shlokn/autogkb huggingface dataset:
Article: Pharmacogenetic Randomized Trial for Cocaine Abuse: Disulfiram and α1A-adrenoceptor gene variation
Gene: ADRA1A
Variant/haplotype: rs1048101
Drug(s): disulfiram
Phenotype category: Efficacy
Significant: yes
Association: Genotypes AA + AG is associated with increased response to disulfiram in people with Cocaine-Related Disorders as compared to genotype GG.
Notes: alleles complemented to plus chromosomal strand. Significance measured for untreated vs treated for each genotype group. "As shown in Figure 1, cocaine positive urines for the TT/TC genotype group during the two baseline weeks were 78% for disulfiram and 80% for placebo. These rates dropped during the last two weeks of treatment to 52% for disulfiram and to 73% for placebo. In comparison, cocaine urines for the CC genotype group during the two baseline weeks were 86% for disulfiram and 80% for placebo. These rates were relatively unchanged during the last two weeks of treatment at 81% for disulfiram and to 82% for placebo. " Authors showed interaction between this variant and the DBH rs1611115 variant.
Article: CYP3A5, ABCB1 and SLCO1B1 Polymorphisms and Pharmacokinetics and Virologic Outcome of Lopinavir/Ritonavir in HIV-infected Children
Gene: SLCO1B1
Variant/haplotype: rs4149056
Drug(s): lopinavir, ritonavir
Phenotype category: Metabolism/PK
Significant: no
Association: Allele C is not associated with response to lopinavir or ritonavir in children with HIV Infections as compared to allele T.
Notes: No significant association between this variant and virologic suppression in patients treated with lopinavir/ritonavir. Variant referred to in the paper as T512C.
Article: Genome-Wide Association and Functional Studies Reveal Novel Pharmacological Mechanisms for Allopurinol
Gene: NTNG1
Variant/haplotype: rs61816456
Drug(s): allopurinol
Phenotype category: Efficacy
Significant: no
Association: Allele A is associated with increased response to allopurinol as compared to allele G.
Notes: Response to allopurinol was determined by whether serum uric acid concentrations decreased following allopurinol treatment.
Article: Effect of CYP4F2 Polymorphisms on Ticagrelor Pharmacokinetics in Healthy Chinese Volunteers
Gene: CYP3A5
Variant/haplotype: rs15524
Drug(s): AR-C124910XX, ticagrelor
Phenotype category: Metabolism/PK
Significant: no
Association: Genotypes AG + GG is not associated with decreased concentrations of AR-C124910XX or ticagrelor in healthy individuals as compared to genotype AA.
Notes: from TABLE 4 Ticagrelor pharmacokinetic parameters based on genotypes without statistical significance and TABLE 5; AR-C124910XX pharmacokinetic parameters based on genotypes without statistical significance
Article: Leveraging an Electronic Health Record-Linked Biorepository to Generate a Metformin Pharmacogenomics Hypothesis
Gene: FMO1
Variant/haplotype: rs13376631
Drug(s): metformin
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with response to metformin in people with Diabetes Mellitus as compared to allele A.
Notes: EHR-linked and EHR-based phenotyping methods were used to study common variants within FMO5. Efficacy was assessed by A1c levels extracted from EHR records. The SNP was marginally significant after correction for multiple testing.
Article: Genetic predictors of the maximum doses patients receive during clinical use of the anti-epileptic drugs carbamazepine and phenytoin
Gene: SCN1A
Variant/haplotype: rs3812718
Drug(s): phenytoin
Phenotype category: Dosage
Significant: yes
Association: Allele T is associated with increased dose of phenytoin in people with Epilepsy as compared to allele C.
Article: Cytochrome P450 Genetic Variation Associated with Tamoxifen Biotransformation in American Indian and Alaska Native People
Gene: CYP3A4
Variant/haplotype: CYP3A4 poor metabolizer and intermediate metabolizer genotypes
Drug(s): endoxifen
Phenotype category: Metabolism/PK
Significant: no
Association: CYP3A4 poor metabolizer and intermediate metabolizer genotypes are not associated with concentrations of endoxifen in women with Breast Neoplasms.
Article: Association of Genetic Polymorphisms with Warfarin Dose Requirements in Chinese Patients
Gene: CYP2C19
Variant/haplotype: rs3814637
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Genotype CC is associated with increased dose of warfarin as compared to genotypes CT + TT.
Notes: "The mean warfarin dose in patients with the CYP2C19 rs3814637CC genotype was 3.39mg/day, which was higher than that in patients with the CYP2C19 rs3814637TT genotype (2.00mg/day)."
Article: Germline Genetic Variants in TEK, ANGPT1, ANGPT2, MMP9, FGF2 and VEGFA Are Associated with Pathologic Complete Response to Bevacizumab in Breast Cancer Patients
Gene: FGF2
Variant/haplotype: rs1960669
Drug(s): bevacizumab
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to bevacizumab in women with Breast Neoplasms as compared to allele C.
Notes: Please note that alleles have been complemented to the positive strand.
Article: Comprehensive Ara-C SNP score predicts leukemic cell intracellular ara-CTP levels in pediatric acute myeloid leukemia patients
Gene: CTPS1
Variant/haplotype: rs11577910
Drug(s): ara-CTP
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype AG is associated with increased concentrations of ara-CTP in children with Leukemia, Myeloid, Acute as compared to genotype GG.
Notes: No AA homozygotes observed.
Article: CALCA and TRPV1 genes polymorphisms are related to a good outcome in female chronic migraine patients treated with OnabotulinumtoxinA
Gene: GABRQ
Variant/haplotype: rs3810651
Drug(s): botulinum toxin type a
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with response to botulinum toxin type a in women with Migraine NOS as compared to allele A.
Notes: No significant difference in allele frequency between responders and non-responders.
Article: Genetic Variation of VKORC1 and CYP4F2 Genes Related to Warfarin Maintenance Dose in Patients with Myocardial Infarction
Gene: VKORC1
Variant/haplotype: rs7294
Drug(s): warfarin
Phenotype category: Dosage, Efficacy
Significant: no
Association: Allele T is associated with increased dose of warfarin in people with Myocardial Infarction as compared to allele C.
Notes: This is VKORC1*3.  There was a significant association when analyzed alone, but the effect was so small that it was negligible when analyzed with VKORC1*2,CYP2C9*2 and CYP2C9*3.
Article: RUNX transcription factors: association with pediatric asthma and modulated by maternal smoking
Gene: RUNX1
Variant/haplotype: rs11702779
Drug(s): methacholine chloride
Phenotype category: Other
Significant: yes
Association: Genotypes AG + GG are associated with increased response to methacholine chloride in children with Asthma.
Notes: This is for children who WERE exposed to maternal smoking in utero.
Article: CYP3A4 and CYP3A5 Polymorphisms and Blood Pressure Response to Amlodipine among African-American Men and Women with Early Hypertensive Renal Disease
Gene: CYP3A4
Variant/haplotype: rs2246709
Drug(s): amlodipine
Phenotype category: Efficacy
Significant: no
Association: Genotypes AG + GG are not associated with response to amlodipine in women with Hypertension as compared to genotype AA.
Notes: No significant change in the likelihood of a woman reaching a target mean arterial pressure concentration of <= 92 mmHg or <= 107 mmHg was seen between genotypes. Please note alleles have been complemented to the plus chromosomal strand.
Article: Prospective study of the UGT1A1*27 gene polymorphism during irinotecan therapy in patients with lung cancer: Results of Lung Oncology Group in Kyusyu (LOGIK1004B)
Gene: UGT1A1
Variant/haplotype: UGT1A1*1, UGT1A1*6, UGT1A1*28
Drug(s): irinotecan
Phenotype category: Efficacy
Significant: no
Association: UGT1A1 *6 + *28 are not associated with response to irinotecan in people with Lung Neoplasms as compared to UGT1A1 *1/*1.
Notes: Neither the *6 nor the *28 alleles were associated with tumor response rate, progression free survival or overall survival.
Article: The population pharmacokinetics of R- and S-warfarin: effect of genetic and clinical factors
Gene: CYP2C19
Variant/haplotype: rs3814637
Drug(s): warfarin
Phenotype category: Other, Metabolism/PK
Significant: not stated
Association: Allele T is associated with decreased clearance of warfarin as compared to allele C.
Notes: For R-Warfarin in a model that included bodyweight, age and CYP3A4 rs2242480.
Article: Genetic variation in the UGT1A locus is associated with simvastatin efficacy in a clinical practice setting
Gene: UGT1A9
Variant/haplotype: rs12052787
Drug(s): simvastatin
Phenotype category: Efficacy
Significant: yes
Association: Allele T is associated with increased response to simvastatin as compared to allele C.
Notes: The mean Emax (maximum decrease in LDL-C) was 59.77 ± 22.68, 64.24 ± 24.56, and 61.42 ± 4.617mg/dl, for patients with 0, 1 or 2 copies of the minor T allele.  There is a nominally significant association between Emax with this variant.
Article: An Expanded Analysis of Pharmacogenetics Determinants of Efavirenz Response that Includes 3′-UTR Single Nucleotide Polymorphisms among Black South African HIV/AIDS Patients
Gene: CYP1A2
Variant/haplotype: rs45564134
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: no
Association: Allele G is not associated with concentrations of efavirenz in people with HIV Infections as compared to genotypes G/del + del/del.
Notes: Presented as G and deletion
Article: CYP2D6 Genotyping as an alternative to phenotyping for determination of metabolic status in a clinical trial setting
Gene: CYP2D6
Variant/haplotype: CYP2D6*3, CYP2D6*4
Drug(s): debrisoquine, dextromethorphan
Phenotype category: Metabolism/PK
Significant: not stated
Association: CYP2D6 *3/*4 is associated with metabolism of debrisoquine or dextromethorphan.
Notes: Out of 558 subjects previously phenotyped for clinical studies and genotyped for this study, 46 PM were found.  1 of these 46 was *3/*4.   One *3/*4 had been phenotyped on dextromethorphan as EM.
Article: An Expanded Analysis of Pharmacogenetics Determinants of Efavirenz Response that Includes 3′-UTR Single Nucleotide Polymorphisms among Black South African HIV/AIDS Patients
Gene: CYP2B6
Variant/haplotype: rs707265
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: no
Association: Genotype AA is not associated with concentrations of efavirenz in people with HIV Infections as compared to genotypes AG + GG.
Article: Tell-Tale SNPs: The Role of CYP2B6 in Methadone Fatalities
Gene: CYP2B6
Variant/haplotype: rs8192719
Drug(s): methadone
Phenotype category: Metabolism/PK
Significant: no
Association: Allele T is not associated with concentrations of methadone as compared to allele C.
Article: Haloperidol plasma concentration in Japanese psychiatric subjects with gene duplication of CYP2D6
Gene: CYP2D6
Variant/haplotype: CYP2D6*1, CYP2D6*2, CYP2D6*10
Drug(s): haloperidol
Phenotype category: Metabolism/PK
Significant: no
Association: CYP2D6 *2 + *10 are not associated with increased metabolism of haloperidol as compared to CYP2D6 *1.
Notes: No association was seen between CYP2D6 genotype and plasma concentration of haloperidol. Duplication of the *2 allele also showed no association with plasma concentration of haloperidol.
Article: Gene‐Wide Tagging Study of the Association Between KCNT1 Polymorphisms and the Susceptibility and Efficacy of Genetic Generalized Epilepsy in Chinese Population
Gene: KCNT1
Variant/haplotype: rs10776850
Drug(s): antiepileptics
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to antiepileptics in people with Epilepsy, Generalized as compared to allele T.
Notes: No significant differences in genotype frequencies were seen between patients who were responsive to antiepileptic drugs (n=279; those who had not experienced any type of seizure for a minimum of 1 year after receiving antiepileptic drugs) and patients who were resistant to antiepileptic drugs (n=204; those who had at least four seizures during the previous year while trying at least three antiepileptic medications at the maximal tolerated doses).
Article: Lack of Association between Opioid-Receptor Genotypes and Smoking Cessation Outcomes in a Randomized, Controlled Naltrexone Trial
Gene: OPRM1
Variant/haplotype: rs1294092
Drug(s): naltrexone
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with response to naltrexone in people with Tobacco Use Disorder as compared to allele A.
Notes: No significant association between this variant and smoking quit rate when naltrexone was used as augmentation to nicotine patch therapy.
Article: Population Pharmacokinetic Quantification of CYP2D6 Activity in Codeine Metabolism in Ambulatory Surgical Patients for Model-Informed Precision Dosing
Gene: CYP2D6
Variant/haplotype: CYP2D6*10, CYP2D6*41
Drug(s): morphine
Phenotype category: Metabolism/PK
Significant: not stated
Association: CYP2D6 *41 is associated with increased exposure to morphine in people with Pain, Postoperative as compared to CYP2D6 *10.
Notes: "patients carrying the CYP2D6*41 allele had consistently higher AUC/F as compared with patients carrying the CYP2D6*10 allele." "In accordance with these results, our study demonstrates that the CYP2D6*10 decreased function allele shows higher apparent CYP2D6 activity than the CYP2D6*41 allele"
Article: Gene Variations of Sixth Complement Component Affecting Tacrolimus Metabolism in Patients with Liver Transplantation for Hepatocellular Carcinoma
Gene: C6
Variant/haplotype: rs6865420
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: no
Association: Genotype AC is not associated with dose-adjusted trough concentrations of tacrolimus in people with liver transplantation as compared to genotypes AA + CC.
Notes: No significant difference was seen when considering DONOR genotype at week 3 of treatment. Patients with hepatocellular carcinoma.
Article: Development of a physiology-directed population pharmacokinetic and pharmacodynamic model for characterizing the impact of genetic and demographic factors on clopidogrel response in healthy adults
Gene: CYP2C19
Variant/haplotype: CYP2C19*1, CYP2C19*2, CYP2C19*17
Drug(s): clopidogrel
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2C19 *1/*2 + *2/*17 + *2/*2 are associated with decreased metabolism of clopidogrel in healthy individuals as compared to CYP2C19 *1/*1 + *1/*17.
Notes: In the Amish PAPI study, age, BMI, CYP2C19*2 polymorphism and CES1 G143E polymorphism were the only statistically significant (p < 0.01) covariates characterizing interindividual differences in clopidogrel elimination/bioactivation and on-treatment platelet reactivity.
Article: Pharmacogenetic study of seven polymorphisms in three nicotinic acetylcholine receptor subunits in smoking-cessation therapies
Gene: CHRNA5
Variant/haplotype: rs503464
Drug(s): bupropion, nicotine, varenicline
Phenotype category: Efficacy
Significant: yes
Association: Allele A is associated with increased response to bupropion, nicotine and varenicline in people with Tobacco Use Disorder as compared to allele T.
Notes: Authors looked at the effect of variants on response to the smoking cessation therapies varenicline, bupropion and nicotine replacement therapy.
Article: Effects of OPRM1 and ABCB1 gene polymorphisms on the analgesic effect and dose of sufentanil after thoracoscopic-assisted radical resection of lung cancer
Gene: ABCB1
Variant/haplotype: rs1128503
Drug(s): sufentanil
Phenotype category: Dosage
Significant: yes
Association: Genotypes AA + AG are associated with increased dose of sufentanil in people with Lung Neoplasms and Pain, Postoperative as compared to genotype GG.
Notes: Patients with the AA genotype had significantly increased sufentanil consumption compared to patients with the AG or GG genotypes, while those with the AG genotype had significantly increased compared to patients with the GG genotype. Please note that alleles have been complemented to the positive strand.
Article: IL28B genetic variations are associated with high sustained virological response (SVR) of interferon-α plus ribavirin therapy in Taiwanese chronic HCV infection
Gene: IFNL3
Variant/haplotype: rs12980275
Drug(s): peginterferon alfa-2b, ribavirin
Phenotype category: Efficacy
Significant: yes
Association: Genotypes AG + GG is associated with decreased response to peginterferon alfa-2b and ribavirin in people with Hepatitis C, Chronic as compared to genotype AA.
Notes: This genotype has decreased association with sustained virological response (SVR).
Article: CYP2C8*3 predicts benefit/risk profile in breast cancer patients receiving neoadjuvant paclitaxel
Gene: CYP2C8
Variant/haplotype: CYP2C8*1, CYP2C8*3
Drug(s): cyclophosphamide, doxorubicin
Phenotype category: Efficacy
Significant: no
Association: CYP2C8 *1/*3 + *3/*3 is not associated with increased response to cyclophosphamide and doxorubicin in women with Breast Neoplasms as compared to CYP2C8 *1/*1.
Notes: Response = complete clinical response (cCR).  9.0% vs 10.3%.
Article: Combined study of genetic and epigenetic biomarker risperidone treatment efficacy in Chinese Han schizophrenia patients
Gene: UGT1A3
Variant/haplotype: rs6706232
Drug(s): risperidone
Phenotype category: Efficacy
Significant: no
Association: Allele A is associated with increased response to risperidone in people with Schizophrenia as compared to allele G.
Notes: The A allele was initially significantly more frequent in patients designated as 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: Methadone Dosage and Plasma Levels, SNPs of OPRM1 Gene and Age of First Drug Use Were Associated With Outcomes of Methadone Maintenance Treatment
Gene: OPRM1
Variant/haplotype: rs675026
Drug(s): methadone
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with response to methadone in people with Heroin Dependence as compared to allele A.
Notes: This SNP was not significantly associated with compliance with methadone maintenance therapy or 'negative rate of morphine urine test'.; Please note that alleles have been complemented to the positive strand.
Article: Influence of TCF7L2 gene variants on the therapeutic response to the dipeptidylpeptidase-4 inhibitor linagliptin
Gene: TCF7L2
Variant/haplotype: rs7903146
Drug(s): linagliptin
Phenotype category: Efficacy
Significant: yes
Association: Genotypes CC + CT is associated with increased clinical benefit to linagliptin in people with Diabetes Mellitus, Type 2 as compared to genotype TT.
Notes: "Linagliptin lowered HbA1c meaningfully in all three genotypes of rs7903146 (non-risk variant carriers CC [n = 356]: −0.82% [−9.0 mmol/mol], p < 0.0001; heterozygous CT [n = 264]: −0.77% [−8.4 mmol/mol], p < 0.0001; homozygous risk variant carriers TT [n = 73]: −0.57% [−6.2 mmol/mol], p < 0.0006). No significant treatment differences were seen between CC and CT patients, although HbA1c response was reduced in TT compared with CC patients (~0.26% [~2.8 mmol/mol], p = 0.0182)."
Article: Pharmacogenetics of TNF inhibitor response in rheumatoid arthritis utilizing the two-component disease activity score
Gene: EYA4
Variant/haplotype: rs17301249
Drug(s): adalimumab, certolizumab pegol, etanercept, infliximab, Tumor necrosis factor alpha (TNF-alpha) inhibitors
Phenotype category: Efficacy
Significant: yes
Association: Allele C is associated with decreased response to adalimumab, certolizumab pegol, etanercept, infliximab or Tumor necrosis factor alpha (TNF-alpha) inhibitors in people with Arthritis, Rheumatoid as compared to allele G.
Notes: as measured by change in 2C-DAS28. Table 2 shows change was a positive value for this variant suggesting increased 2C-DAS28 and less response, it was not attributed to a particular allele at this rs number location so assumed minor allele based on dbSNP frequencies.
Article: Replication study of polymorphisms associated with response to methotrexate in patients with rheumatoid arthritis
Gene: TYMS
Variant/haplotype: rs2244500
Drug(s): methotrexate
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to methotrexate in people with Arthritis, Rheumatoid as compared to allele G.
Article: CYP4F2 Is a Vitamin K1 Oxidase: An Explanation for Altered Warfarin Dose in Carriers of the V433M Variant
Gene: CYP4F2
Variant/haplotype: rs2108622
Drug(s): Vitamin K and analogues
Phenotype category: Metabolism/PK
Significant: not stated
Association: Allele T is associated with decreased metabolism of Vitamin K as compared to allele C.
Notes: Human Liver Microsomes carrying T had lower vitamin K1 oxidation as well as a decreased steady-state hepatic concentration of Vitamin K1 oxidase. HLM-CC: generated metabolite at 0.85 pmol/min/mg microsomal protein.  CT: 0.44 pmol/min/mg; TT: 0.21 pmol/min/mg.; Amount of CYP4F2:  CC:11.3 pmol/mg microsomal protein; CT:7.2 pmol/mg; TT: 2.5 pmol/mg.
Article: Pharmacokinetics and Pharmacogenomics of Once-Daily Raltegravir and Atazanavir in Healthy Volunteers
Gene: UGT1A1
Variant/haplotype: UGT1A1*28
Drug(s): raltegravir
Phenotype category: Metabolism/PK
Significant: no
Association: UGT1A1 *28 is not associated with metabolism of raltegravir in healthy individuals.
Notes: Only one participant was homozygous for 2 UGT1A1 reduced-function alleles and had the lowest raltegravir-glucuronide/raltegravir ratio regardless of atazanavir dosing. Using linear mixed-effect modeling, participants with 1 or 2 reduced-function alleles had nearly identical ratio compared to those with the reference UGT1A *1/*1. In linear regression analysis after adjusting for atazanavir, the ratio of raltegravir-glucuronide AUC to the raltegravir AUC was no different in those with reduced-function alleles than in those with the reference allele (1.19-fold change).
Article: Optimal predictor for 6-mercaptopurine intolerance in Chinese children with acute lymphoblastic leukemia: NUDT15, TPMT, or ITPA genetic variants?
Gene: ITPA
Variant/haplotype: rs1127354
Drug(s): mercaptopurine
Phenotype category: Dosage, Toxicity
Significant: no
Association: Allele A is not associated with decreased dose of mercaptopurine in children with Precursor Cell Lymphoblastic Leukemia-Lymphoma as compared to allele C.
Notes: as measured by 6-MP dose intensity, which is a measure dose adjustment due to toxicity calculated by the ratio of the prescribed 6-MP dose over the protocol dose of 50 mg/m2/d.
Article: Replication study of polymorphisms associated with response to methotrexate in patients with rheumatoid arthritis
Variant/haplotype: rs1703794
Drug(s): methotrexate
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with response to methotrexate in people with Arthritis, Rheumatoid as compared to allele C.
Article: Effect of CYP4F2 Polymorphisms on Ticagrelor Pharmacokinetics in Healthy Chinese Volunteers
Gene: CYP2C9
Variant/haplotype: rs1057911
Drug(s): AR-C124910XX, ticagrelor
Phenotype category: Metabolism/PK
Significant: no
Association: Genotype AT is not associated with decreased concentrations of AR-C124910XX or ticagrelor in healthy individuals as compared to genotype AA.
Notes: from TABLE 4 Ticagrelor pharmacokinetic parameters based on genotypes without statistical significance and TABLE 5; AR-C124910XX pharmacokinetic parameters based on genotypes without statistical significance