shlokn/autogkb huggingface dataset:
Article: Gemcitabine Metabolic and Transporter Gene Polymorphisms Are Associated with Drug Toxicity and Efficacy in Patients with Locally Advanced Pancreatic Cancer
Gene: DCK
Variant/haplotype: rs12648166
Drug(s): gemcitabine
Phenotype category: Efficacy, Toxicity
Significant: no
Association: Genotype AA is not associated with increased response to gemcitabine in people with Pancreatic Neoplasms as compared to genotypes AG + GG.
Notes: Tumor response to therapy, progression free survival, and risk of neutropenia development did not significantly differ between genotype groups.
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: rs3192723
Drug(s): methadone
Phenotype category: Efficacy
Significant: no
Association: Genotype CC is associated with decreased response to methadone in people with Heroin Dependence as compared to genotypes CT + TT.
Notes: Patients with the CC genotype had a lower 'negative rate of morphine urine test' than patients with the CT or TT genotypes. However, this SNP was not significantly associated with MMT compliance in the study.; Note that although this variant is located in MTRF1L, it is discussed in the paper as being an OPRM1 SNP.; Please note that alleles have been complemented to the positive strand.
Article: Influence of ABCC2 and ABCC4 Polymorphisms on Tenofovir Plasma Concentrations in Thai HIV-Infected Patients
Gene: ABCC2
Variant/haplotype: rs3740066
Drug(s): tenofovir
Phenotype category: Metabolism/PK
Significant: no
Association: Genotypes CT + TT is not associated with concentrations of tenofovir in people with HIV Infections as compared to genotype CC.
Article: Clinical Evaluation of Cisplatin Sensitivity Germline Polymorphisms in Neoadjuvant Chemotherapy for Urothelial Cancer
Gene: MLLT3
Variant/haplotype: rs10964552
Drug(s): cisplatin
Phenotype category: Efficacy
Significant: yes
Association: Genotypes AA + AC are associated with decreased response to cisplatin in people with Urinary Bladder Neoplasms as compared to genotype CC.
Notes: This SNP was significantly associated with stage <pT2 (downstaging after neoadjuvant chemotherapy) in the discovery cohort, but not the replication cohort. This measurement was a secondary analysis.
Article: The impact of ABCB1, CYP3A4/5 and ABCG2 gene polymorphisms on rivaroxaban trough concentrations and bleeding events in patients with non-valvular atrial fibrillation
Gene: ABCB1
Variant/haplotype: rs4148738
Drug(s): rivaroxaban
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype CC is associated with increased dose-adjusted trough concentrations of rivaroxaban in people with Atrial Fibrillation as compared to genotypes CT + TT.
Article: Low heritability in pharmacokinetics of talinolol: a pharmacogenetic twin study on the heritability of the pharmacokinetics of talinolol, a putative probe drug of MDR1 and other membrane transporters
Gene: ABCG2
Variant/haplotype: rs2231137
Drug(s): talinolol
Phenotype category: Metabolism/PK
Significant: no
Association: Allele C is not associated with clearance of talinolol in healthy individuals as compared to allele T.
Notes: This was a twin study of monozygotic and dizygotic twins.
Article: TRAF1/C5 but Not PTPRC Variants Are Potential Predictors of Rheumatoid Arthritis Response to Anti-Tumor Necrosis Factor Therapy
Gene: TRAF1
Variant/haplotype: rs3761847
Drug(s): Tumor necrosis factor alpha (TNF-alpha) inhibitors
Phenotype category: Efficacy
Significant: yes
Association: Allele G is associated with decreased response to Tumor necrosis factor alpha (TNF-alpha) inhibitors in people with Arthritis, Rheumatoid as compared to allele A.
Notes: using either the absolute change in DAS28 or the proportion of good responders and non-responders as outcomes. The G allele is also a susceptibility factor for RA related to TNF signaling.
Article: Comparative efficacy and safety of sitagliptin or gliclazide combined with metformin in treatment-naive patients with type 2 diabetes: A single-center, prospective, randomized, controlled, noninferiority study with genetic polymorphism analysis
Gene: CDKAL1
Variant/haplotype: rs7754840
Drug(s): sitagliptin
Phenotype category: Efficacy
Significant: no
Association: Genotype CG is associated with increased response to sitagliptin in people with Diabetes Mellitus, Type 2.
Notes: "Patients with the rs7754840 CG genotype showed a median improvement of 1.44 (IQR, 1.38–1.72) in the study group compared with 1.09 (IQR, 0.79–1.17) in the control group (P = .053). "
Article: Association studies of dopamine synthesis and metabolism genes with multiple phenotypes of heroin dependence
Gene: TH
Variant/haplotype: rs10770140
Drug(s): heroin
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with response to heroin as compared to allele C.
Notes: Although an association was initially observed, it lost significance following Bonferroni correction.
Article: Genetic and nongenetic factors associated with warfarin dose requirements in Egyptian patients
Gene: CYP2C9
Variant/haplotype: rs28371686
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Allele G is associated with decreased dose of warfarin as compared to allele C.
Notes: This SNP defines CYP2C9*5. CYP2C9 *2,*3,*4,*5,*8 were grouped into three groups for testing: *1/*1 vs. *1/*2 + *1/*3 + *1/*4 + *1/*5 + *1/*8 vs *2/*2 + *2/*3 + *3/*3 + *5/*5. People having one or two variant alleles had lower dose requirements than people who were *1/*1.
Article: A variation in NOS1AP gene is associated with repaglinide efficacy on insulin resistance in type 2 diabetes of Chinese
Gene: NOS1AP
Variant/haplotype: rs10494366
Drug(s): repaglinide
Phenotype category: Dosage, Efficacy
Significant: yes
Association: Allele T is associated with increased response to repaglinide in people with Diabetes Mellitus, Type 2 as compared to allele G.
Notes: TT subjects had more serious insulin resistance at baseline, but had increased response (HOMA-IR) to repaglinide than TG  and GG subjects.  TG subjects had a lesser response, while GG subjects had an increase in HOMA-IR after treatments.
Article: Implications of OPRM1 and CYP2B6 variants on treatment outcomes in methadone-maintained patients in Ontario: Exploring sex differences
Gene: OPRM1
Variant/haplotype: rs10485058
Drug(s): methadone
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with response to methadone in people with Opioid-Related Disorders as compared to allele A.
Notes: No association between this SNP and odds of continued opioid use or risk of relapse in patients undergoing MMT. Significance threshold was set to p<0.017.
Article: A Genome-Wide Association Study Confirms VKORC1, CYP2C9, and CYP4F2 as Principal Genetic Determinants of Warfarin Dose
Gene: CYP2C9
Variant/haplotype: rs1799853
Drug(s): warfarin
Phenotype category: Dosage, Metabolism/PK
Significant: yes
Association: Allele T is associated with decreased dose of warfarin as compared to allele C.
Article: Association of Polygenic Score for Schizophrenia and HLA Antigen and Inflammation Genes With Response to Lithium in Bipolar Affective Disorder: A Genome-Wide Association Study
Variant/haplotype: rs66486766
Drug(s): lithium
Phenotype category: Efficacy
Significant: yes
Association: Allele A is associated with decreased response to lithium in people with Bipolar Disorder as compared to allele G.
Article: Pharmacogenetic interactions of efavirenz or rifampin and isoniazid with levonorgestrel emergency contraception during treatment of HIV or tuberculosis
Gene: CYP2B6
Variant/haplotype: CYP2B6 poor metabolizer
Drug(s): levonorgestrel
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2B6 poor metabolizer is associated with increased clearance of levonorgestrel in women with HIV Infections as compared to CYP2B6 normal metabolizer.
Notes: Study investigated the effect on steady-state drugs used to treat HIV or tuberculosis on the pharmacokinetics of single dose levonorgestrel. Association found in the cohort treated with efavirenz.; Poor metabolizers defined as having one of the following genotypes:; 1) rs3745274 TT, rs28399499 TT and rs4803419 CC; 2) rs3745274 GT, rs28399499 CT and rs4803419 CC; 3) rs3745274 GG, rs28399499 CC and rs4803419 CC
Article: Impact of ABCC2 1249G>A and −24C>T Polymorphisms on Lacosamide Efficacy and Plasma Concentrations in Uygur Pediatric Patients With Epilepsy in China
Gene: ABCC2
Variant/haplotype: rs717620
Drug(s): lacosamide
Phenotype category: Efficacy
Significant: yes
Association: Allele T is associated with increased resistance to lacosamide in children with Epilepsy as compared to allele C.
Notes: "the proportion of patients with the ABCC2 1249G>A (rs2273697) A; allele and ABCC2 -24C>T (rs717620) T allele in the drug-resistant group was; significantly higher than that in the drug-responsive group"
Article: Impact of the CYP4F2 gene polymorphisms on the warfarin maintenance dose: A systematic review and meta-analysis
Gene: CYP4F2
Variant/haplotype: rs2108622
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Allele T is associated with increased dose of warfarin as compared to allele C.
Notes: 22 studies with 4,549 were included in the meta-analysis.  Most studies were in Chinese patients but 5 were not (2 Japanese, 1 Korean, 1 Indian, 1 Turkish) and one was in a non-specific "Asian" population. Most individuals were prescribed warfarin for heart valve replacement, AF, DVT, pulmonary embolism and stroke.
Article: Influence of OATP1B1 and BCRP polymorphisms on the pharmacokinetics and pharmacodynamics of rosuvastatin in elderly and young Korean subjects
Gene: SLCO1B1
Variant/haplotype: rs4149056
Drug(s): rosuvastatin
Phenotype category: Metabolism/PK
Significant: no
Association: Genotypes CC + CT are associated with increased concentrations of rosuvastatin as compared to genotype TT.
Notes: SLCO1B1 521T > C was also partially associated with a higher AUC of rosuvastatin in young subjects and a less pronounced increasing trend in elderly subjects (p > 0.05 for both). However, it was not statistically significant.
Article: Association studies of dopamine synthesis and metabolism genes with multiple phenotypes of heroin dependence
Gene: DBH
Variant/haplotype: rs129915
Drug(s): heroin
Phenotype category: Dosage
Significant: no
Association: Allele G is not associated with dose of heroin in people with Heroin Dependence as compared to allele A.
Article: Genome-Wide Association Study of Serum Creatinine Levels during Vancomycin Therapy
Variant/haplotype: rs3008608
Drug(s): vancomycin
Phenotype category: Metabolism/PK
Significant: no
Association: Allele A is not associated with trough concentration of vancomycin as compared to allele G.
Notes: The SNP was not associated with trough levels of vancomycin (first vancomycin trough documented in EMR after at least 3 doses vancomycin). Elimination constants were also calculated.
Article: Population pharmacokinetics and pharmacogenomics of apixaban in Japanese adult patients with atrial fibrillation
Gene: ABCB1
Variant/haplotype: rs1128503
Drug(s): apixaban
Phenotype category: Metabolism/PK
Significant: no
Association: Genotypes AA + AG are not associated with clearance of apixaban in people with Atrial Fibrillation as compared to genotype GG.
Article: Effects of CYP2D6 gene polymorphism on plasma concentration and therapeutic effect of olanzapine
Gene: CYP2D6
Variant/haplotype: CYP2D6*1, CYP2D6*2, CYP2D6*10, CYP2D6*34, CYP2D6*39
Drug(s): olanzapine
Phenotype category: Metabolism/PK
Significant: no
Association: CYP2D6 *10/*10 (assigned as intermediate metabolizer phenotype) is associated with increased concentrations of olanzapine in people with Schizophrenia as compared to CYP2D6 *1/*1 + *1/*34 + *1/*39 + *2/*2 + *2/*34 + *2/*39 + *10/*39 + *39/*39 (assigned as normal metabolizer phenotype) .
Notes: The EMs group showed a trend of lower olanzapine plasma concentrations and C/D ratios than the IMs group at different time points (Fig. 1A and B). Interestingly, the olanzapine concentration in the Unknowns group exhibited a noticeable decrease at 8 weeks, leading to a lower trend of concentrations compared to the other two groups (Fig. 1A and B). However, the difference was not statistically significant."The results showed no significant differences in plasma olanzapine concentrations, treatment response, or the occurrence of adverse effects among different CYP2D6 genotypes
Article: Genome-Wide Association Study of Serum Creatinine Levels during Vancomycin Therapy
Variant/haplotype: rs35762933
Drug(s): vancomycin
Phenotype category: Metabolism/PK
Significant: no
Association: Allele T is not associated with trough concentration of vancomycin as compared to allele C.
Notes: The SNP was not associated with trough levels of vancomycin (first vancomycin trough documented in EMR after at least 3 doses vancomycin). Elimination constants were also calculated.
Article: ABCB1 Variation and Treatment Response in AIDS Patients: Initial Results of the Henan Cohort
Gene: ABCB1
Variant/haplotype: rs1045642
Drug(s): lamivudine, nevirapine
Phenotype category: Efficacy
Significant: not stated
Association: Allele A is associated with response to lamivudine or nevirapine in people with HIV Infections as compared to allele G.
Notes: This paper was unclear as to which allele was associated with increased or decreased response as measured by change in CD4+ T cell counts. The significance of this association was greater if rs2032582 was included.
Article: Impact of CYP2D6, CYP3A5, CYP2C9 and CYP2C19 polymorphisms on tamoxifen pharmacokinetics in Asian breast cancer patients
Gene: CYP3A5
Variant/haplotype: CYP3A5*1, CYP3A5*3
Drug(s): 4-hydroxytamoxifen, endoxifen, N-desmethyltamoxifen, tamoxifen
Phenotype category: Metabolism/PK
Significant: no
Association: CYP3A5 *3 is not associated with concentrations of 4-hydroxytamoxifen, endoxifen, n-desmethyltamoxifen and tamoxifen in women with Breast Neoplasms as compared to CYP3A5 *1.
Notes: Patients (pre- (83%) and postmenopausal (17%)) with ER and/or PR positive breast tumors, which received 20 mg tamoxifen daily. Patients taking CYP2D6 inhibitors were excluded. DNA extracted from blood.
Article: Clinical Evaluation of Cisplatin Sensitivity Germline Polymorphisms in Neoadjuvant Chemotherapy for Urothelial Cancer
Gene: RARS1
Variant/haplotype: rs244898
Drug(s): cisplatin
Phenotype category: Efficacy
Significant: yes
Association: Genotype TT is associated with increased response to cisplatin in people with Urinary Bladder Neoplasms as compared to genotypes CC + CT.
Notes: This SNP was significantly associated with complete pathologic response in the discovery cohort, but not the replication cohort.
Article: Prediction of phenprocoumon maintenance dose and phenprocoumon plasma concentration by genetic and non-genetic parameters
Gene: F7
Variant/haplotype: rs510335
Drug(s): phenprocoumon
Phenotype category: Dosage, Metabolism/PK
Significant: no
Association: Genotype GG is not associated with increased dose of phenprocoumon as compared to genotypes GT + TT.
Notes: Daily dose of phenprocoumon is not significantly associated with this SNP. Daily dose is negatively correlated with age. This study published an algorithm for daily dose that includes height, although height was not significant in univariate analysis. This SNP is also not significantly associated with phenprocoumon concentration.
Article: Influence of FMO3 and CYP3A4 Polymorphisms on the Pharmacokinetics of Teneligliptin in Humans
Gene: FMO3
Variant/haplotype: rs2266780
Drug(s): teneligliptin
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotypes AG + GG is associated with decreased clearance of teneligliptin in men as compared to genotype AA.
Notes: effect described for (rs2266780/rs2266782). Significant for clearance, Cmax, and AUC.
Article: Pharmacokinetic Profiles of Lansoprazole in Patients With Morbid Obesity Post‐Roux‐en‐Y Gastric Bypass Surgery
Gene: CYP2C19
Variant/haplotype: CYP2C19*1
Drug(s): lansoprazole
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2C19 *1/*1 is associated with decreased exposure to lansoprazole in people with history of gastric bypass surgery.
Notes: "Our findings support this evidence, as we observed that CYP2C19 normal metabolizers (CYP2C19 *1/*1) generally exhibit lower systemic exposure to lansoprazole at 6 weeks post‐RYGB, with a significant reduction in Cmax. In contrast, no significant pharmacokinetic changes were observed in CYP2C19 intermediate metabolizers (CYP2C19 *1/*2 & *1/*3) post‐surgery. Based on these results, we suggest that CYP2C19 enzyme activity increases after RYGB surgery, particularly in CYP2C19 normal metabolizers. The increases in enzyme activity, leading to enhanced hepatic CL, are likely associated with weight reduction and decreased liver fat content, as described above."
Article: Pharmacogenomics of aromatase inhibitors in postmenopausal breast cancer and additional mechanisms of anastrozole action
Variant/haplotype: rs1437153
Drug(s): anastrozole
Phenotype category: Efficacy
Significant: yes
Association: Allele T is associated with decreased response to anastrozole in women with Breast Neoplasms as compared to allele G.
Notes: Response was measured by the decrease in estrogen levels over the course of treatment.
Article: IL28B expression depends on a novel TT/-G polymorphism which improves HCV clearance prediction
Gene: IFNL4
Variant/haplotype: rs11322783
Drug(s): peginterferon alfa-2b, ribavirin
Phenotype category: Efficacy
Significant: yes
Association: Genotype GG is associated with decreased response to peginterferon alfa-2b and ribavirin in people with Hepatitis C, Chronic as compared to genotypes G/TT + TT/TT.
Notes: This genotype consists of T deletion adjacent to a T to G substitution (TT/-G) and is associated with sustained virological response (SVR).
Article: Replication study of polymorphisms associated with response to methotrexate in patients with rheumatoid arthritis
Gene: ABCB1
Variant/haplotype: rs1045642
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: Genome-wide association study of patient and clinician rated global impression severity during antipsychotic treatment
Gene: PDE4D
Variant/haplotype: rs2164660
Drug(s): quetiapine
Phenotype category: Efficacy
Significant: yes
Association: Allele A is associated with increased response to quetiapine in people with Schizophrenia as compared to allele G.
Notes: The number of A alleles present in a patient was negatively associated with PGI score. Please note that this variant is in high linkage disequilibrium with rs17742120 and rs17382202.
Article: Inhaled corticosteroid treatment modulates ZNF432 gene variant's effect on bronchodilator response in asthmatics
Gene: ZNF432
Variant/haplotype: rs3752120
Drug(s): budesonide, corticosteroids, fluticasone propionate, fluticasone/salmeterol
Phenotype category: Efficacy
Significant: yes
Association: Genotype TT is associated with decreased response to budesonide, corticosteroids, fluticasone propionate or fluticasone/salmeterol in people with Asthma.
Notes: This is stated as "Having 2 copies of the mutant allele and not being treated with inhaled corticosteroids produces a higher bronchodilator response than having 2 mutant alleles and being treated with inhaled corticosteroids(ICS)."  By "mutant" allele, presumably the minor allele (T) is meant.  CAMP has 3 arms: budesonide,nedocromil and placebo.  Subjects in the budesonide arm were considered exposed to ICS.  For LOCCS(which was used as a replication cohort), subjects who said that they had used ICS either daily or 2-6x/wk over the past 6 months were considered to have used ICS.  Subjects who responded: "1-2x/month", "<1x/month" or "never" were considered to not have used ICS.  A comparison between genotypes was not done.  The authors state that the clinical implication is not clear,and that "Inhaled corticosteroids appear to modulate the association of bronchodilator response with variant(s) in the ZNF432 gene among adults and children with asthma."
Article: Association between single nucleotide polymorphisms in the mu opioid receptor gene (OPRM1) and self-reported responses to alcohol in American Indians
Gene: OPRM1
Variant/haplotype: rs506247
Drug(s): ethanol
Phenotype category: Efficacy
Significant: no
Association: Allele C is not associated with response to ethanol as compared to allele A.
Notes: Please note that alleles have been complemented to the positive strand. No significant association between this variant and any individual item or total score on the Subjective High Assessment Scale-Expectations (SHAS-E) questionnaire.
Article: Effect of NLRP3 inflammasome genes polymorphism on disease susceptibility and response to TNF-α inhibitors in Iraqi patients with rheumatoid arthritis
Gene: CARD8
Variant/haplotype: rs2043211
Drug(s): etanercept, infliximab
Phenotype category: Efficacy
Significant: yes
Association: Genotype TT is associated with decreased response to etanercept or infliximab in people with Arthritis, Rheumatoid as compared to genotypes AA + AT.
Notes: caution, this is an A/T SNP in a gene on the minus strand. Authors show T as minor allele which suggests is reported on plus strand. Responders = ΔDAS-28 ≥ 1.2 and DAS-28 ≤ 3.2, Non-responders = ΔDAS-28 ≤ 1.2 and DAS28 ≤ 5.1 (Table 1)
Article: Meta-analysis of the effects of CYP3A5*3 gene polymorphisms on tacrolimus blood concentration and effectiveness in Chinese patients with membranous nephropathy
Gene: CYP3A5
Variant/haplotype: rs776746
Drug(s): tacrolimus
Phenotype category: Efficacy
Significant: yes
Association: Genotypes CT + TT is associated with decreased dose-adjusted trough concentrations of tacrolimus in people with Glomerulonephritis, Membranous as compared to genotype CC.
Notes: "The meta-analysis results showed that at ≤1 month [SMD = −1.93, 95% CI (−2.79, −1.08), p < 0.001], 1–6 months [SMD = −2.25, 95% CI (−2.71, −1.79), p < 0.001], and ≥6 months [SMD = −2.36, 95% CI (−2.86, −1.86), p < 0.001], the TAC C0/D levels of CYP3A5 expressers in MN patients were lower than those of CYP3A5 non-expressers (Figure 3)." "AA + AG genotype (referred to as expressers) and the GG genotype (referred to as non-expressers)"
Article: Impact of IL28B, APOH and ITPA Polymorphisms on Efficacy and Safety of TVR- or BOC-Based Triple Therapy in Treatment-Experienced HCV-1 Patients with Compensated Cirrhosis from the ANRS CO20-CUPIC Study
Gene: APOH
Variant/haplotype: rs1801689
Drug(s): boceprevir, peginterferon alfa-2a, peginterferon alfa-2b, ribavirin, telaprevir
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with increased response to boceprevir, peginterferon alfa-2a, peginterferon alfa-2b, ribavirin or telaprevir in people with Hepatitis C, Chronic as compared to allele C.
Notes: This variant was not significantly associated with SVR to triple therapy including telaprevir or boceprevir in patients with compensated cirrhosis chronically infected with HCV-1.
Article: Association and cis-mQTL analysis of variants in CHRNA3-A5, CHRNA7, CHRNB2, and CHRNB4 in relation to nicotine dependence in a Chinese Han population
Gene: CHRNA3
Variant/haplotype: rs3743074
Drug(s): nicotine
Phenotype category: Other
Significant: no
Association: Allele G is not associated with exposure to nicotine in men as compared to allele A.
Notes: No significant association between this allele and status as a smoker or non-smoker.