shlokn/autogkb huggingface dataset:
Article: Novel Gene Polymorphisms for Stable Warfarin Dose in a Korean Population: Genome-Wide Association Study
Gene: VKORC1
Variant/haplotype: rs9934438
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Genotype GG is associated with increased dose of warfarin in people with heart valve replacement as compared to genotypes AA + AG.
Notes: in univariate analysis of patients on stable dose. "VKORC1 rs9934438 GG genotype required 9.74 ± 2.18 mg/day, whereas those with AA and AG genotypes needed 5.41 ± 1.84 mg/day"
Article: Enantiospecific Pharmacogenomics of Fluvastatin
Gene: CYP2C9
Variant/haplotype: rs77760615
Drug(s): fluvastatin
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele G is associated with increased concentrations of fluvastatin in healthy individuals as compared to allele A.
Notes: This variant is significantly associated with increased area under the plasma concentration-time curve (AUC) of both 3R,5S-fluvastatin and 3S,5R-fluvastatin and total fluvastatin. The AUC was 82% larger per copy of the variant allele. This variant is in complete LD with CYP2C9*3.
Article: Contribution of Cytochrome P450 and ABCB1 Genetic Variability on Methadone Pharmacokinetics, Dose Requirements, and Response
Gene: CYP2C19
Variant/haplotype: CYP2C19*1, CYP2C19*2
Drug(s): methadone
Phenotype category: Efficacy
Significant: no
Association: CYP2C19 *1/*2 + *2/*2 are not associated with response to methadone in people with Opioid-Related Disorders as compared to CYP2C19 *1/*1.
Notes: No significant difference in genotype or phenotype frequencies between responders and non-responders, as defined by drug misuse during methadone maintenance therapy. No details about which specific variants/alleles were tested for.
Article: The impact of diuretic use and ABCG2 genotype on the predictive performance of a published allopurinol dosing tool
Gene: SLC22A11
Variant/haplotype: rs17300741
Drug(s): allopurinol
Phenotype category: Dosage
Significant: no
Association: Allele G is not associated with dose of allopurinol in people with Gout as compared to allele A.
Article: Association of genetic variation in pharmacodynamic factors with methadone dose required for effective treatment of opioid addiction
Gene: BDNF
Variant/haplotype: rs7934165
Drug(s): methadone
Phenotype category: Dosage
Significant: no
Association: Genotype AA is associated with increased dose of methadone in people with Heroin Dependence as compared to genotypes AG + GG.
Notes: This association was not statistically significant after permutation analysis based on 40,000 replicates, or statistically significant after adjusting for testing for multiple SNPs (Bonferroni correction). Note; this SNP was in LD with rsrs10835210 (r^2>0.7) and not independent. Alleles were reported as T/C, here they are complemented with A representing T and G representing C for the positive chromosomal strand.
Article: Comprehensive Ara-C SNP score predicts leukemic cell intracellular ara-CTP levels in pediatric acute myeloid leukemia patients
Gene: SLC28A1
Variant/haplotype: rs11853372
Drug(s): ara-CTP
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype TT is associated with decreased concentrations of ara-CTP in children with Leukemia, Myeloid, Acute as compared to genotypes GG + GT.
Article: IL-3 and CTLA4 gene polymorphisms may influence the tacrolimus dose requirement in Chinese kidney transplant recipients
Gene: CYP3A4
Variant/haplotype: rs2242480
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype CC is associated with increased exposure to tacrolimus in people with Kidney Transplantation as compared to genotypes CT + TT.
Notes: This association was significant in CYP3A5 nonexpressers and CYP3A5 expressers. The time of measurement for a significant association was 7 days after transplantation for the CYP3A5 expressers and 90 days after transplantation for the CYP3A5 nonexpressers. For CYP3A5  expressers, a significant difference in exposure was not observed at time 30 and 90 days after transplantation. In the CYP3A5 nonexpressers, a significant difference in exposure was seen at 90 days post transplantation but not at day 7 or 30.
Article: Comparison of Functional Variants in IFNL4 and IFNL3 for Association with Hepatitis C Virus Clearance
Gene: IFNL4
Variant/haplotype: rs11322783
Drug(s): peginterferon alfa-2a, ribavirin
Phenotype category: Efficacy
Significant: yes
Association: Genotypes G/TT + TT/TT are associated with increased response to peginterferon alfa-2a and ribavirin in people with Hepatitis C, Chronic as compared to genotype GG.
Notes: in African-American patients.  The associations were stronger for IFNL4-rs368234815 than rs4803217 for undetectable HCV RNA at week 24 in Virahep C (p=0.03) and week 20 in HALT-C (p=0.03).
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): isoniazid
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 increased concentrations of isoniazid 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). "There was a significant difference in isoniazid AUC0–7 h between acetylator groups. The overall median isoniazid AUC0–7 h for slow, intermediate, and fast acetylators was 13.09 µg.h/mL, 6.09 µg.h/mL, and 3.73 µg.h/mL, respectively. The variation of AUC0–7 h between the slow genotype group and the other two groups is high (p < 0.001)." "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 included 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: VKORC1 and Novel CYP2C9 Variation Predict Warfarin Response in Alaska Native and American Indian People
Gene: CYP4F2
Variant/haplotype: rs3093153
Drug(s): warfarin
Phenotype category: Dosage
Significant: no
Association: Allele C is not associated with dose of warfarin as compared to allele A.
Notes: in Alaska Native and American Indian People.
Article: Effects of CYP2C9*1/*13 on the pharmacokinetics and pharmacodynamics of meloxicam
Gene: CYP2C9
Variant/haplotype: CYP2C9*1, CYP2C9*13
Drug(s): meloxicam
Phenotype category: PD, Metabolism/PK
Significant: yes
Association: CYP2C9 *1/*13 is associated with decreased metabolism of meloxicam in healthy individuals as compared to CYP2C9 *1/*1.
Notes: Individuals with *1/*13 had 2.43- and 1.46-fold higher  AUC and Cmax  than in the CYP2C9*1/*1 group. The oral clearance of meloxicam is 37.9% of wild type. The CYP2C9*1/*13 genotype is also associated with increased pharmacodynamic effects of meloxicam. Individuals with *1/*13 had greater inhibition of TXB2 generation ( lower rate of TXB(2) production) than in the CYP2C9*1/*1 group.
Article: Pretransplant 4β‐hydroxycholesterol does not predict tacrolimus exposure or dose requirements during the first days after kidney transplantation
Gene: CYP3A5
Variant/haplotype: CYP3A5*1, CYP3A5*3
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP3A5 *1 is associated with decreased trough concentration of tacrolimus in people with Kidney Transplantation as compared to CYP3A5 *3.
Notes: CYP3A5 *1A genotype was associated with lower trough tacrolimus concentrations (C0) (beta = (-1.739) (95% CI: (-2.517) – (-0.962); P <0.001)) and lower C0/dose ratios (beta = (-0.675) (95% CI: (-0.938) – (-0.412); P <0.001)
Article: Effects of UGT1A1*28 polymorphism on raloxifene pharmacokinetics and pharmacodynamics
Gene: UGT1A1
Variant/haplotype: UGT1A1*1, UGT1A1*28
Drug(s): raloxifene 6-glucuronide, raloxifene-4′-glucuronide
Phenotype category: Metabolism/PK
Significant: yes
Association: UGT1A1 *28/*28 is associated with increased concentrations of raloxifene 6-glucuronide and raloxifene-4′-glucuronide in women with Osteoporosis as compared to UGT1A1 *1/*1 + *1/*28.
Notes: M1 is raloxifene 6-glucuronide, M2 is raloxifene-4-glucuronide.
Article: Polymorphisms in the VKORC1 gene are strongly associated with warfarin dosage requirements in patients receiving anticoagulation
Gene: VKORC1
Variant/haplotype: rs2884737
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Allele C is associated with decreased dose of warfarin as compared to allele A.
Article: Influence of pharmacogenetic polymorphisms and demographic variables on metformin pharmacokinetics in an admixed Brazilian cohort
Gene: SLC47A2
Variant/haplotype: rs12943590
Drug(s): metformin
Phenotype category: Metabolism/PK
Significant: no
Association: Allele A is not associated with exposure to metformin as compared to allele G.
Article: Cholinergic receptor nicotinic alpha 5 subunit polymorphisms are associated with smoking cessation success in women
Gene: CHRNA3
Variant/haplotype: rs1051730
Drug(s): bupropion, nicotine, varenicline
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to bupropion, nicotine or varenicline in people with Tobacco Use Disorder as compared to allele G.
Notes: No significant effect of genotype on likelihood of being abstinent from smoking at 6 months after starting pharmacotherapy for smoking cessation. Please note that alleles have been complemented to the positive strand.
Article: Lack of Association between Opioid-Receptor Genotypes and Smoking Cessation Outcomes in a Randomized, Controlled Naltrexone Trial
Gene: OPRD1
Variant/haplotype: rs204076
Drug(s): naltrexone
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with response to naltrexone in people with Tobacco Use Disorder as compared to allele A.
Notes: No significant association between this variant and smoking quit rate when naltrexone was used as augmentation to nicotine patch therapy. This is a T/A/G SNP. Based on allele frequencies reported by dbSNP, it has been assumed that the major allele in this study is A and the minor allele is T.
Article: Potentially Functional SNPs (pfSNPs) as Novel Genomic Predictors of 5-FU Response in Metastatic Colorectal Cancer Patients
Gene: UMPS
Variant/haplotype: rs3772810
Drug(s): capecitabine, fluorouracil
Phenotype category: Efficacy
Significant: no
Association: Allele G is associated with decreased response to capecitabine and fluorouracil in people with Neoplasm Metastasis as compared to allele A.
Notes: pfSNP identified 2800 SNPS associated with key-words: 5-FU, capecitabine and oxilaplatin and colorectal cancer. Various criteria were used to determine 1536 SNPs to genotype. These SNPs were genotyped in a discovery cohort (N=62) and tested in a validation cohort (N=27). Both cohorts consisted of patients with colorectal cancer metastasis in liver. 36 SNPs were initially significantly associated with drug response but only 3 remained significant in the validation cohort (before Bonferroni correction): rs2291078 A, rs3772809 G, rs3772810 G. All three SNPs were in perfect LD, and were initially associated with the non-responder phenotype, but the association did not remain significant after Bonferroni correction.
Article: Genetic variants in CYP2B6 and CYP2A6 explain interindividual variation in efavirenz plasma concentrations of HIV-infected children with diverse ethnic origin
Gene: ABCB1
Variant/haplotype: rs1045642
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: no
Association: Allele A is not associated with concentrations of efavirenz in children with HIV Infections as compared to allele G.
Notes: This is stated in the paper, but supporting data is not shown.
Article: Robust Stimulation of W1282X-CFTR Channel Activity by a Combination of Allosteric Modulators
Gene: CFTR
Variant/haplotype: rs77010898
Drug(s): curcumin, ivacaftor
Phenotype category: Efficacy
Significant: yes
Association: Genotypes AA + AG are associated with response to curcumin and ivacaftor in people with Cystic Fibrosis as compared to genotype GG.
Notes: This is a cell based study with measuring channel activity in polarized FRT epithelial monolayers.
Article: PTPRD gene associated with blood pressure response to atenolol and resistant hypertension
Gene: PTPRD
Variant/haplotype: rs4742610
Drug(s): trandolapril, verapamil
Phenotype category: Efficacy
Significant: yes
Association: Allele T is associated with resistance to trandolapril and verapamil in people with Hypertension as compared to allele C.
Notes: This was associated with resistant hypertension in whites and Hispanics in the international verapamil SR trandolapril study (meta-analysis P=3.2×10-5).
Article: Azathioprine Biotransformation in Young Patients with Inflammatory Bowel Disease: Contribution of Glutathione-S Transferase M1 and A1 Variants
Gene: TPMT
Variant/haplotype: rs1142345
Drug(s): azathioprine
Phenotype category: Dosage
Significant: yes
Association: Genotype CT is associated with decreased dose of azathioprine in children with Colitis, Ulcerative or Crohn Disease as compared to genotype TT.
Notes: alleles complemented. No CC (*3C/(3C) homozygotes were reported.
Article: Ethnic Stratification of the Association of RGS4 Variants with Antipsychotic Treatment Response in Schizophrenia
Gene: RGS4
Variant/haplotype: rs2842030
Drug(s): olanzapine, perphenazine
Phenotype category: Efficacy
Significant: not stated
Association: Genotype TT is associated with increased response to olanzapine and perphenazine in people with Schizophrenia as compared to genotypes GG + GT.
Notes: compared to quetiapine, risperidone or ziprasidone based on Positive and Negative Syndrome Scale (PANSS) positive scores
Article: Haplotypes of P2RX7 gene polymorphisms are associated with both cold pain sensitivity and analgesic effect of fentanyl
Gene: P2RX7
Variant/haplotype: rs208293
Drug(s): fentanyl
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with dose of fentanyl in people with Pain, Postoperative as compared to allele G.
Notes: No significant association between this variant and 24-h postoperative fentanyl use or perioperative fentanyl use.
Article: Genotypic and Phenotypic Factors Influencing Drug Response in Mexican Patients With Type 2 Diabetes Mellitus
Gene: CYP2C9
Variant/haplotype: rs1799853
Drug(s): sulfonamides, urea derivatives
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with response to sulfonamides, urea derivatives in people with Diabetes Mellitus as compared to allele C.
Notes: This is the defining SNP of CYP2C9*2
Article: Donor CYP3A5 genotype influences tacrolimus disposition on the first day after paediatric liver transplantation
Gene: CYP3A4
Variant/haplotype: CYP3A4*1, CYP3A4*22
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: no
Association: CYP3A4 *1/*22 + *22/*22 are not associated with metabolism of tacrolimus in children with liver transplantation as compared to CYP3A4 *1/*1.
Notes: DONOR liver genotypes. No significant difference in tacrolimus trough concentration or dose-adjusted trough concentration was seen between the genotypes.
Article: Polymorphisms of the KCNQ1 gene are associated with the therapeutic responses of sulfonylureas in Chinese patients with type 2 diabetes
Gene: KCNQ1
Variant/haplotype: rs2237892
Drug(s): gliclazide
Phenotype category: Efficacy
Significant: yes
Association: Allele T is associated with increased clinical benefit to gliclazide in people with Diabetes Mellitus, Type 2 as compared to allele C.
Notes: "Regarding rs2237892, there were more responders among the rare TT allele homozygotes TT; 57.1% of the TT homozygotes responded, compared with only 15.9% of the CC homozygotes. The heterozygote CT group exhibited an intermediate response rate. The odds ratio for the T allele with respect to treatment success was 2.533 (95% CI: 1.283–4.999, P=0.007) compared with the rs2237892 C allele. "
Article: CBR1 and CBR3 pharmacogenetics and their influence on doxorubicin disposition in Asian breast cancer patients
Gene: CBR1
Variant/haplotype: rs9024
Drug(s): doxorubicin
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype GG is associated with increased clearance of doxorubicin in people with Breast Neoplasms as compared to genotype AG.
Article: The International SSRI Pharmacogenomics Consortium (ISPC): a genome-wide association study of antidepressant treatment response
Gene: ANGPT2
Variant/haplotype: rs11989215
Drug(s): Selective serotonin reuptake inhibitors
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with response to Selective serotonin reuptake inhibitors in people with Depressive Disorder, Major as compared to allele A.
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: A Physiologically Based Pharmacokinetic Approach to Recommend an Individual Dose of Tacrolimus in Adult Heart Transplant Recipients
Gene: CYP3A4
Variant/haplotype: rs2242480
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotypes CT + TT is associated with increased clearance of tacrolimus in people with heart transplantation as compared to genotype CC.
Notes: "CYP3A4*18B genotypes were also significant covariates of CL/F. For CYP3A4*18B, there was a significant difference in CL/F of different genotypes: 25.4 ± 12.0 L/h for CYP3A4*18B*18B/*1*18B, and 16.3 ± 10.5 L/h for CYP3A4*1*1 (p < 0.001)." "CYP3A4*18B (rs2242480)"
Article: The effect of potent CYP2D6 inhibition on the pharmacokinetics and safety of deutetrabenazine in healthy volunteers
Gene: CYP2D6
Variant/haplotype: CYP2D6 intermediate metabolizer genotype
Drug(s): alpha-dihydrodeutetrabenazine, beta-dihydrodeutetrabenazine
Phenotype category: Metabolism/PK
Significant: not stated
Association: CYP2D6 intermediate metabolizer is associated with increased exposure to alpha-dihydrodeutetrabenazine and beta-dihydrodeutetrabenazine in healthy individuals as compared to CYP2D6 normal metabolizer.
Notes: Maximum exposure to α-HTBZ and β-HTBZ is slightly higher in IM compared to EM in the absence of paroxetine but comparable between IM and EM in the presence of the inhibitor.
Article: Genome-wide association study of patient and clinician rated global impression severity during antipsychotic treatment
Gene: ATP1A2
Variant/haplotype: rs6688363
Drug(s): olanzapine
Phenotype category: Efficacy
Significant: yes
Association: Allele T is associated with decreased response to olanzapine in people with Schizophrenia as compared to allele C.
Notes: The number of T alleles present in a patient was positively associated with CGI-S score.
Article: Leveraging an Electronic Health Record-Linked Biorepository to Generate a Metformin Pharmacogenomics Hypothesis
Variant/haplotype: rs2076322
Drug(s): metformin
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with response to metformin in people with Diabetes Mellitus as compared to allele A.
Notes: EHR-linked and EHR-based phenotyping methods were used to study common variants within FMO5. Efficacy was assessed by A1c levels extracted from EHR records.
Article: CYP3A4*1B and CYP3A5*3 SNPs significantly impact the response of Egyptian candidates to high-intensity statin therapy to atorvastatin
Gene: CYP3A4
Variant/haplotype: rs2740574
Drug(s): atorvastatin
Phenotype category: Efficacy
Significant: yes
Association: Genotype CC is associated with decreased response to atorvastatin in people with Cardiovascular Disease or Hyperlipidemias as compared to genotypes CT + TT.
Notes: as measured by decreased triglycerides. "The percentage reduction in the serum TG concentration was lower in the CYP3A4*1B (C/C) (wild genotype) group than in the C/T and T/T genotype groups (P value < 0.05). The percentage reduction in serum TG was 4.84 ± 24.32 in the CYP3A4*1B (C/C) genotype group (Table 5). Among the CYP3A4*1B (C/T) and (T/T) genotype carriers, the serum TG percentage reductions were 25.51 ± 8.35% and 26.70 ± 10.17%, respectively (Table 5)."
Article: Rare versus common variants in pharmacogenetics: SLCO1B1 variation and methotrexate disposition
Gene: SLCO1B1
Variant/haplotype: SLCO1B1*1, SLCO1B1*20, SLCO1B1*37
Drug(s): methotrexate
Phenotype category: Metabolism/PK
Significant: yes
Association: SLCO1B1 *20 is associated with increased clearance of methotrexate in children with Precursor Cell Lymphoblastic Leukemia-Lymphoma as compared to SLCO1B1 *1 + *37.
Notes: Please note *1B was mentioned in the article. SLCO1B1*1B was consolidated into  SLCO1B1*37  by PharmVar in 2021.
Article: Implications of OPRM1 and CYP2B6 variants on treatment outcomes in methadone-maintained patients in Ontario: Exploring sex differences
Gene: OPRM1
Variant/haplotype: rs1799971
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: High metabolic N-oxidation of voriconazole in a patient with refractory aspergillosis and CYP2C19*17/*17 genotype
Gene: CYP2C19
Variant/haplotype: CYP2C19*17
Drug(s): voriconazole
Phenotype category: Efficacy
Significant: not stated
Association: CYP2C19 *17/*17 is associated with decreased response to voriconazole in women with Mycoses.
Notes: Case report. A 26-year-old woman with an acute mixed lymphoid and myeloid leukemia met criteria for probable pulmonary aspergillosis and was treated with voriconazole. The patient showed low serum concentrations of the drug, which remained low even after dose increase, and a lack of response. She was found to have the CYP2C19 *17/*17 genotype. Once she was switched to caspofungin, the fungal infection was controlled.  The authors note that co-medications and disease-induced modulation of the CYP2C19 and CYP3A4 activities cannot be excluded as explanations for the low concentrations of voriconazole.
Article: Association between UGT2B7 gene polymorphisms and fentanyl sensitivity in patients undergoing painful orthognathic surgery
Gene: UGT2B7
Variant/haplotype: rs7439366
Drug(s): fentanyl
Phenotype category: Dosage
Significant: no
Association: Genotype TT is not associated with dose of fentanyl in people with Pain, Postoperative as compared to genotypes CC + CT.
Notes: There was no significant difference in 24 hour fentanyl use between the genotype groups.
Article: Influence of pharmacogenetic polymorphisms and demographic variables on metformin pharmacokinetics in an admixed Brazilian cohort
Gene: SLC47A1
Variant/haplotype: rs2252281
Drug(s): metformin
Phenotype category: Metabolism/PK
Significant: no
Association: Allele C is not associated with exposure to metformin as compared to allele T.