shlokn/autogkb huggingface dataset:
Article: Pharmacogenetics of tenofovir clearance among Southern Africans living with HIV
Gene: CYP2A7P1, CYP2B6
Variant/haplotype: rs3745274
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 3.3E-3.
Article: The Association of Transporter Genes Polymorphisms and Lung Cancer Chemotherapy Response
Gene: POU2F2
Variant/haplotype: rs2444933
Drug(s): platinum
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with response to platinum in people with Lung Neoplasms as compared to allele C.
Notes: 26 SNPs were selected which satisfied the following criteria: 1) SNPs were from HapMap Project Phase II of the Han Chinese population 2) were haplotype tagger SNPs 3) SNP minor allele frequency was higher than 5% in Han Chinese 4) the pairwise linkage disequilibrium correlation coefficient (r-squared) was greater than 0.8. After Bonferroni corrections no SNPs remained significantly associated with platinum drug efficacy.
Article: Genetic and nongenetic factors associated with warfarin dose requirements in Egyptian patients
Gene: CYP2C9
Variant/haplotype: rs1799853
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Allele T is associated with decreased dose of warfarin as compared to allele C.
Notes: This SNP defines CYP2C9*2. CYP2C9 *2,*3,*4,*5,*8 were grouped into three groups for testing: *1/*1 vs. *1/*2 + *1/*3 + *1/*4 + *1/*5 + *1/*8 vs *2/*2 + *2/*3 + *3/*3 + *5/*5.  People having one or two variant alleles had lower dose requirements than people who were *1/*1.
Article: Analysis of Genetic and Clinical Factors Associated with Buprenorphine Response
Gene: ADAMTSL2
Variant/haplotype: rs756770
Drug(s): buprenorphine
Phenotype category: Efficacy
Significant: yes
Association: Allele A is associated with increased response to buprenorphine in people with Opioid-Related Disorders as compared to allele C.
Notes: Authors note that this association is nominally significant.
Article: COMT Val158Met, BDNF Val66Met, and OPRM1 Asn40Asp and Methamphetamine Dependence Treatment Response: Preliminary Investigation
Gene: BDNF
Variant/haplotype: rs6265
Drug(s): modafinil
Phenotype category: Efficacy
Significant: no
Association: Allele C is not associated with response to modafinil in people with methamphetamine dependence as compared to allele T.
Notes: No significant association between this variant and Treatment Effectiveness Scores following modafinil treatment compared to placebo.
Article: Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) Potentiator VX-770 (Ivacaftor) Opens the Defective Channel Gate of Mutant CFTR in a Phosphorylation-dependent but ATP-independent Manner
Gene: CFTR
Variant/haplotype: rs113993960
Drug(s): ivacaftor
Phenotype category: Efficacy
Significant: not stated
Association: Allele del is associated with increased response to ivacaftor.
Notes: In vitro studies using proteoliposomes containing CFTR, or CFTR with the G551D mutation (rs75527207 allele A), or CFTR with the F508del mutation (rs113993960 allele del).  Ivacaftor in the presence of ATP potentiated channel activity of CFTR-F508del.
Article: Impact of Pharmacogenetic Markers of CYP2B6, Clinical Factors, and Drug-Drug Interaction on Efavirenz Concentrations in HIV/Tuberculosis-Coinfected Patients
Gene: CYP2B6
Variant/haplotype: CYP2B6*1
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2B6 *1/*1 is associated with increased clearance of efavirenz in people with HIV.
Notes: *1/*1 is associated with low plasma efavirenz concentrations (units = mg/L), as shown through multivariate analysis. Fasting plasma efavirenz concentrations were measured 12 hours after the last dose, and after 12 weeks of treatment.
Article: Influence of genetic, biological and pharmacological factors on warfarin dose in a Southern Brazilian population of European ancestry
Gene: CYP2C9
Variant/haplotype: CYP2C9*1, CYP2C9*2, CYP2C9*3
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: CYP2C9 *1/*2 + *1/*3 + *2/*2 + *2/*3 is associated with decreased dose of warfarin as compared to CYP2C9 *1/*1.
Notes: in a Southern Brazilian population of European ancestry.
Article: Impact of Pharmacogenetic Testing on Clozapine Treatment Efficacy in Patients with Treatment-Resistant Schizophrenia
Gene: SLC6A4
Variant/haplotype: SLC6A4 HTTLPR long form (L allele), SLC6A4 HTTLPR short form (S allele)
Drug(s): clozapine, n-desmethylclozapine
Phenotype category: Metabolism/PK
Significant: yes
Association: SLC6A4 HTTLPR short form (S allele) is associated with decreased concentrations of clozapine and n-desmethylclozapine in people with Schizophrenia as compared to SLC6A4 HTTLPR long form (L allele).
Notes: "Our analysis showed that only when comparing the mean plasma levels of CLZ and NCLZ for 5-HTTLPR S allele carriers versus L allele carriers, a significant difference was obtained (370 vs. 445 ng/mL CLZ plasma levels p = 0.008; 232 vs. 263 ng/mL NCLZ plasma levels p = 0.049). The S allele carriers showed the lowest CLZ and NCLZ plasma levels versus L allele carriers."
Article: Effect of CYP3A5 and CYP3A4 Genetic Variants on Fentanyl Pharmacokinetics in a Pediatric Population
Gene: ABCB1
Variant/haplotype: rs1045642
Drug(s): fentanyl
Phenotype category: Metabolism/PK
Significant: no
Association: Allele G is not associated with clearance of fentanyl in children as compared to allele A (assigned as normal metabolizer phenotype) .
Article: No major role of norepinephrine transporter gene variations in the cardiostimulant effects of MDMA
Gene: SLC6A2
Variant/haplotype: rs1861647
Drug(s): 3,4-methylenedioxymethamphetamine
Phenotype category: Other
Significant: yes
Association: Genotype GG is associated with increased response to 3,4-methylenedioxymethamphetamine as compared to genotypes AA + AG.
Notes: The GG genotype was associated with increased heart rate, but  not with plasma concentrations  nor mean arterial pressure.
Article: Effects of CYP2C19 Loss-of-Function Variants on the Eradication of H. pylori Infection in Patients Treated with Proton Pump Inhibitor-Based Triple Therapy Regimens: A Meta-Analysis of Randomized Clinical Trials
Gene: CYP2C19
Variant/haplotype: CYP2C19*1
Drug(s): rabeprazole
Phenotype category: Efficacy
Significant: no
Association: CYP2C19 *1/*1 is not associated with response to rabeprazole in people with Helicobacter Infections.
Notes: as compared to the *1/*2 or *1/*3 genotype, or the *2/*2, *2/*3 or *3/*3 genotype. No significant differences in eradication rate of Helicobacter pylori (H. pylori) were seen between any of the genotype groups.This was a meta-analysis and included 13 studies. Patients were treated with the drugs anywhere from 7-14 days, and also received the antibiotics amoxicillin and clarithromycin or amoxicillin and metronidazole as part of triple therapy.
Article: CYP2C9*61, a rare missense variant identified in a Puerto Rican patient with low warfarin dose requirements
Gene: CYP2C9
Variant/haplotype: rs202201137
Drug(s): warfarin
Phenotype category: Dosage
Significant: no
Association: Allele G is associated with decreased dose of warfarin.
Notes: in a single individual who also had "factors like the advanced age of the patient, liver function, co-morbidities, drug-to-drug interactions and the presence of other polymorphisms (CYP2C9*2 and CYP2C9*5) "
Article: ABCC2 Polymorphisms and Haplotype are Associated with Drug Resistance in Chinese Epileptic Patients
Gene: ABCC2
Variant/haplotype: rs717620
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: Genotypic variation in the SV2C gene impacts response to atypical antipsychotics the CATIE Study
Gene: SV2C
Variant/haplotype: rs12655684
Drug(s): ziprasidone
Phenotype category: Efficacy
Significant: no
Association: Genotype CC is not associated with response to ziprasidone in people with Schizophrenia as compared to genotypes CT + TT.
Notes: Not significant after correction for multiple testing using the False Discovery Rate. Response was assessed by change in the total Positive and Negative Syndrome Scale (PANSS) score.
Article: Subgroup Differences in Response to 8 Weeks of Ledipasvir/Sofosbuvir for Chronic Hepatitis C
Gene: IFNL3, IFNL4
Variant/haplotype: rs12979860
Drug(s): ledipasvir, sofosbuvir
Phenotype category: Efficacy
Significant: yes
Association: Genotype CC is associated with increased response to ledipasvir and sofosbuvir in people with Hepatitis C as compared to genotypes CT + TT.
Notes: in HCV genotype 1 patients. Patients with the CC genotype have higher SVR rates than patients with the TT genotype. The SVR rate was 98.9% in women and 98.2% in individuals with the rs12979860-CC genotype, 95.1% in patients with the CT genotype and 90.9% in TT genotype patients. Black patients had a lower SVR rate than individuals of other racial groups; however, that association did not reach statistical significance (P= 0.08)
Article: Atazanavir pharmacokinetics in genetically determined CYP3A5 expressors versus non-expressors
Gene: ABCB1
Variant/haplotype: rs2032582
Drug(s): atazanavir
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype AA is associated with increased clearance of atazanavir in healthy individuals as compared to genotypes AC + CC.
Notes: For the haplotype "1236C/2677G/3435C" "subjects with zero CGC copies had faster atazanavir CL/F and lower Cmin compared with individuals with one or two CGC copies" (complemented to plus chromosomal strand). In this two-phase study, healthy participants were given atazanavir only for 7 days and then were co-administered ritonavir as a booster for days 8-14. The results here are for day 1-7 (atazanavir alone). By the end of day 7 oral clearance of atazanavir was 0.25, 0.18, 0.17 L/h/kg in people with 0, 1 or 2 copies of the haplotype, respectively. Cmin was 66, 159 and 209 ng/mL in people with 0,1 or 2 copies, respectively.
Article: Genetic polymorphisms in human CYP2A6 gene causing impaired nicotine metabolism
Gene: CYP2A6
Variant/haplotype: rs5031016
Drug(s): nicotine
Phenotype category: Other, Metabolism/PK
Significant: no
Association: Allele G is associated with decreased metabolism of nicotine as compared to allele A.
Notes: This is a SNP within the CYP2A6*7 or *10 allele. Individuals with these alleles or *4 had impaired nicotine metabolism in this study. Statistics were comparing metabolism levels in Japanese and Korean subjects, rather than these alleles compared to wildtype.
Article: Effects of various factors on steady-state plasma concentrations of risperidone and 9-hydroxyrisperidone: lack of impact of MDR-1 genotypes
Gene: ABCB1
Variant/haplotype: rs2032582
Drug(s): risperidone
Phenotype category: Metabolism/PK
Significant: no
Association: Allele C is not associated with increased metabolism of risperidone in people with Schizophrenia as compared to allele A.
Notes: No association was seen between this SNP and metabolism of risperidone.
Article: Association between imatinib transporters and metabolizing enzymes genotype and response in newly diagnosed chronic myeloid leukemia patients receiving imatinib therapy
Gene: ABCB1
Variant/haplotype: rs1045642
Drug(s): imatinib
Phenotype category: Efficacy
Significant: yes
Association: Genotypes AA + AG is associated with decreased response to imatinib in people with Leukemia, Myelogenous, Chronic, BCR-ABL Positive as compared to genotype GG.
Notes: Patients with the AA or AG genotype had a decreased likelihood of achieving complete molecular response (CMR) within 12 months, as compared to those with the GG genotype. CMR was classified based on BCR-ABL to control gene transcript ratios, expressed on the International Scale; CMR was a ratio <= 0.0032%. Please note that alleles have been complemented to the plus chromosomal strand, and that this SNP was listed as rs60023214.
Article: CYP2D6 Genotyping for Optimization of Tamoxifen Therapy in Indonesian Women with ER+ Breast Cancer
Gene: CYP2D6
Variant/haplotype: CYP2D6*1, CYP2D6*2, CYP2D6*10, CYP2D6*36
Drug(s): tamoxifen
Phenotype category: Dosage
Significant: not stated
Association: CYP2D6 *10/*36 (assigned as intermediate metabolizer phenotype) is associated with increased dose of tamoxifen in women with Breast Neoplasms as compared to CYP2D6 *1/*36 + *2/*10 + *1/*1 + *2/*36 + *1/*10 + *10/*10 (assigned as normal metabolizer phenotype) .
Notes: " The statistical analysis at baseline showed that the endoxifen level of the PMs-IMs was significantly lower than NM (p < 0.001)." "A follow-up consultation was individually scheduled for each participant to inform treatment adjustment, where relevant. There were 83 NMs who were advised to continue taking the standard dose of 20 mg daily. Meanwhile, there were 65 IMs and 2 PMs who were given a recommendation to adjust their tamoxifen dose to 40 mg daily. However, a total of 17 IMs and 2 PMs were deemed clinically unfit for tamoxifen dosage increase and recommended to switch to aromatase inhibitor. Individuals switching to aromatase inhibitors were not followed up further for assessment of metabolite levels changes, side effect monitoring, and survival analysis as tamoxifen is this study’s drug of interest. "
Article: Single Dose, CYP2D6 Genotype-Stratified Pharmacokinetic Study of Atomoxetine in Children with ADHD
Gene: CYP2D6
Variant/haplotype: CYP2D6*1, CYP2D6*2, CYP2D6*3, CYP2D6*4, CYP2D6*4xN, CYP2D6*5, CYP2D6*9, CYP2D6*10, CYP2D6*17, CYP2D6*29, CYP2D6*41
Drug(s): atomoxetine
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2D6 *4/*4xN + *4/*4 are associated with increased concentrations of atomoxetine in children with Attention Deficit Disorder with Hyperactivity as compared to CYP2D6 *1/*1 + *1/ *2 + *2/*4 + *1/*4 + *1/*3 + *2/*5 + *10/*41 + *9/*29 + *5/*17 + *4/*9.
Notes: single dose study with an average of 0.43 mg/kg. Children received either  a single dose of 10, 18, 25, 30 or 40 mg atomoxetine depending on body weight. Cmax of 4 hydroxy atomoxetine was lower in PM (two no function alleles) as compared to EM (one or two functional alleles) (p<0.002 or p<0.001) but not significantly different to IM (one reduced and one no function allele).
Article: GENE AND GENE BY SEX ASSOCIATIONS WITH INITIAL SENSITIVITY TO NICOTINE IN NONSMOKERS
Gene: ANKK1, DRD2
Variant/haplotype: rs1800497
Drug(s): nicotine
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to nicotine in healthy individuals as compared to allele G.
Notes: Please note that alleles have been complemented to the positive strand. No significant association between this variant and nicotine reward, perception, mood or reinforcement or physiological responses to nicotine.
Article: Influence of ABCB1 gene polymorphisms on the pharmacokinetics of verapamil among healthy Chinese Han ethnic subjects
Gene: ABCB1
Variant/haplotype: rs2032582
Drug(s): verapamil
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype CC is associated with decreased metabolism of verapamil in healthy individuals as compared to genotypes AA + AC.
Notes: Patients with the CC genotype had lower oral clearance and higher AUC than patients with the AA or AC genotype. This SNP was studied together with rs1045642. Subjects were non-randomly chosen in order to study patients homozygous for the wildtype at both SNPs, heterozygous for both SNPs, and homozygous for the variant at both SNPs.
Article: Polymorphic Variants of SCN1A and EPHX1 Influence Plasma Carbamazepine Concentration, Metabolism and Pharmacoresistance in a Population of Kosovar Albanian Epileptic Patients
Gene: SCN1A
Variant/haplotype: rs2298771
Drug(s): carbamazepine
Phenotype category: Metabolism/PK
Significant: no
Association: Genotype CC is not associated with dose of carbamazepine in people with Epilepsy as compared to genotypes CT + TT.
Notes: There was no association between dose (mean daily, or mean maintenance) with the genotype. Please note: alleles have been complemented to the + chromosomal strand.
Article: Germline single nucleotide polymorphisms in ERBB3 and BARD1 genes result in a worse relapse free survival response for HER2-positive breast cancer patients treated with adjuvant based docetaxel, carboplatin and trastuzumab (TCH)
Gene: ERBB3
Variant/haplotype: rs773123
Drug(s): carboplatin, docetaxel, trastuzumab
Phenotype category: Efficacy
Significant: yes
Association: Allele A is associated with decreased response to carboplatin, docetaxel and trastuzumab in women with Breast Neoplasms.
Notes: When compared to women who received different treatment regimens. Response was defined as likelihood of achieving relapse-free survival.
Article: Gemcitabine Metabolic and Transporter Gene Polymorphisms Are Associated with Drug Toxicity and Efficacy in Patients with Locally Advanced Pancreatic Cancer
Gene: SLC28A2
Variant/haplotype: rs1060896
Drug(s): gemcitabine
Phenotype category: Efficacy, Toxicity
Significant: no
Association: Genotype AA is not associated with increased response to gemcitabine in people with Pancreatic Neoplasms as compared to genotypes AC + CC.
Notes: Tumor response to therapy, progression free survival, and risk of neutropenia development did not significantly differ between genotype groups.
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: no
Association: Genotype CC is not 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 2/3 infected patients.
Article: Association of Cytochrome P450 Genetic Variants with Clopidogrel Resistance and Outcomes in Acute Ischemic Stroke
Gene: CYP2C19
Variant/haplotype: CYP2C19*1, CYP2C19*2
Drug(s): clopidogrel
Phenotype category: Efficacy
Significant: yes
Association: CYP2C19 *1/*2 + *2/*2 are associated with increased resistance to clopidogrel in people with Stroke as compared to CYP2C19 *1/*1.
Notes: Frequency of CYP2C19*2 (rs4244285) AA/AG genotypes was significantly higher in clopidogrel-resistant patients than in clopidogrel-sensitive patients.
Article: A genome-wide scan for common genetic variants with a large influence on warfarin maintenance dose
Gene: CYP2C9
Variant/haplotype: rs4917639
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Allele C is associated with decreased dose of warfarin as compared to allele A.
Article: Exploring joint effects of genes and the clinical efficacy of morphine for cancer pain: OPRM1 and COMT gene
Gene: COMT
Variant/haplotype: rs4680
Drug(s): morphine
Phenotype category: Efficacy
Significant: yes
Association: Genotypes AG + GG are associated with increased dose of morphine as compared to genotype AA.
Article: Effects of cytochrome P450 2B6 and constitutive androstane receptor genetic variation on Efavirenz plasma concentrations among HIV patients in Kenya
Gene: CYP2B6
Variant/haplotype: rs28399499
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele C is associated with increased concentrations of efavirenz in people with HIV Infections as compared to allele T.
Notes: Described as 983T>C
Article: Pharmacogenetics predictors of methylphenidate efficacy in childhood ADHD
Gene: SLC6A2
Variant/haplotype: rs5569
Drug(s): methylphenidate
Phenotype category: Efficacy
Significant: yes
Association: Genotype GG is associated with increased response to methylphenidate in children with Attention Deficit Disorder with Hyperactivity as compared to genotypes AA + AG.
Article: Effects of CYP3A4*22 polymorphism on trough concentration of tacrolimus in kidney transplantation: a systematic review and meta-analysis
Gene: CYP3A4
Variant/haplotype: CYP3A4*1, CYP3A4*22
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP3A4 *1/*22 + *22/*22 is associated with increased dose-adjusted trough concentrations of tacrolimus in people with Kidney Transplantation as compared to CYP3A4 *1/*1.
Notes: "Therefore, the significant effect of CYP3A4*22 on C0/D and the dose requirement of Tac remained evident even after adjusting for CYP3A5*3."
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: rs524731
Drug(s): ethanol
Phenotype category: Efficacy
Significant: yes
Association: Allele A is associated with increased response to ethanol as compared to allele C.
Notes: The A allele was associated with increased scores in the dizzy, drunk, high and terrible traits on the Subjective High Assessment Scale-Expectations (SHAS-E) questionnaire.
Article: Population pharmacokinetics of unbound mycophenolic acid in adult allogeneic haematopoietic cell transplantation: effect of pharmacogenetic factors
Gene: UGT1A9
Variant/haplotype: rs6714486
Drug(s): mycophenolic acid
Phenotype category: Metabolism/PK
Significant: no
Association: Genotype AA is not associated with metabolism of mycophenolic acid as compared to genotype TT.
Notes: Genotype AA is not associated with any pharmacokinetic parameters measured in the study when exposed to mycophenolic acid as compared to genotype TT.
Article: Genotypic variation in the SV2C gene impacts response to atypical antipsychotics the CATIE Study
Gene: SV2C
Variant/haplotype: rs11960832
Drug(s): olanzapine
Phenotype category: Efficacy
Significant: yes
Association: Genotype TT is associated with decreased response to olanzapine in people with Schizophrenia as compared to genotypes CC + CT.
Notes: Response was assessed by a change in the total Positive and Negative Syndrome Scale (PANSS) score. TT homozygotes had a smaller decrease or an increase in PANSS score compared to C allele carriers.
Article: The impact of non-genetic and genetic factors on a stable warfarin dose in Thai patients
Gene: CYP4F2
Variant/haplotype: rs2108622
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Genotype TT is associated with increased dose of warfarin in people with Atrial Fibrillation, heart valve replacement, Hypertension, Pulmonary, Pulmonary Embolism and Venous Thrombosis as compared to genotype CC.
Article: Population pharmacogenetic-based pharmacokinetic modeling of efavirenz, 7-hydroxy- and 8-hydroxyefavirenz
Gene: CYP2B6
Variant/haplotype: CYP2B6*1, CYP2B6*6
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2B6 *6/*6 is associated with decreased clearance of efavirenz in healthy individuals as compared to CYP2B6 *1/*1 + *1/*6.
Notes: The total clearance of efavirenz was ~30% lower in those with the *6/*6 genotype as compared to those with the *1/*1 or *1/*6 genotype. Population pharmacokinetic modeling.
Article: Prediction of phenprocoumon maintenance dose and phenprocoumon plasma concentration by genetic and non-genetic parameters
Gene: F7
Variant/haplotype: rs510317
Drug(s): phenprocoumon
Phenotype category: Dosage, Metabolism/PK
Significant: no
Association: Genotype GG is not associated with increased dose of phenprocoumon as compared to genotypes AA + AG.
Notes: Daily dose of phenprocoumon is not significantly associated with this SNP. Daily dose is negatively correlated with age. This study published an algorithm for daily dose that includes height, although height was not significant in univariate analysis. This SNP is also not significantly associated with phenprocoumon concentration.