shlokn/autogkb huggingface dataset:
Article: A Pharmacogenetics-Based Warfarin Maintenance Dosing Algorithm from Northern Chinese Patients
Gene: CYP4F2
Variant/haplotype: rs3093105
Drug(s): warfarin
Phenotype category: Dosage
Significant: no
Association: Allele C is not associated with dose of warfarin in people with heart valve replacement as compared to allele A.
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."
Article: The International SSRI Pharmacogenomics Consortium (ISPC): a genome-wide association study of antidepressant treatment response
Variant/haplotype: rs2511398
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: Personalized Tacrolimus Dose Requirement by CYP3A5 but Not ABCB1 or ACE Genotyping in Both Recipient and Donor after Pediatric Liver Transplantation
Gene: ABCB1
Variant/haplotype: rs1045642
Drug(s): tacrolimus
Phenotype category: Dosage
Significant: no
Association: Genotype AA is not associated with concentrations of tacrolimus in children with liver transplantation.
Notes: All liver transplant recipients were given tacrolimus 2-3 days post liver transplantation. Weight adjusted dose and concentration to dose ratio (C/D) were the primary outcomes. Dose and C/D were calculated based on measurements taken on day 3, 7 and 14 post-transplantation as well as the the 1st, 3rd, 6th and 12th month post-transplantation. ABCB1 genotype was not significantly associated with C/D of tacrolimus at any time point.
Article: Association of Pharmacogenetic Markers with Premature Discontinuation of First-line Anti-HIV Therapy: An Observational Cohort Study
Gene: ABCC2
Variant/haplotype: rs2273697
Drug(s): tenofovir
Phenotype category: Toxicity
Significant: no
Association: Genotypes AA + AG is not associated with increased discontinuation of tenofovir in people with HIV Infections as compared to genotype GG.
Article: Multigene predictors of tacrolimus exposure in kidney transplant recipients
Gene: CYP3A4
Variant/haplotype: CYP3A4*22
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: no
Association: CYP3A4 *22 is not associated with trough concentration of tacrolimus in people with Kidney Transplantation.
Notes: No association was observed between CYP3A4*22 genotype and tacrolimus trough concentrations after multivariable analysis adjusting for CYP3A5*1 status and clinical factors. The authors note that the CYP3A4*22 variant was infrequent with a low minor allele frequency. n=35,043 tacrolimus trough concentrations were available for analysis.
Article: The impact of VKORC1-1639 G>A polymorphism on the maintenance dose of oral anticoagulants for thromboembolic prophylaxis in North India: A pilot study
Gene: VKORC1
Variant/haplotype: rs9923231
Drug(s): warfarin
Phenotype category: Dosage, Metabolism/PK
Significant: not stated
Association: Allele T is associated with decreased dose of warfarin as compared to allele C.
Notes: in Indian patients.
Article: Relative contribution of CYP2C9 and VKORC1 genotypes and early INR response to the prediction of warfarin sensitivity during initiation of therapy
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 as compared to CYP2C9 *1/*1.
Article: Pharmacogenetic analysis of high-dose methotrexate treatment in children with osteosarcoma
Gene: NR1I2
Variant/haplotype: rs6785049
Drug(s): methotrexate
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele G is associated with increased concentrations of methotrexate in children with Osteosarcoma as compared to allele A.
Notes: Concentrations refers to concentration at 48 hrs
Article: CYP3A5, ABCB1 and SLCO1B1 Polymorphisms and Pharmacokinetics and Virologic Outcome of Lopinavir/Ritonavir in HIV-infected Children
Gene: SLCO1B1
Variant/haplotype: rs2306283
Drug(s): lopinavir, ritonavir
Phenotype category: Metabolism/PK
Significant: no
Association: Allele G is not associated with response to lopinavir or ritonavir in children with HIV Infections as compared to allele A.
Notes: No association between this variant and virologic suppression in patients treated with lopinavir/ritonavir. Variant referred to in the paper as A388G.
Article: Effects of genetic variants of organic cation transporters on metformin response in newly diagnosed patients with type 2 diabetes
Gene: ALDH3A2
Variant/haplotype: rs4621031
Drug(s): metformin
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with decreased clinical benefit to metformin in people with Diabetes Mellitus, Type 2 as compared to allele C.
Notes: "Other SNPs (rs4621031, rs34399035, rs1800058, and rs11212617) had no significant impact on metformin response. "
Article: Carfilzomib and lenalidomide response related to VEGF and VEGFR2 germline polymorphisms
Gene: KDR
Variant/haplotype: rs1870377
Drug(s): carfilzomib, dexamethasone, lenalidomide
Phenotype category: Efficacy
Significant: yes
Association: Genotypes AT + TT is associated with increased response to carfilzomib, dexamethasone and lenalidomide in people with Multiple Myeloma as compared to genotype AA.
Notes: as measured by "minimum residual disease negativity" (MRD-). Gene is on negative strand, alleles complemented to positive strand. Authors reported for response associated allele as protein change as 472Q.
Article: Personalized Tacrolimus Dose Requirement by CYP3A5 but Not ABCB1 or ACE Genotyping in Both Recipient and Donor after Pediatric Liver Transplantation
Gene: ABCB1
Variant/haplotype: rs1128503
Drug(s): tacrolimus
Phenotype category: Dosage
Significant: no
Association: Genotype AA is not associated with concentrations of tacrolimus in children with liver transplantation.
Notes: All liver transplant recipients were given tacrolimus 2-3 days post liver transplantation. Weight adjusted dose and concentration to dose ratio (C/D) were the primary outcomes. Dose and C/D were calculated based on measurements taken on day 3, 7 and 14 post-transplantation as well as the the 1st, 3rd, 6th and 12th month post-transplantation. ABCB1 genotype was not significantly associated with C/D of tacrolimus at any time point.
Article: Tamoxifen Metabolite Concentrations, CYP2D6 Genotype and Breast Cancer Outcomes
Gene: CYP2D6
Variant/haplotype: CYP2D6 poor metabolizers
Drug(s): tamoxifen
Phenotype category: Metabolism/PK
Significant: no
Association: CYP2D6 poor metabolizer is not associated with increased concentrations of tamoxifen in women with Breast Neoplasms as compared to CYP2D6 normal metabolizer.
Notes: Included were patients with ER-positive tumor who had been taking tamoxifen for at least 4 month. no info on menopausal status. Genotyped using AmpliChip CYP450 Test. (i) nonfunctional (PM) alleles include CYP2D6*3, *4, *5, *6, *7, *8, *11, *14A, *15, *19, *20, and *40, and the *4XN gene duplication; (ii) reduced function (intermediate metabolizer) alleles include CYP2D6*9, *10, *17, *29, *36, and *41, and gene duplications *10XN, *17XN, and *41XN; (iii) fully functional (extensive metabolizer or EM) alleles include CYP2D6*1, *2, and *35 and (iv) increased function (ultrarapid metabolizer) phenotype alleles include gene duplications such as CYP2D6*1XN, *2XN, and *35XN. [pre-menopausal][post-menopausal] [adjuvant] [DNA source: blood] [HWE: yes]
Article: Functional characterization of novel rare CYP2A6 variants and potential implications for clinical outcomes
Gene: CYP2A6
Variant/haplotype: rs143841823
Drug(s): nicotine
Phenotype category: Metabolism/PK
Significant: not stated
Association: Allele G is not associated with metabolism of nicotine as compared to allele A.
Notes: Assigned as neutral function following in vitro assessments, in vivo associations and variant construct functional assignments.
Article: Association of Common C-Reactive Protein (CRP) Gene Polymorphisms With Baseline Plasma CRP Levels and Fenofibrate Response
Gene: CRP
Variant/haplotype: rs1417938
Drug(s): fenofibrate
Phenotype category: Efficacy
Significant: yes
Association: Genotype TT is associated with increased response to fenofibrate in people with Metabolic Syndrome as compared to genotypes AA + AT.
Notes: Patients with the TT genotype had a greater reduction in C-reactive protein (CRP) levels between baseline and 3 weeks of treatment, as compared to carriers of the A allele. In strong linkage disequilibrium with rs3091244 and rs1205 (r2 = 0.4 - 0.9, p < 0.001) and in weak linkage disequilibrium with rs3093059 (r2 = 0.17, p < 0.05).
Article: Possible impact of the CYP2D6*10 polymorphism on the nonlinear pharmacokinetic parameter estimates of paroxetine in Japanese patients with major depressive disorders
Gene: CYP2D6
Variant/haplotype: CYP2D6*2, CYP2D6*5, CYP2D6*10, CYP2D6*39
Drug(s): paroxetine
Phenotype category: Metabolism/PK
Significant: no
Association: CYP2D6 *2/*10 + *10/*39 + *10/*10 + *5/*10 is not associated with concentrations of paroxetine in people with Depressive Disorder, Major as compared to CYP2D6 *39/*39 + *5/*39.
Notes: CYP2D6*2/*10 (n=2), CYP2D6*10/*39 (n=2), CYP2D6*39/*39 (n=2), CYP2D6*10/*10 (n=6), CYP2D6*5/*39 (n=2), and CYP2D6*5/*10 (n=1). The genotypes were grouped as follow: CYP2D6*10 allele carriers and noncarriers. Plasma paroxetine concentrations between the CYP2D6 genotypes using the Mann–Whitney U-test, the plasma concentrations did not differ significantly between the CYP2D6*10 allele carriers and the noncarriers among the patients treated with 20 mg/day, 30 mg/day, or 40 mg/day of paroxetine (P=0.673, P=1.000, and P=0.400, respectively). Km (p=0.008) and Vmax (p=0.022) values were significantly smaller in CYP2D6*10 allele carriers than in the noncarriers.
Article: Polymorphisms in ABCB1 and CYP19A1 genes affect anastrozole plasma concentrations and clinical outcomes in postmenopausal breast cancer patients
Gene: ABCB1
Variant/haplotype: rs1128503
Drug(s): anastrozole
Phenotype category: Metabolism/PK
Significant: no
Association: Genotype GG is not associated with concentrations of anastrozole in women with Breast Neoplasms as compared to genotypes AA + AG.
Notes: Alleles have been complemented to the positive strand.
Article: Association of STAT-3 rs1053004 and VDR rs11574077 With FOLFIRI-Related Gastrointestinal Toxicity in Metastatic Colorectal Cancer Patients
Gene: HNF4A
Variant/haplotype: rs6031587
Drug(s): irinotecan
Phenotype category: Metabolism/PK
Significant: no
Association: Allele T is not associated with metabolism of irinotecan in people with Colorectal Neoplasms as compared to allele C.
Article: Influence of ABCB1 and ABCG2 polymorphisms on doxorubicin disposition in Asian breast cancer patients
Gene: ABCB1
Variant/haplotype: rs1128503
Drug(s): doxorubicin
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype AA is associated with decreased metabolism of doxorubicin in people with Breast Neoplasms as compared to genotype GG.
Notes: Significance given for the haplotype of ABCB1 c.1236C>T, c.2677G>A/T, and c.3435C>T (rs1128503, rs2032582 and rs1045642) which was associated with increased drug exposure and reduced clearance. Patients harboring the CC-GG-CC genotypes had significantly lower peak plasma concentrations of doxorubicinol compared to patients who had TT-TT-TT genotypes (P = 0.03).
Article: SLC22A1-ABCB1 Haplotype Profiles Predict Imatinib Pharmacokinetics in Asian Patients with Chronic Myeloid Leukemia
Gene: SLC22A1
Variant/haplotype: rs628031
Drug(s): imatinib
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype GG is associated with decreased clearance of imatinib in people with Leukemia, Myelogenous, Chronic, BCR-ABL Positive as compared to genotypes AA + AG.
Notes: This SNP was not significantly correlated with imatinib pharmacokinetics individually, but was significant when studied as part of a haplotype including IVS6-878C>A(rs3798168) and IVS7+850C>T polymorphisms. Patients carrying 2 copies of  AGT or CGC haplotypes (rs3798168, rs628031, IVS7+850C>T) had significantly higher (50%) imatinib trough levels and significantly lower (33.4%) clearance than patients with zero or 1 copy.
Article: Haplotypes of P2RX7 gene polymorphisms are associated with both cold pain sensitivity and analgesic effect of fentanyl
Gene: P2RX7
Variant/haplotype: rs2708092
Drug(s): fentanyl
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with dose of fentanyl in people with Pain, Postoperative as compared to allele A.
Notes: No significant association between this variant and 24-h postoperative fentanyl use or perioperative fentanyl use.
Article: Predicting Inhaled Corticosteroid Response in Asthma with Two Associated SNPs
Gene: CRHR1
Variant/haplotype: rs1876828
Drug(s): glucocorticoids
Phenotype category: Efficacy
Significant: yes
Association: Allele T is associated with increased response to glucocorticoids in people with Asthma as compared to allele C.
Notes: as part of a two SNP predictive test of FEV1 change, which identified patients with good or poor steroid response (highest or lowest quartile, respectively). P values are for predictive performance of the test.
Article: Genome-wide association study of patient and clinician rated global impression severity during antipsychotic treatment
Gene: PDE4D
Variant/haplotype: rs17742120
Drug(s): quetiapine
Phenotype category: Efficacy
Significant: yes
Association: Allele G is associated with increased response to quetiapine in people with Schizophrenia as compared to allele A.
Notes: The number of G alleles present in a patient was negatively associated with PGI score. Please note that this variant is in high linkage disequilibrium with rs17382202 and rs2164660.
Article: Genetic predictors of the maximum doses patients receive during clinical use of the anti-epileptic drugs carbamazepine and phenytoin
Gene: CYP2C9
Variant/haplotype: rs1057910
Drug(s): phenytoin
Phenotype category: Dosage, Metabolism/PK
Significant: yes
Association: Allele C is associated with increased dose of phenytoin in people with Epilepsy as compared to allele A.
Article: Combined study of genetic and epigenetic biomarker risperidone treatment efficacy in Chinese Han schizophrenia patients
Gene: CYP2E1
Variant/haplotype: rs2515641
Drug(s): risperidone
Phenotype category: Efficacy
Significant: no
Association: Allele T is associated with increased response to risperidone in people with Schizophrenia as compared to allele C.
Notes: The T allele was initially significantly more frequent in patients designated as responders to risperidone (i.e. >50% reduction in PANSS score compared to the cohort average). However, significance was lost following correction for multiple testing.
Article: The role of IL10 and IL17 gene polymorphisms in treatment response in children and adolescents with severe asthma
Gene: IL17A
Variant/haplotype: rs3819024
Drug(s): budesonide, fluticasone/salmeterol, formoterol, omalizumab
Phenotype category: Efficacy
Significant: yes
Association: Genotypes AG + GG is associated with decreased clinical benefit to budesonide, fluticasone/salmeterol, formoterol or omalizumab in children with Asthma as compared to genotype AA.
Notes: as measured by FEV1. "Asthma patients with the AG or GG genotype showed less bronchodilator responsiveness than did those with the AA genotype (p < 0.05; Mann-Whitney test). " "Some patients were using dry-powder inhalers that delivered a combination of budesonide and formoterol, whereas others were using pressurized metered-dose inhalers that delivered a combination of fluticasone and salmeterol or omalizumab only"
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*2, CYP2C19*17
Drug(s): lansoprazole, omeprazole
Phenotype category: Efficacy
Significant: yes
Association: CYP2C19 *1/*1 + *1/*17 are associated with decreased response to lansoprazole or omeprazole in healthy individuals as compared to CYP2C19 *1/*2 + *2/*17 + *2/*2.
Notes: Based on cumulative mean percentage of time with intragastric pH>4 on day 1.
Article: Influence of RGS2 on Sertraline Treatment for Social Anxiety Disorder
Gene: HTR2A
Variant/haplotype: rs6313
Drug(s): sertraline
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to sertraline in people with Anxiety Disorders as compared to allele G.
Notes: rs6313 was not associated with significant differences in change in LSAS score in patients receiving sertraline.
Article: Adrenergic receptor genotype influences heart failure severity and β-blocker response in children with dilated cardiomyopathy
Gene: ADRB1
Variant/haplotype: rs1801253
Drug(s): Beta Blocking Agents
Phenotype category: Efficacy
Significant: yes
Association: Allele C is associated with increased response to Beta Blocking Agents in children with Cardiomyopathy, Dilated as compared to allele G.
Notes: Study looked at effect of 'high-risk' genotypes (i.e. genotypes of one or more of rs61767072 del, rs1801253 C or rs1042713 A alleles) on response to beta-blockers. Patients with more 'high-risk' alleles showed a greater response to beta-blockers than those with fewer 'high-risk' alleles.
Article: The International SSRI Pharmacogenomics Consortium (ISPC): a genome-wide association study of antidepressant treatment response
Gene: MIR7-2
Variant/haplotype: rs1470108
Drug(s): Selective serotonin reuptake inhibitors
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to Selective serotonin reuptake inhibitors in people with Depressive Disorder, Major as compared to allele C.
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: Genome-Wide Association Study of Serum Creatinine Levels during Vancomycin Therapy
Gene: AIDA
Variant/haplotype: rs17163429
Drug(s): vancomycin
Phenotype category: Metabolism/PK
Significant: no
Association: Allele C is not associated with trough concentration of vancomycin as compared to allele T.
Notes: The SNP was not associated with trough levels of vancomycin (first vancomycin trough documented in EMR after at least 3 doses vancomycin). Elimination constants were also calculated.
Article: Genetic Variation of VKORC1 and CYP4F2 Genes Related to Warfarin Maintenance Dose in Patients with Myocardial Infarction
Gene: VKORC1
Variant/haplotype: rs17708472
Drug(s): warfarin
Phenotype category: Dosage, Efficacy
Significant: no
Association: Allele A is associated with increased dose of warfarin in people with Myocardial Infarction as compared to allele G.
Notes: This is VKORC1 *4.  There was a significant association when analyzed alone, but the effect was so small that it was negligible when analyzed with VKORC1*2,CYP2C9*2 and CYP2C9*3.
Article: Influence of Receptor Polymorphisms on the Response to α-Adrenergic Receptor Blockers in Pheochromocytoma Patients
Gene: ADRA2A
Variant/haplotype: rs521674
Drug(s): doxazosin, phenoxybenzamine
Phenotype category: Dosage
Significant: no
Association: Allele T is associated with increased dose of doxazosin or phenoxybenzamine in people with Pheochromocytoma or Paraganglioma as compared to allele A.
Notes: "the T allele of rs521674 in ADRA2A was associated with a three times higher risk (being in a higher dosage step) than the A allele" "However, none of these significances survived the multiple testing correction."
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: rs11103182
Drug(s): antiepileptics
Phenotype category: Efficacy
Significant: no
Association: Allele G 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: ADH single nucleotide polymorphism associations with alcohol metabolism in vivo
Gene: ADH1C
Variant/haplotype: rs1662060
Drug(s): ethanol
Phenotype category: Toxicity, Metabolism/PK
Significant: yes
Association: Allele C is associated with metabolism of ethanol.
Notes: The authors did not report p-value correction for multiple hypotheses (103 snps tested).  Though they report multiple snps are significantly associated with alcohol metabolism (early or late) tested on blood or breath alcohol concentrations, this snp is NOT significant after Bonferroni correction (<0.00049).  Also, the authors did not state which alleles are associated with increased or decreased metabolism.  Instead, they simply report an association with the snp in general.  Note that this gene is on the minus strand.
Article: Prediction of Warfarin Dose in Pediatric Patients: An Evaluation of the Predictive Performance of Several Models
Gene: VKORC1
Variant/haplotype: rs9923231
Drug(s): warfarin
Phenotype category: Dosage
Significant: not stated
Association: Allele G is associated with dose of warfarin in children with Heart Diseases.
Article: Associations between tamoxifen, estrogens, and FSH serum levels during steady state tamoxifen treatment of postmenopausal women with breast cancer
Gene: CYP2D6
Variant/haplotype: CYP2D6*1, CYP2D6*4, CYP2D6*5
Drug(s): 4-hydroxytamoxifen, endoxifen
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2D6 *4/*4 + *4/*5 are associated with decreased concentrations of 4-hydroxytamoxifen and endoxifen in women with as compared to CYP2D6 *1/*1.
Notes: The study observed a relations between the serum levels of 4OHtam and endoxifen and CYP2D6 gene dose effect. Postmenopausal women adjuvantly treated with tamoxifen 20 mg daily with ER positive breast cancer. DNA was extracted from blood and  *3, *4, *5 and *6 were determined.
Article: Genetic variants influenced the risk of bleeding and pharmacodynamics of rivaroxaban in patients with nonvalvular atrial fibrillation: A multicentre prospective cohort study
Gene: PRF1
Variant/haplotype: rs885821
Drug(s): rivaroxaban
Phenotype category: Toxicity
Significant: no
Association: Allele G is associated with increased response to rivaroxaban in people with Atrial Fibrillation as compared to allele A.
Notes: as measured by peak anti‐FXa level.  Association described as "suggestive". "The incidence of bleeding events were significantly related to the peak anti‐FXa level, which were significantly increased in patients with bleeding events than in those without"
Article: Effect of pharmacogenetics on plasma lumefantrine pharmacokinetics and malaria treatment outcome in pregnant women
Gene: CYP3A5
Variant/haplotype: rs776746
Drug(s): lumefantrine
Phenotype category: Efficacy
Significant: no
Association: Allele C is not associated with response to lumefantrine in women with Malaria and Pregnancy as compared to allele T.