shlokn/autogkb huggingface dataset:
Article: CYP2D6 function moderates the pharmacokinetics and pharmacodynamics of 3,4-methylene-dioxymethamphetamine in a controlled study in healthy individuals
Gene: CYP2D6
Variant/haplotype: CYP2D6*1, CYP2D6*2, CYP2D6*3, CYP2D6*4, CYP2D6*5, CYP2D6*6, CYP2D6*9, CYP2D6*10, CYP2D6*41
Drug(s): 3,4-methylenedioxymethamphetamine
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2D6 *4/*4 + *3/*5 is associated with decreased metabolism of 3,4-methylenedioxymethamphetamine as compared to CYP2D6 *1/*4 + *1/*3 + *1/*6 + *2/*4 + *2/*5 + *9/*10 + *1/*41 + *1/*10 + *1/*9 + *2/*10 + *2/*41 + *1/*1 + *1/*2 + *2/*2.
Notes: Alteration in plasma MDMA levels was seen up to 3 h after drug administration but not beyond. Higher Cmax values in CYP2D6 poor metabolizers (PMs) compared with extensive metabolizers (EMs). PMs showing higher AUC6(up to 6hr) values compared with EMs. The Cmax and AUC6 of 3,4-methylene-dioxyamphetamine (MDA) varied across genotypes (F2,136 = 8.82, P < 0.01, and F2,136 = 9.09, P < 0.001, respectively), which were higher in PMs compared with intermediate metabolizers (IMs; P < 0.001) and EMs (P < 0.001).
Article: Dependence of erythromycin metabolism on ABCC2 (MRP2) transport function
Gene: ABCC2
Variant/haplotype: rs717620
Drug(s): erythromycin
Phenotype category: Other, Metabolism/PK
Significant: yes
Association: Genotype TT is associated with increased metabolism of erythromycin as compared to genotypes CC + CT.
Article: IL28B, HLA-C, and KIR Variants Additively Predict Response to Therapy in Chronic Hepatitis C Virus Infection in a European Cohort: A Cross-Sectional Study
Gene: IFNL3
Variant/haplotype: rs8099917
Drug(s): peginterferon alfa-2b, ribavirin
Phenotype category: Efficacy
Significant: yes
Association: Allele G is associated with decreased response to peginterferon alfa-2b and ribavirin in people with Hepatitis C as compared to allele T.
Notes: Response to treatment assessed by whether patients had successfully cleared the virus after six months of therapy.
Article: Gene Variants in CYP2C19 Are Associated with Altered In Vivo Bupropion Pharmacokinetics but Not Bupropion-Assisted Smoking Cessation Outcomes
Gene: CYP2C19
Variant/haplotype: CYP2C19*1, CYP2C19*2
Drug(s): bupropion
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2C19 *2 is associated with increased exposure to bupropion in healthy individuals as compared to CYP2C19 *1.
Notes: Healthy volunteers were given 150 mg of bupropion once a day for 7 days. On day 7 plasma samples were taken every 4 hours for a 24-hour period as well as a complete urine sample. Individuals with at least one CYP2C19*2 allele had a higher steady-state plasma area under the plasma concentration-time curve for bupropion, erythrohydrobupropion and theohydrobupropion as compared to CYP2C19*1. Hydroxybupropion was not significantly different between CYP2C19*1 and CYP2C19*2.
Article: CYP2B6 Genotypes and Early Efavirenz-based HIV Treatment Outcomes in Botswana
Gene: CYP2B6
Variant/haplotype: rs3745274
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: not stated
Association: Genotypes GT + TT is associated with decreased clearance of efavirenz in people with HIV Infections as compared to genotype GG.
Notes: This is for CYP2B6 516G>T.
Article: Potential role of polymorphisms in the transporter genes ENT1 and MATE1/OCT2 in predicting TAS-102 efficacy and toxicity in patients with refractory metastatic colorectal cancer
Gene: SLC29A1
Variant/haplotype: rs760370
Drug(s): tipiracil hydrochloride, trifluridine
Phenotype category: Efficacy
Significant: yes
Association: Genotypes AG + GG is associated with increased response to tipiracil hydrochloride and trifluridine in people with Colorectal Neoplasms as compared to genotype AA.
Notes: The G allele was tested for association alone and with two other SNPs after univariate and multivariate analysis in training (N= 52, Japan) and testing cohorts (N = 127, Italy). It was associated with improved progression-free and overall survival in the training and testing cohorts after univariate and multivariate analyses.  When tested with other SNPs (rs2289669 G>A and rs316019 A>C) it was also associated with overall, but not progression-free survival.
Article: A Genome-Wide Association Study Confirms VKORC1, CYP2C9, and CYP4F2 as Principal Genetic Determinants of Warfarin Dose
Gene: CYP2C9
Variant/haplotype: rs1057910
Drug(s): warfarin
Phenotype category: Dosage, Metabolism/PK
Significant: yes
Association: Allele C is associated with decreased dose of warfarin as compared to allele A.
Article: Cytochrome P450 Genetic Variation Associated with Tamoxifen Biotransformation in American Indian and Alaska Native People
Gene: CYP2D6
Variant/haplotype: CYP2D6 poor metabolizer and intermediate metabolizer genotypes
Drug(s): endoxifen
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2D6 poor metabolizer and intermediate metabolizer genotypes are associated with concentrations of endoxifen in women with Breast Neoplasms.
Article: Lack of Associations of CHRNA5-A3-B4 Genetic Variants with Smoking Cessation Treatment Outcomes in Caucasian Smokers despite Associations with Baseline Smoking
Gene: CHRNA3
Variant/haplotype: rs578776
Drug(s): nicotine
Phenotype category: Metabolism/PK
Significant: no
Association: Allele A is not associated with dose of nicotine in people with Tobacco Use Disorder as compared to allele G.
Notes: The A allele of s578776 was significantly associated with 8% lower cotinine levels, but the association was no longer significant after adjusting for rs16969968 (the per allele effect size was -8.2 ng/mL, CI = -20.24–3.93 and P = 0.19  vs. -18.9 ng/mL without adjustment P = 0.002 ).
Article: High imatinib dose overcomes insufficient response associated with ABCG2 haplotype in chronic myelogenous leukemia patients
Gene: ABCG2
Variant/haplotype: rs2725252
Drug(s): imatinib
Phenotype category: Efficacy
Significant: yes
Association: Genotypes AC + CC is associated with increased response to imatinib in people with Leukemia, Myelogenous, Chronic, BCR-ABL Positive as compared to genotype AA.
Notes: Individuals with the AC or CC genotype had a higher cumulative incidence of major molecular response (CI-MMR, estimated using Sokal score) after 18 months of treatment with a 400mg/day dose of imatinib, as compared to those with the AA genotype. No significant results were seen when considering patients taking a 600mg/day dose (n=107; p < 0.74). The authors note that they used the Benjamini and Hochberg method for multiple testing issues. Please also note that alleles have been complemented to the plus chromosomal strand.
Article: The impact of CES1 genotypes on the pharmacokinetics of methylphenidate in healthy Danish subjects
Gene: CES1
Variant/haplotype: rs71647871
Drug(s): methylphenidate
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele T is associated with decreased metabolism of methylphenidate in healthy individuals as compared to allele C.
Notes: Metabolism assessed through AUC.
Article: Effect of CYP3 A4, CYP3 A5 and ABCB1 gene polymorphisms on the clinical efficacy of tacrolimus in the treatment of nephrotic syndrome
Gene: ABCB1
Variant/haplotype: rs1128503
Drug(s): tacrolimus
Phenotype category: Efficacy
Significant: yes
Association: Genotype AA is associated with increased response to tacrolimus in people with Nephrotic Syndrome as compared to genotypes AG + GG.
Notes: Patients with the AA genotype had a higher effectiveness of clinical treatment as compared to those with the AG or GG genotypes. Effective response included patients with complete or partial remission, and ineffective response included patients with no remission or recurrence.
Article: Genetic variants influenced the risk of bleeding and pharmacodynamics of rivaroxaban in patients with nonvalvular atrial fibrillation: A multicentre prospective cohort study
Gene: PRKAG2
Variant/haplotype: rs13224758
Drug(s): rivaroxaban
Phenotype category: Toxicity
Significant: no
Association: Allele G is associated with increased response to rivaroxaban in people with Atrial Fibrillation as compared to allele A.
Notes: as measured by peak anti‐FXa level. Association described as "suggestive". "The incidence of bleeding events were significantly related to the peak anti‐FXa level, which were significantly increased in patients with bleeding events than in those without"
Article: Associations Between SNPs in Toll-like Receptors and Related Intracellular Signaling Molecules and Immune Responses to Measles Vaccine: Preliminary Results
Gene: TLR3
Variant/haplotype: rs3775291
Drug(s): Measles vaccines
Phenotype category: Efficacy
Significant: yes
Association: Genotype CT is associated with decreased response to Measles vaccines as compared to genotype CC.
Notes: compared to both homozygous genotypes
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
Gene: FAM178B
Variant/haplotype: rs6728642
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: Clinical and genetic factors associated with warfarin maintenance dose in northern Chinese patients with mechanical heart valve replacement
Gene: CYP2C9
Variant/haplotype: CYP2C9*1, CYP2C9*3
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: CYP2C9 *1/*3 + *3/*3 are associated with decreased dose of warfarin in people with heart valve replacement as compared to CYP2C9 *1/*1.
Article: Influence of genetic co-factors on the population pharmacokinetic model for clopidogrel and its active thiol metabolite
Gene: CYP3A4
Variant/haplotype: rs2242480
Drug(s): clopidogrel, clopidogrel thiol metabolite H4
Phenotype category: Metabolism/PK
Significant: no
Association: Allele T is not associated with exposure to clopidogrel or clopidogrel thiol metabolite H4 as compared to allele C.
Notes: Full pharmacokinetic profile was obtained from 17 subjects at  0.5, 1, 2, 3, and 4 h post clopidogrel dose. From 46 subjects samples were collected at 0.5 and 2 h or 1 and 3 h post-dose. Subjects were receiving PCI or elective coronarography.
Article: XRCC3 Thr241Met Polymorphism and Clinical Outcomes of NSCLC Patients Receiving Platinum-Based Chemotherapy: A Systematic Review and Meta-Analysis
Gene: XRCC3
Variant/haplotype: rs861539
Drug(s): Platinum compounds
Phenotype category: Efficacy
Significant: not stated
Association: Allele A is not associated with response to Platinum compounds in people with Carcinoma, Non-Small-Cell Lung as compared to allele G.
Article: A pharmacogenetic study of docetaxel and thalidomide in patients with castration-resistant prostate cancer using the DMET genotyping platform
Gene: CHST3
Variant/haplotype: rs1871450
Drug(s): docetaxel, thalidomide
Phenotype category: Efficacy
Significant: yes
Association: Allele A is associated with increased response to docetaxel and thalidomide in people with Prostatic Neoplasms as compared to allele G.
Notes: (allele inferred by frequency comparison with data in pgkb, actual base not listed in paper)
Article: Impact of ABCG2 polymorphisms on the clinical outcome and toxicity of gefitinib in non-small-cell lung cancer patients
Gene: ABCG2
Variant/haplotype: rs2622604
Drug(s): gefitinib
Phenotype category: Efficacy
Significant: no
Association: Genotype TT is not associated with increased response to gefitinib in people with Carcinoma, Non-Small-Cell Lung as compared to genotypes CC + CT.
Article: Pharmacogenetics of methylphenidate in childhood attention-deficit/hyperactivity disorder: long-term effects
Gene: SLC6A2
Variant/haplotype: rs28386840
Drug(s): methylphenidate
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with response to methylphenidate in children with Attention Deficit Disorder with Hyperactivity as compared to allele A.
Notes: Clinical Global Impression-Severity (CGI-S) scale and the Children’s Global Assessment Scale (CGAS).
Article: Pharmacokinetic-Pharmacodynamic interaction associated with venlafaxine-XR remission in patients with major depressive disorder with history of citalopram / escitalopram treatment failure
Gene: CYP2D6
Variant/haplotype: CYP2D6 ultrarapid metabolizer phenotype
Drug(s): venlafaxine
Phenotype category: Efficacy
Significant: not stated
Association: CYP2D6 ultrarapid metabolizer is associated with increased response to venlafaxine as compared to CYP2D6 poor metabolizer.
Notes: In citalopram non-remission subjects venlafaxine-XR remission was associated with CYP2D6 metabolism phenotype (p = 0.027). Specifically, remission rates were higher among UM (n=5, 71.4%) in comparison to CYP2D6 PM (n=1, 10%).
Article: Pharmacogenetics of tenofovir clearance among Southern Africans living with HIV
Gene: CCDC12
Variant/haplotype: rs4682844
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 6.0E-7.
Article: Association of complement factor H and LOC387715 genotypes with response of exudative age-related macular degeneration to photodynamic therapy
Gene: CFH
Variant/haplotype: rs1061170
Drug(s): Photodynamic therapy
Phenotype category: Efficacy
Significant: yes
Association: Genotype TT is associated with decreased response to photodynamic therapy in people with Macular Degeneration as compared to genotypes CC + CT.
Notes: Visual acuity post-PDT was significantly worse in patients with the TT genotype than for patients with either the TC or CC genotype.  This is interesting because having the C allele puts patients at higher risk of developing age-related macular degeneration.  While this association with PDT was found to be true for the cohort overall (P=0.05), when subjects were separated based on lesion type, significance was only found in patients with predominantly classic lesions, not in those with occult lesions.
Article: Impact of polymorphisms of the GGCX gene on maintenance warfarin dose in Chinese populations: Systematic review and meta-analysis
Gene: GGCX
Variant/haplotype: rs699664
Drug(s): warfarin
Phenotype category: Dosage
Significant: no
Association: Allele T is not associated with dose of warfarin as compared to genotype CC.
Notes: This meta-analysis in Chinese patients showed no difference in mean daily warfarin dose (MDWD) for various genotypes of GGCX  variant rs699664.
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 significant in CYP3A5 nonexpressors but not in CYP3A5 expressers. The time of measurement was 90 days after transplantation. Day 7 and day 30 after transplantation did not show a significant association, though the same trend was seen.
Article: Pharmacogenetic markers of CYP2B6 associated with efavirenz plasma concentrations in HIV-1 infected Thai adults
Gene: CYP2B6
Variant/haplotype: rs8100458
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: no
Association: Genotypes CT + TT are not associated with concentrations of efavirenz in people with HIV Infections as compared to genotype CC.
Article: No association between IFNL3 (IL28B) genotype and response to peginterferon alfa-2a in HBeAg-positive or -negative chronic hepatitis B
Gene: IFNL3
Variant/haplotype: rs12980275
Drug(s): peginterferon alfa-2a
Phenotype category: Efficacy
Significant: no
Association: Genotype AA is not associated with response to peginterferon alfa-2a in people with Hepatitis B, Chronic as compared to genotypes AG + GG.
Notes: The authors found no association between IFNL3 genotype and peginterferon 2a response in either HBeAg-positive or HBeAg-negative chronic hepatitis B patients, in both Asian and White patients.
Article: Predictors of clozapine concentration and psychiatric symptoms in patients with schizophrenia
Gene: UGT1A1
Variant/haplotype: rs4148323
Drug(s): clozapine
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele A is associated with decreased concentrations of clozapine in people with Schizophrenia or Psychotic Disorder as compared to allele G.
Notes: "In the model adjusted for clinical predictors of clozapine concentration, including smoking status and cumulative dose of clozapine, five SNPs (rs28371726 and rs202102799 in CYP2D6; rs4148323 and rs34946978 in UGT1A1; and rs2011404 in UGT1A4) showed significant associations with clozapine concentration. The rs number for each SNP associated with clozapine concentration is shown in Table 3." Table does not state which allele or direction of effect for these SNPs, so assuming minor allele and decreased concentration (beta value in table is negative).
Article: Factors influencing plasma nevirapine levels: a study in HIV-infected children on generic antiretroviral treatment in India
Gene: CYP2B6
Variant/haplotype: rs3745274
Drug(s): nevirapine
Phenotype category: Toxicity, Metabolism/PK
Significant: yes
Association: Genotype TT is associated with decreased clearance of nevirapine in children with HIV Infections as compared to genotypes GG + GT.
Article: OCT1 polymorphism is associated with response and survival time in anti-Parkinsonian drug users
Gene: SLC22A1
Variant/haplotype: rs622342
Drug(s): amantadine, Anticholinergics, levodopa, selegiline
Phenotype category: Dosage, Efficacy
Significant: yes
Association: Allele C is associated with increased dose of amantadine, Anticholinergics, levodopa or selegiline in people with Parkinson Disease.
Notes: For each copy of the C allele, between the first and fifth levodopa prescriptions, the sum of the prescribed doses of all anti-Parkinsonian drugs were 0.34 defined daily dose higher (There was no change seen for the doses of dopamine agonists.)
Article: Angiotensin-converting enzyme gene polymorphism predicts the time-course of blood pressure response to angiotensin converting enzyme inhibition in the AASK trial
Gene: ACE
Variant/haplotype: rs4344
Drug(s): ramipril
Phenotype category: Efficacy
Significant: yes
Association: Genotypes AA + GG are associated with increased response to ramipril in people with Hypertension as compared to genotype AG.
Notes: This SNP was also reported as ACE G12269A. This SNP was in linkage disequilibrium with the ACE Ins/Del (rs1799752), D' = .98, and rs4359, D' = .88. Patients homozygous for this SNP (AA or GG) responded to ACE inhibitor treatment (reached target blood pressure) almost twice as fast as patients heterozygous (AG) for this SNP.
Article: Antipsychotic pharmacogenomics in first episode psychosis: a role for glutamate genes
Gene: GRM7
Variant/haplotype: rs2069062
Drug(s): risperidone
Phenotype category: Efficacy
Significant: yes
Association: Genotype CC is associated with increased response to risperidone in people with as compared to genotypes CG + GG.
Notes: Psychotic-naive or minimal antipsychotic exposure. Improvement measured with Brief Psychiatric Rating Scale.
Article: Attempted validation of 44 reported SNPs associated with tacrolimus troughs in a cohort of kidney allograft recipients
Gene: POR
Variant/haplotype: rs1057868
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: no
Association: Allele T is not associated with trough concentration of tacrolimus in people with Kidney Transplantation and Transplantation as compared to allele C.
Notes: This study was attempting to validate reported variants and tacrolimus trough concentration in a large population of African American and European American kidney transplant patients.
Article: Exploration of CYP450 and drug transporter genotypes and correlations with nevirapine exposure in Malawians
Gene: NR1I2
Variant/haplotype: rs1523130
Drug(s): nevirapine
Phenotype category: Dosage, Metabolism/PK
Significant: no
Association: Genotypes CC + CT are not associated with decreased clearance of nevirapine in people with HIV Infections as compared to genotype TT.
Notes: no association with PK parameters area under the concentration time curve or apparent oral clearance of the drug. [stat_test: univariate and multiple linear regression]
Article: 5-HTR1A and 5-HTR2A genetic polymorphisms and SSRI antidepressant response in depressive Chinese patients
Gene: HTR2A
Variant/haplotype: rs6313
Drug(s): citalopram, fluoxetine, paroxetine, sertraline
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to citalopram, fluoxetine, paroxetine or sertraline in people with Depressive Disorder, Major as compared to allele G.
Notes: Response/remission measured using HAMD.
Article: Predictors of clozapine concentration and psychiatric symptoms in patients with schizophrenia
Gene: DRD4
Variant/haplotype: rs762502
Drug(s): clozapine
Phenotype category: Efficacy
Significant: yes
Association: Allele C is associated with increased clinical benefit to clozapine in people with Schizophrenia or Psychotic Disorder as compared to allele T.
Notes: Alleles complemented. Table does not state which allele or direction of effect for these SNPs, so assuming minor allele and benefit, PANSS beta is in Table negative. "four SNPs in two genes were significantly associated with the total PANSS score: rs7787082 and rs10248420 in ABCB1 and rs2133251840 and rs762502 in DRD4 (Table 5). Among these, only one SNP in DRD4 (rs2133251840) resulted in different total PANSS scores at visits 3 and 4 according to its genotype"
Article: An association of ABCG8: rs11887534 polymorphism and HDL-cholesterol response to statin treatment in the Polish population
Gene: ABCG8
Variant/haplotype: rs11887534
Drug(s): atorvastatin, simvastatin
Phenotype category: Efficacy
Significant: yes
Association: Genotypes CC + CG is associated with decreased clinical benefit to atorvastatin or simvastatin in people with Dyslipidaemia as compared to genotype GG.
Notes: "The only significant differences between both genotype groups of patients; concerned HDL-C concentrations after statin use as well; as absolute and relative changes in HDL-C concentrations.; In contrast to GG homozygotes, patients with GC + CC; genotypes showed a decrease in post-statin HDL-C concentrations, and negative absolute and relative differences; in HDL-C concentrations "
Article: Polymorphisms in the VKORC1 gene are strongly associated with warfarin dosage requirements in patients receiving anticoagulation
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: The impact of CYP2D6*41 on CYP2D6 enzyme activity using phenotyping methods in urine, plasma, and saliva
Gene: CYP2D6
Variant/haplotype: CYP2D6*41
Drug(s): dextromethorphan
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2D6 *41 is associated with decreased metabolism of dextromethorphan in healthy individuals.
Notes: "Statistically significant increases were observed in the salivary, plasma, and urinary MR values in subjects with CYP2D6*1(or *2)/*1(or *2), *1 (or *2)/*41, *10/*41, and *5/*41 (all p values < 0.05). This result means that as compared with the wild type, one CYP2D6*41 allele combined with one full function allele will significantly reduce the enzyme activity. Likewise, one CYP2D6*41 allele combined with one reduced function allele and one CYP2D6*41 allele combined with one nonfunctional allele will reduce the enzyme activity further and further with statistical significance."; CYP2D6*1/*2 (n = 33), CYP2D6*2/*2 (n = 4), CYP2D6*1/*41 (n = 5), CYP2D6*2/*41 (n = 3), CYP2D6*10/*41 (n = 16), and CYP2D6*5/*41 (n = 4)