shlokn/autogkb huggingface dataset:
Article: A Pharmacogenetics-Based Warfarin Maintenance Dosing Algorithm from Northern Chinese Patients
Gene: CYP2C9
Variant/haplotype: rs9332127
Drug(s): warfarin
Phenotype category: Dosage
Significant: no
Association: Allele G is not associated with 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."
Article: Tacrolimus dose requirements in paediatric renal allograft recipients are characterized by a biphasic course determined by age and bone maturation
Gene: ABCB1
Variant/haplotype: rs1045642
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: no
Association: Genotype AA is not associated with concentrations of tacrolimus in children with Kidney Transplantation as compared to genotypes AG + GG.
Notes: Dose-corrected tacrolimus exposure (AUC0-12/doseBW). Please note that alleles have been complemented to the plus chromosomal strand.
Article: Genetic Variants of Pregnane X Receptor (PXR) and CYP2B6 Affect the Induction of Bupropion Hydroxylation by Sodium Ferulate
Gene: CYP2B6
Variant/haplotype: CYP2B6*1, CYP2B6*6
Drug(s): bupropion
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2B6 *1/*6 + *6/*6 are associated with decreased metabolism of bupropion in healthy individuals as compared to CYP2B6 *1/*1.
Notes: Subjects carrying the CYP2B6*6 allele had significantly increased AUCs if bupropion compared to *1/*1 subjects.
Article: Pharmacogenetic study of seven polymorphisms in three nicotinic acetylcholine receptor subunits in smoking-cessation therapies
Gene: CHRNA5
Variant/haplotype: rs55853698
Drug(s): bupropion, nicotine, varenicline
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with response to bupropion, nicotine and varenicline in people with Tobacco Use Disorder as compared to allele T.
Notes: Authors looked at the effect of variants on response to the smoking cessation therapies varenicline, bupropion and nicotine replacement therapy.
Article: Targeted Sequencing Identifies Missense variant in the BEST3 gene associated with Antihypertensive Response to Hydrochlorothiazide
Gene: BEST3
Variant/haplotype: rs61747221
Drug(s): hydrochlorothiazide
Phenotype category: Efficacy
Significant: yes
Association: Genotypes AA + AG is associated with increased response to hydrochlorothiazide in people with Hypertension as compared to genotype GG.
Article: Effects of Mu-Opiate Receptor Gene Polymorphism rs1799971 (A118G) on the Antidepressant and Dissociation Responses in Esketamine Nasal Spray Clinical Trials
Gene: OPRM1
Variant/haplotype: rs1799971
Drug(s): ketamine
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with response to ketamine in people with Depressive Disorder, Major as compared to allele A.
Notes: No significant difference in changes in MADRS scores on days 2 or 28 of treatment with ketamine and  an oral antidepressant compared to treatment with a placebo and an oral antidepressant.
Article: Peginterferon Alfa-2a/Ribavirin treatment efficacy in chronic hepatitis C patients is related to natural killer group 2D gene rs1049174 GC polymorphism
Gene: KLRK1
Variant/haplotype: rs1049174
Drug(s): peginterferon alfa-2b, ribavirin
Phenotype category: Efficacy
Significant: yes
Association: Genotype GG is associated with increased response to peginterferon alfa-2b and ribavirin in people with Hepatitis C, Chronic as compared to genotypes CC + CG.
Notes: in CHC patients with genotype 1a and 1b.
Article: CYP3A5, ABCB1 and SLCO1B1 Polymorphisms and Pharmacokinetics and Virologic Outcome of Lopinavir/Ritonavir in HIV-infected Children
Gene: ABCB1
Variant/haplotype: rs2032582
Drug(s): lopinavir, ritonavir
Phenotype category: Metabolism/PK
Significant: no
Association: Allele A is not associated with exposure to lopinavir or ritonavir in children with HIV Infections as compared to allele C.
Notes: No association between this variant and AUC0-12 of lopinavir or ritonavir in patients treated with lopinavir/ritonavir. Variant referred to in the paper as G2677T.
Article: Prediction Formulas for Individual Opioid Analgesic Requirements Based on Genetic Polymorphism Analyses
Gene: KCNJ6
Variant/haplotype: rs2835859
Drug(s): fentanyl
Phenotype category: Dosage, Efficacy
Significant: yes
Association: Genotype TT is associated with increased dose of fentanyl in people with Pain, Postoperative as compared to genotypes CC + CT.
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: Factors influencing pharmacokinetics of warfarin in African–Americans: implications for pharmacogenetic dosing algorithms
Gene: CYP2C9
Variant/haplotype: CYP2C9*1, CYP2C9*8
Drug(s): warfarin
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2C9 *1/*8 + *8/*8 are associated with decreased clearance of warfarin as compared to CYP2C9 *1/*1.
Notes: in African Americans. Patients with CYP2C9*8 had a 30% reduction in S-warfarin clearance as compared to patients with *1/*1 genotype. CYP2C9*8, but not; CYP2C9*2/*3, and body surface area (BSA)/body weight were determinants of; S-warfarin clearance (CL[S]) in African–American. Dosing algorithm that excludes African-specific variant(s) may lead to prediction errors in African Americans.
Article: ABCC2 Polymorphisms and Haplotype are Associated with Drug Resistance in Chinese Epileptic Patients
Gene: ABCC2
Variant/haplotype: rs3740066
Drug(s): antiepileptics
Phenotype category: Efficacy
Significant: yes
Association: Genotypes CT + TT are associated with increased resistance to antiepileptics in people with Epilepsy as compared to genotype CC.
Notes: This SNP was also part of haplotype associated with response/resistance.
Article: NUDT15 c.415C>T increases risk of 6-mercaptopurine induced myelosuppression during maintenance therapy in children with acute lymphoblastic leukemia
Gene: NUDT15
Variant/haplotype: rs116855232
Drug(s): mercaptopurine
Phenotype category: Dosage
Significant: yes
Association: Genotypes CT + TT is associated with decreased dose of mercaptopurine in children with Precursor Cell Lymphoblastic Leukemia-Lymphoma as compared to genotype CC.
Notes: Children with the CT or TT genotypes received 80.3%, 61.5% and 61.1% of the median cumulative dose of those with the CC genotype at 2, 4 and 6 months of the mercaptopurine maintenance phase, respectively. Additionally, patients with the CT or TT genotype were given a median dose of 28 mg/m2/day, 56% of the standard initial dose.
Article: OPRM1, OPRK1 and COMT Genetic Polymorphisms Associated with Opioid Effects on Experimental Pain: A Randomized, Double-Blind, Placebo-Controlled Study
Gene: COMT
Variant/haplotype: rs4633
Drug(s): morphine
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with response to morphine in healthy individuals as compared to allele C.
Notes: Study-wide significance was set to p<0.017.
Article: Lack of tacrolimus circadian pharmacokinetics and CYP3A5 pharmacogenetics in the early and maintenance stages in Japanese renal transplant recipients
Gene: CYP3A5
Variant/haplotype: CYP3A5*1, CYP3A5*3
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP3A5 *1/*1 + *1/*3 is associated with increased metabolism of tacrolimus in people with Kidney Transplantation as compared to CYP3A5 *3/*3.
Notes: Dose-adjusted AUC0-12 and dose-adjusted trough levels of tacrolimus were decreased in patients with the *1/*1 (TT) or *1/*3 (CT) genotypes ("expressers") as compared to those with the *3/*3 (CC) genotype ("non-expressers"), both in the early (day 28) and maintenance (beyond 1 year) stages. Additionally, body weight-adjusted oral clearance was higher and dose-adjusted Cmax was lower in those with the *1/*1 and *1/*3 genotype as compared to those with the *3/*3 genotype; this was only significant during the early stage after transplant. No significant results were seen for AUC0-12.
Article: Impact of ABCC2 1249G>A and −24C>T Polymorphisms on Lacosamide Efficacy and Plasma Concentrations in Uygur Pediatric Patients With Epilepsy in China
Gene: ABCC2
Variant/haplotype: rs2273697
Drug(s): lacosamide
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype GG is associated with increased concentrations of lacosamide in children with Epilepsy as compared to genotypes AA + AG.
Article: Integration of genetic, clinical, and INR data to refine warfarin dosing
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 as compared to CYP2C9 *1.
Notes: Each CYP2C9*3 allele resulted in a 28% (23-32%) decrease in therapeutic dose on Day 4 or 5 of therapy.
Article: Genome-wide association study of antidepressant response: involvement of the inorganic cation transmembrane transporter activity pathway
Gene: PARP11
Variant/haplotype: rs2532560
Drug(s): antidepressants
Phenotype category: Efficacy
Significant: yes
Association: Allele G is associated with increased response to antidepressants in people with Depressive Disorder, Major as compared to allele A.
Notes: Identity of minor allele not specified, so minor allele of dbSNP used here (G). Remission considered to be score < or equal to 7 at discharge of the Hamilton Rating Scale for Depression (HRSD17). Patients measured at admission and discharge, 4-6 weeks later. Specific antidepressants not listed.
Article: A prospective study to assess the association between genotype, phenotype and Prakriti in individuals on phenytoin monotherapy
Gene: CYP2C9
Variant/haplotype: CYP2C9*1, CYP2C9*3
Drug(s): phenytoin
Phenotype category: Toxicity
Significant: yes
Association: CYP2C9 *1/*3 is associated with increased concentrations of phenytoin in people with Epilepsy as compared to CYP2C9 *1/*1.
Notes: Concentrations in *1/*3 were 3x more likely to have toxic concentrations of phenytoin compared to *1/*1.
Article: Genetic and nongenetic factors associated with warfarin dose requirements in Egyptian patients
Gene: APOC1, APOE
Variant/haplotype: rs7412
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Allele T is associated with decreased dose of warfarin in people with haplotype epsilon2.
Article: A Nanopore Sequencing-based Pharmacogenomic Panel to Personalize Tuberculosis Drug Dosing
Gene: NAT2
Variant/haplotype: NAT2 intermediate acetylator
Drug(s): isoniazid
Phenotype category: Metabolism/PK
Significant: yes
Association: NAT2 intermediate acetylator and rapid acetylator is associated with increased clearance of isoniazid in people with Tuberculosis as compared to NAT2 slow acetylator.
Notes: "Isoniazid clearance was 2.2 times higher among intermediate acetylators and 3.8 times higher among rapid acetylators compared with slow acetylators (p<0.0001)" Variants measured from Table 2: rs1801279 (191G>A), rs1041983 (282C>T), rs1801280 (341T>C), rs1799929 (481C>T), rs1799930 (590G>A), rs1208 (803A>G), rs1799931 (857G>A).
Article: Combined Effect of CYP2B6 and NAT2 Genotype on Plasma Efavirenz Exposure During Rifampin-based Antituberculosis Therapy in the STRIDE Study
Gene: NAT2
Variant/haplotype: NAT2 slow acetylator
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: not stated
Association: NAT2 slow acetylator is associated with increased concentrations of efavirenz in people with HIV infectious disease and Tuberculosis as compared to NAT2 rapid acetylator.
Notes: Genotype for metabolizer status determined from rs1801279, rs1801280, rs1799930, and rs1799931. Patients were taking both efavirenz and antituberculosis therapy. "In participants with CYP2B6 extensive and intermediate metabolizer genotypes, only small differences between efavirenz Cmin concentrations on antituberculosis therapy and off antituberculosis therapy were seen for all NAT2 metabolizer genotypes. In contrast, among the 4 participants with both CYP2B6 and NAT2 slow metabolizer genotypes, efavirenz Cmin concentrations were substantially elevated on antituberculosis therapy compared to off antituberculosis therapy, with differences exceeding 8 µg/mL in 3 of these 4 participants; this was not statistically significant in this subset. One individual with slow CYP2B6 and intermediate NAT2 metabolizer genotypes had a considerably larger efavirenz Cmin concentration on vs off antituberculosis treatment."
Article: Influences of an NR1I2 polymorphism on heterogeneous antiplatelet reactivity responses to clopidogrel and clinical outcomes in acute ischemic stroke patients
Variant/haplotype: rs2487032
Drug(s): clopidogrel
Phenotype category: Efficacy
Significant: yes
Association: Allele A is associated with decreased response to clopidogrel in people with Coronary Artery Disease as compared to allele G.
Notes: This variant is associated with decreased Cmax, decreased AUC of clopidogrel, decreased H4 concentration, and decreased antiplatelet effects of clopidogrel with a higher PRU.
Article: TET2 and CSMD1genes affect SBP response to hydrochlorothiazide in never-treated essential hypertensives
Gene: DIAPH3
Variant/haplotype: rs77876672
Drug(s): hydrochlorothiazide
Phenotype category: Efficacy
Significant: no
Association: Allele C is associated with decreased response to hydrochlorothiazide in people with Essential hypertension as compared to allele T.
Notes: The SNP was discovered in two independent cohorts, although no SNPs reached genome wide significance. The authors then considered P<1 x10^-5 as a threshold for significance (based on the results from a Q-Q plot distribution reference line). Using this revised threshold the authors reported that this SNP was associated with a lower decrease in diastolic blood pressure after hydrochlorothiazide treatment.
Article: Impact of the CYP2C19 Genotype on Voriconazole Exposure in Adults with Invasive Fungal Infections
Gene: CYP2C19
Variant/haplotype: CYP2C19*1, CYP2C19*2, CYP2C19*17
Drug(s): voriconazole
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2C19 *17/*17 is associated with decreased concentrations of voriconazole in people with Mycoses as compared to CYP2C19 *1/*1 + *1/*2 + *2/*17 + *2/*2.
Notes: The study did not find a significant difference in trough concentration between the NM (*1/*1) (4.27 ± 2.4 mg/l) and the IM/PM (*1/*2 + *2/*17 + *2/*2) (4.13 ± 1.6 mg/l) groups, therefore these groups were combined for comparison. The mean steady-state trough concentrations were 1.35±0.7, 2.97±2.3, and 4.26 ± 2.2 mg/l in patients with the CYP2C19 *17/*17 (UMs), *1/*17 (RMs), and other genotypes, respectively (P=0.02 for both the *17/*17 and *1/*17 genotypes compared with other genotypes. More subjects with the RM/UM phenotype had a subtherapeutic trough concentration (52 vs. 16%, P = 0.0028).
Article: Pharmacogenomics and Placebo Response in a Randomized Clinical Trial in Asthma
Variant/haplotype: rs2392165
Drug(s): budesonide
Phenotype category: Efficacy
Significant: yes
Association: Genotypes AG + GG are associated with increased response to budesonide in children with Asthma as compared to genotype AA.
Notes: The AG and GG genotypes were associated with a greater improvement in coughing and wheezing compared to the AA genotype. Note that this SNP did not reach genome-wide significance in the GWAS.
Article: Clinical and genetic factors associated with warfarin maintenance dose in northern Chinese patients with mechanical heart valve replacement
Gene: CYP4F2
Variant/haplotype: rs2189784
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Genotypes AG + GG are associated with increased dose of warfarin in people with heart valve replacement as compared to genotype AA.
Article: MMP-2 and MMP-9 gene polymorphisms act as biological indicators for ulinastatin efficacy in patients with severe acute pancreatitis
Gene: MMP9
Variant/haplotype: rs3918242
Drug(s): ulinastatin
Phenotype category: Efficacy
Significant: yes
Association: Allele T is associated with increased response to ulinastatin in people with Pancreatitis as compared to allele C.
Article: Pharmacogenetics of tenofovir clearance among Southern Africans living with HIV
Gene: ATIC
Variant/haplotype: rs4673993
Drug(s): tenofovir
Phenotype category: Metabolism/PK
Significant: no
Association: Allele C is not associated with clearance of tenofovir in people with HIV Infections as compared to allele T.
Notes: Significance threshold was set at 3.3E-3.
Article: HLA-G 3’UTR Polymorphisms Impact the Prognosis of Stage II-III CRC Patients in Fluoropyrimidine-Based Treatment
Gene: HLA-G
Variant/haplotype: rs9380142
Drug(s): capecitabine, fluorouracil
Phenotype category: Efficacy
Significant: yes
Association: Genotype GG is associated with decreased response to capecitabine or fluorouracil in people with Colorectal Neoplasms as compared to genotypes AA + AG.
Notes: The authors examined disease free survival (DFS) as well as overall survival (OS). The GG genotype was associated with decreased DFS and OS.
Article: RRM1 and RRM2 pharmacogenetics: association with phenotypes in HapMap cell lines and acute myeloid leukemia patients
Gene: RRM2B
Variant/haplotype: rs1265138
Drug(s): cladribine, cytarabine
Phenotype category: Efficacy
Significant: yes
Association: Genotype AA is associated with increased response to cladribine and cytarabine in children with Leukemia, Myeloid, Acute as compared to genotypes AG + GG.
Notes: More patients with a complete response after the first induction therapy were seen in the AA genotype group. No multiple testing adjustments were performed: 7 SNPs were investigated.
Article: Response to treatment following recently acquired hepatitis C virus infection in a multi-centre collaborative cohort
Gene: IFNL3, IFNL4
Variant/haplotype: rs12979860
Drug(s): peginterferon alfa-2a, peginterferon alfa-2b, ribavirin
Phenotype category: Efficacy
Significant: yes
Association: Genotype CC is associated with increased response to peginterferon alfa-2a, peginterferon alfa-2b and ribavirin in people with Hepatitis C as compared to genotypes CT + TT.
Notes: in HCV genotype 1 infected patients. The association was not significant in HCV genotype 2/3 infected patients.
Article: A GENOME-WIDE ASSOCIATION STUDY OF BRONCHODILATOR RESPONSE IN LATINOS IMPLICATES RARE VARIANTS
Gene: SPATS2L
Variant/haplotype: rs295114
Drug(s): salbutamol
Phenotype category: Efficacy
Significant: no
Association: Allele C is not associated with response to salbutamol in children with Asthma as compared to allele T.
Notes: This SNP was imputed rather than genotyped.  This was assessed as a replication attempt for a previously reported association of a different SPATS2L SNP with response to bronchodilators.  Bonferroni correction was performed according to the number of SNPs included that are within 50 kb up and downstream of SPATS2L.
Article: Effect of pharmacogenetics on plasma lumefantrine pharmacokinetics and malaria treatment outcome in pregnant women
Gene: CYP3A5, ZSCAN25
Variant/haplotype: rs41303343
Drug(s): lumefantrine
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to lumefantrine in women with Malaria and Pregnancy as compared to allele del.
Article: Association of Polygenic Score for Schizophrenia and HLA Antigen and Inflammation Genes With Response to Lithium in Bipolar Affective Disorder: A Genome-Wide Association Study
Gene: FAM177A1
Variant/haplotype: rs79403677
Drug(s): lithium
Phenotype category: Efficacy
Significant: yes
Association: Allele T is associated with decreased response to lithium in people with Bipolar Disorder as compared to allele G.
Article: A genome-wide approach to identify genetic variants that contribute to etoposide-induced cytotoxicity
Gene: SLIT1
Variant/haplotype: rs2784917
Drug(s): etoposide
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype AA is associated with decreased inhibition of etoposide as compared to genotypes AG + GG.
Notes: "Specifically, rs10061997, rs12190776, rs2784917, and rs9730073 were all significant predictors of etoposide IC50. The overall estimate of R2 = 0.40, indicates 40% of the etoposide IC50 variation can be explained by these 4 SNPs in the YRI."
Article: A Genome-Wide Association Study of Citalopram Response in Major Depressive Disorder
Variant/haplotype: rs6127921
Drug(s): citalopram
Phenotype category: Efficacy
Significant: no
Association: Allele C is associated with decreased response to citalopram in people with Depressive Disorder, Major as compared to allele A.
Notes: It was also associated with remission.  Neither association was significant after correction (430,198 SNPs tested).  Authors point out the lack of placebo control.
Article: Dopamine D2 receptor genetic variation and clinical response to antipsychotic drug treatment: A meta-analysis
Gene: DRD2
Variant/haplotype: rs1799732
Drug(s): antipsychotics
Phenotype category: Efficacy
Significant: yes
Association: Allele del is associated with decreased response to antipsychotics in people with Schizophrenia as compared to genotype GG.
Notes: in a meta-analysis.
Article: A Study on CYP2C19 and CYP2D6 Polymorphic Effects on Pharmacokinetics and Pharmacodynamics of Amitriptyline in Healthy Koreans
Gene: CYP2C19
Variant/haplotype: CYP2C19*1, CYP2C19*2, CYP2C19*3
Drug(s): amitriptyline
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2C19 *2/*2 + *2/*3 + *3/*3 is associated with increased exposure to amitriptyline in healthy individuals as compared to CYP2C19 *1/*1.
Article: Pharmacogenetics of tenofovir clearance among Southern Africans living with HIV
Variant/haplotype: rs4816969
Drug(s): tenofovir
Phenotype category: Metabolism/PK
Significant: no
Association: Allele G is not associated with clearance of tenofovir in people with HIV Infections as compared to allele A.
Notes: Significance threshold was set at 5E-9. This variant was in strong linkage disequilibrium with rs9305223 and rs2226443.
Article: Efficacy of the pharmacologic chaperone migalastat in a subset of male patients with the classic phenotype of Fabry disease and migalastat-amenable variants: data from the phase 3 randomized, multicenter, double-blind clinical trial and extension study
Gene: GLA
Variant/haplotype: rs104894827
Drug(s): migalastat
Phenotype category: Efficacy
Significant: not stated
Association: Allele A is associated with increased response to migalastat in people with Fabry Disease.
Notes: Patients carrying the A allele showed improvements in renal function, cardiac geometry (specifically, reductions in left ventricular mass index) and gastrointestinal symptoms as well as reductions in GL-3 inclusions and plasma lyso-Gb3 and an increase in PBMC alpha-Gal A activity when treated with migalastat. Clinical benefit of migalastat was not substantially affected by disease severity. This variant was designated as an 'amenable variant' to migalastat treatment following an in vitro assay where migalastat increased the activity of alpha-Gal A by at least 3%. As all data were derived from post hoc analysis, statistical analyses were not carried out. Variant referred to as Arg356Trp in the paper.
Article: Association between UGT2B7 gene polymorphisms and fentanyl sensitivity in patients undergoing painful orthognathic surgery
Gene: UGT2B7
Variant/haplotype: rs11931604
Drug(s): fentanyl
Phenotype category: Dosage
Significant: no
Association: Allele C is not associated with dose of fentanyl in people with Pain, Postoperative as compared to allele T.
Notes: There was no significant difference in 24 hour fentanyl use between the genotype groups.