shlokn/autogkb huggingface dataset:
Article: CYP3A5, ABCB1 and SLCO1B1 Polymorphisms and Pharmacokinetics and Virologic Outcome of Lopinavir/Ritonavir in HIV-infected Children
Gene: ABCB1
Variant/haplotype: rs1045642
Drug(s): lopinavir, ritonavir
Phenotype category: Metabolism/PK
Significant: no
Association: Allele A is not associated with response to lopinavir or ritonavir in children with HIV Infections as compared to allele G.
Notes: No association between this variant and virologic suppression in patients treated with lopinavir/ritonavir. Variant referred to in the paper as C3435T.
Article: Influence of Methylenetetrahydrofolate Reductase C677T, A1298C, and G80A Polymorphisms on the Survival of Pediatric Patients with Acute Lymphoblastic Leukemia
Gene: MTHFR
Variant/haplotype: rs1801133
Drug(s): methotrexate
Phenotype category: Efficacy
Significant: yes
Association: Genotype AA is associated with increased response to methotrexate in children with Precursor Cell Lymphoblastic Leukemia-Lymphoma.
Notes: Patients with the AA genotype had better overall survival than patients with the AG or GG genotypes. Variant referred to in the paper as C677T. Please note that alleles have been complemented to the positive strand.
Article: Comparative performance of gene-based warfarin dosing algorithms in a multiethnic population
Gene: VKORC1
Variant/haplotype: rs17708472
Drug(s): warfarin
Phenotype category: Dosage
Significant: no
Association: Allele A is not associated with dose of warfarin as compared to allele G.
Notes: Neither the addition of race, number of concurrent medications nor the number of concurrent medications interacting with warfarin enhanced algorithm performance. Similarly, consideration of CYP4F2, CALU or GGCX variant genotypes did not improve algorithms.
Article: β2-Adrenergic Receptor Gene Affects the Heart Rate Response of β-Blockers: Evidence From 3 Clinical Studies
Gene: ADRB2
Variant/haplotype: rs1042713
Drug(s): atenolol, metoprolol
Phenotype category: Efficacy
Significant: yes
Association: Genotype AA is associated with increased response to atenolol or metoprolol in people with Tachycardia as compared to genotypes AG + GG.
Notes: Patients with the AA genotype had a significantly greater decrease in heart rate than patients with the AG or GG genotypes. Note that this association was only significant in white patients.
Article: Association of carbamazepine major metabolism and transport pathway gene polymorphisms and pharmacokinetics in patients with epilepsy
Gene: CYP3A4
Variant/haplotype: rs2740574
Drug(s): carbamazepine
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype TT is associated with increased clearance of carbamazepine in people with Epilepsy as compared to genotypes CC + CT.
Notes: This association was significant in the whole cohort, but not when looking at African American or Caucasian patient sub-cohorts. The C allele occured at a higher frequency in African Americans compared to Caucasians, and the authors suggest that this association may be due to differences in the racial groups (African Americans had a significantly lower clearance p=0.006 and longer half-life p=0.01 of the drug as compared with Caucasians).
Article: Calcium‐channel blockers: Clinical outcome associations with reported pharmacogenetics variants in 32 000 patients
Gene: NUMA1
Variant/haplotype: rs10898815
Drug(s): Dihydropyridine derivatives
Phenotype category: Other
Significant: yes
Association: Genotypes AA + AG is associated with increased discontinuation of Dihydropyridine derivatives as compared to genotype GG.
Notes: "The association for AA was still significant after BenjaminiHochberg adjustment for multiple statistical testing (adjusted p=0.04)."
Article: S-1 plus irinotecan and oxaliplatin for the first-line treatment of patients with metastatic colorectal cancer: a prospective phase II study and pharmacogenetic analysis
Gene: UGT1A1
Variant/haplotype: UGT1A1*28
Drug(s): irinotecan, oxaliplatin, tegafur / gimeracil / oteracil
Phenotype category: Efficacy
Significant: no
Association: UGT1A1 *28 is not associated with response to irinotecan, oxaliplatin and s 1 (combination) in people with Colorectal Neoplasms.
Notes: No significant difference in the objective response rate was seen between those with the *28 allele (54% responders) and those without one (79%).
Article: The Association of Transporter Genes Polymorphisms and Lung Cancer Chemotherapy Response
Gene: LRP1
Variant/haplotype: rs4788184
Drug(s): platinum
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with response to platinum in people with Lung Neoplasms as compared to allele C.
Notes: 26 SNPs were selected which satisfied the following criteria: 1) SNPs were from HapMap Project Phase II of the Han Chinese population 2) were haplotype tagger SNPs 3) SNP minor allele frequency was higher than 5% in Han Chinese 4) the pairwise linkage disequilibrium correlation coefficient (r-squared) was greater than 0.8. After Bonferroni corrections no SNPs remained significantly associated with platinum drug efficacy.
Article: KIF6 gene as a pharmacogenetic marker for lipid-lowering effect in statin treatment
Gene: KIF6
Variant/haplotype: rs20455
Drug(s): rosuvastatin
Phenotype category: Efficacy
Significant: yes
Association: Genotype GG is associated with decreased response to rosuvastatin in people with Hypercholesterolemia as compared to genotype AA.
Notes: Please note that alleles have been complemented to the positive strand. Statistically significant association only seen between genotype and change in c-HDL
Article: Impact of cytochrome P450 2C19 polymorphisms on the pharmacokinetics of tacrolimus when coadministered with voriconazole
Gene: CYP2C19
Variant/haplotype: CYP2C19*1, CYP2C19*2, CYP2C19*3
Drug(s): voriconazole
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2C19 *1/*2 + *1/*3 is associated with increased concentrations of voriconazole in healthy individuals as compared to CYP2C19 *1/*1.
Notes: The maximum plasma concentration (Cmax) and area under the plasma concentration time curve from 0 to 12 hours (AUC0-12) was higher in intermediate metabolizers (*1/*2 n=2; *1/*3 n=4) as compared to extensive metabolizers (*1/*1 n=6).
Article: CYP2B6*6 and CYP2B6*18 Predict Long-Term Efavirenz Exposure Measured in Hair Samples in HIV-Positive South African Women
Gene: CYP2B6
Variant/haplotype: CYP2B6*1, CYP2B6*18
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2B6 *18 is associated with increased concentrations of efavirenz in people with HIV as compared to CYP2B6 *1/*1.
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: rs498974
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: Evaluation of genetic association of neurodevelopment and neuroimmunological genes with antipsychotic treatment response in schizophrenia in Indian populations
Variant/haplotype: rs2513265
Drug(s): antipsychotics
Phenotype category: Efficacy
Significant: yes
Association: Allele A is associated with increased response to antipsychotics in people with Schizophrenia as compared to allele T.
Notes: In low severity schizophrenia patient subgroup
Article: Population pharmacokinetic approach to evaluate the effect of CYP2D6, CYP3A, ABCB1, POR and NR1I2 genotypes on donepezil clearance
Gene: CYP2D6
Variant/haplotype: CYP2D6*4, CYP2D6*5
Drug(s): donepezil
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2D6 *4/*4 + *4/*5 (assigned as poor metabolizer phenotype) is associated with decreased clearance of donepezil in people with Alzheimer Disease.
Notes: Pharmacokinetic model: gender and CYP2D6 metabolizer status explained 11% of the overall variability in donepezil clearance. Model-based simulations were also performed to compared predicted average plasma concentrations with a 10mg once daily dosage regimen suggesting a 43% increase in average plasma concentrations for poor metabolizers. Extensive metabolizers were grouped together (diplotypes *1/*3, *1/*4, *1/*5, *1/*6, *1/*1, *4/*1xN, *6/*1xN).
Article: Pharmacogenomics of aromatase inhibitors in postmenopausal breast cancer and additional mechanisms of anastrozole action
Gene: CSMD1
Variant/haplotype: rs6990851
Drug(s): anastrozole
Phenotype category: Efficacy
Significant: yes
Association: Allele G is associated with increased response to anastrozole in women with Breast Neoplasms as compared to allele A.
Notes: The G allele was significantly associated with a longer breast cancer free interval (BCFI) in MA.27 trial participants. Subsequent in vitro work provided functional validation by demonstrating that the G allele causes expression of CSMD1 to increase in the presence of anastrozole, which results in SMAD3 activation and increased expression of CYP19A1.
Article: Influence of SLCO1B1 polymorphisms on lopinavir C trough in Serbian HIV/AIDS patients
Gene: SLCO1B1
Variant/haplotype: rs11045819
Drug(s): lopinavir
Phenotype category: Metabolism/PK
Significant: no
Association: Allele A is not associated with trough concentration of lopinavir in people with HIV Infections as compared to allele C.
Notes: Although the A allele was initially found to be significantly associated with decreased trough concentrations of lopinavir, this significance was lost following multivariate regression analysis.
Article: Pharmacogenetic Interactions of Rifapentine plus Isoniazid with Efavirenz or Nevirapine
Gene: CYP2B6
Variant/haplotype: CYP2B6 poor metabolizer
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: not stated
Association: CYP2B6 poor metabolizer is associated with increased concentrations of efavirenz in people with HIV Infections.
Notes: CYP2B6 poor metabolizers had greater efavirenz concentrations at all weeks.
Article: Genetic Polymorphisms of Cytokines Might Affect Postoperative Sufentanil Dosage for Analgesia in Patients
Gene: NFKB1
Variant/haplotype: rs3774932
Drug(s): sufentanil
Phenotype category: Dosage
Significant: no
Association: Allele G is not associated with dose of sufentanil in people with Pain, Postoperative as compared to allele A.
Article: Candidate‐Gene Study of Functional Polymorphisms in SLCO1B1 and CYP3A4/5 and the Cholesterol‐Lowering Response to Simvastatin
Gene: SLCO1B1
Variant/haplotype: rs4149056
Drug(s): simvastatin
Phenotype category: Efficacy
Significant: no
Association: Allele C is not associated with response to simvastatin as compared to allele T.
Notes: in African American.
Article: Association studies of dopamine synthesis and metabolism genes with multiple phenotypes of heroin dependence
Gene: TH
Variant/haplotype: rs10770141
Drug(s): heroin
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with response to heroin as compared to allele A.
Notes: Although an association was initially observed, it lost significance following Bonferroni correction.
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: rs648893
Drug(s): ethanol
Phenotype category: Efficacy
Significant: no
Association: Allele G 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: Correlation of N-acetyltransferase 2 genotype and acetylation status with plasma isoniazid concentration and its metabolic ratio in ethiopian tuberculosis patients
Gene: NAT2
Variant/haplotype: NAT2*4, NAT2*6, NAT2*7, NAT2*14, NAT2*16
Drug(s): acetylisoniazid
Phenotype category: Metabolism/PK
Significant: yes
Association: NAT2 *16/*14 + *16/*16 + *16/*6 + *16/*7 + *6/*14 + *6/*6 + *6/*7 (assigned as slow acetylator phenotype) is associated with decreased concentrations of acetylisoniazid in people with Tuberculosis as compared to NAT2 *4/*14 + *4/*16 + *4/*6 + *4/*7 (assigned as intermediate acetylator phenotype) .
Notes: Originally annotated as NAT2 *5/*14 + *5/*5 + *5/*6 + *5/*7 + *6/*14 + *6/*6 + *6/*7 (assigned as slow acetylator phenotype) compared to NAT2 *4/*14 + *4/*5 + *4/*6 + *4/*7 (assigned as intermediate acetylator phenotype). "A significant difference in acetyl-isoniazid concentration was observed between slow and intermediate (p < 0.001) and slow and fast (p = 0.001) acetylators." "The frequency distribution of NAT2*4, *5, *6, *7, and *14 alleles in Ethiopian tuberculosis patients were 14.6%, 47.1%, 31.3%, 5.4%, and 1.7%, respectively. " Based on the Methods section the alleles are determined the following each SNP: C___1204093_20 for NAT2*5 (c.341 T>C, rs1801280), C___1204091_10 for NAT2*6 (c.590G>A, rs1799930), C____572770_20 for NAT2*7 (c.857G>A, rs1799931), C____572770_20 for NAT2*14 (191G>A, rs1801279). Those are mapped for the annotation to *16, *6, *7, *14 as those are defined by the single SNPs.; The arylamine N-acetyltransferases (NATs) database was transitioned into the PharmVar database in March 2024. The alleles in this annotation are mapped as following: NAT2*14A under the *14 core allele; NAT2*5D under the *16 core allele; NAT2*6B under the *6 core allele; NAT2*7A under the *7 core allele.
Article: Methadone dose in heroin-dependent patients: role of clinical factors, comedications, genetic polymorphisms and enzyme activity
Gene: CYP2C19
Variant/haplotype: rs11188072
Drug(s): methadone
Phenotype category: Dosage
Significant: no
Association: Allele C is not associated with dose of methadone in people with Opioid-Related Disorders as compared to allele T.
Notes: Methadone maintenance dose was not associated with genotype of the SNP but it was correlated to the highest dose ever used. Multiple doses versus single dose, body weight, history of cocaine dependence and ethnicity (Asian>Caucasian>African) were independently associated with methadone dose in multiple regression analysis. Please note: alleles were complemented to the + chromosomal strand.
Article: CYP3A5, ABCB1 and SLCO1B1 Polymorphisms and Pharmacokinetics and Virologic Outcome of Lopinavir/Ritonavir in HIV-infected Children
Gene: ABCB1
Variant/haplotype: rs1045642
Drug(s): lopinavir, ritonavir
Phenotype category: Metabolism/PK
Significant: no
Association: Allele A is not associated with clearance of lopinavir or ritonavir in children with HIV Infections as compared to allele G.
Notes: No association between this variant and clearance of lopinavir or ritonavir in patients treated with lopinavir/ritonavir. Variant referred to in the paper as C3435T.
Article: CHRNA4 rs1044396 is associated with smoking cessation in varenicline therapy
Gene: CHRNB2
Variant/haplotype: rs2072660
Drug(s): varenicline
Phenotype category: Efficacy
Significant: no
Association: Genotypes CT + TT are not associated with response to varenicline in people with Tobacco Use Disorder as compared to genotype CC.
Article: Functional genetic variation in the Rev-Erbα pathway and lithium response in the treatment of bipolar disorder
Gene: PER3
Variant/haplotype: rs228642
Drug(s): lithium
Phenotype category: Efficacy
Significant: no
Association: Allele C is not associated with increased response to lithium in people with Bipolar Disorder as compared to allele T.
Article: CYP3A5*3 and CYP3A4*22 Cluster Polymorphism Effects on LCP-Tac Tacrolimus Exposure: Population Pharmacokinetic Approach
Gene: CYP3A5
Variant/haplotype: CYP3A5*1, CYP3A5*3
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP3A5 *3/*3 is associated with increased dose-adjusted trough concentrations of tacrolimus in people with Kidney Transplantation as compared to CYP3A5 *1/*1 + *1/*3.
Notes: "Statistically significant (p < 0.001) differences were found when comparing normalized by dose AUC values between CYP3A5 *1 expressers vs. non-expressers. Similarly, statistically significant (p < 0.001) differences were found when comparing C0 normalized by a dose of CYP3A5 *1 expressers vs. non-expressers."
Article: Tell-Tale SNPs: The Role of CYP2B6 in Methadone Fatalities
Gene: CYP2B6
Variant/haplotype: rs3745274
Drug(s): methadone
Phenotype category: Metabolism/PK
Significant: no
Association: Allele T is not associated with concentrations of methadone as compared to allele G.
Article: CYP2B6 Pharmacogenetics–Based In Vitro–In Vivo Extrapolation of Efavirenz Clearance by Physiologically Based Pharmacokinetic Modeling
Gene: CYP2B6
Variant/haplotype: CYP2B6*1, CYP2B6*6
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: no
Association: CYP2B6 *1/*1 + *1/*6 is not associated with clearance of efavirenz in healthy individuals as compared to CYP2B6 *6/*6.
Notes: Following a 600-mg oral dose of efavirenz, no significant difference in oral clearance was seen between the two genotype groups. However, the authors suggest this is due to an inadequate number of subjects with the *6/*6 genotype (n=3). Those with the *6/*6 genotype had a 30% reduction in clearance and a 27% increase in area under the concentration-time curve from 0-infinity (AUC0-inf).
Article: Contribution of the activities of CYP3A, CYP2D6, CYP1A2 and other potential covariates to the disposition of methadone in patients undergoing methadone maintenance treatment
Gene: CYP2D6
Variant/haplotype: CYP2D6 poor metabolizer phenotype
Drug(s): methadone
Phenotype category: Metabolism/PK
Significant: not stated
Association: CYP2D6 poor metabolizer is not associated with trough concentration of methadone as compared to CYP2D6 normal metabolizer.
Notes: CYP2D6 phenotype, as assessed by dextromethorphan metabolism did not significantly contribute to variance in methadone trough plasma concentrations.
Article: AHR-dependent genes and response to MTX therapy in rheumatoid arthritis patients
Gene: AHRR
Variant/haplotype: rs2292596
Drug(s): methotrexate
Phenotype category: Efficacy
Significant: not stated
Association: Allele G is associated with decreased response to methotrexate in people with Arthritis, Rheumatoid as compared to allele C.
Notes: The authors state that there is an association, but the significance is unclear and requires further functional studies.
Article: Impact of the novel CYP2C:TG haplotype and CYP2B6 variants on sertraline exposure in a large patient population
Gene: CYP2C19
Variant/haplotype: CYP2C19*1, CYP2C19*17
Drug(s): sertraline
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2C19 *1/*17 + *17/*17 are associated with decreased concentrations of sertraline as compared to CYP2C19 *1/*1.
Notes: Compared with the ref- erence group (CYP2C19*1/*1), a lower sertraline serum concentration was observed in CYP2C19*17/*17 (21.6% decrease, n = 44, p = 0.003), CYP2C:TG/CYP2C:TG (21.2% decrease, n = 26, p = 0.022), CYP2C19*17/ CYP2C:TG (20.0% decrease, n = 65, p = 0.003), and CYP2C19*1/*17 (17.0% decrease, n = 150, p < 0.001).
Article: Efavirenz inhibits the human ether-a-go-go related current (hERG) and induces QT interval prolongation in CYP2B6*6*6 allele carriers
Gene: CYP2B6
Variant/haplotype: CYP2B6*1, CYP2B6*6
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2B6 *6/*6 is associated with increased concentrations of efavirenz in healthy individuals as compared to CYP2B6 *1/*1 + *1/*6.
Article: The influence of CYP3A, PPARA, and POR genetic variants on the pharmacokinetics of tacrolimus and cyclosporine in renal transplant recipients
Gene: PPARA
Variant/haplotype: rs4253728
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: no
Association: Genotype AA is not associated with metabolism of tacrolimus in people with Kidney Transplantation as compared to allele G.
Notes: A single steady-state concentration of tacrolimus was collected for each patient 2-7 wks post-transplant and compared to dose of tacrolimus administered to patients at Oslo University Hospital. Reported concentrations are "steady-state dose-adjusted concentration" of tacrolimus.  Steady-state is defined as at least 3 days after last dose adjustment for Tac and 4 days for cyclosporine.
Article: Ivacaftor in a young boy with the rare gating mutation S549R - use of lung clearance index to track progress: a case report
Gene: CFTR
Variant/haplotype: rs121909005
Drug(s): ivacaftor
Phenotype category: Efficacy
Significant: not stated
Association: Allele G is associated with response to ivacaftor in children with Cystic Fibrosis.
Notes: Case report of a pediatric cystic fibrosis patient (genotype S549R/1717-1G>A) being treated with ivacaftor. Improvements in body weight, cough frequency, sputum production, physical performance, sweat chloride level and FEV1 were reported following six weeks of treatment. Paper does not state if rs121908757 or rs121909005 is the causative variant of S549R.
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: ANGPT2
Variant/haplotype: rs10102851
Drug(s): bevacizumab
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with response to bevacizumab in women with Breast Neoplasms as compared to allele A.
Article: Genetic variation in OPRD1 and the response to treatment for opioid dependence with buprenorphine in European American females
Gene: OPRD1
Variant/haplotype: rs529520
Drug(s): buprenorphine
Phenotype category: Efficacy
Significant: yes
Association: Genotype AA is associated with decreased response to buprenorphine in women with Opioid-Related Disorders as compared to genotype CC.
Notes: Opioid dependence. Four cohorts were analyzed. The first three were women taking buprenorphine or methadone, women taking only buprenorphine and women taking only methadone, where opiod-positive urine drug screens or missing urine drug screens were both considered a "positive" drug screen. The fourth was women taking only buprenorphine were missing urine drug screens were coded as "missing" and not as "positive". No significant results were seen when considering women only taking methadone, but significant results were seen for all other cohorts: women with the AA genotype were more likely to have opioid-; "positive" urine drug screens, as compared to those with the CC genotype. Patients were treated with buprenorphine or methadone for 24 weeks.
Article: A preliminary pharmacogenetic investigation of adverse events from topiramate in heavy drinkers
Gene: GRIK1
Variant/haplotype: rs2832407
Drug(s): topiramate
Phenotype category: Efficacy
Significant: yes
Association: Genotypes AA + AC is associated with decreased response to topiramate in people with Alcohol-Related Disorders as compared to genotype CC.
Notes: 75.5% of participants met the criteria for an alcohol use disorder. At target dose (week 5 of treatment), carriers of the A allele reported a higher percentage of heavy drinking days (%HDD), as compared to those with the CC genotype (controlling for baseline %HDD).
Article: Variation in P450 oxidoreductase (POR) A503V and flavin containing monooxygenase (FMO)-3 E158K is associated with minor alterations in nicotine metabolism but does not alter cigarette consumption
Gene: FMO3
Variant/haplotype: rs2266782
Drug(s): nicotine
Phenotype category: Metabolism/PK
Significant: no
Association: Genotypes AA + AG is associated with decreased metabolism of nicotine in CYP2A6 reduced, but not normal, metabolizers as compared to genotype GG.
Notes: This was described as a trend towards higher nicotine AUC.  Participants received 4 mg oral nicotine.