shlokn/autogkb huggingface dataset:
Article: Cholinergic receptor nicotinic alpha 5 subunit polymorphisms are associated with smoking cessation success in women
Gene: CHRNA2
Variant/haplotype: rs2472553
Drug(s): bupropion, nicotine, varenicline
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to bupropion, nicotine or varenicline in people with Tobacco Use Disorder as compared to allele G.
Notes: No significant effect of genotype on likelihood of being abstinent from smoking at 6 months after starting pharmacotherapy for smoking cessation. Please note that alleles have been complemented to the positive strand.
Article: Pharmacogenetics of tenofovir clearance among Southern Africans living with HIV
Gene: CYP2B6
Variant/haplotype: rs28399499
Drug(s): tenofovir
Phenotype category: Metabolism/PK
Significant: no
Association: Allele C is not associated with clearance of tenofovir in people with HIV Infections as compared to allele T.
Notes: Significance threshold was set at 3.3E-3.
Article: Association between Polymorphisms in Vascular Endothelial Growth Factor Gene and Response to Chemotherapies in Colorectal Cancer: A Meta-Analysis
Gene: VEGFA
Variant/haplotype: rs833061
Drug(s): bevacizumab, capecitabine, fluorouracil, irinotecan, leucovorin, oxaliplatin
Phenotype category: Efficacy
Significant: no
Association: Allele C is not associated with response to bevacizumab, capecitabine, fluorouracil, irinotecan, leucovorin and oxaliplatin in people with Colorectal Neoplasms as compared to allele T.
Notes: Response was determined by RECIST criteria. In a subgroup analysis excluding the use of anti-angiogenic agents (e.g. bevacuzimab) no significant association was found for any genotypes and response to chemotherapy.
Article: Germline Polymorphisms as Biomarkers of Tumor Response in Colorectal Cancer Patients Treated with Anti-EGFR Monoclonal Antibodies: A Systematic Review and Meta-Analysis
Gene: CCND1
Variant/haplotype: rs9344
Drug(s): cetuximab, panitumumab
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to cetuximab or panitumumab in people with Colorectal Neoplasms as compared to allele G.
Notes: Meta-analysis with 5 studies. This variant was listed as rs17852153 in the original article. The authors did not provide the exact number of patients but stated that "the median number of patients per analysis was 110 (range 50 - 740)". Most definitions of response were variations of the RECIST criteria.
Article: Methadone pharmacogenetics in vitro and in vivo: Metabolism by CYP2B6 polymorphic variants and genetic variability in pediatric disposition
Gene: CYP2B6
Variant/haplotype: CYP2B6*1, CYP2B6*6, CYP2B6*7, CYP2B6*9, CYP2B6*18
Drug(s): (S)-methadone
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2B6 *6 + *7 + *9 + *18 is associated with decreased clearance of (S)-methadone in children with Scoliosis as compared to CYP2B6 *1/*1.
Notes: effect was reported as "S-methadone clearance was significantly associated with CYP2B6 polymorphisms,; specifically the number of CYP2B6 slow metabolizer alleles" and listed "CYP2B6 slow metabolizer alleles in the study population included *6,*7,*9,*18"
Article: Association of Pharmacogenetic Markers with Premature Discontinuation of First-line Anti-HIV Therapy: An Observational Cohort Study
Gene: ABCB1
Variant/haplotype: rs1045642
Drug(s): atazanavir, ritonavir
Phenotype category: Toxicity
Significant: no
Association: Genotypes AA + AG is not associated with increased discontinuation of atazanavir and ritonavir in people with HIV Infections as compared to genotype GG.
Notes: atazanavir boosted with ritonavir
Article: Association of corticotropin releasing hormone receptor 2 (CRHR2) genetic variants with acute bronchodilator response in asthma
Gene: CRHR2
Variant/haplotype: rs2267715
Drug(s): salbutamol
Phenotype category: Efficacy
Significant: yes
Association: Allele G is associated with decreased response to salbutamol in people with Asthma as compared to allele A.
Article: Interactive Modeling for Ongoing Utility of Pharmacogenetic Diagnostic Testing: Application for Warfarin Therapy
Gene: VKORC1
Variant/haplotype: rs9923231
Drug(s): warfarin
Phenotype category: Dosage, Efficacy
Significant: yes
Association: Allele T is associated with increased response to warfarin as compared to allele C.
Notes: The plasma S-warfarin concentration required to yield the target INR response for each genotype: CC, 0.68 mg/L; TC, 0.48 mg/L; TT, 0.27 mg/L.
Article: IL28B genotype is associated with differential expression of intrahepatic interferon-stimulated genes in chronic hepatitis C patients
Gene: IFNL3, IFNL4
Variant/haplotype: rs12979860
Drug(s): peginterferon alfa-2a, peginterferon alfa-2b, ribavirin
Phenotype category: Efficacy
Significant: yes
Association: Genotype CC is associated with increased response to peginterferon alfa-2a, peginterferon alfa-2b and ribavirin in people with Hepatitis C, Chronic as compared to genotypes CT + TT.
Notes: The subtype of peginterferon alpha was not specified.  The association was with SVR(sustained viral response).  Patients were monoinfected with HCV genotype 1. Nonresponders and relapsers were grouped together.  Allele frequency listed is for entire cohort of 61.
Article: The Association of Transporter Genes Polymorphisms and Lung Cancer Chemotherapy Response
Gene: AQP9
Variant/haplotype: rs1554203
Drug(s): platinum
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to platinum in people with Lung Neoplasms as compared to allele G.
Notes: 26 SNPs were selected which satisfied the following criteria: 1) SNPs were from HapMap Project Phase II of the Han Chinese population 2) were haplotype tagger SNPs 3) SNP minor allele frequency was higher than 5% in Han Chinese 4) the pairwise linkage disequilibrium correlation coefficient (r-squared) was greater than 0.8. After Bonferroni corrections no SNPs remained significantly associated with platinum drug efficacy.
Article: A Single Site Population Study to Investigate CYP2D6 Phenotype of Patients with Persistent Non-Malignant Pain
Gene: CYP2D6
Variant/haplotype: CYP2D6 normal metabolizers
Drug(s): codeine
Phenotype category: Efficacy
Significant: not stated
Association: CYP2D6 normal metabolizer is associated with increased response to codeine in people with Pain as compared to CYP2D6 intermediate metabolizer and poor metabolizer.
Notes: All CYP2D6 PMs, IMs and UMs in the study cohort were categorized as non-responders to codeine. Patients were genotyped for the *1, *2, *3, *4, *5, *6, *9, *10, *41 alleles as well as for allele duplication. Note that patients with a CYP2D6 activity score of 1 were assigned as normal metabolizers.
Article: Prediction of Warfarin Dose in Pediatric Patients: An Evaluation of the Predictive Performance of Several Models
Gene: CYP2C9
Variant/haplotype: CYP2C9*1, CYP2C9*3
Drug(s): warfarin
Phenotype category: Dosage
Significant: not stated
Association: CYP2C9 *3 is associated with dose of warfarin in children with Heart Diseases as compared to CYP2C9 *1.
Article: The paraoxonase-1 pathway is not a major bioactivation pathway of clopidogrel in vitro
Gene: CYP2C19
Variant/haplotype: CYP2C19*1, CYP2C19*2
Drug(s): clopidogrel
Phenotype category: Metabolism/PK
Significant: not stated
Association: CYP2C19 *2/*2 is associated with decreased metabolism of clopidogrel as compared to CYP2C19 *1/*1.
Notes: This comparison was done in pooled human liver microsomes.  Production of clopidogrel's active metabolite from 2-oxo-clopidogrel was measured.
Article: Monitoring of peripheral blood cluster of differentiation 4+ adenosine triphosphate activity and CYP3A5 genotype to determine the pharmacokinetics, clinical effects and complications of tacrolimus in patients with autoimmune diseases
Gene: CYP3A5
Variant/haplotype: CYP3A5*1, CYP3A5*3
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP3A5 *1/*1 + *1/*3 is associated with decreased concentrations of tacrolimus in people with Autoimmune Diseases as compared to CYP3A5 *3/*3.
Notes: Patients with the *1/*1 + *1/*3 genotypes had lower tacrolimus concentrations (p=0.0108) and concentration/dose ratio (p=0.0056) as compared to those with the *3/*3 genotype.
Article: Population pharmacokinetic analyses for belzutifan to inform dosing considerations and labeling
Gene: UGT2B17
Variant/haplotype: UGT2B17 poor metabolizer
Drug(s): belzutifan
Phenotype category: Metabolism/PK
Significant: not stated
Association: UGT2B17 poor metabolizer is associated with increased concentrations of belzutifan in people with von Hippel-Lindau Disease or Carcinoma, Renal Cell.
Notes: variants genotyped are not specified, nor are which variants are considered PM. "A population pharmacokinetic (PK) model was built, using NONMEM® v7.3, based on demographics/PK data from 3 clinical pharmacology (food effect, formulation bridging, genotype/race effect) and 2 clinical (phase 1 dose escalation/expansion in RCC and other solid tumors; phase 2 in VHL patients) studies." "UGT2B17 and CYP2C19 poor metabolizers (PM) were estimated to have a 3.2-fold higher area under the plasma concentration-time curve (AUC) compared to UGT2B17 extensive metabolizer and CYP2C19 non-PM patients."
Article: Association studies of dopamine synthesis and metabolism genes with multiple phenotypes of heroin dependence
Gene: TH
Variant/haplotype: rs3842727
Drug(s): heroin
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with response to heroin as compared to allele G.
Notes: No significant association between this variant and strength of euphoria on first heroin use.
Article: Relevance of CYP2B6 and CYP2D6 genotypes to methadone pharmacokinetics and response in the OPAL study
Gene: CYP2D6
Variant/haplotype: CYP2D6 poor and ultrarapid metabolizers
Drug(s): methadone
Phenotype category: Dosage
Significant: no
Association: CYP2D6 poor metabolizer and ultrarapid metabolizer are not associated with dose of methadone in people with Opioid-Related Disorders as compared to CYP2D6 normal metabolizer.
Article: Response Prediction in Chronic Hepatitis C by Assessment of IP-10 and IL28B-Related Single Nucleotide Polymorphisms
Gene: IFNL3
Variant/haplotype: rs12980275
Drug(s): peginterferon alfa-2a, peginterferon alfa-2b, ribavirin
Phenotype category: Efficacy
Significant: no
Association: Genotype AA is not associated with increased response to peginterferon alfa-2a, peginterferon alfa-2b and ribavirin in people with Hepatitis C as compared to genotypes AG + GG.
Notes: This SNP was associated with response in univariate analysis, but not in multivariate analysis. Significantly lower baseline plasma levels of IP-10 were associated with this SNP. Lower levels of IP-10 were found to be statistically significantly associated with better treatment outcome.
Article: Combined study of genetic and epigenetic biomarker risperidone treatment efficacy in Chinese Han schizophrenia patients
Gene: CYP1B1
Variant/haplotype: rs10012
Drug(s): risperidone
Phenotype category: Efficacy
Significant: no
Association: Allele C is associated with decreased response to risperidone in people with Schizophrenia as compared to allele G.
Notes: The C allele was initially significantly more frequent in patients designated as non-responders to risperidone (i.e. <50% reduction in PANSS score compared to the cohort average). However, significance was lost following correction for multiple testing.
Article: Pharmacokinetics of Intravenous Voriconazole in Obese Patients: Implications of CYP2C19 Homozygous Poor Metabolizer Genotype
Gene: CYP2C19
Variant/haplotype: CYP2C19*2
Drug(s): voriconazole
Phenotype category: Metabolism/PK
Significant: not stated
Association: CYP2C19 *2/*2 (assigned as poor metabolizer phenotype) is associated with increased concentrations of voriconazole.
Notes: Case report: 17 yo Hispanic obese (BMI: 35) male receiving voriconazole for suspected aspergillosis. Elevated levels remained elevated (5.8 ug/ml) despite decreased dose to 4mg/kg every 12 hours. Drug discontinued due to QTc prolongation possibly related to electrolyte abnormalities and elevated voriconazole concentrations.
Article: Adiponectin Gene Polymorphism rs2241766 T/G Is Associated with Response to Pioglitazone Treatment in Type 2 Diabetic Patients from Southern China
Gene: ADIPOQ
Variant/haplotype: rs3774261
Drug(s): pioglitazone
Phenotype category: Efficacy
Significant: no
Association: Genotypes AG + GG are not associated with response to pioglitazone in people with Diabetes Mellitus as compared to genotype AA.
Notes: Response was defined as "any decrease greater than (or equal to) 15%" of glycated hemoglobin (HbA1C%).  The AA genotype was associated with a greater decrease in waist circumference as compared to the AG and GG genotypes after pioglitazone therapy (p=0.019) although the AG and GG genotypes were associated with a greater decrease in fasting insulin as compared to the AA genotype (p=0.03).
Article: Oxidative Stress-Related Genetic Polymorphisms Are Associated with the Prognosis of Metastatic Gastric Cancer Patients Treated with Epirubicin, Oxaliplatin and 5-Fluorouracil Combination Chemotherapy
Gene: NQO1
Variant/haplotype: rs1800566
Drug(s): epirubicin, fluorouracil, oxaliplatin
Phenotype category: Efficacy
Significant: yes
Association: Genotypes AA + AG are associated with decreased response to epirubicin, fluorouracil and oxaliplatin in people with Neoplasm Metastasis and Stomach Neoplasms as compared to genotype GG.
Notes: Response refers to survival (progression free and overall). rs1800566 AG/AA genotype was an independent predictive factor of poor PFS. Please note: the alleles reported here are complemented to the + chromosomal strand.
Article: Normalization of Sweat Chloride Concentration and Clinical Improvement With Ivacaftor in a Patient With Cystic Fibrosis With Mutation S549N
Gene: CFTR
Variant/haplotype: rs121908755
Drug(s): ivacaftor
Phenotype category: Efficacy
Significant: not stated
Association: Allele A is associated with response to ivacaftor in children with Cystic Fibrosis.
Notes: A girl with rapidly advancing lung disease was treated with ivacaftor and after 6 weeks of treatment showed clinical improvement (including normalization of sweat chloride, cough was cleared within 3 weeks, ability to engage in school exercise classes by 4 weeks, weight gain, and significantly improved lung function). She had the gating variant CFTR S549N, as well as the class I CFTR variant 1811+1.6kbA>G.
Article: Limited predictive value of achieving beneficial plasma (Z)-endoxifen threshold level by CYP2D6 genotyping in tamoxifen-treated Polish women with breast cancer
Gene: CYP2D6
Variant/haplotype: CYP2D6*1, CYP2D6*2, CYP2D6*3, CYP2D6*4, CYP2D6*5, CYP2D6*6
Drug(s): endoxifen
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2D6 *4/*4 + *3/*4 + *4/*5 + *4/*6 are associated with decreased concentrations of endoxifen in women with Breast Neoplasms as compared to CYP2D6 *1/*2 + *1/*1 + *2/*2.
Notes: Pre- and post menopausal patients received 20 mg/day tamoxifen for at least 1 month (median duration 21.5 month). DNA source was blood and CYP2D6 was genotyped with TaqMan allelic discrimination assays. PM (non-functional) alleles include: CYP2D6*3, *4, *5, *6, *7; IM (reduced function) alleles include: CYP2D6*9, *10, *17, *41; EM (wt; fully functional) alleles include CYP2D6*1 and *2; UM (increased function) alleles include: duplication of EM variants of the gene, such as CYP2D6*1XN and *2XN. Patients were assigned a CYP2D6 genotype depending on the combination of alleles they carry, as PM/PM, IM/PM, IM/IM, EM/PM, EM/IM, EM/EM or EM/UM.
Article: Genetic Variation of VKORC1 and CYP4F2 Genes Related to Warfarin Maintenance Dose in Patients with Myocardial Infarction
Gene: CYP4F2
Variant/haplotype: rs2108622
Drug(s): warfarin
Phenotype category: Dosage, Efficacy
Significant: no
Association: Allele C is not associated with dose of warfarin in people with Myocardial Infarction as compared to allele T.
Notes: This SNP showed a weak but not significant association with dosage when analyzed alone, and when analyzed with CYP2C9*2,CYP2C9*3 and VKORC1*2, also provided no significant contribution.
Article: Association of Common C-Reactive Protein (CRP) Gene Polymorphisms With Baseline Plasma CRP Levels and Fenofibrate Response
Gene: CRP
Variant/haplotype: rs1205
Drug(s): fenofibrate
Phenotype category: Efficacy
Significant: no
Association: Genotype CC is not associated with response to fenofibrate in people with Metabolic Syndrome as compared to genotypes CT + TT.
Notes: No significant difference in the change of C-reactive protein (CRP) levels between baseline and 3 weeks of treatment, was seen between genotypes. In strong linkage disequilibrium with rs3091244 and rs1417938 (r2 = 0.4 - 0.9, p < 0.001) and in weak linkage disequilibrium with rs3093059 (r2 = 0.17, p < 0.05).
Article: Pharmacogenomics study on cadherin 2 network with regard to HIV infection and methadone treatment outcome
Gene: CDH2
Variant/haplotype: rs17446819
Drug(s): methadone
Phenotype category: Efficacy
Significant: yes
Association: Genotype CC is associated with increased response to methadone as compared to genotypes AA + AC.
Notes: Association between SNP and response to methadone is not directly shown in the paper. Genotype AA is associated with increased concentrations of CDH2 in plasma and individuals with increased CDH2 levels had an improved response to methadone treatment (p=0.005).
Article: Genetic variants in CYP2B6 and CYP2A6 explain interindividual variation in efavirenz plasma concentrations of HIV-infected children with diverse ethnic origin
Gene: CYP2B6
Variant/haplotype: rs3745274
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype TT is associated with increased concentrations of efavirenz in children with HIV Infections.
Notes: Allele also known as CYP2B6*6.
Article: Dual specificity phosphatase-1 as a pharmacogenetic modifier of inhaled steroid response among asthma patients
Gene: DUSP1
Variant/haplotype: rs881152
Drug(s): salbutamol
Phenotype category: Efficacy
Significant: yes
Association: Allele G is associated with increased response to salbutamol in people with Asthma as compared to allele A.
Notes: Subjects were taking inhaled corticosteroids.  When the Puerto-Rican and Mexican American cohorts from the GALA study were analyzed separately, the same association was significant in the Puerto-Ricans but not in the Mexican Americans.
Article: Combined Effect of CYP2B6 and NAT2 Genotype on Plasma Efavirenz Exposure During Rifampin-based Antituberculosis Therapy in the STRIDE Study
Gene: CYP2B6
Variant/haplotype: CYP2B6 poor metabolizer
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: not stated
Association: CYP2B6 poor metabolizer is associated with increased concentrations of efavirenz in people with HIV infectious disease and Tuberculosis as compared to CYP2B6 normal metabolizer.
Notes: Genotype for metabolizer status determined from rs3745274, rs28399499, and rs4803419. Patients were taking both efavirenz and antituberculosis therapy.  "In participants with CYP2B6 extensive and intermediate metabolizer genotypes, only small differences between efavirenz Cmin concentrations on antituberculosis therapy and off antituberculosis therapy were seen for all NAT2 metabolizer genotypes. In contrast, among the 4 participants with both CYP2B6 and NAT2 slow metabolizer genotypes, efavirenz Cmin concentrations were substantially elevated on antituberculosis therapy compared to off antituberculosis therapy, with differences exceeding 8 µg/mL in 3 of these 4 participants; this was not statistically significant in this subset. One individual with slow CYP2B6 and intermediate NAT2 metabolizer genotypes had a considerably larger efavirenz Cmin concentration on vs off antituberculosis treatment."
Article: Effects of erythromycin on voriconazole pharmacokinetics and association with CYP2C19 polymorphism
Gene: CYP2C19
Variant/haplotype: CYP2C19*1, CYP2C19*2, CYP2C19*3
Drug(s): voriconazole
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2C19 *2/*2 + *2/*3 (assigned as poor metabolizer phenotype) is associated with decreased metabolism of voriconazole in healthy individuals as compared to CYP2C19 *1/*1 + *1/*2 + *1/*3.
Notes: The authors report that extensive metabolizers (*1/*1) and heterozygote extensive metabolizers (*1/*2 or *1/*3) had decreased elimination half life (hours), AUC (0-24, 0-infinity) (h*µg/mL), and increased apparent oral clearance (mL/min) of voriconazole when compared to poor metabolizers (*2/*2 +*2/*3). No significant difference was reported when comparing the same PK parameters between *1/*1 to *1/*2+*1/*3. Additionally, no significant differences were seen for maximum plasma concentrations (Cmax) or time to Cmax (Tmax).
Article: Genetic variants in CYP2B6 and CYP2A6 explain interindividual variation in efavirenz plasma concentrations of HIV-infected children with diverse ethnic origin
Gene: CYP3A5
Variant/haplotype: rs41303343
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: no
Association: Allele A is not associated with concentrations of efavirenz in children with HIV Infections as compared to allele del.
Notes: This is stated in the paper, but supporting data is not shown.; Allele also known as CYP3A5*7
Article: A GENOME-WIDE ASSOCIATION STUDY OF BRONCHODILATOR RESPONSE IN LATINOS IMPLICATES RARE VARIANTS
Gene: ADCY9
Variant/haplotype: rs144315541
Drug(s): salbutamol
Phenotype category: Efficacy
Significant: yes
Association: Genotype AG is associated with increased response to salbutamol in children with Asthma as compared to genotype GG.
Notes: The allele associated with increased response and low frequency is not explicitly stated.  Response is increased for carriers of the rare, minor allele.  GALAII genotyping was done using the Affymetrix LAT1 Array, which was designed to capture Latino population variation.  This was assessed as a replication attempt for a previously reported association of a different ADCY9 SNP with response to bronchodilators.  Bonferroni correction was performed according to the number of SNPs included that are within 50 kb up and downstream of ADCY9.
Article: Warfarin Dosage Response Related Pharmacogenetics in Chinese Population
Gene: CYP4F2
Variant/haplotype: rs2108622
Drug(s): warfarin
Phenotype category: Dosage
Significant: no
Association: Genotypes CT + TT are not associated with dose of warfarin in people with heart valve replacement as compared to genotype CC.
Notes: 158/220 patients had the target INR (1.5–2.5). The comparison of weekly warfarin maintenance dose was among patients of different genotypes. Differences in maintenance dose were not observed in patients with variant genotypes of CYP4F2 s2108622. Please note: the alleles are complemented to the + chromosomal strand.
Article: Genetic polymorphisms in the long noncoding RNA MIR2052HG offer a pharmacogenomic basis for the response of breast cancer patients to aromatase inhibitor therapy
Variant/haplotype: rs2891356
Drug(s): anastrozole, exemestane
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with increased response to anastrozole and exemestane in women with Breast Neoplasms as compared to allele A.
Notes: Patients included postmenopausal women with resected stage I–III breast cancer that was ERa and/or PgR positive and randomized to five years of anastrozole or exemestane. Did not reach statistical significance for GWAS (P<5 x 10^-8).
Article: Deciphering the Interleukin 28B Variants That Better Predict Response to Pegylated Interferon-α and Ribavirin Therapy in HCV/HIV-1 Coinfected Patients
Gene: IFNL3
Variant/haplotype: rs28416813
Drug(s): peginterferon alfa-2b, ribavirin
Phenotype category: Efficacy
Significant: yes
Association: Genotype CC is associated with increased response to peginterferon alfa-2b and ribavirin in people with Hepatitis C and HIV Infections as compared to genotypes CG + GG.
Notes: This genotype is associated with sustained virological response (SVR).