shlokn/autogkb huggingface dataset:
Article: Warfarin Dosage Response Related Pharmacogenetics in Chinese Population
Gene: CYP2C9
Variant/haplotype: rs1057910
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Genotype AA is associated with increased dose of warfarin in people with heart valve replacement as compared to genotype AC.
Notes: 158/220 patients had the target INR (1.5–2.5). The comparison of weekly warfarin maintenance dose was among patients of different genotypes. The mean maintenance dose per week was significantly lower in the rs1057910 AC genotype (15.31±5.26 mg/w) vs the AA genotype (21.21±6.98 mg/w, p = 0.002 ANOVA). rs9923231 and rs1057910 had significant effects on maintenance dose (rs9923231: coefficient was 1.398, p < 0.001; rs1057910: coefficient was-0.994, p < 0.001) and together explained apx. 32.0% of warfarin maintenance dose variability.
Article: Functional characterization of novel rare CYP2A6 variants and potential implications for clinical outcomes
Gene: CYP2A6
Variant/haplotype: rs778019189
Drug(s): nicotine
Phenotype category: Metabolism/PK
Significant: not stated
Association: Allele G is associated with decreased metabolism of nicotine as compared to allele A.
Notes: Assigned as loss-of-function following in vitro assessments, in vivo associations and variant construct functional assignments. Please note that alleles have been complemented to the positive strand.
Article: Warfarin Anticoagulant Therapy: A Southern Italy Pharmacogenetics-Based Dosing Model
Gene: CYP2C9
Variant/haplotype: CYP2C9*1, CYP2C9*2, CYP2C9*3
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: CYP2C9 *2 + *3 are associated with decreased dose of warfarin in people with Cardiovascular Diseases as compared to CYP2C9 *1.
Notes: Patients with the *2 or *3 alleles showed significantly lower doses (17% or 32%, respectively) of warfarin as compared to patients with the wildtype genotype (*1/*1). When studied together with VKORC1 1639G/A, patients carrying variants in both genes needed between 34.8% and 84% of the dose needed for patients wildtype for both genes.
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*6
Drug(s): irinotecan, oxaliplatin, tegafur / gimeracil / oteracil
Phenotype category: Efficacy
Significant: no
Association: UGT1A1 *6 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 *6 allele (85% responders) and those without one (64%).
Article: Genomic Association Analysis of Common Variants Influencing Antihypertensive Response to Hydrochlorothiazide
Variant/haplotype: rs4376293
Drug(s): "diuretics", "hydrochlorothiazide", "Thiazides, plain"
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with response to diuretics, hydrochlorothiazide or Thiazides, plain in people with Hypertension as compared to allele C.
Notes: Significance was not attained. Observations: 2.50 mm Hg increased reduction of systolic blood pressure per A allele in PEAR + GERA, 0.38 mm Hg decreased reduction of systolic blood pressure per A allele in NORDIL, and 1.77 mm Hg increased reduction of systolic blood pressure per A allele in PEAR + GERA + NORDIL.
Article: VKORC1 Asp36Tyr geographic distribution and its impact on warfarin dose requirements in Egyptians
Gene: VKORC1
Variant/haplotype: rs61742245
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Genotypes AA + AC are associated with increased dose of warfarin as compared to genotype CC.
Notes: Egyptian carriers of the VKORC1 rs61742245 A allele (Tyr 36) showed higher warfarin dose requirement (57.1 ± 29.4 mg/week) than those with the CC (Asp36Asp) genotype (35.8 ± 16.6 mg/week; p<0.03). "This SNP was most frequent among Kenyans and Sudanese, with a minor allele frequency (MAF) of 6% followed by Saudi Arabians and Egyptians with a MAF of 3% and 2.5%, respectively. It was not detected in West Africans (Ghana), and a large cohort of African Americans."
Article: The role of organic anion-transporting polypeptides and their common genetic variants in mycophenolic acid pharmacokinetics
Gene: SLCO1B3
Variant/haplotype: rs7311358
Drug(s): mycophenolate mofetil
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele A is associated with decreased clearance of mycophenolate mofetil in people with Kidney Transplantation as compared to allele G.
Notes: This association was found for the haplotype of 334T>G/699G>A (rs4149117G/rs7311358A).  Patients were also treated with sirolimus or tacrolimus (results did not differ between these treatments so were pooled).
Article: Genetic-based dosing in orthopedic patients beginning warfarin therapy
Gene: CYP2C9
Variant/haplotype: CYP2C9*1, CYP2C9*3
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: CYP2C9 *3 is associated with decreased dose of warfarin in people with total knee or hip arthroplasty as compared to CYP2C9 *1.
Notes: *3 was associated with 38.1 %(95% CI 29.3 -45.7%) reduction in therapeutic dose (defined as the dose that gave an INR in the target therapeutic range after 7 consecutive days) per copy.
Article: Sunitinib-induced severe toxicities in a Japanese patient with the ABCG2 421 AA genotype
Gene: ABCG2
Variant/haplotype: rs2231142
Drug(s): n-desethyl sunitinib, sunitinib
Phenotype category: Toxicity, Metabolism/PK
Significant: no
Association: Genotype TT is associated with increased concentrations of n-desethyl sunitinib and sunitinib in women with Carcinoma, Renal Cell.
Notes: in a single case study. Authors state "Therefore, we speculated that the extremely high plasma concentrations of sunitinib and SU12662 caused by the ABCG2 421 AA genotype might have resulted in severe toxicities to the patient."
Article: ABCB1 (MDR1) genetic variants are associated with methadone doses required for effective treatment of heroin dependence
Gene: ABCB1
Variant/haplotype: rs2032582
Drug(s): methadone
Phenotype category: Dosage
Significant: no
Association: Allele A is not associated with dose of methadone in people with Heroin Dependence as compared to allele C.
Notes: Please note that alleles have been complemented to the positive strand. Alleles were not associated with the need for a higher (>150mg) or lower (<150 mg) dose of methadone.
Article: Fixed dose capecitabine is feasible: results from a pharmacokinetic and pharmacogenetic study in metastatic breast cancer
Gene: SLC28A1
Variant/haplotype: rs2290272
Drug(s): capecitabine
Phenotype category: Metabolism/PK
Significant: no
Association: Allele A is not associated with metabolism of capecitabine in people with Breast Neoplasms as compared to allele G.
Notes: Please note that these alleles were listed as G and T within the paper. No significant differences in the area under the concentration-time curve from 0 to infinity (AUCinf) were seen between any of the genotypes (CC, AC, AA). Nor were any significant differences seen between these genotypes when considering the capecitabine metabolites 5'-DFCR, 5'-DFUR or 5'FU (5'-fluorouracil).
Article: Pharmacokinetics of Efavirenz when Co-administered with Rifampin in TB/HIV Co-infected Patients: Pharmacogenetic Effect of CYP2B6 Variation
Gene: CYP2B6
Variant/haplotype: rs3745274
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype TT is associated with increased concentrations of efavirenz in people with HIV Infections and Tuberculosis as compared to genotypes GG + GT.
Article: Cholinergic receptor nicotinic alpha 5 subunit polymorphisms are associated with smoking cessation success in women
Gene: CHRNA5
Variant/haplotype: rs16969968
Drug(s): bupropion, nicotine, varenicline
Phenotype category: Efficacy
Significant: yes
Association: Genotypes AA + AG are associated with increased response to bupropion, nicotine or varenicline in women with Tobacco Use Disorder as compared to genotype GG.
Notes: Women with the AA or AG genotypes were more likely to be abstinent from smoking at 6 months after starting pharmacotherapy for smoking cessation compared to those with the GG genotype.
Article: Rare versus common variants in pharmacogenetics: SLCO1B1 variation and methotrexate disposition
Gene: SLCO1B1
Variant/haplotype: SLCO1B1*1, SLCO1B1*14, SLCO1B1*37
Drug(s): methotrexate
Phenotype category: Metabolism/PK
Significant: yes
Association: SLCO1B1 *14 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: Pharmacogenetic Predictors of Adverse Events and Response to Chemotherapy in Metastatic Colorectal Cancer: Results From North American Gastrointestinal Intergroup Trial N9741
Gene: DPYD
Variant/haplotype: rs3918290
Drug(s): FOLFIRI, FOLFOX, irinotecan, oxaliplatin
Phenotype category: Efficacy
Significant: no
Association: Genotype CT is not associated with response to FOLFIRI, FOLFOX, irinotecan or oxaliplatin in people with Colorectal Neoplasms as compared to genotype CC.
Notes: Patients were taking either IFL (irinotecan + fluorouracil + leucovorin; n=114), FOLFOX (fluorouracil + oxaliplatin + leucovorin; n=299) or IROX (irinotecan + oxaliplatin; n=107). No significant association was seen between this variant and confirmed response rate, overall survival or time to progression in any of the treatment groups (no analyses were undertaken for the FOLFOX group) OR all treatment groups considered together. Significance level was set at 0.01.
Article: Pharmacogenetic-Based Efavirenz Dose Modification: Suggestions for an African Population and the Different CYP2B6 Genotypes
Gene: ABCB1
Variant/haplotype: rs3842
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele C is associated with metabolism of efavirenz in people with HIV Infections as compared to allele T.
Notes: Steady-state plasma concentration from HIV infected patients treated with EFV were used to calculate baseline biochemistries, CD4 counts, and viral load. The authors used non-linear mixed effect modeling to created a PK model of efavirenz. Significant covariates predicted to affect PK of efavirenz were included in the final model. rs3842 T>C was considered a significant factor in covariate analysis and included in the final pharmacokinetic model.
Article: Exploring the Role of Alcohol Metabolizing Genotypes in a 12-Week Clinical Trial of Naltrexone for Alcohol Use Disorder
Gene: ALDH2
Variant/haplotype: rs671
Drug(s): naltrexone
Phenotype category: Efficacy
Significant: yes
Association: Allele G is associated with increased response to naltrexone in men with Alcoholism as compared to allele A.
Notes: The G allele is also referred to as the ALDH2*2 allele in the paper. Patients carrying the G allele reported fewer drinking days during naltrexone treatment.
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: rs3842
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: no
Association: Allele C is not associated with concentrations of efavirenz in children with HIV Infections as compared to allele T.
Notes: This is stated in the paper, but supporting data is not shown.
Article: Resequencing of serotonin-related genes and association of tagging SNPs to citalopram response
Gene: HTR2A
Variant/haplotype: rs6313
Drug(s): citalopram
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to citalopram in people with Depressive Disorder, Major as compared to allele G.
Article: Novel and replicated clinical and genetic risk factors for toxicity from high-dose methotrexate in pediatric acute lymphoblastic leukemia
Gene: ABCC4
Variant/haplotype: rs7317112
Drug(s): methotrexate
Phenotype category: Metabolism/PK
Significant: not stated
Association: Allele G is associated with decreased clearance of methotrexate in children with Precursor Cell Lymphoblastic Leukemia-Lymphoma as compared to allele A.
Notes: "The G allele of rs7317112, an intronic variant of ABCC4, was the other SNP with a clear; association with prolonged MTX clearance"
Article: Adiponectin Gene Polymorphism rs2241766 T/G Is Associated with Response to Pioglitazone Treatment in Type 2 Diabetic Patients from Southern China
Gene: ADIPOQ
Variant/haplotype: rs1063537
Drug(s): pioglitazone
Phenotype category: Efficacy
Significant: no
Association: Genotype CC are not associated with response to pioglitazone in people with Diabetes Mellitus as compared to genotypes CT + TT.
Notes: Response was defined as "any decrease greater than (or equal to) 15%" of glycated hemoglobin (HbA1C%).
Article: Associations between CES1 variants and dosing and adverse effects in children taking methylphenidate
Gene: CES1
Variant/haplotype: rs114119971
Drug(s): methylphenidate
Phenotype category: Dosage
Significant: yes
Association: Genotype CG is associated with decreased dose of methylphenidate in children with Attention Deficit Disorder with Hyperactivity as compared to genotype GG.
Notes: Authors never explicitly state which allele is associated with lower dose but do show that it is minor allele which is observed in only two individuals. The frequencies in gnomAD for all populations show G as major allele and C as minor allele.  "The individuals with the rs114119971 SNV had a significantly lower weight-based dose (0.42 mg/kg) as compared to those without (0.88 mg/kg; p < 0.001)."
Article: Effect of NAT2, GSTM1 and CYP2E1 genetic polymorphisms on plasma concentration of isoniazid and its metabolites in patients with tuberculosis, and the assessment of exposure-response relationships
Gene: NAT2
Variant/haplotype: NAT2 slow acetylator
Drug(s): isoniazid
Phenotype category: Efficacy
Significant: no
Association: NAT2 slow acetylator is associated with decreased clinical benefit to isoniazid in people with Tuberculosis as compared to NAT2 intermediate acetylator.
Notes: "A trend of association between NAT2 phenotypes and; tSCC was detected, with SA having 80% lower odds of tSCC within; 60 days in comparison to IA (OR = 0.2; 95% CI, 0.03–1.22); however,; statistical significance was not reached (p = 0.069) (Table 5)."
Article: Genetic Polymorphisms of Cytokines Might Affect Postoperative Sufentanil Dosage for Analgesia in Patients
Gene: CXCL8
Variant/haplotype: rs4073
Drug(s): sufentanil
Phenotype category: Dosage
Significant: no
Association: Allele T is not associated with dose of sufentanil in people with Pain, Postoperative as compared to allele A.
Article: CYP2D6 Genetic Variation and Beta-Blocker Maintenance Dose in Patients with Heart Failure
Gene: CYP2D6
Variant/haplotype: CYP2D6*4
Drug(s): carvedilol
Phenotype category: Dosage
Significant: no
Association: CYP2D6 *4 is associated with increased dose of carvedilol in people with Heart Failure.
Notes: A trend was observed between the *4 allele and an increased maintenance dose of carvedilol.
Article: Genetic determinants of serum bilirubin using inferred native American gene variants in Chilean adolescents
Gene: UGT1A1
Variant/haplotype: rs887829
Drug(s): bilirubin
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype TT is associated with increased concentrations of bilirubin in children as compared to genotypes CC + CT.
Notes: "By considering the deconvoluted genotypes with NAT origin, we found that the variant with the strongest association was also rs887829, upstream of the UGT1A1 gene, beta = 0.35 mg/dL total bilirubin, p = 3.29 × 10−17, with a frequency of 34.2% in the NAT component of GOCS (Table 2; Supplementary Table S5)." "The variant rs887829 near UGT1A1 explained 34.98% of the variation in total bilirubin levels, while the rs1910167 variant near SLCO1B1 only explained 4.61%. "
Article: A pharmacokinetic comparison of two voriconazole formulations and the effect of CYP2C19 polymorphism on their pharmacokinetic profiles
Gene: CYP2C19
Variant/haplotype: CYP2C19*1, CYP2C19*2, CYP2C19*3
Drug(s): voriconazole
Phenotype category: Metabolism/PK
Significant: not stated
Association: CYP2C19 *1/*2 + *1/*3 + *2/*2 + *2/*3 + *3/*3 (assigned as intermediate metabolizer and poor metabolizer phenotype) is associated with increased concentrations of voriconazole in healthy individuals as compared to CYP2C19 *1/*1 (assigned as normal metabolizer phenotype) .
Notes: Area under the concentration-time curve from dosing to last quantifiable concentration (AUClast) and maximum plasma concentration (Cmax) were greatest in CYP2C19 poor metabolizers (PMs; *2/*2 + *2/*3 + *3/*3), followed by intermediate metabolizers (IMs; *1/*2 + *1/*3) and then extensive metabolizers (EMs; *1/*1). The AUClast was 2.35-fold greater in PMs vs EMs, and 1.27-fold greater in IMs vs EMs. The intrasubject coefficient of variation (CV) for Cmax was 44% greater in PMs vs EMs, and 22% greater in IMs vs EMs. The intrasubject CV for AUClast was 71% greater for PMs vs EMs, and 135% greater for IMs vs EMs. However, no statistical analyses were provided for these differences. The authors also note that one individual with the *1/*17 genotype had an AUClast close to that of the EM group, and one with the *2/*17 genotype had an AUClast close to that of the IM group. Two voriconazole formulations were studied in this paper (SYP-1018 and Vfend), and these results apply to both formulations.
Article: Genetic factors influencing warfarin dose in Black-African patients: a systematic review and meta-analysis
Gene: VKORC1
Variant/haplotype: rs2359612
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Genotypes AA + AG are associated with decreased dose of warfarin as compared to genotype GG.
Notes: In this meta-analysis of warfarin Dose in Black-African Patients, this variant is associated with 17.3mg/week less warfarin dose requirement compared to wild-type homozygotes.
Article: Genetic Variants Associated With Response to Platinum-Based Chemotherapy in Non-Small Cell Lung Cancer Patients: A Field Synopsis and Meta‐Analysis
Gene: ERCC2
Variant/haplotype: rs1799793
Drug(s): Platinum compounds
Phenotype category: Efficacy
Significant: yes
Association: Genotypes CT + TT is associated with increased resistance to Platinum compounds in people with Carcinoma, Non-Small-Cell Lung as compared to genotype CC.
Notes: " Under the dominant model, ERCC2 rs1799793 was associated with an increased risk of PBC chemoresistance (OR = 1.186, 95% CI = 1.000–1.407), although the association was at borderline significance (p = 0.049). Similarly, an increased risk of chemoresistance was observed for under the allele model (OR = 1.311, 95% CI = 1.082–1.590, p < 0.01" Alleles complemented to plus chromosomal strand.
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: rs1461773
Drug(s): ethanol
Phenotype category: Efficacy
Significant: yes
Association: Allele A is associated with increased response to ethanol as compared to allele G.
Notes: Please note that alleles have been complemented to the positive strand. The T allele was associated with increased scores in the dizzy, drunk, high, nausea, talkative and uncomfortable traits as well as increased total score on the Subjective High Assessment Scale-Expectations (SHAS-E) questionnaire.
Article: CYP4F2 genetic variant alters required warfarin dose
Gene: CYP4F2
Variant/haplotype: rs2108622
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Genotype CC is associated with decreased dose of warfarin as compared to genotypes CT + TT.
Notes: 4% to 12% increase in the warfarin dose per T allele. This is in Whites presumably of European descent.
Article: The association of gene polymorphisms of adenosine and dopamine receptors with the response to caffeine citrate treatment in infants with apnea of prematurity: a prospective nested case-control study
Gene: ADORA1
Variant/haplotype: rs10920573
Drug(s): caffeine
Phenotype category: Efficacy
Significant: yes
Association: Genotype CC is associated with decreased clinical benefit to caffeine in infants with Apnea of prematurity as compared to genotypes CT + TT.
Notes: "In the univariate logistic regression analysis, the CC genotype of ADORA1 rs10920573 (TT / TC vs. CC: OR, 2.89; 95% CI, 1.30–6.40), TC genotype of ADORA2B rs2015353 (TT / CC vs. TC: OR, 2.56; 95% CI, 1.28–5.12), AG genotype of DRD3 rs7625282 (AA / GG vs. AG: OR, 2.15; 95% CI, 1.17–3.96), and CT genotype of DRD3 rs6280 (CC / TT vs. CT: OR, 2.36; 95% CI, 1.29–4.30) were identified as risk factors for non-response to caffeine citrate in preterm infants. " "CC genotype of ADORA1 rs10920573 (aOR, 3.51; 95% CI, 1.34–9.25) and CT genotype of DRD3 rs6280 (aOR, 3.19; 95% CI, 1.53–6.65) were identified as independent risk factors for non-response to caffeine citrate in preterm infants. "
Article: Association of ABCB1 and FLT3 Polymorphisms with Toxicities and Survival in Asian Patients Receiving Sunitinib for Renal Cell Carcinoma
Gene: FLT3
Variant/haplotype: rs1933437
Drug(s): sunitinib
Phenotype category: Efficacy
Significant: no
Association: Genotype AA is not associated with response to sunitinib in people with Carcinoma, Renal Cell as compared to genotypes AG + GG.
Notes: The genotype was not associated with progression free survival, or overall survival either. Clinical benefit was defined as either partial response or stable disease. Please note, alleles have been complemented to the + chromosomal strand.
Article: Influence of genetic polymorphisms in P2Y12 receptor signaling pathway on antiplatelet response to clopidogrel in coronary heart disease
Gene: ITGB3
Variant/haplotype: rs3785873
Drug(s): clopidogrel
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with increased resistance to clopidogrel in people with Coronary Disease as compared to allele G.
Article: Genetic Polymorphisms of Cytokines Might Affect Postoperative Sufentanil Dosage for Analgesia in Patients
Gene: REL
Variant/haplotype: rs842647
Drug(s): sufentanil
Phenotype category: Dosage
Significant: no
Association: Allele A is not associated with dose of sufentanil in people with Pain, Postoperative as compared to allele G.
Article: Influence of SLCO1B1 and CYP2C8 gene polymorphisms on rosiglitazone pharmacokinetics in healthy volunteers
Gene: CYP2C8
Variant/haplotype: CYP2C8*1, CYP2C8*3
Drug(s): rosiglitazone
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2C8 *1/*3 is associated with decreased concentrations of rosiglitazone in healthy individuals as compared to CYP2C8 *1/*1.
Notes: CYP2C8*1/*3 genotype (n=7) had significantly lower rosiglitazone area under the plasma concentration–time curve (AUC) and significantly higher rosiglitazone oral clearance, compared with CYP2C8 wild-type homozygotes.
Article: Pharmacogenetics of TNF inhibitor response in rheumatoid arthritis utilizing the two-component disease activity score
Gene: CERS6
Variant/haplotype: rs13393173
Drug(s): adalimumab, certolizumab pegol, etanercept, infliximab, Tumor necrosis factor alpha (TNF-alpha) inhibitors
Phenotype category: Efficacy
Significant: yes
Association: Allele A is associated with increased response to adalimumab, certolizumab pegol, etanercept, infliximab or Tumor necrosis factor alpha (TNF-alpha) inhibitors in people with Arthritis, Rheumatoid as compared to allele G.
Notes: as measured by change in 2C-DAS28. Table 2 shows change was a negative value for this variant suggesting decreased 2C-DAS28 and increased response, it was not attributed to a particular allele at this rs number location so assumed minor allele based on dbSNP frequencies.