shlokn/autogkb huggingface dataset:
Article: Pharmacogenetics for Genes Associated with Age-Related Macular Degeneration (AMD) in the Comparison of AMD Treatments Trials (CATT)
Gene: HTRA1
Variant/haplotype: rs11200638
Drug(s): bevacizumab, ranibizumab
Phenotype category: Efficacy
Significant: no
Association: Genotype AA is not associated with response to bevacizumab or ranibizumab in people with Macular Degeneration as compared to genotypes AG + GG.
Notes: No significant differences in mean visual acuity (units = letters), mean visual acuity change from baseline (units = letters), >= 15-letter increase from baseline (%), mean number of injections, retinal thickness (%, units = um), mean change in total foveal thickness from baseline (units = um), dry on optical coherence tomography (%), leakage on fluorescein angiography (%) or mean change in lesion size from baseline (units = disc area) after 1 year of treatment were seen between genotypes. p <= 0.01 was considered statistically significant to adjust for multiple comparisons.
Article: Warfarin Anticoagulant Therapy: A Southern Italy Pharmacogenetics-Based Dosing Model
Gene: CYP4F2
Variant/haplotype: rs2108622
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Genotypes CC + CT is associated with decreased dose of warfarin in people with Cardiovascular Diseases as compared to genotype TT.
Notes: This SNP was presented as CYP4F2 1297G>A. Patients with the TT allele showed significantly higher doses of warfarin as compared to patients carrying the wildtype allele, C. However, this effect was small as the difference in dose between wildtype (CC) and homozygous variant (TT) genotypes was 0.6 mg/day.
Article: Evaluation of genetic association of neurodevelopment and neuroimmunological genes with antipsychotic treatment response in schizophrenia in Indian populations
Gene: ADCY2
Variant/haplotype: rs1544938
Drug(s): antipsychotics
Phenotype category: Efficacy
Significant: yes
Association: Allele C is associated with increased response to antipsychotics in people with Schizophrenia as compared to allele G.
Notes: In high severity schizophrenia patient subgroup
Article: Dosing strategies for de novo once-daily extended release tacrolimus in kidney transplant recipients based on CYP3A5 genotype
Gene: CYP3A5
Variant/haplotype: CYP3A5*1
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP3A5 *1 is associated with increased time to response to tacrolimus in people with Kidney Transplantation.
Notes: CYP3A5 variants tested: "CYP3A5*3 (rs776746), CYP3A5*6 (rs10264272), and CYP3A5*7 (rs41303343)". "Mean time to therapeutic tacrolimus trough concentration was longer in CYP3A5 intermediate and extensive metabolizers compared to CYP3A5 non-expressers"
Article: Attempted validation of 44 reported SNPs associated with tacrolimus troughs in a cohort of kidney allograft recipients
Gene: CTLA4
Variant/haplotype: rs16840252
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. This SNP is a proxy for rs4553808. Authors described association as suggestive in the AA population but it did not survive multiple testing correction and the authors did not state which allele was the associated allele.
Article: Effect of CYP2C19*2 and *17 mutations on pharmacodynamics and kinetics of proton pump inhibitors in Caucasians
Gene: CYP2C19
Variant/haplotype: CYP2C19*1, CYP2C19*17
Drug(s): omeprazole, pantoprazole
Phenotype category: Metabolism/PK
Significant: no
Association: CYP2C19 *1/*1 is not associated with metabolism of omeprazole or pantoprazole in healthy individuals as compared to CYP2C19 *1/*17.
Notes: No significant differences in area under the concentration-time curve (AUC) were seen between the two genotypes in subjects taking omeprazole (20 mg/day) or pantoprazole (40 mg/day). Subjects were treated with either drug for 6 days, in a crossover fashion; AUC was measured on day 1 and day 6 after initiation of treatment.
Article: Polymorphisms of SLC19A1 80 G>A, MTHFR 677 C>T, and Tandem TS Repeats Influence Pharmacokinetics, Acute Liver Toxicity, and Vomiting in Children With Acute Lymphoblastic Leukemia Treated With High Doses of Methotrexate
Gene: SLC19A1
Variant/haplotype: rs1051266
Drug(s): methotrexate
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype TT is associated with increased steady-state concentration of methotrexate in children with Precursor Cell Lymphoblastic Leukemia-Lymphoma as compared to genotypes CC + CT.
Notes: SNP is referred to in the paper as 80 G>A and was mapped to rs1051266 by PharmGKB. Please note that alleles have been complemented to the positive strand.
Article: Pharmacogenetics of tenofovir clearance among Southern Africans living with HIV
Variant/haplotype: rs7902657
Drug(s): tenofovir
Phenotype category: Metabolism/PK
Significant: no
Association: Allele T is not associated with clearance of tenofovir in people with HIV Infections as compared to allele G.
Notes: Significance threshold was set at 6.0E-7.
Article: Relationship between Lipid Phenotypes, Overweight, Lipid Lowering Drug Response and KIF6 and HMG-CoA Genotypes in a Subset of the Brisighella Heart Study Population
Gene: KIF6
Variant/haplotype: rs9462535
Drug(s): hmg coa reductase inhibitors
Phenotype category: Efficacy
Significant: no
Association: Genotypes AC + CC are not associated with response to hmg coa reductase inhibitors as compared to genotype AA.
Notes: With regard to lipid-lowering therapy with statins, the authors did not find any association between HMG-CoA or KIF6 genotypes and achievement of <130 mg/dL LDL-C level.
Article: Pharmacokinetics of Bupropion and Its Pharmacologically Active Metabolites in Pregnancy
Gene: CYP2C19
Variant/haplotype: CYP2C19*2, CYP2C19*3, CYP2C19*17
Drug(s): bupropion
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2C19 *2 + *3 (assigned as intermediate metabolizer and poor metabolizer phenotype) are associated with decreased metabolism of bupropion in women with Pregnancy as compared to CYP2C19 *17 (assigned as normal metabolizer phenotype) .
Article: Associations between CES1 variants and dosing and adverse effects in children taking methylphenidate
Gene: CES1
Variant/haplotype: rs4122238
Drug(s): methylphenidate
Phenotype category: Dosage
Significant: no
Association: Genotypes AG + GG is associated with decreased dose of methylphenidate in children with Attention Deficit Disorder with Hyperactivity as compared to genotype AA.
Notes: Authors never explicitly state which allele is associated with lower dose but do show that it is major allele in figure 5. The frequencies in gnomAD for all populations show G as major allele and A as minor allele.  This was not significant after Benjamini-Hochberg correction for multiple hypothesis testing which the authors state "may be too stringent".
Article: Effect of CYP3A4*22, CYP3A5*3, and CYP3A Combined Genotypes on Cyclosporine, Everolimus, and Tacrolimus Pharmacokinetics in Renal Transplantation
Gene: CYP3A5
Variant/haplotype: CYP3A5*1, CYP3A5*3
Drug(s): cyclosporine, everolimus
Phenotype category: Metabolism/PK
Significant: no
Association: CYP3A5 *1/*1 + *1/*3 is not associated with clearance of cyclosporine or everolimus in people with Kidney Transplantation as compared to CYP3A5 *3/*3.
Article: Lack of Association between Opioid-Receptor Genotypes and Smoking Cessation Outcomes in a Randomized, Controlled Naltrexone Trial
Gene: OPRM1
Variant/haplotype: rs1799971
Drug(s): naltrexone
Phenotype category: Efficacy
Significant: no
Association: Allele G 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.
Article: Influence of genetic polymorphisms in the folate pathway on toxicity after high-dose methotrexate treatment in pediatric osteosarcoma
Gene: ATIC
Variant/haplotype: rs2372536
Drug(s): methotrexate
Phenotype category: Metabolism/PK
Significant: no
Association: Allele G is not associated with concentrations of methotrexate in children with Osteosarcoma as compared to allele C.
Article: Association of carbamazepine major metabolism and transport pathway gene polymorphisms and pharmacokinetics in patients with epilepsy
Gene: NR1I2
Variant/haplotype: rs4688040
Drug(s): carbamazepine
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele T is associated with increased metabolism of carbamazepine in people with Epilepsy as compared to allele G.
Notes: This association was significant in the whole cohort. As measured by a higher carbamazepine-10-11 epoxide: carbamazepine ratio.
Article: Predictive Value of UGT1A1*28 Polymorphism In Irinotecan-based Chemotherapy
Gene: UGT1A1
Variant/haplotype: UGT1A1*1, UGT1A1*28
Drug(s): irinotecan
Phenotype category: Efficacy
Significant: no
Association: UGT1A1 *1/*28 + *28/*28 is not associated with increased response to irinotecan in people with Lung Neoplasms as compared to UGT1A1 *1/*1.
Notes: Meta-analysis of studies of Asian subjects with lung cancer (small-cell and non-small cell) from China, Korea, and Japan treated with irinotecan-based chemotherapy.
Article: The PlA1/A2 polymorphism of glycoprotein IIIa in relation to efficacy of antiplatelet drugs: a systematic review and meta-analysis
Gene: ITGB3
Variant/haplotype: rs5918
Drug(s): aspirin, clopidogrel
Phenotype category: Efficacy
Significant: no
Association: Allele C is not associated with resistance to aspirin or clopidogrel as compared to allele T.
Notes: Allele C = PIA2, allele T = PIA1.
Article: Fc‐gamma receptor polymorphisms, cetuximab therapy, and overall survival in the CCTG CO.20 trial of metastatic colorectal cancer
Gene: FCGR2A
Variant/haplotype: rs1801274
Drug(s): cetuximab
Phenotype category: Efficacy
Significant: yes
Association: Genotype AA is associated with increased response to cetuximab in people with Colorectal Neoplasms as compared to genotypes AG + GG.
Notes: Overall survival and progression-free survival were used as indicators of response to cetuximab.
Article: The effects of CYP2D6 and CYP3A activities on the pharmacokinetics of immediate release oxycodone
Gene: CYP2D6
Variant/haplotype: CYP2D6 poor metabolizer genotype
Drug(s): oxymorphone
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2D6 poor metabolizer is associated with decreased exposure to oxymorphone in healthy individuals as compared to CYP2D6 ultrarapid metabolizer.
Notes: The AUC for oxymorphone was significantly lower in poor metabolizers than in ultrarapid metabolizers.
Article: Exploration of CYP450 and drug transporter genotypes and correlations with nevirapine exposure in Malawians
Gene: CYP3A4
Variant/haplotype: rs2740574
Drug(s): nevirapine
Phenotype category: Dosage, Metabolism/PK
Significant: no
Association: Genotype CC is not associated with decreased clearance of nevirapine in people with HIV Infections as compared to genotypes CT + 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: The International SSRI Pharmacogenomics Consortium (ISPC): a genome-wide association study of antidepressant treatment response
Variant/haplotype: rs2566255
Drug(s): Selective serotonin reuptake inhibitors
Phenotype category: Efficacy
Significant: no
Association: Allele C is not associated with response to Selective serotonin reuptake inhibitors in people with Depressive Disorder, Major as compared to allele G.
Notes: The allele did not reach genome wide significance in the discovery or replication cohorts. GWA analyses were performed for two phenotypes: ‘% change in HRSD-17 score’ (% HRSD defined as the change in HRSD-17 score divided by the baseline score) and ‘response’ (defined as greater than or equal to 50% reduction in HRSD-17 score from baseline to 4-week visit).
Article: Polymorphisms in methotrexate transporters and their relationship to plasma methotrexate levels, toxicity of high-dose methotrexate, and outcome of pediatric acute lymphoblastic leukemia
Gene: SLCO1B1
Variant/haplotype: rs4149056
Drug(s): methotrexate
Phenotype category: Metabolism/PK
Significant: no
Association: Genotypes CT + TT are not associated with concentrations of methotrexate in children with Precursor Cell Lymphoblastic Leukemia-Lymphoma as compared to genotype CC.
Notes: There is no association between selected SNPs and methotrexate plasma level at 48 h between the first dose of methotrexate infusion. med. MTX concentration: TC+TT (0.45 (0.09–41.63)) vs. CC 1.1. (0.15–7.53)).
Article: Pharmacogenetic association of the APOA1/C3/A4/A5 gene cluster and lipid responses to fenofibrate: the Genetics of Lipid-Lowering Drugs and Diet Network study
Gene: APOA5
Variant/haplotype: rs3135506
Drug(s): fenofibrate
Phenotype category: Efficacy
Significant: yes
Association: Genotypes CC + CG are associated with increased response to fenofibrate in people with Hypertriglyceridemia as compared to genotype GG.
Notes: Carriers of the C allele had greater decreases in plasma triglyceride (TG) and high-density lipoprotein (HDL) levels over 3 weeks of treatment, as compared to GG homozygotes.
Article: Attempted validation of 44 reported SNPs associated with tacrolimus troughs in a cohort of kidney allograft recipients
Gene: SLCO1B3
Variant/haplotype: rs4149117
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: no
Association: Allele G is not associated with trough concentration of tacrolimus in people with Kidney Transplantation and Transplantation as compared to allele T.
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. Authors described association as suggestive in the AA population but it did not survive multiple testing correction and the authors did not state which allele was the associated allele.
Article: DRD2, DRD3, and HTR2A Single-Nucleotide Polymorphisms Involvement in High Treatment Resistance to Atypical Antipsychotic Drugs
Gene: DRD2
Variant/haplotype: rs1799732
Drug(s): antipsychotics
Phenotype category: Efficacy
Significant: yes
Association: Allele G is associated with increased resistance to antipsychotics in people with Mood Disorders or Schizophrenia as compared to allele del.
Notes: "Furthermore, the DRD2 rs1799732 I|I vs. D|I genotype significantly predicted the; HTR group membership (OR = 12.079; B = 2.491; p = 0.037) (Table 3)."
Article: Prediction Formulas for Individual Opioid Analgesic Requirements Based on Genetic Polymorphism Analyses
Variant/haplotype: rs2952768
Drug(s): fentanyl
Phenotype category: Dosage, Efficacy
Significant: yes
Association: Genotype CC is associated with increased dose of fentanyl in people with Pain, Postoperative as compared to genotypes CT + TT.
Notes: A formula was developed to predict individual opioid use during the first 24-h post-operative period for patients who underwent craniofacial surgery. The post-operative period R squared values were higher when genotype information was included. In the first group fentanyl was administered by IV, on demand, with a bolus dose of 20 micrograms and a 10 minute lockout period 24-h post-op.
Article: Tafenoquine treatment of Plasmodium vivax malaria: suggestive evidence that CYP2D6 reduced metabolism is not associated with relapse in the Phase 2b DETECTIVE trial
Gene: CYP2D6
Variant/haplotype: CYP2D6*1, CYP2D6*2, CYP2D6*4, CYP2D6*9, CYP2D6*10, CYP2D6*41
Drug(s): tafenoquine
Phenotype category: Efficacy
Significant: no
Association: CYP2D6 *4/*41 + *1/*4 + *10/*10 + *10/*41 + *2/*4 + *41/*41 is not associated with decreased response to tafenoquine in people with Malaria as compared to CYP2D6 *1/*10 + *1/*41 + *1/*9 + *2/*10 + *2/*41 + *1/*1 + *1/*2 + *2/*2.
Notes: Please not patients are co-treated with chloroquine. No evidence of association between CYP2D6 IM phenotype and increased frequency of clinical relapse of P. vivax infection was seen in either of the TQ treatment groups. Genotyped with Affymetrix® DMET-Plus array. Phenotype grouping: poor metabolizers two no function alleles; intermediate metabolizers (IM) one null and one decreased function allele or two decreased function alleles, or one null allele and one normal allele; extensive metabolizers (EM) if they carried two normal alleles or one normal allele and one deficient allele.
Article: Polymorphisms in methotrexate transporters and their relationship to plasma methotrexate levels, toxicity of high-dose methotrexate, and outcome of pediatric acute lymphoblastic leukemia
Gene: SLCO1B1
Variant/haplotype: rs11045879
Drug(s): methotrexate
Phenotype category: Efficacy
Significant: no
Association: Allele C is not associated with response to methotrexate in children with Precursor Cell Lymphoblastic Leukemia-Lymphoma as compared to allele T.
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: Metabolism/PK
Significant: yes
Association: NAT2 slow acetylator is associated with increased concentrations of isoniazid in people with Tuberculosis as compared to NAT2 intermediate acetylator.
Notes: "More specifically, INH AUC0–6h and INH Cmax; values were significantly higher, while AcINH AUC0–6h values were; significantly lower in NAT2 slow acetylators. Also, median values of; both AcINH/INH and INA/INH ratios were significantly lower in; the NAT2 SA group." "A 1211-bp fragment, which contains the entire coding region of; NAT2 was amplified by PCR" alleles were assigned using the Greek nomenclature database. "individuals were; classified as rapid (carrying two rapid NAT2 alleles), intermediate; (one rapid and one slow allele) or slow (two slow alleles) acetylators." No fast acetylators were observed.
Article: Replication study of polymorphisms associated with response to methotrexate in patients with rheumatoid arthritis
Gene: MTRR
Variant/haplotype: rs162040
Drug(s): methotrexate
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to methotrexate in people with Arthritis, Rheumatoid as compared to allele C.
Article: A Pharmacogenetics-Based Warfarin Maintenance Dosing Algorithm from Northern Chinese Patients
Gene: VKORC1
Variant/haplotype: rs7294
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Allele T is associated with increased dose of warfarin in people with heart valve replacement as compared to allele C.
Notes: Samples, genotypes and INRs from a cohort of 551 patients were used to derive an algorithm which was used to predict daily warfarin maintenance dose in a second cohort of 236 patients. Note: the authors state that "SNPs were tested for deviations from HWE using the chi-squared test, and for their association with the warfarin dose by Spearman correlation analysis using a *co-dominant* model." rs7294 remained significantly associated with warfarin maintenance dose in the multivariate analysis.
Article: CYP4F2 rs2108622: a minor significant genetic factor of warfarin dose in Han Chinese patients with mechanical heart valve replacement
Gene: CYP4F2
Variant/haplotype: rs2108622
Drug(s): warfarin
Phenotype category: Dosage, Efficacy
Significant: yes
Association: Genotypes CT + TT are associated with increased dose of warfarin in people with mechanical heart valve replacement as compared to genotype CC.
Notes: 3.2 mg/day vs. 2.9 mg/day.  There were only 15 TT patients.
Article: Human Polymorphisms in the Glutathione Transferase Zeta 1/Maleylacetoacetate Isomerase Gene Influence the Toxicokinetics of Dichloroacetate
Gene: GSTZ1, POMT2
Variant/haplotype: rs7975
Drug(s): dichloroacetic acid
Phenotype category: Toxicity, Metabolism/PK
Significant: no
Association: Allele G is associated with decreased clearance of dichloroacetic acid in children with Mitochondrial Diseases.
Notes: The statement above is meant for a haplotype rather than for the allele. For the various possible haplotype combinations involving rs7975,rs7972,rs1046428, the slowest clearance and the highest urinary excretion of unmetabolized C(13)-DCA was observed for a subject homozygous for G for rs7975,G for rs7972, T for rs1046428.
Article: Independent and interactive effects of OPRM1 and DAT1 polymorphisms on alcohol consumption and subjective responses in social drinkers
Gene: SLC6A3
Variant/haplotype: rs28363170
Drug(s): ethanol
Phenotype category: Toxicity
Significant: yes
Association: Allele del is associated with increased exposure to ethanol in healthy individuals as compared to allele GGGGGCCCTGCATGCGTCCTGGGGTAGTACACGCTCCAGT.
Notes: This variant is a VNTR; the 'del' allele represented the 9-repeat allele, while the 'GGG...' allele represents the 10-repeat allele. Subjects with the 9-repeat allele had a significantly increased odds ratio for reporting more drinking days compared to subjects carrying the 10-repeat allele. The authors note an epistatic effect, where the presence of the rs1799971 G allele in OPRM1 reduced the effect of the 9-repeat allele on the number of drinking days. There was no significant association between rs28363170 and number of drinks per drinking day or number of heavy drinking days.
Article: Variability in plasma rifampicin concentrations and role of SLCO1B1, ABCB1, AADAC2 and CES2 genotypes in Ethiopian patients with tuberculosis
Gene: AADAC
Variant/haplotype: rs1803155
Drug(s): rifampin
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype GG is associated with decreased exposure to rifampin in people with Tuberculosis as compared to genotypes AA + AG.
Notes: "We  found a  significant association between AADAC c.841G>A genotype and rifampicin Cmax, which was sig-nificantly higher in  carriers of  the  mutant variant allele (A/A, G/A) than in  those with wild-type G/G  genotype" "AADAC c.841GG and ABCB1 c.4036A>GAA genotype groups and  male patients had a  higher risk  of  low  rifampicin plasma exposure than females."
Article: Association studies of dopamine synthesis and metabolism genes with multiple phenotypes of heroin dependence
Gene: DBH
Variant/haplotype: rs1611114
Drug(s): heroin
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with response to heroin as compared to allele C.
Notes: No significant association between this variant and strength of euphoria on first heroin use.
Article: Relationships of related genetic polymorphisms and individualized medication of tacrolimus in patients with renal transplantation
Gene: CYP3A5
Variant/haplotype: CYP3A5*1, CYP3A5*3
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP3A5 *3 is associated with increased dose-adjusted trough concentrations of tacrolimus in people with Kidney Transplantation as compared to CYP3A5 *1.
Notes: CYP3A5*3 was positively correlated with tacrolimus dose-adjusted trough concentrations (C/D). In multiple regression analysis, the factors with statistical significance toward C/D were CYP3A5*3, hematocrit and albumin. CYP3A5*3 explained 23.5% of individual variations in C/D, followed by hematocrit (3.3%) and albumin (1.5%).
Article: Genome-Wide Association and Functional Studies Reveal Novel Pharmacological Mechanisms for Allopurinol
Gene: PKD2
Variant/haplotype: rs2725215
Drug(s): allopurinol
Phenotype category: Efficacy
Significant: no
Association: Allele T is associated with decreased response to allopurinol as compared to allele C.
Notes: Response to allopurinol was determined by whether serum uric acid concentrations decreased following allopurinol treatment.