obo/CHEBI_17303", "pgxCategory": "Toxicity"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1448603303", "evidenceLevel": "3", "literature": ["25558980"], "variantId": "1_46399999_A_G", "variantRsId": "rs3766246", "targetFromSourceId": "ENSG00000117480", "variantFunctionalConsequenceId": "intron_variant", "variantOverlappingGeneId": "ENSG00000117480", "genotype": "GG", "genotypeAnnotationText": "Children with the GG genotype who are undergoing a tonsillectomy may have a decreased risk for post-operative nausea and vomiting (PONV) when treated with morphine as compared to patients with the AA or AG genotype. Other genetic and clinical factors may also influence risk of PONV.", "drugText": "morphine", "drugId": "http://purl.obolibrary.org/obo/CHEBI_17303", "pgxCategory": "Toxicity"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1043880328", "evidenceLevel": "3", "literature": ["21435719"], "variantRsId": "rs4630", "targetFromSourceId": "ENSG00000277656", "genotype": "AA", "genotypeAnnotationText": "Patients with the AA genotype may have increased likelihood of Neurotoxicity when treated with thalidomide in people with Multiple Myeloma as compared to patients with the AG genotype. Other clinical or genetic factors may also influence a patient's response to thalidomide.", "drugText": "thalidomide", "drugId": "http://purl.obolibrary.org/obo/CHEBI_9513", "pgxCategory": "Toxicity", "phenotypeText": "Multiple Myeloma", "phenotypeFromSourceId": "http://www.ebi.ac.uk/efo/EFO_0001378"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1043880328", "evidenceLevel": "3", "literature": ["21435719"], "variantRsId": "rs4630", "targetFromSourceId": "ENSG00000277656", "genotype": "AG", "genotypeAnnotationText": "Patients with the AG genotype may have decreased likelihood of Neurotoxicity when treated with thalidomide in people with Multiple Myeloma as compared to patients with the AA genotype. Other clinical or genetic factors may also influence a patient's response to thalidomide.", "drugText": "thalidomide", "drugId": "http://purl.obolibrary.org/obo/CHEBI_9513", "pgxCategory": "Toxicity", "phenotypeText": "Multiple Myeloma", "phenotypeFromSourceId": "http://www.ebi.ac.uk/efo/EFO_0001378"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1043880328", "evidenceLevel": "3", "literature": ["21435719"], "variantRsId": "rs4630", "targetFromSourceId": "ENSG00000277656", "genotype": "GG", "genotypeAnnotationText": "Patients with the GG genotype may have decreased likelihood of Neurotoxicity when treated with thalidomide in people with Multiple Myeloma as compared to patients with the AA genotype. Other clinical or genetic factors may also influence a patient's response to thalidomide.", "drugText": "thalidomide", "drugId": "http://purl.obolibrary.org/obo/CHEBI_9513", "pgxCategory": "Toxicity", "phenotypeText": "Multiple Myeloma", "phenotypeFromSourceId": "http://www.ebi.ac.uk/efo/EFO_0001378"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "targetFromSourceId": "ENSG00000197110", "variantFunctionalConsequenceId": "upstream_gene_variant", "variantOverlappingGeneId": "ENSG00000197110", "genotype": "CC", "genotypeAnnotationText": "Patients with the rs12979860 CC genotype and hepatitis C infection may have increased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CT or TT genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugText": "boceprevir", "drugId": "http://purl.obolibrary.org/obo/CHEBI_68621", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "targetFromSourceId": "ENSG00000197110", "variantFunctionalConsequenceId": "upstream_gene_variant", "variantOverlappingGeneId": "ENSG00000197110", "genotype": "CT", "genotypeAnnotationText": "Patients with the rs12979860 CT genotype and hepatitis C infection may have decreased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CC genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugText": "boceprevir", "drugId": "http://purl.obolibrary.org/obo/CHEBI_68621", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "targetFromSourceId": "ENSG00000197110", "variantFunctionalConsequenceId": "upstream_gene_variant", "variantOverlappingGeneId": "ENSG00000197110", "genotype": "TT", "genotypeAnnotationText": "Patients with the rs12979860 TT genotype and hepatitis C infection may have decreased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CC genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugText": "boceprevir", "drugId": "http://purl.obolibrary.org/obo/CHEBI_68621", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "targetFromSourceId": "ENSG00000272395", "variantFunctionalConsequenceId": "upstream_gene_variant", "variantOverlappingGeneId": "ENSG00000197110", "genotype": "CC", "genotypeAnnotationText": "Patients with the rs12979860 CC genotype and hepatitis C infection may have increased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CT or TT genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugText": "boceprevir", "drugId": "http://purl.obolibrary.org/obo/CHEBI_68621", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "targetFromSourceId": "ENSG00000272395", "variantFunctionalConsequenceId": "upstream_gene_variant", "variantOverlappingGeneId": "ENSG00000197110", "genotype": "CT", "genotypeAnnotationText": "Patients with the rs12979860 CT genotype and hepatitis C infection may have decreased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CC genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugText": "boceprevir", "drugId": "http://purl.obolibrary.org/obo/CHEBI_68621", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "targetFromSourceId": "ENSG00000272395", "variantFunctionalConsequenceId": "upstream_gene_variant", "variantOverlappingGeneId": "ENSG00000197110", "genotype": "TT", "genotypeAnnotationText": "Patients with the rs12979860 TT genotype and hepatitis C infection may have decreased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CC genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugText": "boceprevir", "drugId": "http://purl.obolibrary.org/obo/CHEBI_68621", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "targetFromSourceId": "ENSG00000197110", "variantFunctionalConsequenceId": "upstream_gene_variant", "variantOverlappingGeneId": "ENSG00000197110", "genotype": "CC", "genotypeAnnotationText": "Patients with the rs12979860 CC genotype and hepatitis C infection may have increased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CT or TT genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugText": "peginterferon alfa-2a", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "targetFromSourceId": "ENSG00000197110", "variantFunctionalConsequenceId": "upstream_gene_variant", "variantOverlappingGeneId": "ENSG00000197110", "genotype": "CT", "genotypeAnnotationText": "Patients with the rs12979860 CT genotype and hepatitis C infection may have decreased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CC genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugText": "peginterferon alfa-2a", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "targetFromSourceId": "ENSG00000197110", "variantFunctionalConsequenceId": "upstream_gene_variant", "variantOverlappingGeneId": "ENSG00000197110", "genotype": "TT", "genotypeAnnotationText": "Patients with the rs12979860 TT genotype and hepatitis C infection may have decreased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CC genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugText": "peginterferon alfa-2a", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "targetFromSourceId": "ENSG00000272395", "variantFunctionalConsequenceId": "upstream_gene_variant", "variantOverlappingGeneId": "ENSG00000197110", "genotype": "CC", "genotypeAnnotationText": "Patients with the rs12979860 CC genotype and hepatitis C infection may have increased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CT or TT genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugText": "peginterferon alfa-2a", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "targetFromSourceId": "ENSG00000272395", "variantFunctionalConsequenceId": "upstream_gene_variant", "variantOverlappingGeneId": "ENSG00000197110", "genotype": "CT", "genotypeAnnotationText": "Patients with the rs12979860 CT genotype and hepatitis C infection may have decreased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CC genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugText": "peginterferon alfa-2a", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "targetFromSourceId": "ENSG00000272395", "variantFunctionalConsequenceId": "upstream_gene_variant", "variantOverlappingGeneId": "ENSG00000197110", "genotype": "TT", "genotypeAnnotationText": "Patients with the rs12979860 TT genotype and hepatitis C infection may have decreased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CC genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugText": "peginterferon alfa-2a", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "targetFromSourceId": "ENSG00000197110", "variantFunctionalConsequenceId": "upstream_gene_variant", "variantOverlappingGeneId": "ENSG00000197110", "genotype": "CC", "genotypeAnnotationText": "Patients with the rs12979860 CC genotype and hepatitis C infection may have increased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CT or TT genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugText": "peginterferon alfa-2b", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "targetFromSourceId": "ENSG00000197110", "variantFunctionalConsequenceId": "upstream_gene_variant", "variantOverlappingGeneId": "ENSG00000197110", "genotype": "CT", "genotypeAnnotationText": "Patients with the rs12979860 CT genotype and hepatitis C infection may have decreased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CC genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugText": "peginterferon alfa-2b", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "targetFromSourceId": "ENSG00000197110", "variantFunctionalConsequenceId": "upstream_gene_variant", "variantOverlappingGeneId": "ENSG00000197110", "genotype": "TT", "genotypeAnnotationText": "Patients with the rs12979860 TT genotype and hepatitis C infection may have decreased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CC genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugText": "peginterferon alfa-2b", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "targetFromSourceId": "ENSG00000272395", "variantFunctionalConsequenceId": "upstream_gene_variant", "variantOverlappingGeneId": "ENSG00000197110", "genotype": "CC", "genotypeAnnotationText": "Patients with the rs12979860 CC genotype and hepatitis C infection may have increased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CT or TT genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugText": "peginterferon alfa-2b", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "targetFromSourceId": "ENSG00000272395", "variantFunctionalConsequenceId": "upstream_gene_variant", "variantOverlappingGeneId": "ENSG00000197110", "genotype": "CT", "genotypeAnnotationText": "Patients with the rs12979860 CT genotype and hepatitis C infection may have decreased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CC genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugText": "peginterferon alfa-2b", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "targetFromSourceId": "ENSG00000272395", "variantFunctionalConsequenceId": "upstream_gene_variant", "variantOverlappingGeneId": "ENSG00000197110", "genotype": "TT", "genotypeAnnotationText": "Patients with the rs12979860 TT genotype and hepatitis C infection may have decreased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CC genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugText": "peginterferon alfa-2b", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "targetFromSourceId": "ENSG00000197110", "variantFunctionalConsequenceId": "upstream_gene_variant", "variantOverlappingGeneId": "ENSG00000197110", "genotype": "CC", "genotypeAnnotationText": "Patients with the rs12979860 CC genotype and hepatitis C infection may have increased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CT or TT genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugText": "ribavirin", "drugId": "http://purl.obolibrary.org/obo/CHEBI_63580", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "targetFromSourceId": "ENSG00000197110", "variantFunctionalConsequenceId": "upstream_gene_variant", "variantOverlappingGeneId": "ENSG00000197110", "genotype": "CT", "genotypeAnnotationText": "Patients with the rs12979860 CT genotype and hepatitis C infection may have decreased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CC genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugText": "ribavirin", "drugId": "http://purl.obolibrary.org/obo/CHEBI_63580", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "targetFromSourceId": "ENSG00000197110", "variantFunctionalConsequenceId": "upstream_gene_variant", "variantOverlappingGeneId": "ENSG00000197110", "genotype": "TT", "genotypeAnnotationText": "Patients with the rs12979860 TT genotype and hepatitis C infection may have decreased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CC genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugText": "ribavirin", "drugId": "http://purl.obolibrary.org/obo/CHEBI_63580", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "targetFromSourceId": "ENSG00000272395", "variantFunctionalConsequenceId": "upstream_gene_variant", "variantOverlappingGeneId": "ENSG00000197110", "genotype": "CC", "genotypeAnnotationText": "Patients with the rs12979860 CC genotype and hepatitis C infection may have increased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CT or TT genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugText": "ribavirin", "drugId": "http://purl.obolibrary.org/obo/CHEBI_63580", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "targetFromSourceId": "ENSG00000272395", "variantFunctionalConsequenceId": "upstream_gene_variant", "variantOverlappingGeneId": "ENSG00000197110", "genotype": "CT", "genotypeAnnotationText": "Patients with the rs12979860 CT genotype and hepatitis C infection may have decreased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CC genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugText": "ribavirin", "drugId": "http://purl.obolibrary.org/obo/CHEBI_63580", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "targetFromSourceId": "ENSG00000272395", "variantFunctionalConsequenceId": "upstream_gene_variant", "variantOverlappingGeneId": "ENSG00000197110", "genotype": "TT", "genotypeAnnotationText": "Patients with the rs12979860 TT genotype and hepatitis C infection may have decreased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CC genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugText": "ribavirin", "drugId": "http://purl.obolibrary.org/obo/CHEBI_63580", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1449309937", "evidenceLevel": "1A", "literature": ["27857962", "11389482"], "variantId": "19_38499645_GGAGGAG_GGAG", "variantRsId": "rs121918596", "targetFromSourceId": "ENSG00000196218", "variantFunctionalConsequenceId": "inframe_deletion", "variantOverlappingGeneId": "ENSG00000196218", "genotype": "GAG/GAG", "genotypeAnnotationText": "Patients with the rs121918596 GAG/GAG genotype may have a decreased, but not absent, risk for malignant hyperthermia based on this variant when treated with volatile anesthetics (desflurane, enflurane, halothane, isoflurane, methoxyflurane, sevoflurane) and/or succinylcholine as compared to patients with the del/del or del/GAG genotypes. Other genetic or clinical factors may also influence the risk for malignant hyperthermia.", "drugText": "desflurane", "drugId": "http://purl.obolibrary.org/obo/CHEBI_4445", "pgxCategory": "Toxicity", "phenotypeText": "Malignant Hyperthermia", "phenotypeFromSourceId": "http://www.orpha.net/ORDO/Orphanet_423"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1449309937", "evidenceLevel": "1A", "literature": ["27857962", "11389482"], "variantId": "19_38499645_GGAGGAG_GGAG", "variantRsId": "rs121918596", "targetFromSourceId": "ENSG00000196218", "variantFunctionalConsequenceId": "inframe_deletion", "variantOverlappingGeneId": "ENSG00000196218", "genotype": "del/GAG", "genotypeAnnotationText": "Patients with the rs121918596 del/GAG genotype may develop malignant hyperthermia when treated with volatile anesthetics (desflurane, enflurane, halothane, isoflurane, methoxyflurane, sevoflurane) and/or succinylcholine as compared to patients with the GAG/GAG genotype. Other genetic or clinical factors may also influence the risk for malignant hyperthermia.", "drugText": "desflurane", "drugId": "http://purl.obolibrary.org/obo/CHEBI_4445", "pgxCategory": "Toxicity", "phenotypeText": "Malignant Hyperthermia", "phenotypeFromSourceId": "http://www.orpha.net/ORDO/Orphanet_423"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1449309937", "evidenceLevel": "1A", "literature": ["27857962", "11389482"], "variantId": "19_38499645_GGAGGAG_GGAG", "variantRsId": "rs121918596", "targetFromSourceId": "ENSG00000196218", "variantFunctionalConsequenceId": "inframe_deletion", "variantOverlappingGeneId": "ENSG00000196218", "genotype": "del/del", "genotypeAnnotationText": "Patients with the rs121918596 del/del genotype may develop malignant hyperthermia when treated with volatile anesthetics (desflurane, enflurane, halothane, isoflurane, methoxyflurane, sevoflurane) and/or succinylcholine as compared to patients with the GAG/GAG genotype. Other genetic or clinical factors may also influence the risk for malignant hyperthermia.", "drugText": "desflurane", "drugId": "http://purl.obolibrary.org/obo/CHEBI_4445", "pgxCategory": "Toxicity", "phenotypeText": "Malignant Hyperthermia", "phenotypeFromSourceId": "http://www.orpha.net/ORDO/Orphanet_423"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1449309937", "evidenceLevel": "1A", "literature": ["27857962", "11389482"], "variantId": "19_38499645_GGAGGAG_GGAG", "variantRsId": "rs121918596", "targetFromSourceId": "ENSG00000196218", "variantFunctionalConsequenceId": "inframe_deletion", "variantOverlappingGeneId": "ENSG00000196218", "genotype": "GAG/GAG", "genotypeAnnotationText": "Patients with the rs121918596 GAG/GAG genotype may have a decreased, but not absent, risk for malignant hyperthermia based on this variant when treated with volatile anesthetics (desflurane, enflurane, halothane, isoflurane, methoxyflurane, sevoflurane) and/or succinylcholine as compared to patients with the del/del or del/GAG genotypes. Other genetic or clinical factors may also influence the risk for malignant hyperthermia.", "drugText": "enflurane", "drugId": "http://purl.obolibrary.org/obo/CHEBI_4792", "pgxCategory": "Toxicity", "phenotypeText": "Malignant Hyperthermia", "phenotypeFromSourceId": "http://www.orpha.net/ORDO/Orphanet_423"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1449309937", "evidenceLevel": "1A", "literature": ["27857962", "11389482"], "variantId": "19_38499645_GGAGGAG_GGAG", "variantRsId": "rs121918596", "targetFromSourceId": "ENSG00000196218", "variantFunctionalConsequenceId": "inframe_deletion", "variantOverlappingGeneId": "ENSG00000196218", "genotype": "del/GAG", "genotypeAnnotationText": "Patients with the rs121918596 del/GAG genotype may develop malignant hyperthermia when treated with volatile anesthetics (desflurane, enflurane, halothane, isoflurane, methoxyflurane, sevoflurane) and/or succinylcholine as compared to patients with the GAG/GAG genotype. Other genetic or clinical factors may also influence the risk for malignant hyperthermia.", "drugText": "enflurane", "drugId": "http://purl.obolibrary.org/obo/CHEBI_4792", "pgxCategory": "Toxicity", "phenotypeText": "Malignant Hyperthermia", "phenotypeFromSourceId": "http://www.orpha.net/ORDO/Orphanet_423"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1449309937", "evidenceLevel": "1A", "literature": ["27857962", "11389482"], "variantId": "19_38499645_GGAGGAG_GGAG", "variantRsId": "rs121918596", "targetFromSourceId": "ENSG00000196218", "variantFunctionalConsequenceId": "inframe_deletion", "variantOverlappingGeneId": "ENSG00000196218", "genotype": "del/del", "genotypeAnnotationText": "Patients with the rs121918596 del/del genotype may develop malignant hyperthermia when treated with volatile anesthetics (desflurane, enflurane, halothane, isoflurane, methoxyflurane, sevoflurane) and/or succinylcholine as compared to patients with the GAG/GAG genotype. Other genetic or clinical factors may also influence the risk for malignant hyperthermia.", "drugText": "enflurane", "drugId": "http://purl.obolibrary.org/obo/CHEBI_4792", "pgxCategory": "Toxicity", "phenotypeText": "Malignant Hyperthermia", "phenotypeFromSourceId": "http://www.orpha.net/ORDO/Orphanet_423"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1449309937", "evidenceLevel": "1A", "literature": ["27857962", "11389482"], "variantId": "19_38499645_GGAGGAG_GGAG", "variantRsId": "rs121918596", "targetFromSourceId": "ENSG00000196218", "variantFunctionalConsequenceId": "inframe_deletion", "variantOverlappingGeneId": "ENSG00000196218", "genotype": "GAG/GAG", "genotypeAnnotationText": "Patients with the rs121918596 GAG/GAG genotype may have a decreased, but not absent, risk for malignant hyperthermia based on this variant when treated with volatile anesthetics (desflurane, enflurane, halothane, isoflurane, methoxyflurane, sevoflurane) and/or succinylcholine as compared to patients with the del/del or del/GAG genotypes. Other genetic or clinical factors may also influence the risk for malignant hyperthermia.", "drugText": "halothane", "drugId": "http://purl.obolibrary.org/obo/CHEBI_5615", "pgxCategory": "Toxicity", "phenotypeText": "Malignant Hyperthermia", "phenotypeFromSourceId": "http://www.orpha.net/ORDO/Orphanet_423"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1449309937", "evidenceLevel": "1A", "literature": ["27857962", "11389482"], "variantId": "19_38499645_GGAGGAG_GGAG", "variantRsId": "rs121918596", "targetFromSourceId": "ENSG00000196218", "variantFunctionalConsequenceId": "inframe_deletion", "variantOverlappingGeneId": "ENSG00000196218", "genotype": "del/GAG", "genotypeAnnotationText": "Patients with the rs121918596 del/GAG genotype may develop malignant hyperthermia when treated with volatile anesthetics (desflurane, enflurane, halothane, isoflurane, methoxyflurane, sevoflurane) and/or succinylcholine as compared to patients with the GAG/GAG genotype. Other genetic or clinical factors may also influence the risk for malignant hyperthermia.", "drugText": "halothane", "drugId": "http://purl.obolibrary.org/obo/CHEBI_5615", "pgxCategory": "Toxicity", "phenotypeText": "Malignant Hyperthermia", "phenotypeFromSourceId": "http://www.orpha.net/ORDO/Orphanet_423"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1449309937", "evidenceLevel": "1A", "literature": ["27857962", "11389482"], "variantId": "19_38499645_GGAGGAG_GGAG", "variantRsId": "rs121918596", "targetFromSourceId": "ENSG00000196218", "variantFunctionalConsequenceId": "inframe_deletion", "variantOverlappingGeneId": "ENSG00000196218", "genotype": "del/del", "genotypeAnnotationText": "Patients with the rs121918596 del/del genotype may develop malignant hyperthermia when treated with volatile anesthetics (desflurane, enflurane, halothane, isoflurane, methoxyflurane, sevoflurane) and/or succinylcholine as compared to patients with the GAG/GAG genotype. Other genetic or clinical factors may also influence the risk for malignant hyperthermia.", "drugText": "halothane", "drugId": "http://purl.obolibrary.org/obo/CHEBI_5615", "pgxCategory": "Toxicity", "phenotypeText": "Malignant Hyperthermia", "phenotypeFromSourceId": "http://www.orpha.net/ORDO/Orphanet_423"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1449309937", "evidenceLevel": "1A", "literature": ["27857962", "11389482"], "variantId": "19_38499645_GGAGGAG_GGAG", "variantRsId": "rs121918596", "targetFromSourceId": "ENSG00000196218", "variantFunctionalConsequenceId": "inframe_deletion", "variantOverlappingGeneId": "ENSG00000196218", "genotype": "GAG/GAG", "genotypeAnnotationText": "Patients with the rs121918596 GAG/GAG genotype may have a decreased, but not absent, risk for malignant hyperthermia based on this variant when treated with volatile anesthetics (desflurane, enflurane, halothane, isoflurane, methoxyflurane, sevoflurane) and/or succinylcholine as compared to patients with the del/del or del/GAG genotypes. Other genetic or clinical factors may also influence the risk for malignant hyperthermia.", "drugText": "isoflurane", "drugId": "http://purl.obolibrary.org/obo/CHEBI_6015", "pgxCategory": "Toxicity", "phenotypeText": "Malignant Hyperthermia", "phenotypeFromSourceId": "http://www.orpha.net/ORDO/Orphanet_423"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1449309937", "evidenceLevel": "1A", "literature": ["27857962", "11389482"], "variantId": "19_38499645_GGAGGAG_GGAG", "variantRsId": "rs121918596", "targetFromSourceId": "ENSG00000196218", "variantFunctionalConsequenceId": "inframe_deletion", "variantOverlappingGeneId": "ENSG00000196218", "genotype": "del/GAG", "genotypeAnnotationText": "Patients with the rs121918596 del/GAG genotype may develop malignant hyperthermia when treated with volatile anesthetics (desflurane, enflurane, halothane, isoflurane, methoxyflurane, sevoflurane) and/or succinylcholine as compared to patients with the GAG/GAG genotype. Other genetic or clinical factors may also influence the risk for malignant hyperthermia.", "drugText": "isoflurane", "drugId": "http://purl.obolibrary.org/obo/CHEBI_6015", "pgxCategory": "Toxicity", "phenotypeText": "Malignant Hyperthermia", "phenotypeFromSourceId": "http://www.orpha.net/ORDO/Orphanet_423"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1449309937", "evidenceLevel": "1A", "literature": ["27857962", "11389482"], "variantId": "19_38499645_GGAGGAG_GGAG", "variantRsId": "rs121918596", "targetFromSourceId": "ENSG00000196218", "variantFunctionalConsequenceId": "inframe_deletion", "variantOverlappingGeneId": "ENSG00000196218", "genotype": "del/del", "genotypeAnnotationText": "Patients with the rs121918596 del/del genotype may develop malignant hyperthermia when treated with volatile anesthetics (desflurane, enflurane, halothane, isoflurane, methoxyflurane, sevoflurane) and/or succinylcholine as compared to patients with the GAG/GAG genotype. Other genetic or clinical factors may also influence the risk for malignant hyperthermia.", "drugText": "isoflurane", "drugId": "http://purl.obolibrary.org/obo/CHEBI_6015", "pgxCategory": "Toxicity", "phenotypeText": "Malignant Hyperthermia", "phenotypeFromSourceId": "http://www.orpha.net/ORDO/Orphanet_423"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1449309937", "evidenceLevel": "1A", "literature": ["27857962", "11389482"], "variantId": "19_38499645_GGAGGAG_GGAG", "variantRsId": "rs121918596", "targetFromSourceId": "ENSG00000196218", "variantFunctionalConsequenceId": "inframe_deletion", "variantOverlappingGeneId": "ENSG00000196218", "genotype": "GAG/GAG", "genotypeAnnotationText": "Patients with the rs121918596 GAG/GAG genotype may have a decreased, but not absent, risk for malignant hyperthermia based on this variant when treated with volatile anesthetics (desflurane, enflurane, halothane, isoflurane, methoxyflurane, sevoflurane) and/or succinylcholine as compared to patients with the del/del or del/GAG genotypes. Other genetic or clinical factors may also influence the risk for malignant hyperthermia.", "drugText": "methoxyflurane", "drugId": "http://purl.obolibrary.org/obo/CHEBI_6843", "pgxCategory": "Toxicity", "phenotypeText": "Malignant Hyperthermia", "phenotypeFromSourceId": "http://www.orpha.net/ORDO/Orphanet_423"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1449309937", "evidenceLevel": "1A", "literature": ["27857962", "11389482"], "variantId": "19_38499645_GGAGGAG_GGAG", "variantRsId": "rs121918596", "targetFromSourceId": "ENSG00000196218", "variantFunctionalConsequenceId": "inframe_deletion", "variantOverlappingGeneId": "ENSG00000196218", "genotype": "del/GAG", "genotypeAnnotationText": "Patients with the rs121918596 del/GAG genotype may develop malignant hyperthermia when treated with volatile anesthetics (desflurane, enflurane, halothane, isoflurane, methoxyflurane, sevoflurane) and/or succinylcholine as compared to patients with the GAG/GAG genotype. Other genetic or clinical factors may also influence the risk for malignant hyperthermia.", "drugText": "methoxyflurane", "drugId": "http://purl.obolibrary.org/obo/CHEBI_6843", "pgxCategory": "Toxicity", "phenotypeText": "Malignant Hyperthermia", "phenotypeFromSourceId": "http://www.orpha.net/ORDO/Orphanet_423"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1449309937", "evidenceLevel": "1A", "literature": ["27857962", "11389482"], "variantId": "19_38499645_GGAGGAG_GGAG", "variantRsId": "rs121918596", "targetFromSourceId": "ENSG00000196218", "variantFunctionalConsequenceId": "inframe_deletion", "variantOverlappingGeneId": "ENSG00000196218", "genotype": "del/del", "genotypeAnnotationText": "Patients with the rs121918596 del/del genotype may develop malignant hyperthermia when treated with volatile anesthetics (desflurane, enflurane, halothane, isoflurane, methoxyflurane, sevoflurane) and/or succinylcholine as compared to patients with the GAG/GAG genotype. Other genetic or clinical factors may also influence the risk for malignant hyperthermia.", "drugText": "methoxyflurane", "drugId": "http://purl.obolibrary.org/obo/CHEBI_6843", "pgxCategory": "Toxicity", "phenotypeText": "Malignant Hyperthermia", "phenotypeFromSourceId": "http://www.orpha.net/ORDO/Orphanet_423"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1449309937", "evidenceLevel": "1A", "literature": ["27857962", "11389482"], "variantId": "19_38499645_GGAGGAG_GGAG", "variantRsId": "rs121918596", "targetFromSourceId": "ENSG00000196218", "variantFunctionalConsequenceId": "inframe_deletion", "variantOverlappingGeneId": "ENSG00000196218", "genotype": "GAG/GAG", "genotypeAnnotationText": "Patients with the rs121918596 GAG/GAG genotype may have a decreased, but not absent, risk for malignant hyperthermia based on this variant when treated with volatile anesthetics (desflurane, enflurane, halothane, isoflurane, methoxyflurane, sevoflurane) and/or succinylcholine as compared to patients with the del/del or del/GAG genotypes. Other genetic or clinical factors may also influence the risk for malignant hyperthermia.", "drugText": "sevoflurane", "drugId": "http://purl.obolibrary.org/obo/CHEBI_9130", "pgxCategory": "Toxicity", "phenotypeText": "Malignant Hyperthermia", "phenotypeFromSourceId": "http://www.orpha.net/ORDO/Orphanet_423"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1449309937", "evidenceLevel": "1A", "literature": ["27857962", "11389482"], "variantId": "19_38499645_GGAGGAG_GGAG", "variantRsId": "rs121918596", "targetFromSourceId": "ENSG00000196218", "variantFunctionalConsequenceId": "inframe_deletion", "variantOverlappingGeneId": "ENSG00000196218", "genotype": "del/GAG", "genotypeAnnotationText": "Patients with the rs121918596 del/GAG genotype may develop malignant hyperthermia when treated with volatile anesthetics (desflurane, enflurane, halothane, isoflurane, methoxyflurane, sevoflurane) and/or succinylcholine as compared to patients with the GAG/GAG genotype. Other genetic or clinical factors may also influence the risk for malignant hyperthermia.", "drugText": "sevoflurane", "drugId": "http://purl.obolibrary.org/obo/CHEBI_9130", "pgxCategory": "Toxicity", "phenotypeText": "Malignant Hyperthermia", "phenotypeFromSourceId": "http://www.orpha.net/ORDO/Orphanet_423"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1449309937", "evidenceLevel": "1A", "literature": ["27857962", "11389482"], "variantId": "19_38499645_GGAGGAG_GGAG", "variantRsId": "rs121918596", "targetFromSourceId": "ENSG00000196218", "variantFunctionalConsequenceId": "inframe_deletion", "variantOverlappingGeneId": "ENSG00000196218", "genotype": "del/del", "genotypeAnnotationText": "Patients with the rs121918596 del/del genotype may develop malignant hyperthermia when treated with volatile anesthetics (desflurane, enflurane, halothane, isoflurane, methoxyflurane, sevoflurane) and/or succinylcholine as compared to patients with the GAG/GAG genotype. Other genetic or clinical factors may also influence the risk for malignant hyperthermia.", "drugText": "sevoflurane", "drugId": "http://purl.obolibrary.org/obo/CHEBI_9130", "pgxCategory": "Toxicity", "phenotypeText": "Malignant Hyperthermia", "phenotypeFromSourceId": "http://www.orpha.net/ORDO/Orphanet_423"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1449309937", "evidenceLevel": "1A", "literature": ["27857962", "11389482"], "variantId": "19_38499645_GGAGGAG_GGAG", "variantRsId": "rs121918596", "targetFromSourceId": "ENSG00000196218", "variantFunctionalConsequenceId": "inframe_deletion", "variantOverlappingGeneId": "ENSG00000196218", "genotype": "GAG/GAG", "genotypeAnnotationText": "Patients with the rs121918596 GAG/GAG genotype may have a decreased, but not absent, risk for malignant hyperthermia based on this variant when treated with volatile anesthetics (desflurane, enflurane, halothane, isoflurane, methoxyflurane, sevoflurane) and/or succinylcholine as compared to patients with the del/del or del/GAG genotypes. Other genetic or clinical factors may also influence the risk for malignant hyperthermia.", "drugText": "succinylcholine", "drugId": "http://purl.obolibrary.org/obo/CHEBI_45652", "pgxCategory": "Toxicity", "phenotypeText": "Malignant Hyperthermia", "phenotypeFromSourceId": "http://www.orpha.net/ORDO/Orphanet_423"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1449309937", "evidenceLevel": "1A", "literature": ["27857962", "11389482"], "variantId": "19_38499645_GGAGGAG_GGAG", "variantRsId": "rs121918596", "targetFromSourceId": "ENSG00000196218", "variantFunctionalConsequenceId": "inframe_deletion", "variantOverlappingGeneId": "ENSG00000196218", "genotype": "del/GAG", "genotypeAnnotationText": "Patients with the rs121918596 del/GAG genotype may develop malignant hyperthermia when treated with volatile anesthetics (desflurane, enflurane, halothane, isoflurane, methoxyflurane, sevoflurane) and/or succinylcholine as compared to patients with the GAG/GAG genotype. Other genetic or clinical factors may also influence the risk for malignant hyperthermia.", "drugText": "succinylcholine", "drugId": "http://purl.obolibrary.org/obo/CHEBI_45652", "pgxCategory": "Toxicity", "phenotypeText": "Malignant Hyperthermia", "phenotypeFromSourceId": "http://www.orpha.net/ORDO/Orphanet_423"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1449309937", "evidenceLevel": "1A", "literature": ["27857962", "11389482"], "variantId": "19_38499645_GGAGGAG_GGAG", "variantRsId": "rs121918596", "targetFromSourceId": "ENSG00000196218", "variantFunctionalConsequenceId": "inframe_deletion", "variantOverlappingGeneId": "ENSG00000196218", "genotype": "del/del", "genotypeAnnotationText": "Patients with the rs121918596 del/del genotype may develop malignant hyperthermia when treated with volatile anesthetics (desflurane, enflurane, halothane, isoflurane, methoxyflurane, sevoflurane) and/or succinylcholine as compared to patients with the GAG/GAG genotype. Other genetic or clinical factors may also influence the risk for malignant hyperthermia.", "drugText": "succinylcholine", "drugId": "http://purl.obolibrary.org/obo/CHEBI_45652", "pgxCategory": "Toxicity", "phenotypeText": "Malignant Hyperthermia", "phenotypeFromSourceId": "http://www.orpha.net/ORDO/Orphanet_423"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1447680028", "evidenceLevel": "3", "literature": ["26633805"], "variantId": "6_29830805_-_ATTTGTTCATGCCT", "variantRsId": "rs371194629", "targetFromSourceId": "ENSG00000233095", "genotype": "ATTTGTTCATGCCT/ATTTGTTCATGCCT", "genotypeAnnotationText": "Patients with colorectal cancer and the HLA-G ATTTGTTCATGCCT/ATTTGTTCATGCCT genotype may have better response to capecitabine or fluorouracil as compared to patients with the HLA-G del/del genotypes. Other clinical and genetic factors may also influence response to capecitabine or fluorouracil in patients with colorectal cancer.", "drugText": "capecitabine", "drugId": "http://purl.obolibrary.org/obo/CHEBI_31348", "pgxCategory": "Efficacy", "phenotypeText": "Colorectal Neoplasms"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1447680028", "evidenceLevel": "3", "literature": ["26633805"], "variantId": "6_29830805_-_ATTTGTTCATGCCT", "variantRsId": "rs371194629", "targetFromSourceId": "ENSG00000276051", "genotype": "ATTTGTTCATGCCT/ATTTGTTCATGCCT", "genotypeAnnotationText": "Patients with colorectal cancer and the HLA-G ATTTGTTCATGCCT/ATTTGTTCATGCCT genotype may have better response to capecitabine or fluorouracil as compared to patients with the HLA-G del/del genotypes. Other clinical and genetic factors may also influence response to capecitabine or fluorouracil in patients with colorectal cancer.", "drugText": "capecitabine", "drugId": "http://purl.obolibrary.org/obo/CHEBI_31348", "pgxCategory": "Efficacy", "phenotypeText": "Colorectal Neoplasms"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1447680028", "evidenceLevel": "3", "literature": ["26633805"], "variantId": "6_29830805_-_ATTTGTTCATGCCT", "variantRsId": "rs371194629", "targetFromSourceId": "ENSG00000235680", "genotype": "ATTTGTTCATGCCT/ATTTGTTCATGCCT", "genotypeAnnotationText": "Patients with colorectal cancer and the HLA-G ATTTGTTCATGCCT/ATTTGTTCATGCCT genotype may have better response to capecitabine or fluorouracil as compared to patients with the HLA-G del/del genotypes. Other clinical and genetic factors may also influence response to capecitabine or fluorouracil in patients with colorectal cancer.", "drugText": "capecitabine", "drugId": "http://purl.obolibrary.org/obo/CHEBI_31348", "pgxCategory": "Efficacy", "phenotypeText": "Colorectal Neoplasms"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1447680028", "evidenceLevel": "3", "literature": ["26633805"], "variantId": "6_29830805_-_ATTTGTTCATGCCT", "variantRsId": "rs371194629", "targetFromSourceId": "ENSG00000230413", "genotype": "ATTTGTTCATGCCT/ATTTGTTCATGCCT", "genotypeAnnotationText": "Patients with colorectal cancer and the HLA-G ATTTGTTCATGCCT/ATTTGTTCATGCCT genotype may have better response to capecitabine or fluorouracil as compared to patients with the HLA-G del/del genotypes. Other clinical and genetic factors may also influence response to capecitabine or fluorouracil in patients with colorectal cancer.", "drugText": "capecitabine", "drugId": "http://purl.obolibrary.org/obo/CHEBI_31348", "pgxCategory": "Efficacy", "phenotypeText": "Colorectal Neoplasms"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1447680028", "evidenceLevel": "3", "literature": ["26633805"], "variantId": "6_29830805_-_ATTTGTTCATGCCT", "variantRsId": "rs371194629", "targetFromSourceId": "ENSG00000235346", "genotype": "ATTTGTTCATGCCT/ATTTGTTCATGCCT", "genotypeAnnotationText": "Patients with colorectal cancer and the HLA-G ATTTGTTCATGCCT/ATTTGTTCATGCCT genotype may have better response to capecitabine or fluorouracil as compared to patients with the HLA-G del/del genotypes. Other clinical and genetic factors may also influence response to capecitabine or fluorouracil in patients with colorectal cancer.", "drugText": "capecitabine", "drugId": "http://purl.obolibrary.org/obo/CHEBI_31348", "pgxCategory": "Efficacy", "phenotypeText": "Colorectal Neoplasms"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1447680028", "evidenceLevel": "3", "literature": ["26633805"], "variantId": "6_29830805_-_ATTTGTTCATGCCT", "variantRsId": "rs371194629", "targetFromSourceId": "ENSG00000237216", "genotype": "ATTTGTTCATGCCT/ATTTGTTCATGCCT", "genotypeAnnotationText": "Patients with colorectal cancer and the HLA-G ATTTGTTCATGCCT/ATTTGTTCATGCCT genotype may have better response to capecitabine or fluorouracil as compared to patients with the HLA-G del/del genotypes. Other clinical and genetic factors may also influence response to capecitabine or fluorouracil in patients with colorectal cancer.", "drugText": "capecitabine", "drugId": "http://purl.obolibrary.org/obo/CHEBI_31348", "pgxCategory": "Efficacy", "phenotypeText": "Colorectal Neoplasms"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1447680028", "evidenceLevel": "3", "literature": ["26633805"], "variantId": "6_29830805_-_ATTTGTTCATGCCT", "variantRsId": "rs371194629", "targetFromSourceId": "ENSG00000206506", "genotype": "ATTTGTTCATGCCT/ATTTGTTCATGCCT", "genotypeAnnotationText": "Patients with colorectal cancer and the HLA-G ATTTGTTCATGCCT/ATTTGTTCATGCCT genotype may have better response to capecitabine or fluorouracil as compared to patients with the HLA-G del/del genotypes. Other clinical and genetic factors may also influence response to capecitabine or fluorouracil in patients with colorectal cancer.", "drugText": "capecitabine", "drugId": "http://purl.obolibrary.org/obo/CHEBI_31348", "pgxCategory": "Efficacy", "phenotypeText": "Colorectal Neoplasms"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1447680028", "evidenceLevel": "3", "literature": ["26633805"], "variantId": "6_29830805_-_ATTTGTTCATGCCT", "variantRsId": "rs371194629", "targetFromSourceId": "ENSG00000204632", "genotype": "ATTTGTTCATGCCT/ATTTGTTCATGCCT", "genotypeAnnotationText": "Patients with colorectal cancer and the HLA-G ATTTGTTCATGCCT/ATTTGTTCATGCCT genotype may have better response to capecitabine or fluorouracil as compared to patients with the HLA-G del/del genotypes. Other clinical and genetic factors may also influence response to capecitabine or fluorouracil in patients with colorectal cancer.", "drugText": "capecitabine", "drugId": "http://purl.obolibrary.org/obo/CHEBI_31348", "pgxCategory": "Efficacy", "phenotypeText": "Colorectal Neoplasms"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1447680028", "evidenceLevel": "3", "literature": ["26633805"], "variantId": "6_29830805_-_ATTTGTTCATGCCT", "variantRsId": "rs371194629", "targetFromSourceId": "ENSG00000233095", "genotype": "del/ATTTGTTCATGCCT", "genotypeAnnotationText": "Patients with colorectal cancer and the HLA-G del/ATTTGTTCATGCCT genotype may have better response to capecitabine or fluorouracil as compared to patients with the HLA-G del/del genotypes. Other clinical and genetic factors may also influence response to capecitabine or fluorouracil in patients with colorectal cancer.", "drugText": "capecitabine", "drugId": "http://purl.obolibrary.org/obo/CHEBI_31348", "pgxCategory": "Efficacy", "phenotypeText": "Colorectal Neoplasms"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1447680028", "evidenceLevel": "3", "literature": ["26633805"], "variantId": "6_29830805_-_ATTTGTTCATGCCT", "variantRsId": "rs371194629", "targetFromSourceId": "ENSG00000276051", "genotype": "del/ATTTGTTCATGCCT", "genotypeAnnotationText": "Patients with colorectal cancer and the HLA-G del/ATTTGTTCATGCCT genotype may have better response to capecitabine or fluorouracil as compared to patients with the HLA-G del/del genotypes. Other clinical and genetic factors may also influence response to capecitabine or fluorouracil in patients with colorectal cancer.", "drugText": "capecitabine", "drugId": "http://purl.obolibrary.org/obo/CHEBI_31348", "pgxCategory": "Efficacy", "phenotypeText": "Colorectal Neoplasms"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1447680028", "evidenceLevel": "3", "literature": ["26633805"], "variantId": "6_29830805_-_ATTTGTTCATGCCT", "variantRsId": "rs371194629", "targetFromSourceId": "ENSG00000235680", "genotype": "del/ATTTGTTCATGCCT", "genotypeAnnotationText": "Patients with colorectal cancer and the HLA-G del/ATTTGTTCATGCCT genotype may have better response to capecitabine or fluorouracil as compared to patients with the HLA-G del/del genotypes. Other clinical and genetic factors may also influence response to capecitabine or fluorouracil in patients with colorectal cancer.", "drugText": "capecitabine", "drugId": "http://purl.obolibrary.org/obo/CHEBI_31348", "pgxCategory": "Efficacy", "phenotypeText": "Colorectal Neoplasms"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1447680028", "evidenceLevel": "3", "literature": ["26633805"], "variantId": "6_29830805_-_ATTTGTTCATGCCT", "variantRsId": "rs371194629", "targetFromSourceId": "ENSG00000230413", "genotype": "del/ATTTGTTCATGCCT", "genotypeAnnotationText": "Patients with colorectal cancer and the HLA-G del/ATTTGTTCATGCCT genotype may have better response to capecitabine or fluorouracil as compared to patients with the HLA-G del/del genotypes. 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Other clinical and genetic factors may also influence response to capecitabine or fluorouracil in patients with colorectal cancer.", "drugText": "fluorouracil", "drugId": "http://purl.obolibrary.org/obo/CHEBI_46345", "pgxCategory": "Efficacy", "phenotypeText": "Colorectal Neoplasms"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1447680028", "evidenceLevel": "3", "literature": ["26633805"], "variantId": "6_29830805_-_ATTTGTTCATGCCT", "variantRsId": "rs371194629", "targetFromSourceId": "ENSG00000230413", "genotype": "del/del", "genotypeAnnotationText": "Patients with colorectal cancer and the HLA-G del/del genotype may have a worse response to capecitabine or fluorouracil as compared to patients with the HLA-G del/ATTTGTTCATGCCT or ATTTGTTCATGCCT/ATTTGTTCATGCCT genotypes. 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Other clinical and genetic factors may also influence response to capecitabine or fluorouracil in patients with colorectal cancer.", "drugText": "fluorouracil", "drugId": "http://purl.obolibrary.org/obo/CHEBI_46345", "pgxCategory": "Efficacy", "phenotypeText": "Colorectal Neoplasms"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1447680028", "evidenceLevel": "3", "literature": ["26633805"], "variantId": "6_29830805_-_ATTTGTTCATGCCT", "variantRsId": "rs371194629", "targetFromSourceId": "ENSG00000206506", "genotype": "del/del", "genotypeAnnotationText": "Patients with colorectal cancer and the HLA-G del/del genotype may have a worse response to capecitabine or fluorouracil as compared to patients with the HLA-G del/ATTTGTTCATGCCT or ATTTGTTCATGCCT/ATTTGTTCATGCCT genotypes. Other clinical and genetic factors may also influence response to capecitabine or fluorouracil in patients with colorectal cancer.", "drugText": "fluorouracil", "drugId": "http://purl.obolibrary.org/obo/CHEBI_46345", "pgxCategory": "Efficacy", "phenotypeText": "Colorectal Neoplasms"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1447680028", "evidenceLevel": "3", "literature": ["26633805"], "variantId": "6_29830805_-_ATTTGTTCATGCCT", "variantRsId": "rs371194629", "targetFromSourceId": "ENSG00000204632", "genotype": "del/del", "genotypeAnnotationText": "Patients with colorectal cancer and the HLA-G del/del genotype may have a worse response to capecitabine or fluorouracil as compared to patients with the HLA-G del/ATTTGTTCATGCCT or ATTTGTTCATGCCT/ATTTGTTCATGCCT genotypes. Other clinical and genetic factors may also influence response to capecitabine or fluorouracil in patients with colorectal cancer.", "drugText": "fluorouracil", "drugId": "http://purl.obolibrary.org/obo/CHEBI_46345", "pgxCategory": "Efficacy", "phenotypeText": "Colorectal Neoplasms"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "targetFromSourceId": "ENSG00000176890", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2 or 2R/2R genotype may have an increased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 2R/3R or 3R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugText": "fluorouracil", "drugId": "http://purl.obolibrary.org/obo/CHEBI_46345", "pgxCategory": "Efficacy", "phenotypeText": "overall survival"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "targetFromSourceId": "ENSG00000176890", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3 or 2R/3R genotype may have an increased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 3R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugText": "fluorouracil", "drugId": "http://purl.obolibrary.org/obo/CHEBI_46345", "pgxCategory": "Efficacy", "phenotypeText": "overall survival"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "targetFromSourceId": "ENSG00000176890", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)3/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3 or 3R/3R genotype may have a decreased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 2R/2R or 2R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugText": "fluorouracil", "drugId": "http://purl.obolibrary.org/obo/CHEBI_46345", "pgxCategory": "Efficacy", "phenotypeText": "overall survival"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "targetFromSourceId": "ENSG00000176890", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2 or 2R/2R genotype may have an increased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 2R/3R or 3R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugText": "FOLFIRI", "pgxCategory": "Efficacy", "phenotypeText": "overall survival"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "targetFromSourceId": "ENSG00000176890", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3 or 2R/3R genotype may have an increased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 3R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugText": "FOLFIRI", "pgxCategory": "Efficacy", "phenotypeText": "overall survival"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "targetFromSourceId": "ENSG00000176890", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)3/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3 or 3R/3R genotype may have a decreased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 2R/2R or 2R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugText": "FOLFIRI", "pgxCategory": "Efficacy", "phenotypeText": "overall survival"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "targetFromSourceId": "ENSG00000176890", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2 or 2R/2R genotype may have an increased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 2R/3R or 3R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugText": "FOLFOX", "pgxCategory": "Efficacy", "phenotypeText": "overall survival"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "targetFromSourceId": "ENSG00000176890", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3 or 2R/3R genotype may have an increased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 3R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugText": "FOLFOX", "pgxCategory": "Efficacy", "phenotypeText": "overall survival"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "targetFromSourceId": "ENSG00000176890", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)3/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3 or 3R/3R genotype may have a decreased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 2R/2R or 2R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugText": "FOLFOX", "pgxCategory": "Efficacy", "phenotypeText": "overall survival"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "targetFromSourceId": "ENSG00000176890", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2 or 2R/2R genotype may have an increased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 2R/3R or 3R/3R genotype. However, conflicting evidence has been reported. 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However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugText": "fluorouracil", "drugId": "http://purl.obolibrary.org/obo/CHEBI_46345", "pgxCategory": "Efficacy", "phenotypeText": "progression-free survival"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "targetFromSourceId": "ENSG00000176890", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)3/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3 or 3R/3R genotype may have a decreased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 2R/2R or 2R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugText": "fluorouracil", "drugId": "http://purl.obolibrary.org/obo/CHEBI_46345", "pgxCategory": "Efficacy", "phenotypeText": "progression-free survival"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "targetFromSourceId": "ENSG00000176890", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2 or 2R/2R genotype may have an increased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 2R/3R or 3R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugText": "FOLFIRI", "pgxCategory": "Efficacy", "phenotypeText": "progression-free survival"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "targetFromSourceId": "ENSG00000176890", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3 or 2R/3R genotype may have an increased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 3R/3R genotype. However, conflicting evidence has been reported. 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However, conflicting evidence has been reported. 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However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugText": "FOLFOX", "pgxCategory": "Efficacy", "phenotypeText": "progression-free survival"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "targetFromSourceId": "ENSG00000176890", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3 or 2R/3R genotype may have an increased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 3R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugText": "FOLFOX", "pgxCategory": "Efficacy", "phenotypeText": "progression-free survival"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "targetFromSourceId": "ENSG00000176890", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)3/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3 or 3R/3R genotype may have a decreased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 2R/2R or 2R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugText": "FOLFOX", "pgxCategory": "Efficacy", "phenotypeText": "progression-free survival"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1444668808", "evidenceLevel": "3", "literature": ["11593098", "11910301"], "variantId": "17_63488530_ATACAGTCACTTTT_ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCATACAGTCACTTTT", "variantRsId": "rs1799752", "targetFromSourceId": "ENSG00000159640", "variantFunctionalConsequenceId": "intron_variant", "variantOverlappingGeneId": "ENSG00000159640", "genotype": "ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC", "genotypeAnnotationText": "Hypertensive patients with the rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC genotype may have an increased response to irbesartan as compared to patients with the ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/del or del/del genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to irbesartan.", "drugText": "irbesartan", "drugId": "http://purl.obolibrary.org/obo/CHEBI_5959", "pgxCategory": "Efficacy", "phenotypeText": "Hypertension", "phenotypeFromSourceId": "http://www.ebi.ac.uk/efo/EFO_0000537"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1444668808", "evidenceLevel": "3", "literature": ["11593098", "11910301"], "variantId": "17_63488530_ATACAGTCACTTTT_ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCATACAGTCACTTTT", "variantRsId": "rs1799752", "targetFromSourceId": "ENSG00000159640", "variantFunctionalConsequenceId": "intron_variant", "variantOverlappingGeneId": "ENSG00000159640", "genotype": "ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/del", "genotypeAnnotationText": "Hypertensive patients with the rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/del genotype may have a decreased response to irbesartan as compared to patients with the ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to irbesartan.", "drugText": "irbesartan", "drugId": "http://purl.obolibrary.org/obo/CHEBI_5959", "pgxCategory": "Efficacy", "phenotypeText": "Hypertension", "phenotypeFromSourceId": "http://www.ebi.ac.uk/efo/EFO_0000537"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1444668808", "evidenceLevel": "3", "literature": ["11593098", "11910301"], "variantId": "17_63488530_ATACAGTCACTTTT_ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCATACAGTCACTTTT", "variantRsId": "rs1799752", "targetFromSourceId": "ENSG00000159640", "variantFunctionalConsequenceId": "intron_variant", "variantOverlappingGeneId": "ENSG00000159640", "genotype": "del/del", "genotypeAnnotationText": "Hypertensive patients with the rs1799752 del/del genotype may have a decreased response to irbesartan as compared to patients with the ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to irbesartan.", "drugText": "irbesartan", "drugId": "http://purl.obolibrary.org/obo/CHEBI_5959", "pgxCategory": "Efficacy", "phenotypeText": "Hypertension", "phenotypeFromSourceId": "http://www.ebi.ac.uk/efo/EFO_0000537"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1444668808", "evidenceLevel": "3", "literature": ["11593098", "11910301"], "variantId": "17_63488530_ATACAGTCACTTTT_ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCATACAGTCACTTTT", "variantRsId": "rs1799752", "targetFromSourceId": "ENSG00000159640", "variantFunctionalConsequenceId": "intron_variant", "variantOverlappingGeneId": "ENSG00000159640", "genotype": "ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC", "genotypeAnnotationText": "Hypertensive patients with the rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC genotype may have an increased response to irbesartan as compared to patients with the ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/del or del/del genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to irbesartan.", "drugText": "irbesartan", "drugId": "http://purl.obolibrary.org/obo/CHEBI_5959", "pgxCategory": "Efficacy", "phenotypeText": "Hypertrophy, Left Ventricular"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1444668808", "evidenceLevel": "3", "literature": ["11593098", "11910301"], "variantId": "17_63488530_ATACAGTCACTTTT_ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCATACAGTCACTTTT", "variantRsId": "rs1799752", "targetFromSourceId": "ENSG00000159640", "variantFunctionalConsequenceId": "intron_variant", "variantOverlappingGeneId": "ENSG00000159640", "genotype": "ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/del", "genotypeAnnotationText": "Hypertensive patients with the rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/del genotype may have a decreased response to irbesartan as compared to patients with the ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to irbesartan.", "drugText": "irbesartan", "drugId": "http://purl.obolibrary.org/obo/CHEBI_5959", "pgxCategory": "Efficacy", "phenotypeText": "Hypertrophy, Left Ventricular"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1444668808", "evidenceLevel": "3", "literature": ["11593098", "11910301"], "variantId": "17_63488530_ATACAGTCACTTTT_ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCATACAGTCACTTTT", "variantRsId": "rs1799752", "targetFromSourceId": "ENSG00000159640", "variantFunctionalConsequenceId": "intron_variant", "variantOverlappingGeneId": "ENSG00000159640", "genotype": "del/del", "genotypeAnnotationText": "Hypertensive patients with the rs1799752 del/del genotype may have a decreased response to irbesartan as compared to patients with the ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to irbesartan.", "drugText": "irbesartan", "drugId": "http://purl.obolibrary.org/obo/CHEBI_5959", "pgxCategory": "Efficacy", "phenotypeText": "Hypertrophy, Left Ventricular"} \ No newline at end of file +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1450375701", "evidenceLevel": "3", "literature": ["30924126"], "variantRsId": "rs4659982", "genotype": "AA", "genotypeAnnotationText": "Patients with the AA genotype may have a decreased response to allopurinol as compared to patients with the AC, CC or CT genotypes. Other genetic and clinical factors may also affect a patient's response to allopurinol.", "drugFromSource": "allopurinol", "drugId": "http://purl.obolibrary.org/obo/CHEBI_40279", "pgxCategory": "Efficacy"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1450375701", "evidenceLevel": "3", "literature": ["30924126"], "variantRsId": "rs4659982", "genotype": "AC", "genotypeAnnotationText": "Patients with the AC genotype may have an increased response to allopurinol as compared to patients with the AA, AT or TT genotypes. Other genetic and clinical factors may also affect a patient's response to allopurinol.", "drugFromSource": "allopurinol", "drugId": "http://purl.obolibrary.org/obo/CHEBI_40279", "pgxCategory": "Efficacy"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1450375701", "evidenceLevel": "3", "literature": ["30924126"], "variantRsId": "rs4659982", "genotype": "AT", "genotypeAnnotationText": "Patients with the AT genotype may have a decreased response to allopurinol as compared to patients with the AC, CC or CT genotypes. Other genetic and clinical factors may also affect a patient's response to allopurinol.", "drugFromSource": "allopurinol", "drugId": "http://purl.obolibrary.org/obo/CHEBI_40279", "pgxCategory": "Efficacy"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1450375701", "evidenceLevel": "3", "literature": ["30924126"], "variantRsId": "rs4659982", "genotype": "CC", "genotypeAnnotationText": "Patients with the CC genotype may have an increased response to allopurinol as compared to patients with the AA, AT or TT genotypes. Other genetic and clinical factors may also affect a patient's response to allopurinol.", "drugFromSource": "allopurinol", "drugId": "http://purl.obolibrary.org/obo/CHEBI_40279", "pgxCategory": "Efficacy"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1450375701", "evidenceLevel": "3", "literature": ["30924126"], "variantRsId": "rs4659982", "genotype": "CT", "genotypeAnnotationText": "Patients with the CT genotype may have an increased response to allopurinol as compared to patients with the AA, AT or TT genotypes. Other genetic and clinical factors may also affect a patient's response to allopurinol.", "drugFromSource": "allopurinol", "drugId": "http://purl.obolibrary.org/obo/CHEBI_40279", "pgxCategory": "Efficacy"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1450375701", "evidenceLevel": "3", "literature": ["30924126"], "variantRsId": "rs4659982", "genotype": "TT", "genotypeAnnotationText": "Patients with the TT genotype may have a decreased response to allopurinol as compared to patients with the AC, CC or CT genotypes. Other genetic and clinical factors may also affect a patient's response to allopurinol.", "drugFromSource": "allopurinol", "drugId": "http://purl.obolibrary.org/obo/CHEBI_40279", "pgxCategory": "Efficacy"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1448603303", "evidenceLevel": "3", "literature": ["25558980"], "variantId": "1_46399999_A_G", "variantRsId": "rs3766246", "variantFunctionalConsequenceId": "intron_variant", "targetFromSourceId": "ENSG00000117480", "genotype": "AA", "genotypeAnnotationText": "Children with the AA genotype who are undergoing a tonsillectomy may have an increased risk for post-operative nausea and vomiting (PONV) when treated with morphine as compared to patients with the GG genotype. Other genetic and clinical factors may also influence risk of PONV.", "drugFromSource": "morphine", "drugId": "http://purl.obolibrary.org/obo/CHEBI_17303", "pgxCategory": "Toxicity"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1448603303", "evidenceLevel": "3", "literature": ["25558980"], "variantId": "1_46399999_A_G", "variantRsId": "rs3766246", "variantFunctionalConsequenceId": "intron_variant", "targetFromSourceId": "ENSG00000117480", "genotype": "AG", "genotypeAnnotationText": "Children with the AG genotype who are undergoing a tonsillectomy may have an increased risk for post-operative nausea and vomiting (PONV) when treated with morphine as compared to patients with the GG genotype. Other genetic and clinical factors may also influence risk of PONV.", "drugFromSource": "morphine", "drugId": "http://purl.obolibrary.org/obo/CHEBI_17303", "pgxCategory": "Toxicity"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1448603303", "evidenceLevel": "3", "literature": ["25558980"], "variantId": "1_46399999_A_G", "variantRsId": "rs3766246", "variantFunctionalConsequenceId": "intron_variant", "targetFromSourceId": "ENSG00000117480", "genotype": "GG", "genotypeAnnotationText": "Children with the GG genotype who are undergoing a tonsillectomy may have a decreased risk for post-operative nausea and vomiting (PONV) when treated with morphine as compared to patients with the AA or AG genotype. Other genetic and clinical factors may also influence risk of PONV.", "drugFromSource": "morphine", "drugId": "http://purl.obolibrary.org/obo/CHEBI_17303", "pgxCategory": "Toxicity"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1043880328", "evidenceLevel": "3", "literature": ["21435719"], "variantRsId": "rs4630", "genotype": "AA", "genotypeAnnotationText": "Patients with the AA genotype may have increased likelihood of Neurotoxicity when treated with thalidomide in people with Multiple Myeloma as compared to patients with the AG genotype. Other clinical or genetic factors may also influence a patient's response to thalidomide.", "drugFromSource": "thalidomide", "drugId": "http://purl.obolibrary.org/obo/CHEBI_9513", "pgxCategory": "Toxicity", "phenotypeText": "Multiple Myeloma", "phenotypeFromSourceId": "http://www.ebi.ac.uk/efo/EFO_0001378"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1043880328", "evidenceLevel": "3", "literature": ["21435719"], "variantRsId": "rs4630", "genotype": "AG", "genotypeAnnotationText": "Patients with the AG genotype may have decreased likelihood of Neurotoxicity when treated with thalidomide in people with Multiple Myeloma as compared to patients with the AA genotype. Other clinical or genetic factors may also influence a patient's response to thalidomide.", "drugFromSource": "thalidomide", "drugId": "http://purl.obolibrary.org/obo/CHEBI_9513", "pgxCategory": "Toxicity", "phenotypeText": "Multiple Myeloma", "phenotypeFromSourceId": "http://www.ebi.ac.uk/efo/EFO_0001378"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1043880328", "evidenceLevel": "3", "literature": ["21435719"], "variantRsId": "rs4630", "genotype": "GG", "genotypeAnnotationText": "Patients with the GG genotype may have decreased likelihood of Neurotoxicity when treated with thalidomide in people with Multiple Myeloma as compared to patients with the AA genotype. Other clinical or genetic factors may also influence a patient's response to thalidomide.", "drugFromSource": "thalidomide", "drugId": "http://purl.obolibrary.org/obo/CHEBI_9513", "pgxCategory": "Toxicity", "phenotypeText": "Multiple Myeloma", "phenotypeFromSourceId": "http://www.ebi.ac.uk/efo/EFO_0001378"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "variantFunctionalConsequenceId": "upstream_gene_variant", "targetFromSourceId": "ENSG00000197110", "genotype": "CC", "genotypeAnnotationText": "Patients with the rs12979860 CC genotype and hepatitis C infection may have increased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CT or TT genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugFromSource": "boceprevir", "drugId": "http://purl.obolibrary.org/obo/CHEBI_68621", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "variantFunctionalConsequenceId": "upstream_gene_variant", "targetFromSourceId": "ENSG00000197110", "genotype": "CT", "genotypeAnnotationText": "Patients with the rs12979860 CT genotype and hepatitis C infection may have decreased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CC genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugFromSource": "boceprevir", "drugId": "http://purl.obolibrary.org/obo/CHEBI_68621", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "variantFunctionalConsequenceId": "upstream_gene_variant", "targetFromSourceId": "ENSG00000197110", "genotype": "TT", "genotypeAnnotationText": "Patients with the rs12979860 TT genotype and hepatitis C infection may have decreased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CC genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugFromSource": "boceprevir", "drugId": "http://purl.obolibrary.org/obo/CHEBI_68621", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "variantFunctionalConsequenceId": "upstream_gene_variant", "targetFromSourceId": "ENSG00000197110", "genotype": "CC", "genotypeAnnotationText": "Patients with the rs12979860 CC genotype and hepatitis C infection may have increased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CT or TT genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugFromSource": "peginterferon alfa-2a", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "variantFunctionalConsequenceId": "upstream_gene_variant", "targetFromSourceId": "ENSG00000197110", "genotype": "CT", "genotypeAnnotationText": "Patients with the rs12979860 CT genotype and hepatitis C infection may have decreased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CC genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugFromSource": "peginterferon alfa-2a", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "variantFunctionalConsequenceId": "upstream_gene_variant", "targetFromSourceId": "ENSG00000197110", "genotype": "TT", "genotypeAnnotationText": "Patients with the rs12979860 TT genotype and hepatitis C infection may have decreased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CC genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugFromSource": "peginterferon alfa-2a", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "variantFunctionalConsequenceId": "upstream_gene_variant", "targetFromSourceId": "ENSG00000197110", "genotype": "CC", "genotypeAnnotationText": "Patients with the rs12979860 CC genotype and hepatitis C infection may have increased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CT or TT genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugFromSource": "peginterferon alfa-2b", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "variantFunctionalConsequenceId": "upstream_gene_variant", "targetFromSourceId": "ENSG00000197110", "genotype": "CT", "genotypeAnnotationText": "Patients with the rs12979860 CT genotype and hepatitis C infection may have decreased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CC genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugFromSource": "peginterferon alfa-2b", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "variantFunctionalConsequenceId": "upstream_gene_variant", "targetFromSourceId": "ENSG00000197110", "genotype": "TT", "genotypeAnnotationText": "Patients with the rs12979860 TT genotype and hepatitis C infection may have decreased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CC genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugFromSource": "peginterferon alfa-2b", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "variantFunctionalConsequenceId": "upstream_gene_variant", "targetFromSourceId": "ENSG00000197110", "genotype": "CC", "genotypeAnnotationText": "Patients with the rs12979860 CC genotype and hepatitis C infection may have increased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CT or TT genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugFromSource": "ribavirin", "drugId": "http://purl.obolibrary.org/obo/CHEBI_63580", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "variantFunctionalConsequenceId": "upstream_gene_variant", "targetFromSourceId": "ENSG00000197110", "genotype": "CT", "genotypeAnnotationText": "Patients with the rs12979860 CT genotype and hepatitis C infection may have decreased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CC genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugFromSource": "ribavirin", "drugId": "http://purl.obolibrary.org/obo/CHEBI_63580", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1183680546", "evidenceLevel": "1A", "literature": ["27711230", "22626609", "26191484", "26670100", "28469811"], "variantId": "19_39248147_C_T", "variantRsId": "rs12979860", "variantFunctionalConsequenceId": "upstream_gene_variant", "targetFromSourceId": "ENSG00000197110", "genotype": "TT", "genotypeAnnotationText": "Patients with the rs12979860 TT genotype and hepatitis C infection may have decreased response to triple therapy (boceprevir, peginterferon alfa-2a/2b and ribavirin) as compared to patients with the CC genotype. Other genetic and clinical factors may also influence response to boceprevir-peginterferon based therapy.", "drugFromSource": "ribavirin", "drugId": "http://purl.obolibrary.org/obo/CHEBI_63580", "pgxCategory": "Efficacy", "phenotypeText": "Hepatitis C, Chronic"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1449309937", "evidenceLevel": "1A", "literature": ["27857962", "11389482"], "variantId": "19_38499645_GGAGGAG_GGAG", "variantRsId": "rs121918596", "variantFunctionalConsequenceId": "inframe_deletion", "targetFromSourceId": "ENSG00000196218", "genotype": "GAG/GAG", "genotypeAnnotationText": "Patients with the rs121918596 GAG/GAG genotype may have a decreased, but not absent, risk for malignant hyperthermia based on this variant when treated with volatile anesthetics (desflurane, enflurane, halothane, isoflurane, methoxyflurane, sevoflurane) and/or succinylcholine as compared to patients with the del/del or del/GAG genotypes. Other genetic or clinical factors may also influence the risk for malignant hyperthermia.", "drugFromSource": "desflurane", "drugId": "http://purl.obolibrary.org/obo/CHEBI_4445", "pgxCategory": "Toxicity", "phenotypeText": "Malignant Hyperthermia", "phenotypeFromSourceId": "http://www.orpha.net/ORDO/Orphanet_423"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1449309937", "evidenceLevel": "1A", "literature": ["27857962", "11389482"], "variantId": "19_38499645_GGAGGAG_GGAG", "variantRsId": "rs121918596", "variantFunctionalConsequenceId": "inframe_deletion", "targetFromSourceId": "ENSG00000196218", "genotype": "del/GAG", "genotypeAnnotationText": "Patients with the rs121918596 del/GAG genotype may develop malignant hyperthermia when treated with volatile anesthetics (desflurane, enflurane, halothane, isoflurane, methoxyflurane, sevoflurane) and/or succinylcholine as compared to patients with the GAG/GAG genotype. Other genetic or clinical factors may also influence the risk for malignant hyperthermia.", "drugFromSource": "desflurane", "drugId": "http://purl.obolibrary.org/obo/CHEBI_4445", "pgxCategory": "Toxicity", "phenotypeText": "Malignant Hyperthermia", "phenotypeFromSourceId": "http://www.orpha.net/ORDO/Orphanet_423"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1449309937", "evidenceLevel": "1A", "literature": ["27857962", "11389482"], "variantId": "19_38499645_GGAGGAG_GGAG", "variantRsId": "rs121918596", "variantFunctionalConsequenceId": "inframe_deletion", "targetFromSourceId": "ENSG00000196218", "genotype": "del/del", "genotypeAnnotationText": "Patients with the rs121918596 del/del genotype may develop malignant hyperthermia when treated with volatile anesthetics (desflurane, enflurane, halothane, isoflurane, methoxyflurane, sevoflurane) and/or succinylcholine as compared to patients with the GAG/GAG genotype. Other genetic or clinical factors may also influence the risk for malignant hyperthermia.", "drugFromSource": "desflurane", "drugId": "http://purl.obolibrary.org/obo/CHEBI_4445", "pgxCategory": "Toxicity", "phenotypeText": "Malignant Hyperthermia", "phenotypeFromSourceId": "http://www.orpha.net/ORDO/Orphanet_423"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1449309937", "evidenceLevel": "1A", "literature": ["27857962", "11389482"], "variantId": "19_38499645_GGAGGAG_GGAG", "variantRsId": "rs121918596", "variantFunctionalConsequenceId": "inframe_deletion", "targetFromSourceId": "ENSG00000196218", "genotype": "GAG/GAG", "genotypeAnnotationText": "Patients with the rs121918596 GAG/GAG genotype may have a decreased, but not absent, risk for malignant hyperthermia based on this variant when treated with volatile anesthetics (desflurane, enflurane, halothane, isoflurane, methoxyflurane, sevoflurane) and/or succinylcholine as compared to patients with the del/del or del/GAG genotypes. Other genetic or clinical factors may also influence the risk for malignant hyperthermia.", "drugFromSource": "enflurane", "drugId": "http://purl.obolibrary.org/obo/CHEBI_4792", "pgxCategory": "Toxicity", "phenotypeText": "Malignant Hyperthermia", "phenotypeFromSourceId": "http://www.orpha.net/ORDO/Orphanet_423"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1449309937", "evidenceLevel": "1A", "literature": ["27857962", "11389482"], "variantId": "19_38499645_GGAGGAG_GGAG", "variantRsId": "rs121918596", "variantFunctionalConsequenceId": "inframe_deletion", "targetFromSourceId": "ENSG00000196218", "genotype": "del/GAG", "genotypeAnnotationText": "Patients with the rs121918596 del/GAG genotype may develop malignant hyperthermia when treated with volatile anesthetics (desflurane, enflurane, halothane, isoflurane, methoxyflurane, sevoflurane) and/or succinylcholine as compared to patients with the GAG/GAG genotype. Other genetic or clinical factors may also influence the risk for malignant hyperthermia.", "drugFromSource": "enflurane", "drugId": "http://purl.obolibrary.org/obo/CHEBI_4792", "pgxCategory": "Toxicity", "phenotypeText": "Malignant Hyperthermia", "phenotypeFromSourceId": "http://www.orpha.net/ORDO/Orphanet_423"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1449309937", "evidenceLevel": "1A", "literature": ["27857962", "11389482"], "variantId": "19_38499645_GGAGGAG_GGAG", "variantRsId": "rs121918596", "variantFunctionalConsequenceId": "inframe_deletion", "targetFromSourceId": "ENSG00000196218", "genotype": "del/del", "genotypeAnnotationText": "Patients with the rs121918596 del/del genotype may develop malignant hyperthermia when treated with volatile anesthetics (desflurane, enflurane, halothane, isoflurane, methoxyflurane, sevoflurane) and/or succinylcholine as compared to patients with the GAG/GAG genotype. Other genetic or clinical factors may also influence the risk for malignant hyperthermia.", "drugFromSource": "enflurane", "drugId": "http://purl.obolibrary.org/obo/CHEBI_4792", "pgxCategory": "Toxicity", "phenotypeText": "Malignant Hyperthermia", "phenotypeFromSourceId": "http://www.orpha.net/ORDO/Orphanet_423"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1449309937", "evidenceLevel": "1A", "literature": ["27857962", "11389482"], "variantId": "19_38499645_GGAGGAG_GGAG", "variantRsId": "rs121918596", "variantFunctionalConsequenceId": "inframe_deletion", "targetFromSourceId": "ENSG00000196218", "genotype": "GAG/GAG", "genotypeAnnotationText": "Patients with the rs121918596 GAG/GAG genotype may have a decreased, but not absent, risk for malignant hyperthermia based on this variant when treated with volatile anesthetics (desflurane, enflurane, halothane, isoflurane, methoxyflurane, sevoflurane) and/or succinylcholine as compared to patients with the del/del or del/GAG genotypes. Other genetic or clinical factors may also influence the risk for malignant hyperthermia.", "drugFromSource": "halothane", "drugId": "http://purl.obolibrary.org/obo/CHEBI_5615", "pgxCategory": "Toxicity", "phenotypeText": "Malignant Hyperthermia", "phenotypeFromSourceId": "http://www.orpha.net/ORDO/Orphanet_423"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1449309937", "evidenceLevel": "1A", "literature": ["27857962", "11389482"], "variantId": "19_38499645_GGAGGAG_GGAG", "variantRsId": "rs121918596", "variantFunctionalConsequenceId": "inframe_deletion", "targetFromSourceId": "ENSG00000196218", "genotype": "del/GAG", "genotypeAnnotationText": "Patients with the rs121918596 del/GAG genotype may develop malignant hyperthermia when treated with volatile anesthetics (desflurane, enflurane, halothane, isoflurane, methoxyflurane, sevoflurane) and/or succinylcholine as compared to patients with the GAG/GAG genotype. Other genetic or clinical factors may also influence the risk for malignant hyperthermia.", "drugFromSource": "halothane", "drugId": "http://purl.obolibrary.org/obo/CHEBI_5615", "pgxCategory": "Toxicity", "phenotypeText": "Malignant Hyperthermia", "phenotypeFromSourceId": "http://www.orpha.net/ORDO/Orphanet_423"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1449309937", "evidenceLevel": "1A", "literature": ["27857962", "11389482"], "variantId": "19_38499645_GGAGGAG_GGAG", "variantRsId": "rs121918596", "variantFunctionalConsequenceId": "inframe_deletion", "targetFromSourceId": "ENSG00000196218", "genotype": "del/del", "genotypeAnnotationText": "Patients with the rs121918596 del/del genotype may develop malignant hyperthermia when treated with volatile anesthetics (desflurane, enflurane, halothane, isoflurane, methoxyflurane, sevoflurane) and/or succinylcholine as compared to patients with the GAG/GAG genotype. Other genetic or clinical factors may also influence the risk for malignant hyperthermia.", "drugFromSource": "halothane", "drugId": "http://purl.obolibrary.org/obo/CHEBI_5615", "pgxCategory": "Toxicity", "phenotypeText": "Malignant Hyperthermia", "phenotypeFromSourceId": "http://www.orpha.net/ORDO/Orphanet_423"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1449309937", "evidenceLevel": "1A", "literature": ["27857962", "11389482"], "variantId": "19_38499645_GGAGGAG_GGAG", "variantRsId": "rs121918596", "variantFunctionalConsequenceId": "inframe_deletion", "targetFromSourceId": "ENSG00000196218", "genotype": "GAG/GAG", "genotypeAnnotationText": "Patients with the rs121918596 GAG/GAG genotype may have a decreased, but not absent, risk for malignant hyperthermia based on this variant when treated with volatile anesthetics (desflurane, enflurane, halothane, isoflurane, methoxyflurane, sevoflurane) and/or succinylcholine as compared to patients with the del/del or del/GAG genotypes. Other genetic or clinical factors may also influence the risk for malignant hyperthermia.", "drugFromSource": "isoflurane", "drugId": "http://purl.obolibrary.org/obo/CHEBI_6015", "pgxCategory": "Toxicity", "phenotypeText": "Malignant Hyperthermia", "phenotypeFromSourceId": "http://www.orpha.net/ORDO/Orphanet_423"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1449309937", "evidenceLevel": "1A", "literature": ["27857962", "11389482"], "variantId": "19_38499645_GGAGGAG_GGAG", "variantRsId": "rs121918596", "variantFunctionalConsequenceId": "inframe_deletion", "targetFromSourceId": "ENSG00000196218", "genotype": "del/GAG", "genotypeAnnotationText": "Patients with the rs121918596 del/GAG genotype may develop malignant hyperthermia when treated with volatile anesthetics (desflurane, enflurane, halothane, isoflurane, methoxyflurane, sevoflurane) and/or succinylcholine as compared to patients with the GAG/GAG genotype. Other genetic or clinical factors may also influence the risk for malignant hyperthermia.", "drugFromSource": "isoflurane", "drugId": "http://purl.obolibrary.org/obo/CHEBI_6015", "pgxCategory": "Toxicity", "phenotypeText": "Malignant Hyperthermia", "phenotypeFromSourceId": "http://www.orpha.net/ORDO/Orphanet_423"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1449309937", "evidenceLevel": "1A", "literature": ["27857962", "11389482"], "variantId": "19_38499645_GGAGGAG_GGAG", "variantRsId": "rs121918596", "variantFunctionalConsequenceId": "inframe_deletion", "targetFromSourceId": "ENSG00000196218", "genotype": "del/del", "genotypeAnnotationText": "Patients with the rs121918596 del/del genotype may develop malignant hyperthermia when treated with volatile anesthetics (desflurane, enflurane, halothane, isoflurane, methoxyflurane, sevoflurane) and/or succinylcholine as compared to patients with the GAG/GAG genotype. Other genetic or clinical factors may also influence the risk for malignant hyperthermia.", "drugFromSource": "isoflurane", "drugId": "http://purl.obolibrary.org/obo/CHEBI_6015", "pgxCategory": "Toxicity", "phenotypeText": "Malignant Hyperthermia", "phenotypeFromSourceId": "http://www.orpha.net/ORDO/Orphanet_423"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1449309937", "evidenceLevel": "1A", "literature": ["27857962", "11389482"], "variantId": "19_38499645_GGAGGAG_GGAG", "variantRsId": "rs121918596", "variantFunctionalConsequenceId": "inframe_deletion", "targetFromSourceId": "ENSG00000196218", "genotype": "GAG/GAG", "genotypeAnnotationText": "Patients with the rs121918596 GAG/GAG genotype may have a decreased, but not absent, risk for malignant hyperthermia based on this variant when treated with volatile anesthetics (desflurane, enflurane, halothane, isoflurane, methoxyflurane, sevoflurane) and/or succinylcholine as compared to patients with the del/del or del/GAG genotypes. Other genetic or clinical factors may also influence the risk for malignant hyperthermia.", "drugFromSource": "methoxyflurane", "drugId": "http://purl.obolibrary.org/obo/CHEBI_6843", "pgxCategory": "Toxicity", "phenotypeText": "Malignant Hyperthermia", "phenotypeFromSourceId": "http://www.orpha.net/ORDO/Orphanet_423"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1449309937", "evidenceLevel": "1A", "literature": ["27857962", "11389482"], "variantId": "19_38499645_GGAGGAG_GGAG", "variantRsId": "rs121918596", "variantFunctionalConsequenceId": "inframe_deletion", "targetFromSourceId": "ENSG00000196218", "genotype": "del/GAG", "genotypeAnnotationText": "Patients with the rs121918596 del/GAG genotype may develop malignant hyperthermia when treated with volatile anesthetics (desflurane, enflurane, halothane, isoflurane, methoxyflurane, sevoflurane) and/or succinylcholine as compared to patients with the GAG/GAG genotype. Other genetic or clinical factors may also influence the risk for malignant hyperthermia.", "drugFromSource": "methoxyflurane", "drugId": "http://purl.obolibrary.org/obo/CHEBI_6843", "pgxCategory": "Toxicity", "phenotypeText": "Malignant Hyperthermia", "phenotypeFromSourceId": "http://www.orpha.net/ORDO/Orphanet_423"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1449309937", "evidenceLevel": "1A", "literature": ["27857962", "11389482"], "variantId": "19_38499645_GGAGGAG_GGAG", "variantRsId": "rs121918596", "variantFunctionalConsequenceId": "inframe_deletion", "targetFromSourceId": "ENSG00000196218", "genotype": "del/del", "genotypeAnnotationText": "Patients with the rs121918596 del/del genotype may develop malignant hyperthermia when treated with volatile anesthetics (desflurane, enflurane, halothane, isoflurane, methoxyflurane, sevoflurane) and/or succinylcholine as compared to patients with the GAG/GAG genotype. Other genetic or clinical factors may also influence the risk for malignant hyperthermia.", "drugFromSource": "methoxyflurane", "drugId": "http://purl.obolibrary.org/obo/CHEBI_6843", "pgxCategory": "Toxicity", "phenotypeText": "Malignant Hyperthermia", "phenotypeFromSourceId": "http://www.orpha.net/ORDO/Orphanet_423"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1449309937", "evidenceLevel": "1A", "literature": ["27857962", "11389482"], "variantId": "19_38499645_GGAGGAG_GGAG", "variantRsId": "rs121918596", "variantFunctionalConsequenceId": "inframe_deletion", "targetFromSourceId": "ENSG00000196218", "genotype": "GAG/GAG", "genotypeAnnotationText": "Patients with the rs121918596 GAG/GAG genotype may have a decreased, but not absent, risk for malignant hyperthermia based on this variant when treated with volatile anesthetics (desflurane, enflurane, halothane, isoflurane, methoxyflurane, sevoflurane) and/or succinylcholine as compared to patients with the del/del or del/GAG genotypes. Other genetic or clinical factors may also influence the risk for malignant hyperthermia.", "drugFromSource": "sevoflurane", "drugId": "http://purl.obolibrary.org/obo/CHEBI_9130", "pgxCategory": "Toxicity", "phenotypeText": "Malignant Hyperthermia", "phenotypeFromSourceId": "http://www.orpha.net/ORDO/Orphanet_423"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1449309937", "evidenceLevel": "1A", "literature": ["27857962", "11389482"], "variantId": "19_38499645_GGAGGAG_GGAG", "variantRsId": "rs121918596", "variantFunctionalConsequenceId": "inframe_deletion", "targetFromSourceId": "ENSG00000196218", "genotype": "del/GAG", "genotypeAnnotationText": "Patients with the rs121918596 del/GAG genotype may develop malignant hyperthermia when treated with volatile anesthetics (desflurane, enflurane, halothane, isoflurane, methoxyflurane, sevoflurane) and/or succinylcholine as compared to patients with the GAG/GAG genotype. Other genetic or clinical factors may also influence the risk for malignant hyperthermia.", "drugFromSource": "sevoflurane", "drugId": "http://purl.obolibrary.org/obo/CHEBI_9130", "pgxCategory": "Toxicity", "phenotypeText": "Malignant Hyperthermia", "phenotypeFromSourceId": "http://www.orpha.net/ORDO/Orphanet_423"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1449309937", "evidenceLevel": "1A", "literature": ["27857962", "11389482"], "variantId": "19_38499645_GGAGGAG_GGAG", "variantRsId": "rs121918596", "variantFunctionalConsequenceId": "inframe_deletion", "targetFromSourceId": "ENSG00000196218", "genotype": "del/del", "genotypeAnnotationText": "Patients with the rs121918596 del/del genotype may develop malignant hyperthermia when treated with volatile anesthetics (desflurane, enflurane, halothane, isoflurane, methoxyflurane, sevoflurane) and/or succinylcholine as compared to patients with the GAG/GAG genotype. Other genetic or clinical factors may also influence the risk for malignant hyperthermia.", "drugFromSource": "sevoflurane", "drugId": "http://purl.obolibrary.org/obo/CHEBI_9130", "pgxCategory": "Toxicity", "phenotypeText": "Malignant Hyperthermia", "phenotypeFromSourceId": "http://www.orpha.net/ORDO/Orphanet_423"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1449309937", "evidenceLevel": "1A", "literature": ["27857962", "11389482"], "variantId": "19_38499645_GGAGGAG_GGAG", "variantRsId": "rs121918596", "variantFunctionalConsequenceId": "inframe_deletion", "targetFromSourceId": "ENSG00000196218", "genotype": "GAG/GAG", "genotypeAnnotationText": "Patients with the rs121918596 GAG/GAG genotype may have a decreased, but not absent, risk for malignant hyperthermia based on this variant when treated with volatile anesthetics (desflurane, enflurane, halothane, isoflurane, methoxyflurane, sevoflurane) and/or succinylcholine as compared to patients with the del/del or del/GAG genotypes. Other genetic or clinical factors may also influence the risk for malignant hyperthermia.", "drugFromSource": "succinylcholine", "drugId": "http://purl.obolibrary.org/obo/CHEBI_45652", "pgxCategory": "Toxicity", "phenotypeText": "Malignant Hyperthermia", "phenotypeFromSourceId": "http://www.orpha.net/ORDO/Orphanet_423"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1449309937", "evidenceLevel": "1A", "literature": ["27857962", "11389482"], "variantId": "19_38499645_GGAGGAG_GGAG", "variantRsId": "rs121918596", "variantFunctionalConsequenceId": "inframe_deletion", "targetFromSourceId": "ENSG00000196218", "genotype": "del/GAG", "genotypeAnnotationText": "Patients with the rs121918596 del/GAG genotype may develop malignant hyperthermia when treated with volatile anesthetics (desflurane, enflurane, halothane, isoflurane, methoxyflurane, sevoflurane) and/or succinylcholine as compared to patients with the GAG/GAG genotype. Other genetic or clinical factors may also influence the risk for malignant hyperthermia.", "drugFromSource": "succinylcholine", "drugId": "http://purl.obolibrary.org/obo/CHEBI_45652", "pgxCategory": "Toxicity", "phenotypeText": "Malignant Hyperthermia", "phenotypeFromSourceId": "http://www.orpha.net/ORDO/Orphanet_423"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1449309937", "evidenceLevel": "1A", "literature": ["27857962", "11389482"], "variantId": "19_38499645_GGAGGAG_GGAG", "variantRsId": "rs121918596", "variantFunctionalConsequenceId": "inframe_deletion", "targetFromSourceId": "ENSG00000196218", "genotype": "del/del", "genotypeAnnotationText": "Patients with the rs121918596 del/del genotype may develop malignant hyperthermia when treated with volatile anesthetics (desflurane, enflurane, halothane, isoflurane, methoxyflurane, sevoflurane) and/or succinylcholine as compared to patients with the GAG/GAG genotype. Other genetic or clinical factors may also influence the risk for malignant hyperthermia.", "drugFromSource": "succinylcholine", "drugId": "http://purl.obolibrary.org/obo/CHEBI_45652", "pgxCategory": "Toxicity", "phenotypeText": "Malignant Hyperthermia", "phenotypeFromSourceId": "http://www.orpha.net/ORDO/Orphanet_423"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1447680028", "evidenceLevel": "3", "literature": ["26633805"], "variantId": "6_29830805_-_ATTTGTTCATGCCT", "variantRsId": "rs371194629", "genotype": "ATTTGTTCATGCCT/ATTTGTTCATGCCT", "genotypeAnnotationText": "Patients with colorectal cancer and the HLA-G ATTTGTTCATGCCT/ATTTGTTCATGCCT genotype may have better response to capecitabine or fluorouracil as compared to patients with the HLA-G del/del genotypes. Other clinical and genetic factors may also influence response to capecitabine or fluorouracil in patients with colorectal cancer.", "drugFromSource": "capecitabine", "drugId": "http://purl.obolibrary.org/obo/CHEBI_31348", "pgxCategory": "Efficacy", "phenotypeText": "Colorectal Neoplasms"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1447680028", "evidenceLevel": "3", "literature": ["26633805"], "variantId": "6_29830805_-_ATTTGTTCATGCCT", "variantRsId": "rs371194629", "genotype": "del/ATTTGTTCATGCCT", "genotypeAnnotationText": "Patients with colorectal cancer and the HLA-G del/ATTTGTTCATGCCT genotype may have better response to capecitabine or fluorouracil as compared to patients with the HLA-G del/del genotypes. Other clinical and genetic factors may also influence response to capecitabine or fluorouracil in patients with colorectal cancer.", "drugFromSource": "capecitabine", "drugId": "http://purl.obolibrary.org/obo/CHEBI_31348", "pgxCategory": "Efficacy", "phenotypeText": "Colorectal Neoplasms"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1447680028", "evidenceLevel": "3", "literature": ["26633805"], "variantId": "6_29830805_-_ATTTGTTCATGCCT", "variantRsId": "rs371194629", "genotype": "del/del", "genotypeAnnotationText": "Patients with colorectal cancer and the HLA-G del/del genotype may have a worse response to capecitabine or fluorouracil as compared to patients with the HLA-G del/ATTTGTTCATGCCT or ATTTGTTCATGCCT/ATTTGTTCATGCCT genotypes. Other clinical and genetic factors may also influence response to capecitabine or fluorouracil in patients with colorectal cancer.", "drugFromSource": "capecitabine", "drugId": "http://purl.obolibrary.org/obo/CHEBI_31348", "pgxCategory": "Efficacy", "phenotypeText": "Colorectal Neoplasms"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1447680028", "evidenceLevel": "3", "literature": ["26633805"], "variantId": "6_29830805_-_ATTTGTTCATGCCT", "variantRsId": "rs371194629", "genotype": "ATTTGTTCATGCCT/ATTTGTTCATGCCT", "genotypeAnnotationText": "Patients with colorectal cancer and the HLA-G ATTTGTTCATGCCT/ATTTGTTCATGCCT genotype may have better response to capecitabine or fluorouracil as compared to patients with the HLA-G del/del genotypes. Other clinical and genetic factors may also influence response to capecitabine or fluorouracil in patients with colorectal cancer.", "drugFromSource": "fluorouracil", "drugId": "http://purl.obolibrary.org/obo/CHEBI_46345", "pgxCategory": "Efficacy", "phenotypeText": "Colorectal Neoplasms"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1447680028", "evidenceLevel": "3", "literature": ["26633805"], "variantId": "6_29830805_-_ATTTGTTCATGCCT", "variantRsId": "rs371194629", "genotype": "del/ATTTGTTCATGCCT", "genotypeAnnotationText": "Patients with colorectal cancer and the HLA-G del/ATTTGTTCATGCCT genotype may have better response to capecitabine or fluorouracil as compared to patients with the HLA-G del/del genotypes. Other clinical and genetic factors may also influence response to capecitabine or fluorouracil in patients with colorectal cancer.", "drugFromSource": "fluorouracil", "drugId": "http://purl.obolibrary.org/obo/CHEBI_46345", "pgxCategory": "Efficacy", "phenotypeText": "Colorectal Neoplasms"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1447680028", "evidenceLevel": "3", "literature": ["26633805"], "variantId": "6_29830805_-_ATTTGTTCATGCCT", "variantRsId": "rs371194629", "genotype": "del/del", "genotypeAnnotationText": "Patients with colorectal cancer and the HLA-G del/del genotype may have a worse response to capecitabine or fluorouracil as compared to patients with the HLA-G del/ATTTGTTCATGCCT or ATTTGTTCATGCCT/ATTTGTTCATGCCT genotypes. Other clinical and genetic factors may also influence response to capecitabine or fluorouracil in patients with colorectal cancer.", "drugFromSource": "fluorouracil", "drugId": "http://purl.obolibrary.org/obo/CHEBI_46345", "pgxCategory": "Efficacy", "phenotypeText": "Colorectal Neoplasms"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2 or 2R/2R genotype may have an increased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 2R/3R or 3R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugFromSource": "fluorouracil", "drugId": "http://purl.obolibrary.org/obo/CHEBI_46345", "pgxCategory": "Efficacy", "phenotypeText": "overall survival"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3 or 2R/3R genotype may have an increased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 3R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugFromSource": "fluorouracil", "drugId": "http://purl.obolibrary.org/obo/CHEBI_46345", "pgxCategory": "Efficacy", "phenotypeText": "overall survival"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)3/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3 or 3R/3R genotype may have a decreased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 2R/2R or 2R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugFromSource": "fluorouracil", "drugId": "http://purl.obolibrary.org/obo/CHEBI_46345", "pgxCategory": "Efficacy", "phenotypeText": "overall survival"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2 or 2R/2R genotype may have an increased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 2R/3R or 3R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugFromSource": "FOLFIRI", "pgxCategory": "Efficacy", "phenotypeText": "overall survival"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3 or 2R/3R genotype may have an increased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 3R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugFromSource": "FOLFIRI", "pgxCategory": "Efficacy", "phenotypeText": "overall survival"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)3/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3 or 3R/3R genotype may have a decreased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 2R/2R or 2R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugFromSource": "FOLFIRI", "pgxCategory": "Efficacy", "phenotypeText": "overall survival"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2 or 2R/2R genotype may have an increased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 2R/3R or 3R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugFromSource": "FOLFOX", "pgxCategory": "Efficacy", "phenotypeText": "overall survival"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3 or 2R/3R genotype may have an increased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 3R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugFromSource": "FOLFOX", "pgxCategory": "Efficacy", "phenotypeText": "overall survival"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)3/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3 or 3R/3R genotype may have a decreased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 2R/2R or 2R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugFromSource": "FOLFOX", "pgxCategory": "Efficacy", "phenotypeText": "overall survival"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2 or 2R/2R genotype may have an increased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 2R/3R or 3R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugFromSource": "fluorouracil", "drugId": "http://purl.obolibrary.org/obo/CHEBI_46345", "pgxCategory": "Efficacy", "phenotypeText": "progression-free survival"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3 or 2R/3R genotype may have an increased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 3R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugFromSource": "fluorouracil", "drugId": "http://purl.obolibrary.org/obo/CHEBI_46345", "pgxCategory": "Efficacy", "phenotypeText": "progression-free survival"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)3/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3 or 3R/3R genotype may have a decreased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 2R/2R or 2R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugFromSource": "fluorouracil", "drugId": "http://purl.obolibrary.org/obo/CHEBI_46345", "pgxCategory": "Efficacy", "phenotypeText": "progression-free survival"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2 or 2R/2R genotype may have an increased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 2R/3R or 3R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugFromSource": "FOLFIRI", "pgxCategory": "Efficacy", "phenotypeText": "progression-free survival"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3 or 2R/3R genotype may have an increased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 3R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugFromSource": "FOLFIRI", "pgxCategory": "Efficacy", "phenotypeText": "progression-free survival"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)3/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3 or 3R/3R genotype may have a decreased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 2R/2R or 2R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugFromSource": "FOLFIRI", "pgxCategory": "Efficacy", "phenotypeText": "progression-free survival"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2 or 2R/2R genotype may have an increased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 2R/3R or 3R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugFromSource": "FOLFOX", "pgxCategory": "Efficacy", "phenotypeText": "progression-free survival"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3 or 2R/3R genotype may have an increased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 3R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugFromSource": "FOLFOX", "pgxCategory": "Efficacy", "phenotypeText": "progression-free survival"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1451114960", "evidenceLevel": "3", "literature": ["19384296", "21919605", "20385995", "20165956", "20932673", "14522928", "15918040", "21167658", "20665215", "25232828", "16249645", "11913730", "28972045"], "variantRsId": "rs45445694", "genotype": "(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3", "genotypeAnnotationText": "Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)3/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3 or 3R/3R genotype may have a decreased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 2R/2R or 2R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy.", "drugFromSource": "FOLFOX", "pgxCategory": "Efficacy", "phenotypeText": "progression-free survival"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1444668808", "evidenceLevel": "3", "literature": ["11593098", "11910301"], "variantId": "17_63488530_ATACAGTCACTTTT_ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCATACAGTCACTTTT", "variantRsId": "rs1799752", "variantFunctionalConsequenceId": "intron_variant", "targetFromSourceId": "ENSG00000159640", "genotype": "ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC", "genotypeAnnotationText": "Hypertensive patients with the rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC genotype may have an increased response to irbesartan as compared to patients with the ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/del or del/del genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to irbesartan.", "drugFromSource": "irbesartan", "drugId": "http://purl.obolibrary.org/obo/CHEBI_5959", "pgxCategory": "Efficacy", "phenotypeText": "Hypertension", "phenotypeFromSourceId": "http://www.ebi.ac.uk/efo/EFO_0000537"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1444668808", "evidenceLevel": "3", "literature": ["11593098", "11910301"], "variantId": "17_63488530_ATACAGTCACTTTT_ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCATACAGTCACTTTT", "variantRsId": "rs1799752", "variantFunctionalConsequenceId": "intron_variant", "targetFromSourceId": "ENSG00000159640", "genotype": "ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/del", "genotypeAnnotationText": "Hypertensive patients with the rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/del genotype may have a decreased response to irbesartan as compared to patients with the ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to irbesartan.", "drugFromSource": "irbesartan", "drugId": "http://purl.obolibrary.org/obo/CHEBI_5959", "pgxCategory": "Efficacy", "phenotypeText": "Hypertension", "phenotypeFromSourceId": "http://www.ebi.ac.uk/efo/EFO_0000537"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1444668808", "evidenceLevel": "3", "literature": ["11593098", "11910301"], "variantId": "17_63488530_ATACAGTCACTTTT_ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCATACAGTCACTTTT", "variantRsId": "rs1799752", "variantFunctionalConsequenceId": "intron_variant", "targetFromSourceId": "ENSG00000159640", "genotype": "del/del", "genotypeAnnotationText": "Hypertensive patients with the rs1799752 del/del genotype may have a decreased response to irbesartan as compared to patients with the ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to irbesartan.", "drugFromSource": "irbesartan", "drugId": "http://purl.obolibrary.org/obo/CHEBI_5959", "pgxCategory": "Efficacy", "phenotypeText": "Hypertension", "phenotypeFromSourceId": "http://www.ebi.ac.uk/efo/EFO_0000537"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1444668808", "evidenceLevel": "3", "literature": ["11593098", "11910301"], "variantId": "17_63488530_ATACAGTCACTTTT_ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCATACAGTCACTTTT", "variantRsId": "rs1799752", "variantFunctionalConsequenceId": "intron_variant", "targetFromSourceId": "ENSG00000159640", "genotype": "ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC", "genotypeAnnotationText": "Hypertensive patients with the rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC genotype may have an increased response to irbesartan as compared to patients with the ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/del or del/del genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to irbesartan.", "drugFromSource": "irbesartan", "drugId": "http://purl.obolibrary.org/obo/CHEBI_5959", "pgxCategory": "Efficacy", "phenotypeText": "Hypertrophy, Left Ventricular"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1444668808", "evidenceLevel": "3", "literature": ["11593098", "11910301"], "variantId": "17_63488530_ATACAGTCACTTTT_ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCATACAGTCACTTTT", "variantRsId": "rs1799752", "variantFunctionalConsequenceId": "intron_variant", "targetFromSourceId": "ENSG00000159640", "genotype": "ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/del", "genotypeAnnotationText": "Hypertensive patients with the rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/del genotype may have a decreased response to irbesartan as compared to patients with the ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to irbesartan.", "drugFromSource": "irbesartan", "drugId": "http://purl.obolibrary.org/obo/CHEBI_5959", "pgxCategory": "Efficacy", "phenotypeText": "Hypertrophy, Left Ventricular"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1444668808", "evidenceLevel": "3", "literature": ["11593098", "11910301"], "variantId": "17_63488530_ATACAGTCACTTTT_ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCATACAGTCACTTTT", "variantRsId": "rs1799752", "variantFunctionalConsequenceId": "intron_variant", "targetFromSourceId": "ENSG00000159640", "genotype": "del/del", "genotypeAnnotationText": "Hypertensive patients with the rs1799752 del/del genotype may have a decreased response to irbesartan as compared to patients with the ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to irbesartan.", "drugFromSource": "irbesartan", "drugId": "http://purl.obolibrary.org/obo/CHEBI_5959", "pgxCategory": "Efficacy", "phenotypeText": "Hypertrophy, Left Ventricular"} \ No newline at end of file From f33c21ad80be6699e9d5879d6eaa30f0f35ac638 Mon Sep 17 00:00:00 2001 From: April Shen Date: Wed, 5 Jul 2023 15:17:40 +0100 Subject: [PATCH 05/13] debug output genes table --- opentargets_pharmgkb/evidence_generation.py | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/opentargets_pharmgkb/evidence_generation.py b/opentargets_pharmgkb/evidence_generation.py index 302db12..abb58f6 100644 --- a/opentargets_pharmgkb/evidence_generation.py +++ b/opentargets_pharmgkb/evidence_generation.py @@ -55,7 +55,7 @@ def pipeline(clinical_annot_path, clinical_alleles_path, clinical_evidence_path, output.write('\n'.join(json.dumps(ev) for ev in evidence)) # Final count report - gene_comparison_counts(evidence_table, counts) + gene_comparison_counts(evidence_table, counts, debug_path=f'{output_path}_genes.csv') counts.report() @@ -235,7 +235,7 @@ def generate_clinical_annotation_evidence(created_date, row): return evidence_string -def gene_comparison_counts(df, counts): +def gene_comparison_counts(df, counts, debug_path=None): # Map PGKB genes mapped_genes = explode_and_map_genes(df) # Re-group by ID column @@ -245,3 +245,6 @@ def gene_comparison_counts(df, counts): ) # Compare sets of genes counts.pgkb_vep_gene_diff = len(genes_table[genes_table['all_pgkb_genes'] != genes_table['all_vep_genes']]) + # Debug dump genes table + if debug_path: + genes_table.to_csv(debug_path) From f9fa1ff900d077662a81343ed0f0e9538cb0ecd7 Mon Sep 17 00:00:00 2001 From: April Shen Date: Wed, 5 Jul 2023 15:45:32 +0100 Subject: [PATCH 06/13] update requirements --- requirements.txt | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/requirements.txt b/requirements.txt index 95187f5..d06e9f7 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,6 +1,6 @@ numpy==1.24.3 pandas==1.5.3 pytest==7.2.2 -requests==2.28.2 +requests==2.31.0 retry==0.9.2 -cmat @ git+https://github.com/apriltuesday/eva-opentargets.git@refactor#egg=cmat \ No newline at end of file +cmat @ git+https://github.com/EBIvariation/eva-opentargets.git#egg=cmat \ No newline at end of file From 90cbe16ca9bf2d5538c4ccef9ed1bc560e9e7e66 Mon Sep 17 00:00:00 2001 From: April Shen Date: Wed, 5 Jul 2023 16:24:26 +0100 Subject: [PATCH 07/13] simplify command line args --- README.md | 11 +++++++++++ bin/generate_evidence.py | 10 ++-------- opentargets_pharmgkb/evidence_generation.py | 9 ++++++++- tests/test_evidence_generation.py | 5 +---- 4 files changed, 22 insertions(+), 13 deletions(-) diff --git a/README.md b/README.md index 37b422c..05374b8 100644 --- a/README.md +++ b/README.md @@ -1,2 +1,13 @@ # opentargets-pharmgkb Pipeline to provide evidence strings for Open Targets from PharmGKB + +Download data: +``` +wget https://api.pharmgkb.org/v1/download/file/data/clinicalAnnotations.zip +wget https://api.pharmgkb.org/v1/download/file/data/drugs.zip + +unzip -j clinicalAnnotations.zip "*.tsv" -d . +unzip -j clinicalAnnotations.zip "CREATED*.txt" -d . +unzip -j drugs.zip "*.tsv" -d . +rm clinicalAnnotations.zip drugs.zip +``` \ No newline at end of file diff --git a/bin/generate_evidence.py b/bin/generate_evidence.py index 89a5664..3100eee 100644 --- a/bin/generate_evidence.py +++ b/bin/generate_evidence.py @@ -4,10 +4,7 @@ from opentargets_pharmgkb import evidence_generation parser = argparse.ArgumentParser('Generates Open Targets evidence strings from PharmGKB data') -parser.add_argument('--clinical-annot-path', help='Path to clinical_annotations.tsv', required=True) -parser.add_argument('--clinical-alleles-path', help='Path to clinical_ann_alleles.tsv', required=True) -parser.add_argument('--clinical-evidence-path', help='Path to clinical_ann_evidence.tsv', required=True) -parser.add_argument('--drugs-path', help='Path to drugs.tsv', required=True) +parser.add_argument('--data-dir', help='Directory containing necessary .tsv files from PharmGKB', required=True) parser.add_argument('--created-date', help='Created date of downloaded files (provided by PharmGKB)', required=True) parser.add_argument('--output-path', help='Path to output evidence strings', required=True) @@ -15,10 +12,7 @@ if __name__ == '__main__': args = parser.parse_args() evidence_generation.pipeline( - clinical_annot_path=args.clinical_annot_path, - clinical_alleles_path=args.clinical_alleles_path, - clinical_evidence_path=args.clinical_evidence_path, - drugs_path=args.drugs_path, + data_dir=args.data_dir, created_date=args.created_date, output_path=args.output_path ) diff --git a/opentargets_pharmgkb/evidence_generation.py b/opentargets_pharmgkb/evidence_generation.py index abb58f6..b31f64d 100644 --- a/opentargets_pharmgkb/evidence_generation.py +++ b/opentargets_pharmgkb/evidence_generation.py @@ -1,5 +1,6 @@ import json import multiprocessing +import os from itertools import zip_longest import pandas as pd @@ -14,7 +15,13 @@ ID_COL_NAME = 'Clinical Annotation ID' -def pipeline(clinical_annot_path, clinical_alleles_path, clinical_evidence_path, drugs_path, created_date, output_path): +def pipeline(data_dir, created_date, output_path): + # TODO test file existence + clinical_annot_path = os.path.join(data_dir, 'clinical_annotations.tsv') + clinical_alleles_path = os.path.join(data_dir, 'clinical_ann_alleles.tsv') + clinical_evidence_path = os.path.join(data_dir, 'clinical_ann_evidence.tsv') + drugs_path = os.path.join(data_dir, 'drugs.tsv') + clinical_annot_table = read_tsv_to_df(clinical_annot_path) clinical_alleles_table = read_tsv_to_df(clinical_alleles_path) clinical_evidence_table = read_tsv_to_df(clinical_evidence_path) diff --git a/tests/test_evidence_generation.py b/tests/test_evidence_generation.py index 4e2e032..8a4d34a 100644 --- a/tests/test_evidence_generation.py +++ b/tests/test_evidence_generation.py @@ -31,10 +31,7 @@ def test_pipeline(): output_path = os.path.join(resources_dir, 'test_output.json') expected_path = os.path.join(resources_dir, 'expected_output.json') evidence_generation.pipeline( - clinical_annot_path=os.path.join(resources_dir, 'clinical_annotations.tsv'), - clinical_alleles_path=os.path.join(resources_dir, 'clinical_ann_alleles.tsv'), - clinical_evidence_path=os.path.join(resources_dir, 'clinical_ann_evidence.tsv'), - drugs_path=os.path.join(resources_dir, 'drugs.tsv'), + data_dir=resources_dir, created_date='2023-03-23', output_path=output_path ) From 233a7fc9944e7d6ad37ebc41fe0a76518fb7556e Mon Sep 17 00:00:00 2001 From: April Shen Date: Thu, 6 Jul 2023 11:54:13 +0100 Subject: [PATCH 08/13] fix explode_column for nan --- opentargets_pharmgkb/pandas_utils.py | 3 ++- tests/test_pandas_utils.py | 7 +++++-- 2 files changed, 7 insertions(+), 3 deletions(-) diff --git a/opentargets_pharmgkb/pandas_utils.py b/opentargets_pharmgkb/pandas_utils.py index 582952a..179dbfb 100644 --- a/opentargets_pharmgkb/pandas_utils.py +++ b/opentargets_pharmgkb/pandas_utils.py @@ -1,4 +1,5 @@ import numpy as np +import pandas as pd def none_to_nan(x): @@ -17,5 +18,5 @@ def explode_column(df, source_col, target_col, sep=';'): :return: dataframe with target_col added """ split_cols = df.assign(**{target_col: df[source_col].str.split(sep)}).explode(target_col).reset_index(drop=True) - split_cols[target_col] = split_cols[target_col].map(lambda x: x.strip()) + split_cols[target_col] = split_cols[target_col].map(lambda x: str(x).strip() if pd.notna(x) else np.nan) return split_cols diff --git a/tests/test_pandas_utils.py b/tests/test_pandas_utils.py index 2390e73..443ecbe 100644 --- a/tests/test_pandas_utils.py +++ b/tests/test_pandas_utils.py @@ -1,3 +1,4 @@ +import numpy as np import pandas as pd from opentargets_pharmgkb.pandas_utils import explode_column @@ -7,7 +8,8 @@ def test_explode_column(): df = pd.DataFrame([ [1, 'apple; pear; banana'], [2, 'cat;frog'], - [3, 'something'] + [3, 'something'], + [4, np.nan] ], columns=['A', 'B']) expected = pd.DataFrame([ @@ -16,7 +18,8 @@ def test_explode_column(): [1, 'apple; pear; banana', 'banana'], [2, 'cat;frog', 'cat'], [2, 'cat;frog', 'frog'], - [3, 'something', 'something'] + [3, 'something', 'something'], + [4, np.nan, np.nan] ], columns=['A', 'B', 'C']) result = explode_column(df, 'B', 'C') From a8efed46a02c4a220acf689b72bdb2b0a72c2718 Mon Sep 17 00:00:00 2001 From: April Shen Date: Thu, 6 Jul 2023 14:01:08 +0100 Subject: [PATCH 09/13] fix gene mapping and add more tests --- opentargets_pharmgkb/evidence_generation.py | 14 +++++++++--- tests/resources/clinical_ann_alleles.tsv | 5 ++++- tests/resources/clinical_ann_evidence.tsv | 1 + tests/resources/clinical_annotations.tsv | 1 + tests/resources/expected_output.json | 5 ++++- tests/test_evidence_generation.py | 24 ++++++++++++++++++++- 6 files changed, 44 insertions(+), 6 deletions(-) diff --git a/opentargets_pharmgkb/evidence_generation.py b/opentargets_pharmgkb/evidence_generation.py index b31f64d..8d3280d 100644 --- a/opentargets_pharmgkb/evidence_generation.py +++ b/opentargets_pharmgkb/evidence_generation.py @@ -1,4 +1,5 @@ import json +import logging import multiprocessing import os from itertools import zip_longest @@ -12,15 +13,22 @@ from opentargets_pharmgkb.pandas_utils import none_to_nan, explode_column from opentargets_pharmgkb.variant_coordinates import get_coordinates_for_clinical_annotation +logging.basicConfig() +logger = logging.getLogger(__package__) +logger.setLevel(level=logging.DEBUG) + ID_COL_NAME = 'Clinical Annotation ID' def pipeline(data_dir, created_date, output_path): - # TODO test file existence clinical_annot_path = os.path.join(data_dir, 'clinical_annotations.tsv') clinical_alleles_path = os.path.join(data_dir, 'clinical_ann_alleles.tsv') clinical_evidence_path = os.path.join(data_dir, 'clinical_ann_evidence.tsv') drugs_path = os.path.join(data_dir, 'drugs.tsv') + for p in (clinical_annot_path, clinical_alleles_path, clinical_evidence_path, drugs_path): + if not os.path.exists(p): + logger.error(f'Missing required data file: {p}') + raise ValueError(f'Missing required data file: {p}') clinical_annot_table = read_tsv_to_df(clinical_annot_path) clinical_alleles_table = read_tsv_to_df(clinical_alleles_path) @@ -142,9 +150,9 @@ def explode_and_map_genes(df): ensembl_ids = query_biomart( ('hgnc_symbol', 'split_gene'), ('ensembl_gene_id', 'gene_from_pgkb'), - split_genes['split_gene'].drop_duplicates().tolist() + split_genes['split_gene'].dropna().drop_duplicates().tolist() ) - mapped_genes = pd.merge(split_genes, ensembl_ids, on='split_gene') + mapped_genes = pd.merge(split_genes, ensembl_ids, on='split_gene', how='left') # HGNC could map to more than one ensembl gene id, so must explode again mapped_genes = mapped_genes.explode('gene_from_pgkb').reset_index(drop=True) return mapped_genes diff --git a/tests/resources/clinical_ann_alleles.tsv b/tests/resources/clinical_ann_alleles.tsv index 29794be..6881d34 100644 --- a/tests/resources/clinical_ann_alleles.tsv +++ b/tests/resources/clinical_ann_alleles.tsv @@ -26,4 +26,7 @@ Clinical Annotation ID Genotype/Allele Annotation Text Allele Function 1444668808 del/del Hypertensive patients with the rs1799752 del/del genotype may have a decreased response to irbesartan as compared to patients with the ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to irbesartan. 1451114960 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2 Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2 or 2R/2R genotype may have an increased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 2R/3R or 3R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy. 1451114960 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3 Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3 or 2R/3R genotype may have an increased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 3R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy. -1451114960 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)3/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3 Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)3/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3 or 3R/3R genotype may have a decreased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 2R/2R or 2R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy. +1451114960 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)3/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3 Patients with the rs45445694 (CCGCGCCACTTGGCCTGCCTCCGTCCCG)3/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3 or 3R/3R genotype may have a decreased response or survival when treated with fluorouracil chemotherapy regimens as compared to patients with the 2R/2R or 2R/3R genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to fluorouracil chemotherapy. +1449566379 AA Patients with the AA genotype and hypertension may have an increased response to hydrochlorothiazide treatment, as measured by decreases in systolic and diastolic blood pressure, as compared to patients with the AG or GG genotypes. Other genetic and clinical factors may also affect a patient's response to hydrochlorothiazide. +1449566379 AG Patients with the AG genotype and hypertension may have an increased response to hydrochlorothiazide treatment, as measured by decreases in systolic and diastolic blood pressure, as compared to patients with the GG genotype, but a decreased response as compared to patients with the AA genotype. Other genetic and clinical factors may also affect a patient's response to hydrochlorothiazide. +1449566379 GG Patients with the GG genotype and hypertension may have a decreased response to hydrochlorothiazide treatment, as measured by decreases in systolic and diastolic blood pressure, as compared to patients with the AA or AG genotypes. Other genetic and clinical factors may also affect a patient's response to hydrochlorothiazide. diff --git a/tests/resources/clinical_ann_evidence.tsv b/tests/resources/clinical_ann_evidence.tsv index 853e147..793ed1e 100644 --- a/tests/resources/clinical_ann_evidence.tsv +++ b/tests/resources/clinical_ann_evidence.tsv @@ -69,3 +69,4 @@ Clinical Annotation ID Evidence ID Evidence Type Evidence URL PMID Summary Score 1451114960 827825053 Variant Phenotype Annotation https://www.pharmgkb.org/variantAnnotation/827825053 16249645 Genotype (CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3 is associated with increased survival when treated with cisplatin and fluorouracil in people with Stomach Neoplasms. 0.25 1451114960 769169082 Variant Drug Annotation https://www.pharmgkb.org/variantAnnotation/769169082 11913730 Genotype (CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2 is associated with increased response to fluorouracil in people with Colorectal Neoplasms as compared to genotypes (CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3 + (CCGCGCCACTTGGCCTGCCTCCGTCCCG)3/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3. 1.5 1451114960 1449155868 Variant Phenotype Annotation https://www.pharmgkb.org/variantAnnotation/1449155868 28972045 Genotype (CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)2 is associated with increased overall survival when treated with cisplatin, epirubicin and fluorouracil in people with Esophageal Neoplasms or Stomach Neoplasms as compared to genotypes (CCGCGCCACTTGGCCTGCCTCCGTCCCG)2/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3 + (CCGCGCCACTTGGCCTGCCTCCGTCCCG)3/(CCGCGCCACTTGGCCTGCCTCCGTCCCG)3. 2.5 +1449566379 1449566369 Variant Drug Annotation https://www.pharmgkb.org/variantAnnotation/1449566369 29925376 Genotypes AA + AG is associated with increased response to hydrochlorothiazide in people with Hypertension as compared to genotype GG. 2.5 diff --git a/tests/resources/clinical_annotations.tsv b/tests/resources/clinical_annotations.tsv index 3683872..8b1bfc4 100644 --- a/tests/resources/clinical_annotations.tsv +++ b/tests/resources/clinical_annotations.tsv @@ -8,3 +8,4 @@ Clinical Annotation ID Variant/Haplotypes Gene Level of Evidence Level Override 1448603303 rs3766246 FAAH 3 3.0 Toxicity 1 1 morphine 2021-03-24 https://www.pharmgkb.org/clinicalAnnotation/1448603303 Pediatric 1444668808 rs1799752 ACE 3 Tier 1 VIP 0.75 Efficacy 2 2 irbesartan Hypertension;Hypertrophy, Left Ventricular 2021-09-09 https://www.pharmgkb.org/clinicalAnnotation/1444668808 1451114960 rs45445694 TYMS 3 Tier 1 VIP 3.25 Efficacy 13 13 fluorouracil;FOLFIRI;FOLFOX overall survival;progression-free survival 2021-03-24 https://www.pharmgkb.org/clinicalAnnotation/1451114960 +1449566379 rs11065987 3 2.5 Efficacy 1 1 hydrochlorothiazide Hypertension 2021-03-24 https://www.pharmgkb.org/clinicalAnnotation/1449566379 diff --git a/tests/resources/expected_output.json b/tests/resources/expected_output.json index 0b5b5b5..bc4f1ed 100644 --- a/tests/resources/expected_output.json +++ b/tests/resources/expected_output.json @@ -72,4 +72,7 @@ {"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1444668808", "evidenceLevel": "3", "literature": ["11593098", "11910301"], "variantId": "17_63488530_ATACAGTCACTTTT_ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCATACAGTCACTTTT", "variantRsId": "rs1799752", "variantFunctionalConsequenceId": "intron_variant", "targetFromSourceId": "ENSG00000159640", "genotype": "del/del", "genotypeAnnotationText": "Hypertensive patients with the rs1799752 del/del genotype may have a decreased response to irbesartan as compared to patients with the ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to irbesartan.", "drugFromSource": "irbesartan", "drugId": "http://purl.obolibrary.org/obo/CHEBI_5959", "pgxCategory": "Efficacy", "phenotypeText": "Hypertension", "phenotypeFromSourceId": "http://www.ebi.ac.uk/efo/EFO_0000537"} {"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1444668808", "evidenceLevel": "3", "literature": ["11593098", "11910301"], "variantId": "17_63488530_ATACAGTCACTTTT_ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCATACAGTCACTTTT", "variantRsId": "rs1799752", "variantFunctionalConsequenceId": "intron_variant", "targetFromSourceId": "ENSG00000159640", "genotype": "ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC", "genotypeAnnotationText": "Hypertensive patients with the rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC genotype may have an increased response to irbesartan as compared to patients with the ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/del or del/del genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to irbesartan.", "drugFromSource": "irbesartan", "drugId": "http://purl.obolibrary.org/obo/CHEBI_5959", "pgxCategory": "Efficacy", "phenotypeText": "Hypertrophy, Left Ventricular"} {"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1444668808", "evidenceLevel": "3", "literature": ["11593098", "11910301"], "variantId": "17_63488530_ATACAGTCACTTTT_ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCATACAGTCACTTTT", "variantRsId": "rs1799752", "variantFunctionalConsequenceId": "intron_variant", "targetFromSourceId": "ENSG00000159640", "genotype": "ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/del", "genotypeAnnotationText": "Hypertensive patients with the rs1799752 ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/del genotype may have a decreased response to irbesartan as compared to patients with the ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to irbesartan.", "drugFromSource": "irbesartan", "drugId": "http://purl.obolibrary.org/obo/CHEBI_5959", "pgxCategory": "Efficacy", "phenotypeText": "Hypertrophy, Left Ventricular"} -{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1444668808", "evidenceLevel": "3", "literature": ["11593098", "11910301"], "variantId": "17_63488530_ATACAGTCACTTTT_ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCATACAGTCACTTTT", "variantRsId": "rs1799752", "variantFunctionalConsequenceId": "intron_variant", "targetFromSourceId": "ENSG00000159640", "genotype": "del/del", "genotypeAnnotationText": "Hypertensive patients with the rs1799752 del/del genotype may have a decreased response to irbesartan as compared to patients with the ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to irbesartan.", "drugFromSource": "irbesartan", "drugId": "http://purl.obolibrary.org/obo/CHEBI_5959", "pgxCategory": "Efficacy", "phenotypeText": "Hypertrophy, Left Ventricular"} \ No newline at end of file +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1444668808", "evidenceLevel": "3", "literature": ["11593098", "11910301"], "variantId": "17_63488530_ATACAGTCACTTTT_ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCATACAGTCACTTTT", "variantRsId": "rs1799752", "variantFunctionalConsequenceId": "intron_variant", "targetFromSourceId": "ENSG00000159640", "genotype": "del/del", "genotypeAnnotationText": "Hypertensive patients with the rs1799752 del/del genotype may have a decreased response to irbesartan as compared to patients with the ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC genotype. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence response to irbesartan.", "drugFromSource": "irbesartan", "drugId": "http://purl.obolibrary.org/obo/CHEBI_5959", "pgxCategory": "Efficacy", "phenotypeText": "Hypertrophy, Left Ventricular"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1449566379", "evidenceLevel": "3", "literature": ["29925376"], "variantId": "12_111634620_A_G", "variantRsId": "rs11065987", "genotype": "AA", "genotypeAnnotationText": "Patients with the AA genotype and hypertension may have an increased response to hydrochlorothiazide treatment, as measured by decreases in systolic and diastolic blood pressure, as compared to patients with the AG or GG genotypes. Other genetic and clinical factors may also affect a patient's response to hydrochlorothiazide.", "drugFromSource": "hydrochlorothiazide", "drugId": "http://purl.obolibrary.org/obo/CHEBI_5778", "pgxCategory": "Efficacy", "phenotypeText": "Hypertension", "phenotypeFromSourceId": "http://www.ebi.ac.uk/efo/EFO_0000537"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1449566379", "evidenceLevel": "3", "literature": ["29925376"], "variantId": "12_111634620_A_G", "variantRsId": "rs11065987", "genotype": "AG", "genotypeAnnotationText": "Patients with the AG genotype and hypertension may have an increased response to hydrochlorothiazide treatment, as measured by decreases in systolic and diastolic blood pressure, as compared to patients with the GG genotype, but a decreased response as compared to patients with the AA genotype. Other genetic and clinical factors may also affect a patient's response to hydrochlorothiazide.", "drugFromSource": "hydrochlorothiazide", "drugId": "http://purl.obolibrary.org/obo/CHEBI_5778", "pgxCategory": "Efficacy", "phenotypeText": "Hypertension", "phenotypeFromSourceId": "http://www.ebi.ac.uk/efo/EFO_0000537"} +{"datasourceId": "pharmgkb", "datasourceVersion": "2023-03-23", "datatypeId": "clinical_annotation", "studyId": "1449566379", "evidenceLevel": "3", "literature": ["29925376"], "variantId": "12_111634620_A_G", "variantRsId": "rs11065987", "genotype": "GG", "genotypeAnnotationText": "Patients with the GG genotype and hypertension may have a decreased response to hydrochlorothiazide treatment, as measured by decreases in systolic and diastolic blood pressure, as compared to patients with the AA or AG genotypes. Other genetic and clinical factors may also affect a patient's response to hydrochlorothiazide.", "drugFromSource": "hydrochlorothiazide", "drugId": "http://purl.obolibrary.org/obo/CHEBI_5778", "pgxCategory": "Efficacy", "phenotypeText": "Hypertension", "phenotypeFromSourceId": "http://www.ebi.ac.uk/efo/EFO_0000537"} \ No newline at end of file diff --git a/tests/test_evidence_generation.py b/tests/test_evidence_generation.py index 8a4d34a..360b132 100644 --- a/tests/test_evidence_generation.py +++ b/tests/test_evidence_generation.py @@ -1,9 +1,12 @@ import os +import numpy as np import pandas as pd +import pytest from opentargets_pharmgkb import evidence_generation -from opentargets_pharmgkb.evidence_generation import get_functional_consequences, explode_and_map_drugs, read_tsv_to_df +from opentargets_pharmgkb.evidence_generation import get_functional_consequences, explode_and_map_drugs, \ + read_tsv_to_df, explode_and_map_genes resources_dir = os.path.join(os.path.dirname(__file__), 'resources') @@ -27,6 +30,15 @@ def test_explode_and_map_drugs(): assert annotated_df.loc['peginterferon alfa-2a']['chebi'] is None +def test_explode_and_map_genes(): + df = pd.DataFrame(columns=['Gene'], data=[['IFNL3;IFNL4'], ['HLA-G'], [np.nan]]) + annotated_df = explode_and_map_genes(df) + assert annotated_df.shape == (11, 3) + assert 'ENSG00000272395' in annotated_df['gene_from_pgkb'].values + assert 'ENSG00000235346' in annotated_df['gene_from_pgkb'].values + assert pd.isna(annotated_df['gene_from_pgkb']).any() + + def test_pipeline(): output_path = os.path.join(resources_dir, 'test_output.json') expected_path = os.path.join(resources_dir, 'expected_output.json') @@ -41,3 +53,13 @@ def test_pipeline(): if os.path.exists(output_path): os.remove(output_path) + + +def test_pipeline_missing_file(): + output_path = os.path.join(resources_dir, 'test_output.json') + with pytest.raises(ValueError): + evidence_generation.pipeline( + data_dir=os.path.join(resources_dir, 'nonexistent'), + created_date='2023-03-23', + output_path=output_path + ) From a73fc485ab351ece0cc1f922f384a5fe3b88b545 Mon Sep 17 00:00:00 2001 From: April Shen Date: Thu, 6 Jul 2023 15:16:35 +0100 Subject: [PATCH 10/13] improved gene comparison --- opentargets_pharmgkb/counts.py | 7 ++++++- opentargets_pharmgkb/evidence_generation.py | 13 ++++++++----- 2 files changed, 14 insertions(+), 6 deletions(-) diff --git a/opentargets_pharmgkb/counts.py b/opentargets_pharmgkb/counts.py index ad5d331..097cf81 100644 --- a/opentargets_pharmgkb/counts.py +++ b/opentargets_pharmgkb/counts.py @@ -12,6 +12,8 @@ def __init__(self): self.with_consequence = 0 # self.with_pgkb_gene = 0 self.with_vep_gene = 0 + self.annot_with_pgkb_genes = 0 + self.annot_with_vep_genes = 0 self.pgkb_vep_gene_diff = 0 def report(self): @@ -23,6 +25,9 @@ def report(self): report_str += f'\tWith functional consequence: {self.with_consequence}\n' # report_str += f'\tWith PGKB gene: {self.with_pgkb_gene}\n' report_str += f'\tWith VEP gene: {self.with_vep_gene}\n' - report_str += f'Annotations where PGKB genes != VEP genes: {self.pgkb_vep_gene_diff}\n' + report_str += f'Gene comparisons per annotation\n' + report_str += f'\tWith PGKB genes: {self.annot_with_pgkb_genes}\n' + report_str += f'\tWith VEP genes: {self.annot_with_vep_genes}\n' + report_str += f'\tPGKB genes != VEP genes: {self.pgkb_vep_gene_diff}\n' print(report_str) return report_str diff --git a/opentargets_pharmgkb/evidence_generation.py b/opentargets_pharmgkb/evidence_generation.py index 8d3280d..690cb95 100644 --- a/opentargets_pharmgkb/evidence_generation.py +++ b/opentargets_pharmgkb/evidence_generation.py @@ -70,7 +70,7 @@ def pipeline(data_dir, created_date, output_path): output.write('\n'.join(json.dumps(ev) for ev in evidence)) # Final count report - gene_comparison_counts(evidence_table, counts, debug_path=f'{output_path}_genes.csv') + gene_comparison_counts(evidence_table, counts, debug_path=f'{output_path.rsplit(".", 1)[0]}_genes.csv') counts.report() @@ -255,11 +255,14 @@ def gene_comparison_counts(df, counts, debug_path=None): mapped_genes = explode_and_map_genes(df) # Re-group by ID column genes_table = mapped_genes.groupby(by=ID_COL_NAME).aggregate( - all_pgkb_genes=('gene_from_pgkb', set), - all_vep_genes=('overlapping_gene', set) + all_pgkb_genes=('gene_from_pgkb', lambda x: set(x.dropna())), + all_vep_genes=('overlapping_gene', lambda x: set(x.dropna())) ) # Compare sets of genes - counts.pgkb_vep_gene_diff = len(genes_table[genes_table['all_pgkb_genes'] != genes_table['all_vep_genes']]) + counts.annot_with_pgkb_genes = len(genes_table[genes_table['all_pgkb_genes'] != set()]) + counts.annot_with_vep_genes = len(genes_table[genes_table['all_vep_genes'] != set()]) + neq_genes_table = genes_table[genes_table['all_pgkb_genes'] != genes_table['all_vep_genes']] + counts.pgkb_vep_gene_diff = len(neq_genes_table) # Debug dump genes table if debug_path: - genes_table.to_csv(debug_path) + neq_genes_table.to_csv(debug_path) From 260805c75e6f6f0cc2d8620d458df802a63a0ac9 Mon Sep 17 00:00:00 2001 From: April Shen Date: Fri, 7 Jul 2023 10:13:34 +0100 Subject: [PATCH 11/13] update readme --- README.md | 12 ++++++++---- opentargets_pharmgkb/counts.py | 1 + 2 files changed, 9 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 05374b8..dc18723 100644 --- a/README.md +++ b/README.md @@ -1,13 +1,17 @@ # opentargets-pharmgkb Pipeline to provide evidence strings for Open Targets from PharmGKB -Download data: ``` +# Download data +DATA_DIR= wget https://api.pharmgkb.org/v1/download/file/data/clinicalAnnotations.zip wget https://api.pharmgkb.org/v1/download/file/data/drugs.zip -unzip -j clinicalAnnotations.zip "*.tsv" -d . -unzip -j clinicalAnnotations.zip "CREATED*.txt" -d . -unzip -j drugs.zip "*.tsv" -d . +unzip -j clinicalAnnotations.zip "*.tsv" -d $DATA_DIR +unzip -j clinicalAnnotations.zip "CREATED*.txt" -d $DATA_DIR +unzip -j drugs.zip "*.tsv" -d $DATA_DIR rm clinicalAnnotations.zip drugs.zip + +# Run pipeline +generate_evidence.py --data-dir $DATA_DIR --created-date --output-path evidence.json ``` \ No newline at end of file diff --git a/opentargets_pharmgkb/counts.py b/opentargets_pharmgkb/counts.py index 097cf81..ce6bbe7 100644 --- a/opentargets_pharmgkb/counts.py +++ b/opentargets_pharmgkb/counts.py @@ -12,6 +12,7 @@ def __init__(self): self.with_consequence = 0 # self.with_pgkb_gene = 0 self.with_vep_gene = 0 + # Evaluation counts - after annotation but without exploding self.annot_with_pgkb_genes = 0 self.annot_with_vep_genes = 0 self.pgkb_vep_gene_diff = 0 From 29fbd004464b6ae9b67a72792f4ecb60544a511e Mon Sep 17 00:00:00 2001 From: April Shen Date: Wed, 12 Jul 2023 08:46:04 +0100 Subject: [PATCH 12/13] add counts after exploding by allele --- opentargets_pharmgkb/counts.py | 7 +++++-- opentargets_pharmgkb/evidence_generation.py | 1 + 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/opentargets_pharmgkb/counts.py b/opentargets_pharmgkb/counts.py index ce6bbe7..3b121bd 100644 --- a/opentargets_pharmgkb/counts.py +++ b/opentargets_pharmgkb/counts.py @@ -2,10 +2,12 @@ class ClinicalAnnotationCounts: """Simple class to hold counts for generating clinical annotation evidence.""" def __init__(self): - # Input counts (before exploding by allele, etc.) + # Input counts (before annotation and exploding by drug, etc.) self.clinical_annotations = 0 self.with_rs = 0 - # Output counts (after exploding) + # Counts after exploding by allele + self.allele_annotations = 0 + # Output counts (after annotation and exploding) self.evidence_strings = 0 self.with_chebi = 0 self.with_efo = 0 @@ -20,6 +22,7 @@ def __init__(self): def report(self): report_str = f'\nTotal clinical annotations: {self.clinical_annotations}\n' report_str += f'\tWith RS: {self.with_rs}\n' + report_str += f'Total annotations by allele: {self.allele_annotations}\n' report_str += f'Total evidence strings: {self.evidence_strings}\n' report_str += f'\tWith CHEBI: {self.with_chebi}\n' report_str += f'\tWith EFO phenotype: {self.with_efo}\n' diff --git a/opentargets_pharmgkb/evidence_generation.py b/opentargets_pharmgkb/evidence_generation.py index 690cb95..0cd34fc 100644 --- a/opentargets_pharmgkb/evidence_generation.py +++ b/opentargets_pharmgkb/evidence_generation.py @@ -45,6 +45,7 @@ def pipeline(data_dir, created_date, output_path): # Main processing merged_with_alleles_table = pd.merge(rs_only_table, clinical_alleles_table, on=ID_COL_NAME, how='left') + counts.allele_annotations = len(merged_with_alleles_table) coordinates_table = get_vcf_coordinates(merged_with_alleles_table) consequences_table = get_functional_consequences(coordinates_table) # mapped_genes = explode_and_map_genes(consequences_table) From aa24d59a2de01c3a8b5a5b986c872ea6379da05d Mon Sep 17 00:00:00 2001 From: April Shen Date: Wed, 12 Jul 2023 10:59:01 +0100 Subject: [PATCH 13/13] add counts after each step --- opentargets_pharmgkb/counts.py | 10 +++++++--- opentargets_pharmgkb/evidence_generation.py | 16 ++++++++++------ 2 files changed, 17 insertions(+), 9 deletions(-) diff --git a/opentargets_pharmgkb/counts.py b/opentargets_pharmgkb/counts.py index 3b121bd..a457825 100644 --- a/opentargets_pharmgkb/counts.py +++ b/opentargets_pharmgkb/counts.py @@ -5,8 +5,10 @@ def __init__(self): # Input counts (before annotation and exploding by drug, etc.) self.clinical_annotations = 0 self.with_rs = 0 - # Counts after exploding by allele - self.allele_annotations = 0 + # Counts after exploding by each attribute + self.exploded_alleles = 0 + self.exploded_drugs = 0 + self.exploded_phenotypes = 0 # Output counts (after annotation and exploding) self.evidence_strings = 0 self.with_chebi = 0 @@ -22,7 +24,9 @@ def __init__(self): def report(self): report_str = f'\nTotal clinical annotations: {self.clinical_annotations}\n' report_str += f'\tWith RS: {self.with_rs}\n' - report_str += f'Total annotations by allele: {self.allele_annotations}\n' + report_str += f'Exploded by allele: {self.exploded_alleles}\n' + report_str += f'Exploded by drug: {self.exploded_drugs}\n' + report_str += f'Exploded by phenotype: {self.exploded_phenotypes}\n' report_str += f'Total evidence strings: {self.evidence_strings}\n' report_str += f'\tWith CHEBI: {self.with_chebi}\n' report_str += f'\tWith EFO phenotype: {self.with_efo}\n' diff --git a/opentargets_pharmgkb/evidence_generation.py b/opentargets_pharmgkb/evidence_generation.py index 0cd34fc..27d11dc 100644 --- a/opentargets_pharmgkb/evidence_generation.py +++ b/opentargets_pharmgkb/evidence_generation.py @@ -45,16 +45,20 @@ def pipeline(data_dir, created_date, output_path): # Main processing merged_with_alleles_table = pd.merge(rs_only_table, clinical_alleles_table, on=ID_COL_NAME, how='left') - counts.allele_annotations = len(merged_with_alleles_table) - coordinates_table = get_vcf_coordinates(merged_with_alleles_table) - consequences_table = get_functional_consequences(coordinates_table) - # mapped_genes = explode_and_map_genes(consequences_table) - mapped_drugs = explode_and_map_drugs(consequences_table, drugs_table) + counts.exploded_alleles = len(merged_with_alleles_table) + + mapped_drugs = explode_and_map_drugs(merged_with_alleles_table, drugs_table) + counts.exploded_drugs = len(mapped_drugs) + mapped_phenotypes = explode_and_map_phenotypes(mapped_drugs) + counts.exploded_phenotypes = len(mapped_phenotypes) + + coordinates_table = get_vcf_coordinates(mapped_phenotypes) + consequences_table = get_functional_consequences(coordinates_table) # Add clinical evidence with PMIDs pmid_evidence = clinical_evidence_table[clinical_evidence_table['PMID'].notna()] - evidence_table = pd.merge(mapped_phenotypes, pmid_evidence.groupby(by=ID_COL_NAME).aggregate( + evidence_table = pd.merge(consequences_table, pmid_evidence.groupby(by=ID_COL_NAME).aggregate( publications=('PMID', list)), on=ID_COL_NAME) # Gather output counts