shlokn/autogkb huggingface dataset:
Article: Warfarin Dose Model for the Prediction of Stable Maintenance Dose in Indian Patients
Gene: F7
Variant/haplotype: rs6046
Drug(s): warfarin
Phenotype category: Dosage
Significant: no
Association: Allele A is not associated with dose of warfarin as compared to allele G.
Article: Genetic polymorphisms in key methotrexate pathway genes are associated with response to treatment in rheumatoid arthritis patients
Gene: GGH
Variant/haplotype: rs11545078
Drug(s): methotrexate
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to methotrexate in people with Arthritis, Rheumatoid.
Article: Association of variants in NEDD4L with blood pressure response and adverse cardiovascular outcomes in hypertensive patients treated with thiazide diuretics
Gene: NEDD4L
Variant/haplotype: rs292449
Drug(s): hydrochlorothiazide
Phenotype category: Efficacy
Significant: yes
Association: Genotypes CC + CG are associated with increased response to hydrochlorothiazide in people with Hypertension as compared to genotype GG.
Notes: CC and CG patients had significantly greater reduction in Systolic and in Diastolic Blood pressure than those with GG genotype.  A significant association was also seen between the haplotype rs4149601G/rs292449C and greater response to hydrachlorothiazide in Whites.  The GC SNP creates ambiguity in knowing which strand is being reported on.  The SNP is in a positive chromosomal strand gene, so hopefully the genotypes are being reported in relation to the positive strand.
Article: Effects of FMO3 Polymorphisms on Pharmacokinetics of Sulindac in Chinese Healthy Male Volunteers
Gene: FMO3
Variant/haplotype: rs2266782
Drug(s): sulindac
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype AA is associated with increased exposure to sulindac in healthy individuals as compared to genotype GG.
Notes: Measures of exposure were AUC, Cmax, Tmax, and T1/2.
Article: CYP3A5, ABCB1 and SLCO1B1 Polymorphisms and Pharmacokinetics and Virologic Outcome of Lopinavir/Ritonavir in HIV-infected Children
Gene: CYP3A5
Variant/haplotype: rs776746
Drug(s): lopinavir, ritonavir
Phenotype category: Metabolism/PK
Significant: no
Association: Allele C is not associated with exposure to lopinavir or ritonavir in children with HIV Infections as compared to allele T.
Notes: No association between this variant and AUC0-12 of lopinavir or ritonavir in patients treated with lopinavir/ritonavir. Variant referred to in the paper as A6986G.
Article: The International SSRI Pharmacogenomics Consortium (ISPC): a genome-wide association study of antidepressant treatment response
Gene: LINC00478
Variant/haplotype: rs239022
Drug(s): Selective serotonin reuptake inhibitors
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to Selective serotonin reuptake inhibitors in people with Depressive Disorder, Major as compared to allele G.
Notes: The allele did not reach genome wide significance in the discovery or replication cohorts. GWA analyses were performed for two phenotypes: ‘% change in HRSD-17 score’ (% HRSD defined as the change in HRSD-17 score divided by the baseline score) and ‘response’ (defined as greater than or equal to 50% reduction in HRSD-17 score from baseline to 4-week visit).
Article: Genome-wide association study of a nicotine metabolism biomarker in African American smokers: impact of chromosome 19 genetic influences
Variant/haplotype: rs12459249
Drug(s): nicotine
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele C is associated with decreased metabolism of nicotine as compared to allele T.
Notes: Nicotine metabolism was assessed by measuring participants' nicotine metabolite ratio.
Article: Pharmacogenetic Influence of LOC387715/HTRA1 on the Efficacy of Bevacizumab Treatment for Age-Related Macular Degeneration in a Korean Population
Gene: ARMS2
Variant/haplotype: rs10490924
Drug(s): bevacizumab
Phenotype category: Efficacy
Significant: no
Association: Genotypes GT + TT are not associated with response to bevacizumab in people with Macular Degeneration as compared to genotype GG.
Notes: No significant difference in change in central macular thickness (measured by optical coherence tomography) were seen between any the genotypes, over either 6 or 12 months of treatment.
Article: Prediction Formulas for Individual Opioid Analgesic Requirements Based on Genetic Polymorphism Analyses
Variant/haplotype: rs11959113
Drug(s): fentanyl
Phenotype category: Dosage, Efficacy
Significant: yes
Association: Genotype AA is associated with increased dose of fentanyl in people with Pain, Postoperative as compared to genotypes AG + GG.
Notes: A formula was developed to predict individual opioid use during the first 24-h post-operative period for patients who underwent craniofacial surgery. The post-operative period R squared values were higher when genotype information was included. In the first group fentanyl was administered by IV, on demand, with a bolus dose of 20 micrograms and a 10 minute lockout period 24-h post-op.
Article: Genome-Wide Association Study of Serum Creatinine Levels during Vancomycin Therapy
Variant/haplotype: rs3002130
Drug(s): vancomycin
Phenotype category: Metabolism/PK
Significant: no
Association: Allele C is not associated with trough concentration of vancomycin as compared to allele T.
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: Pharmacokinetics and Safety of Brexpiprazole Following Multiple‐Dose Administration to Japanese Patients With Schizophrenia
Gene: CYP2D6
Variant/haplotype: CYP2D6 intermediate metabolizer
Drug(s): brexpiprazole
Phenotype category: Metabolism/PK
Significant: not stated
Association: CYP2D6 intermediate metabolizer is associated with decreased metabolism of brexpiprazole in people with Schizophrenia as compared to CYP2D6 normal metabolizer.
Notes: 15 and 6 patients were classified as NMs (genotypes including at least 1 active allele) and IMs (genotypes with 2 decreased-activity alleles or 1 decreased-activity allele and 1 inactive allele or 1decreased-activity allele and 1 unknown-activity allele). Metabolic activity was defined as the normal alleles *1 and *2, the decreased-activity alleles *10 and *41, the inactive alleles *4, *5, and *14A, and the unknown-activity alleles *14B, *18, and *21. For PK parameters of brexpiprazole, both Cmax/D and AUC24h/D were higher in IM patients than in EM patients. The Cmax and AUC24h in EM and IM patients of brexpiprazole following multiple administrations of brexpiprazole were 2.6–2.8 and 4.5–5.8 times higher, respectively, on day 14 compared with day 1 based on the accumulation index. CL/F waslower in IM patients than in EM patients.
Article: Association of corticotropin releasing hormone receptor 2 (CRHR2) genetic variants with acute bronchodilator response in asthma
Gene: CRHR2
Variant/haplotype: rs255100
Drug(s): salbutamol
Phenotype category: Efficacy
Significant: yes
Association: Allele A is associated with decreased response to salbutamol in people with Asthma as compared to allele T.
Notes: The A allele of this variant is associated with reduced bronchodilator response in CAMP cohort. However, this association is not significant in the other two cohorts tested.
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): ritonavir
Phenotype category: Metabolism/PK
Significant: no
Association: Allele C is not associated with clearance of ritonavir in children with HIV Infections as compared to allele T.
Notes: No significant association between this variant and clearance of ritonavir in patients treated with lopinavir/ritonavir. Variant referred to in the paper as T512C.
Article: Genetic Polymorphisms of Cytokines Might Affect Postoperative Sufentanil Dosage for Analgesia in Patients
Gene: NFKB1
Variant/haplotype: rs28362491
Drug(s): sufentanil
Phenotype category: Dosage
Significant: no
Association: Allele (ATTG)1 is not associated with dose of sufentanil in people with Pain, Postoperative as compared to allele ATTGATTG.
Article: Race, Gender, and Genetic Polymorphism Contribute to Variability in Acetaminophen Pharmacokinetics, Metabolism, and Protein-Adduct Concentrations in Healthy African-American and European-American Volunteers
Gene: SULT1A1
Variant/haplotype: rs1042028
Drug(s): acetaminophen
Phenotype category: Metabolism/PK
Significant: no
Association: Genotype TT is not associated with decreased metabolism of acetaminophen in healthy individuals as compared to genotypes CC + CT.
Notes: Metabolism here, refers to AUC ratio of Sulfate: APAP. Association was nominally significant initially, but did not remain statistically significant in multiple linear regression. The T allele is also referred to as the *2 allele. Please note: alleles have been complemented to the + chromosomal strand. This variant was originally mapped to rs9282861, which has now been merged into rs1042028.
Article: Pharmacogenetic interactions of efavirenz or rifampin and isoniazid with levonorgestrel emergency contraception during treatment of HIV or tuberculosis
Gene: NAT2
Variant/haplotype: NAT2 intermediate acetylator
Drug(s): levonorgestrel
Phenotype category: Metabolism/PK
Significant: no
Association: NAT2 intermediate acetylator is not associated with clearance of levonorgestrel in women with Tuberculosis as compared to NAT2 rapid acetylator.
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 Isoniazid and rifampin.; Intermediate acetylators were defined as heterozygous for the NAT2*5, *6, *7 or *14 alleles.
Article: No significant influence of OCT1 genotypes on the pharmacokinetics of morphine in adult surgical patients
Gene: SLC22A1
Variant/haplotype: rs72552763
Drug(s): morphine
Phenotype category: Dosage
Significant: no
Association: Allele del is not associated with dose of morphine in people with Pain, Postoperative as compared to allele GAT.
Notes: Analyzed as part of haplotypes with rs12208357, rs34059508 and rs34130495. No significant association between haplotypes and PCA doses of morphine.
Article: ABCC3 Genetic Variants are Associated with Postoperative Morphine-induced Respiratory Depression and Morphine Pharmacokinetics in Children
Gene: ABCC3
Variant/haplotype: rs4148412
Drug(s): morphine-3-glucuronide
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype TT is associated with increased concentrations of morphine-3-glucuronide in children with tonsillectomy as compared to genotypes CC + CT.
Notes: This variant was not significant in the spine surgery cohort. Increases in M6G were also observed but were not significant in either cohort. Alleles were described in paper as A and G, with AA for risk genotype.
Article: Relative contribution of CYP2C9 and VKORC1 genotypes and early INR response to the prediction of warfarin sensitivity during initiation of therapy
Gene: VKORC1
Variant/haplotype: rs9934438
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Allele A is associated with decreased dose of warfarin as compared to allele G.
Article: Integrative genomic analysis of methylphenidate response in attention-deficit/hyperactivity disorder
Gene: ZNF211
Variant/haplotype: rs10420097
Drug(s): methylphenidate
Phenotype category: Efficacy
Significant: no
Association: Allele G is associated with increased response to methylphenidate in people with Attention Deficit Disorder with Hyperactivity.
Notes: The authors carried out a GWAS in a Spanish cohort of pediatric patients, than performed a meta-analysis using data from the Spanish cohort and data from a Brazilian adult patient cohort.; This variant was not significant in the meta-analysis after Bonferroni correction had been applied, and was nominally significant (i.e did not reach genome-wide significance) in the initial GWAS in the Spanish cohort.; Response was measured on the Clinical Global Impression-Improvement scale (CGI-I). A CGI-I score of two points or less after eight weeks of treatment was considered a good response.
Article: IL-3 and CTLA4 gene polymorphisms may influence the tacrolimus dose requirement in Chinese kidney transplant recipients
Gene: CYP3A4
Variant/haplotype: rs4646437
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype GG is associated with increased exposure to tacrolimus in people with Kidney Transplantation as compared to genotypes AA + AG.
Notes: This association was seen for time 7, 30, and 90 days after transplantation. Exposure to CC was higher than CT, which was higher than TT.
Article: Effect of pharmacogenetics on plasma lumefantrine pharmacokinetics and malaria treatment outcome in pregnant women
Gene: CYP2B6
Variant/haplotype: rs28399499
Drug(s): lumefantrine
Phenotype category: Metabolism/PK
Significant: no
Association: Allele C is not associated with concentrations of lumefantrine in women with Malaria and Pregnancy as compared to allele T.
Notes: Median concentrations of lumefantrine 7 days after beginning treatment with artemether-lumefantrine were not significantly different and no more likely to have median concentrations of lumefantrine  >600 ng/ml between genotypes.
Article: Targeted pharmacogenetic analysis of antipsychotic response in the CATIE study
Variant/haplotype: rs11774231
Drug(s): perphenazine
Phenotype category: Efficacy
Significant: yes
Association: Allele C is associated with response to perphenazine in people with Schizophrenia.
Notes: as measured by changes in PANSS-T (positive and negative syndrome scale total score), using a mixed model repeated measures approach. Examined 6789 SNPs - p-value of p< or equal to 5x10-4 was considered significant. It was unclear whether the allele was associated with an increased or decreased response to drug.
Article: Influence of genetic polymorphisms in P2Y12 receptor signaling pathway on antiplatelet response to clopidogrel in coronary heart disease
Gene: P2RY12
Variant/haplotype: rs2046934
Drug(s): clopidogrel
Phenotype category: Efficacy
Significant: no
Association: Genotype AG is not associated with increased resistance to clopidogrel in people with Coronary Disease as compared to genotype GG.
Notes: no AA individuals were observed.
Article: Discordant Associations between SLCO1B1 521T→C and Plasma Levels of Ritonavir-boosted Protease Inhibitors in AIDS Clinical Trials Group Study A5146
Gene: SLCO1B1
Variant/haplotype: rs4149056
Drug(s): amprenavir
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele C is associated with decreased trough concentration of amprenavir in people with HIV Infections as compared to allele T.
Notes: Association was significant in white patients treated with fosamprenavir only. Only 3 Hispanic patients carried the C allele, so statistical analysis could not be carried out. However, the authors note that these patients also tended to have low trough concentrations of amprenavir.
Article: A genetic variant in Rassf1a predicts outcome in mCRC patients treated with cetuximab plus chemotherapy: results from FIRE-3 and JACCRO 05 and 06 trials
Gene: WWTR1
Variant/haplotype: rs3811715
Drug(s): cetuximab
Phenotype category: Efficacy
Significant: no
Association: Genotype GG is not associated with response to cetuximab in people with Colorectal Neoplasms as compared to genotypes AA + AG.
Notes: No significant difference in tumor response, progression-free survival or overall survival was seen between the genotype groups. Patients also receiving treatment with fluorouracil, leucovorin and irinotecan (FOLFIRI). Please note that alleles have been complemented to the plus chromosomal strand.
Article: Hypertension Susceptibility Loci and Blood Pressure Response to Antihypertensives – Results from the Pharmacogenomic Evaluation of Antihypertensive Responses (PEAR) Study
Gene: SH2B3
Variant/haplotype: rs3184504
Drug(s): hydrochlorothiazide
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with response to hydrochlorothiazide in people with Hypertension as compared to allele C.
Notes: Not significant when using Bonferroni-corrected alpha of 0.0014. Response was assessed by change in diastolic blood pressure (DBP) after 9 weeks of treatment.
Article: Influence of ABCC2 and ABCC4 Polymorphisms on Tenofovir Plasma Concentrations in Thai HIV-Infected Patients
Gene: ABCC2
Variant/haplotype: rs717620
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: Investigation of CYP 3A5 and ABCB1 gene polymorphisms in the long-term following renal transplantation: Effects on tacrolimus exposure and kidney function
Gene: ABCB1
Variant/haplotype: rs1045642
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: no
Association: Genotypes AG + GG is not associated with metabolism of tacrolimus in people with Kidney Transplantation as compared to genotype AA.
Notes: No significant difference in dose, trough concentrations or dose-adjusted trough concentrations of tacrolimus were seen between the genotype groups, when adjusting for the influence of the CYP3A5 *3/*3 genotype (i.e. individuals who were carriers of the *1/*3 genotype, or "expressers", were excluded from the analysis). Prior to adjustment for the influence of *3/*3, those with the AG or GG genotype had decreased dose-adjusted trough concentrations of tacrolimus at 24 months post transplant and increased dose requirements at 6 months post-transplant (p<0.05).
Article: Pharmacogenetics of plasma efavirenz exposure in HIV-infected adults and children in South Africa
Gene: CYP2B6
Variant/haplotype: rs28399499
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele C is associated with increased concentrations of efavirenz in people with HIV Infections as compared to allele T.
Notes: When considered as part of a composite (rs3745274 T, rs28399499 C, and rs4803419 T), the C allele was strongly associated with plasma efavirenz concentrations (plasma [EFV]) [beta=0.28, 95% CI (0.21, 0.35) p=2.4 E-11]. In a final multivariable model  the C allele was associated with a 46% increased in plasma [EFV] (beta=0.27). Post-hoc sensitivity analysis, in which two extreme outliers were excluded from analysis (N=111), showed that the C allele was associated with a 48% increase in plasma [EFV]. Multi-level mixed effects models predicted plasma [EFV] as a function of 1) fixed age effect, time after dose, CYP2B6 composite genotype T,C,T and 2) random effects of the individual to account for w/in individual correlations, genotype CT was associated with a 2.1 fold increase in plasma [EFV].
Article: Pharmacogenetics of unboosted atazanavir in HIV-infected individuals in resource-limited settings: a sub-study of the AIDS Clinical Trials Group (ACTG) PEARLS study (NWCS 342)
Gene: SLCO1B1
Variant/haplotype: rs4149056
Drug(s): atazanavir
Phenotype category: Metabolism/PK
Significant: no
Association: Genotype CT (assigned as deficiency phenotype) is not associated with concentrations of atazanavir in people with HIV Infections as compared to genotype TT.
Notes: Looked at CL/F, concentration at 24 hours, and ratios of metabolites M1 and M2 to atazanavir. No CC genotypes identified.
Article: Prediction of Methotrexate Clinical Response in Portuguese Rheumatoid Arthritis Patients: Implication of MTHFR rs1801133 and ATIC rs4673993 Polymorphisms
Gene: ATIC
Variant/haplotype: rs4673993
Drug(s): methotrexate
Phenotype category: Efficacy
Significant: yes
Association: Genotype CC is associated with increased response to methotrexate in people with Arthritis, Rheumatoid as compared to genotypes CT + TT.
Notes: "ATIC 675T carriers were associated with over 4-fold increased risk for nonresponse. "
Article: NUDT15 codon 139 is the best pharmacogenetic marker for predicting thiopurine-induced severe adverse events in Japanese patients with inflammatory bowel disease: a multicenter study
Gene: NUDT15
Variant/haplotype: rs116855232
Drug(s): azathioprine, mercaptopurine
Phenotype category: Dosage
Significant: yes
Association: Genotype TT is associated with decreased dose of azathioprine or mercaptopurine in people with Inflammatory Bowel Diseases as compared to genotypes CC + CT.
Notes: The doses of thiopurines at the time when severe leukopenia was diagnosed were 39.4 ± 3.1 mg/day in TT which was significantly lower than 69.1 ± 28.1 mg/day in CC (8.50E-06) and 54.6 ± 19.1 mg/day in CT (p = 2.46E-02 ),
Article: The CYP19 RS4646 Polymorphism IS Related to the Prognosis of Stage I–II and Operable Stage III Breast Cancer
Gene: CYP19A1
Variant/haplotype: rs4646
Drug(s): anastrozole, letrozole, tamoxifen
Phenotype category: Efficacy
Significant: yes
Association: Genotype AA is associated with increased response to anastrozole, letrozole or tamoxifen in women with Breast Neoplasms as compared to genotypes AC + CC.
Notes: Median follow up time was 96 months and the association was with disease free survival (DFS). Overall there was no difference in DFS by genotype, however when women were split into the pre-menopausal and post-menopausal group, an association was seen between the AA genotype and DFS, but in opposite directions. The AA genotype was associated with shorter DFS in the post-menopausal women and longer DFS in the pre-menopausal women when compared to the AC and CC genotypes (87 months in pre-menopausal AA women, and 48.7 months in pre-menopausal AC+CC women). Chemotherapy included Cyclophosphamide, Doxorubicin/epirubicin and Fluoracil or Doxorubicin, Cyclophosphamide with/without docetaxel, Cyclophosphamide, Epirubicin or Doxorubicin, Cyclophosphamide followed by Docetaxel or weekly Paclitaxel, CAF (Cyclophosphamide, Doxorubicin/Epirubicin and Fluoracil) followed by Docetaxel or weekly Paclitaxel treatment and others, 10 (2.5%) remained unknown.
Article: Assessing the Contribution of Opioid- and Dopamine-Related Genetic Polymorphisms to the Abuse Liability of Oxycodone
Gene: COMT
Variant/haplotype: rs737865
Drug(s): oxycodone
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with response to oxycodone as compared to allele A.
Notes: No association between this variant and analgesic response to oxycodone, as assessed by cold pressor test, subjective effects of oxycodone. Please note that alleles have been complemented to the positive strand.
Article: Warfarin Dose Model for the Prediction of Stable Maintenance Dose in Indian Patients
Gene: GGCX
Variant/haplotype: rs11676382
Drug(s): warfarin
Phenotype category: Dosage
Significant: no
Association: Allele G is not associated with dose of warfarin as compared to allele C.
Article: Association of Variants in Candidate Genes with Lipid Profiles in Women with Early Breast Cancer on Adjuvant Aromatase Inhibitor Therapy
Gene: CYP19A1
Variant/haplotype: rs4775936
Drug(s): triglycerides
Phenotype category: Other
Significant: yes
Association: Allele C is associated with decreased concentrations of triglycerides in women with Breast Neoplasms and Menopause as compared to allele T.
Notes: when taking letrozole and lipid lowering agents (LLA), such as statins. Data are from a sub-analysis of the Exemestane and Letrozole Pharmacogenomics (ELPh) study, where post-menopausal women with early stage breast cancer were randomized to receive exemestane or letrozole. Of the 303 eligible women, 160 were randomized to the letrozole group, 52 of whom were also taking LLA. This SNP was associated with decreases in triglycerides of 33.2 mg/dL (SE 8.9).