shlokn/autogkb huggingface dataset:
Article: Pharmacogenetic meta-analysis of genome-wide association studies of LDL cholesterol response to statins
Variant/haplotype: rs445925
Drug(s): hmg coa reductase inhibitors
Phenotype category: Efficacy
Significant: yes
Association: Allele A is associated with increased response to hmg coa reductase inhibitors as compared to allele G.
Notes: Carriers of the rs445925 A SNP respond to statins with an additional 4.3% increase per allele in LDL-C lowering effect compared with non-carriers.
Article: A genome-wide scan for common genetic variants with a large influence on warfarin maintenance dose
Gene: CYP2C9
Variant/haplotype: rs1057910
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Allele C is associated with decreased dose of warfarin as compared to allele A.
Article: A polymorphism in the OPRM1 3′ untranslated region is associated with methadone efficacy in treating opioid dependence
Gene: OPRM1
Variant/haplotype: rs10485058
Drug(s): methadone
Phenotype category: Efficacy
Significant: yes
Association: Genotype AA is associated with increased response to methadone in people with Opioid-Related Disorders as compared to genotypes AG + GG.
Notes: Methadone patients with the AA genotype were less likely to have opioid-positive urine drug screens as compared to those with the AG and GG genotypes over 24 weeks. This SNP was not associated with response to buprenorphine treatment. A separate cohort of patients (CATS) was also analyzed; this cohort collected self-reported data on ever having had a relapse after a period of abstinence in opioid-dependent individuals. In this cohort, using an additive model, the A allele was found to be significantly associated with never having relapsed.
Article: Pharmacogenetics of tenofovir clearance among Southern Africans living with HIV
Gene: IFNL3, IFNL4
Variant/haplotype: rs12979860
Drug(s): tenofovir
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele C is associated with increased clearance of tenofovir in people with HIV Infections as compared to allele T.
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: APOA1
Variant/haplotype: rs613808
Drug(s): fenofibrate
Phenotype category: Efficacy
Significant: no
Association: Genotypes AA + AG are not associated with response to fenofibrate in people with Hypertriglyceridemia as compared to genotype GG.
Notes: No significant difference in the change in plasma triglyceride (TG) or high-density lipoprotein (HDL) levels between genotypes was seen, after three weeks of treatment with fenofibrate.
Article: Attempted validation of 44 reported SNPs associated with tacrolimus troughs in a cohort of kidney allograft recipients
Gene: CYP3A4
Variant/haplotype: rs4646437
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele A is associated with trough concentration of tacrolimus in people with Kidney Transplantation and Transplantation as compared to allele G.
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 was one of the variants that passed validation in both populations. Direction of effect was not stated.
Article: Population pharmacokinetic approach to evaluate the effect of CYP2D6, CYP3A, ABCB1, POR and NR1I2 genotypes on donepezil clearance
Gene: CYP3A7
Variant/haplotype: CYP3A7*1A, CYP3A7*1C
Drug(s): donepezil
Phenotype category: Metabolism/PK
Significant: no
Association: CYP3A7 *1C/*1C is not associated with clearance of donepezil in people with Alzheimer Disease as compared to CYP3A7 *1A/*1A.
Notes: Diplotypes *1/*1, *1/*1C, *1C/*1C, did not influence donepezil clearance in a covariate model.
Article: Germline Polymorphisms as Biomarkers of Tumor Response in Colorectal Cancer Patients Treated with Anti-EGFR Monoclonal Antibodies: A Systematic Review and Meta-Analysis
Gene: EGF
Variant/haplotype: rs4444903
Drug(s): cetuximab, panitumumab
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with response to cetuximab or panitumumab in people with Colorectal Neoplasms as compared to allele A.
Notes: Meta-analysis with 6 studies. This association was not significant after multiple testing correction. The authors did not provide the exact number of patients but stated that "the median number of patients per analysis was 110 (range 50 - 740)". Most definitions of response were variations of the RECIST criteria.
Article: The Effects of Inherited NUDT15 Polymorphisms on Thiopurine Active Metabolites in Japanese Children with Acute Lymphoblastic Leukemia
Gene: NUDT15
Variant/haplotype: NUDT15*1, NUDT15*2, NUDT15*3, NUDT15*5
Drug(s): mercaptopurine
Phenotype category: Toxicity
Significant: yes
Association: NUDT15 *1/*2 + *1/*3 + *1/*5 are associated with decreased dose of mercaptopurine in children with Precursor Cell Lymphoblastic Leukemia-Lymphoma as compared to NUDT15 *1/*1.
Notes: The mean mercaptopurine (MP) dosages were 48.0 ± 21.2, 34.1 ± 17.0, and 3.2 ± 1.2 mg/m2 for the normal-activity (*1/*1 n=44), intermediate-activity (*1/*2 + *1/*3 + *1/*5 n=10), and low-activity (*2/*3 n=1) NUDT15 groups, respectively (P = 4.8×10-4). TGN (thioguanine nucleotides, not further specified) levels was correlated negatively with the number of NUDT15 risk alleles (P=5.3×10-6) and this association remained significant after adjusting for MP dosage (P = 1.7 × 10 - 6).
Article: Genome-wide association study of antidepressant response: involvement of the inorganic cation transmembrane transporter activity pathway
Gene: MTRF1L
Variant/haplotype: rs766127
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: Pharmacokinetics and response to pravastatin in paediatric patients with familial hypercholesterolaemia and in paediatric cardiac transplant recipients in relation to polymorphisms of the SLCO1B1 and ABCB1 genes
Gene: ABCB1
Variant/haplotype: rs2032582
Drug(s): pravastatin
Phenotype category: Metabolism/PK
Significant: no
Association: Allele C is not associated with metabolism of pravastatin in children with Hyperlipoproteinemia Type II as compared to allele T.
Notes: No significant association was found between PK parameters and this SNP.
Article: Correlation of MDR1 gene polymorphism with propofol combined with remifentanil anesthesia in pediatric tonsillectomy
Gene: ABCB1
Variant/haplotype: rs2032582
Drug(s): propofol, remifentanil
Phenotype category: Efficacy
Significant: no
Association: Allele C is not associated with response to propofol and remifentanil in children as compared to allele T.
Notes: Referred to as 2677 G>T/A Please note that alleles have been complemented to the positive strand.
Article: Pharmacokinetics and pharmacogenetics of the MEK1/2 inhibitor, selumetinib, in Asian and Western healthy subjects: a pooled analysis
Gene: UGT1A1
Variant/haplotype: rs4148323
Drug(s): selumetinib
Phenotype category: Metabolism/PK
Significant: no
Association: Allele G is not associated with dose of selumetinib in healthy individuals as compared to allele A.
Notes: Not associated with normalized dose when allele was assessed within ethnic groups (Asian, White, Black) and when all ethnic groups were pooled together.
Article: Impact of the novel CYP2C:TG haplotype and CYP2B6 variants on sertraline exposure in a large patient population
Gene: CYP2B6
Variant/haplotype: CYP2B6*1, CYP2B6*4
Drug(s): sertraline
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2B6 *1/*4 + *4/*4 are associated with decreased concentrations of sertraline as compared to CYP2B6 *1/*1.
Notes: Compared with the reference group (CYP2B6*1/*1, n = 454), patients carrying the CYP2B6*4 allele had a 17.4% (n = 37, p = 0.022) reduced serum concentration of sertraline.
Article: Positive effects of methylphenidate on hyperactivity are moderated by monoaminergic gene variants in children with autism spectrum disorders
Gene: COMT
Variant/haplotype: rs4680
Drug(s): methylphenidate
Phenotype category: Efficacy
Significant: yes
Association: Genotypes AA + AG is associated with increased response to methylphenidate in children with Autism Spectrum Disorder as compared to genotype GG.
Notes: Positive response defined as Clinical Global Impression-Improvement (CGI-I) rating of 'much improved' or 'very much improved', and decrease in Aberrant Behavior Checklist-Hyperactivity subscale of >25% from baseline. This result was not significant when considering correction for multiple testing (p<0.002).
Article: Bisoprolol responses (PK/PD) in hypertensive patients: A cytochrome P450 (CYP) 2D6 targeted polymorphism study
Gene: CYP2D6
Variant/haplotype: rs1080985
Drug(s): bisoprolol
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype CC is associated with decreased concentrations of bisoprolol in people with Cardiovascular Diseases as compared to genotypes CG + GG.
Notes: "The plasma concentrations of Bisoprolol in CC carriers were significantly lower than GG and CC carriers by 25%, and 51% respectively. Higher systolic and diastolic blood pressure was also observed in CC carriers than GG and CC carriers so there is a window to increase the dose for these patients. The average systolic blood pressure in CC carriers was 139.8 mmHg compared to 128.8 mmHg in GG carriers and 121.5 mmHg in GC carries. Similarly, the average diastolic blood pressure in CC carriers was 79.9 mmHg compared to 73.6 mmHg in GG carriers and 73.7 mmHg in CC carriers."
Article: An Intronic Variant in OPRD1 Predicts Treatment Outcome for Opioid Dependence in African-Americans
Gene: OPRD1
Variant/haplotype: rs678849
Drug(s): buprenorphine
Phenotype category: Efficacy
Significant: yes
Association: Genotype CC is associated with decreased response to buprenorphine in people with Opioid-Related Disorders as compared to genotypes CT + TT.
Notes: Efficacy was determined based on the number of opioid-positive drug screens that each patient had during treatment. Patients with the CC genotype had significantly more positive drug screens during 24 weeks of treatment than the combined group of patients with the CT or TT genotypes.
Article: Interferon-λ3 polymorphisms in pegylated-interferon-α plus ribavirin therapy for genotype-2 chronic hepatitis C
Gene: IFNL3
Variant/haplotype: rs8099917
Drug(s): peginterferon alfa-2a, peginterferon alfa-2b, ribavirin
Phenotype category: Efficacy
Significant: yes
Association: Genotype TT is associated with increased response to peginterferon alfa-2a, peginterferon alfa-2b and ribavirin in people with Hepatitis C as compared to genotypes GG + GT.
Notes: for chronically HCV G2-infected patients who did not achieve rapid virologic response (non-RVR). This variant is not associated SVR for patients infected with genotype-2 chronic hepatitis C and have achieved RVR.
Article: Genomic Association Analysis of Common Variants Influencing Antihypertensive Response to Hydrochlorothiazide
Variant/haplotype: rs238
Drug(s): "diuretics", "hydrochlorothiazide", "Thiazides, plain"
Phenotype category: Efficacy
Significant: yes
Association: Allele A is associated with decreased response to diuretics, hydrochlorothiazide or Thiazides, plain in people with Hypertension as compared to allele G.
Notes: The association was significant in PEAR + GERA, but not in NORDIL (in which the effect was opposite, though small) or in the 3-study meta-analysis.  Observations: 3.11 mm Hg decrease in reduction of systolic blood pressure per A allele  in PEAR + GERA, 0.45 mm Hg greater reduction in systolic blood pressure per A allele in NORDIL and 2.22 mm Hg decrease in reduction of systolic blood pressure per A allele in PEAR + GERA + NORDIL.
Article: CYP4F2 rs2108622: a minor significant genetic factor of warfarin dose in Han Chinese patients with mechanical heart valve replacement
Gene: CYP2C9
Variant/haplotype: CYP2C9*1, CYP2C9*3
Drug(s): warfarin
Phenotype category: Dosage, Efficacy
Significant: yes
Association: CYP2C9 *1/*3 + *3/*3 is associated with decreased dose of warfarin in people with mechanical heart valve replacement as compared to CYP2C9 *1/*1.
Notes: 2.1 mg/day vs 2.9 mg/day
Article: In vivo assessment of the metabolic activity of CYP2D6 diplotypes and alleles
Gene: CYP2D6
Variant/haplotype: CYP2D6 intermediate metabolizers
Drug(s): tamoxifen
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2D6 intermediate metabolizer is associated with increased dose of tamoxifen in women Breast Neoplasms as compared to CYP2D6 normal metabolizer.
Notes: EMs were treated with 20mg/day tamoxifen, while IMs and PMs were treated with 40mg/day. Doubling the dose of tamoxifen resulted in similar endoxifen concentrations for EM/EM vs EM/PM and IM/IM concentration and a higher endoxifen concentration for EM/IM. Endoxifen concentration for IM/PM and PM/PM stayed significantly lower compared to EM/EM. The patients of the cohort (83% White, 15% Black) were genotype with AmpliChip CYP450 test. The variations used to define the star alleles are not reported. The diplotypes of the patients are not reported. The alleles found in the cohort are not explicit reported but graphic 3 shows *1, *2, *35, *9, *10, *17, *29, and *41. The study included UMs and PM but no CYP2D6 star allele is reported for those phenotypes. *1, *2, *35 are grouped as active alleles and any combination of these defines the extensive metabolizer. *9, *10, *17, *29, and *41 are grouped as reduced function alleles. The article subgroups the IMs into EM/IM, EM/PM, IM/IM, IM/PM.
Article: Warfarin Dose Model for the Prediction of Stable Maintenance Dose in Indian Patients
Gene: CYP4F2
Variant/haplotype: rs2108622
Drug(s): warfarin
Phenotype category: Dosage
Significant: no
Association: Allele T is not associated with dose of warfarin as compared to allele C.
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: rs498618
Drug(s): antiepileptics
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to antiepileptics in people with Epilepsy, Generalized as compared to allele G.
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). Please note alleles have been complemented to the plus chromosomal strand.
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, CYP2C19*2, CYP2C19*3
Drug(s): omeprazole
Phenotype category: Efficacy
Significant: no
Association: CYP2C19 *1/*2 + *1/*3 is not associated with response to omeprazole in people with Helicobacter Infections as compared to CYP2C19 *2/*2 + *2/*3 + *3/*3.
Notes: No significant difference in eradication rate of Helicobacter pylori (H. pylori) were seen between the two genotype groups.This was a meta-analysis and included 6 studies. Patients were treated with the drugs anywhere from 7-14 days, and also received the antibiotics amoxicillin and clarithromycin as part of triple therapy.
Article: Deciphering the Interleukin 28B Variants That Better Predict Response to Pegylated Interferon-α and Ribavirin Therapy in HCV/HIV-1 Coinfected Patients
Gene: IFNL3, IFNL4
Variant/haplotype: rs12979860
Drug(s): peginterferon alfa-2b, ribavirin
Phenotype category: Efficacy
Significant: yes
Association: Genotype CC is associated with increased response to peginterferon alfa-2b and ribavirin in people with Hepatitis C and HIV Infections as compared to genotypes CT + TT.
Notes: This genotype is associated with sustained virological response (SVR).
Article: Identification of CYP2C19*4B: pharmacogenetic implications for drug metabolism including clopidogrel responsiveness
Gene: CYP2C19
Variant/haplotype: rs28399504
Drug(s): clopidogrel
Phenotype category: Other
Significant: no
Association: Allele G is associated with decreased metabolism of clopidogrel in people with CYP2C19*17 (rs12248560 T) as compared to allele A.
Notes: This SNP modifies the UM phenotype of CYP2C19*17 to the PM allele CYP2C19*4B.
Article: Association and cis-mQTL analysis of variants in CHRNA3-A5, CHRNA7, CHRNB2, and CHRNB4 in relation to nicotine dependence in a Chinese Han population
Gene: CHRNA5
Variant/haplotype: rs647041
Drug(s): nicotine
Phenotype category: Other
Significant: no
Association: Allele T is not associated with exposure to nicotine in men as compared to allele C.
Notes: No significant association between this allele and status as a smoker or non-smoker.
Article: Implications of OPRM1 and CYP2B6 variants on treatment outcomes in methadone-maintained patients in Ontario: Exploring sex differences
Variant/haplotype: rs73568641
Drug(s): methadone
Phenotype category: Dosage
Significant: no
Association: Allele C is associated with decreased dose of methadone in women with Opioid-Related Disorders as compared to allele T.
Notes: The C allele was associated with reduced dose of methadone in female patients. However, this was not significant. No association was found in male patients. The significance threshold was set at p<0.017. This SNP is described in the paper as an OPRM1 SNP.
Article: Rheumatoid Arthritis Risk Allele PTPRC Is Also Associated With Response to Anti–Tumor Necrosis Factor α Therapy
Gene: PTPRC
Variant/haplotype: rs10919563
Drug(s): adalimumab, etanercept, infliximab
Phenotype category: Efficacy
Significant: yes
Association: Allele G is associated with increased response to adalimumab, etanercept or infliximab in people with Arthritis, Rheumatoid as compared to allele A.
Article: MHC class I-related chain B gene polymorphism is associated with virological response to pegylated interferon plus ribavirin therapy in patients with chronic hepatitis C infection
Gene: IFNL3
Variant/haplotype: rs8099917
Drug(s): peginterferon alfa-2a, peginterferon alfa-2b, ribavirin
Phenotype category: Efficacy
Significant: yes
Association: Genotype TT is associated with increased response to peginterferon alfa-2a, peginterferon alfa-2b and ribavirin in people with Hepatitis C, Chronic and Hepatitis C, Chronic as compared to genotypes GG + GT.
Notes: A multivariate logistic model showed that the IL28B major genotype (TT) was an independent factor contributing to SVR (OR, 7.14; 95% CI, 2.19-23.22; P=0.001).
Article: Personalized Tacrolimus Dose Requirement by CYP3A5 but Not ABCB1 or ACE Genotyping in Both Recipient and Donor after Pediatric Liver Transplantation
Gene: CYP3A5
Variant/haplotype: rs776746
Drug(s): tacrolimus
Phenotype category: Dosage
Significant: yes
Association: Genotype CC is associated with decreased dose of tacrolimus in children with liver transplantation as compared to genotypes CT + TT.
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. Genotype CC is classified as a CYP3A5 non-expresser (*3/*3) and genotypes CT (*1/*3) + TT (*1/*1) are classified as CYP3A5 expressers. The mean tacrolimus dose of non-expressor donor/ non-expresser recipient pairs was lower as compared to all other donor/recipient combinations.
Article: Two Novel Loci of RELN Associated With Antipsychotics Response in Chinese Han Population
Gene: RELN
Variant/haplotype: rs3808035
Drug(s): aripiprazole, olanzapine, perphenazine, quetiapine, risperidone
Phenotype category: Efficacy
Significant: no
Association: Allele C is not associated with response to aripiprazole, olanzapine, perphenazine, quetiapine or risperidone in people with Schizophrenia as compared to allele A.
Notes: Response was assessed by changes in PANSS score. A reduction of 50% or more in PANSS score was classified as a good response.
Article: Pharmacokinetic– pharmacodynamic analysis of the role of CYP2C19 genotypes in short-term rabeprazole-based triple therapy against Helicobacter pylori
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 those with the *1/*2 or *1/*3 genotype, or those with the *2/*2 or *2/*3 genotype. No significant differences in eradication rate of Helicobacter pylori were seen between any of the genotype groups. Subjects were treated with rabeprazole for 7 days, and also received amoxicillin and clarithromycin.
Article: Brain/blood ratios of methadone and ABCB1 polymorphisms in methadone-related deaths
Gene: ABCB1
Variant/haplotype: rs1045642
Drug(s): methadone
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype AA is associated with increased concentrations of methadone as compared to genotypes AG + GG.
Notes: Cases with the AA genotype had higher medulla/blood concentration ratios of methadone compared to the AG and GG genotypes. Please note that alleles have been complemented to the positive strand.
Article: PXR and CAR single nucleotide polymorphisms influence plasma efavirenz levels in South African HIV/AIDS patients
Gene: NR1I2
Variant/haplotype: rs12721616
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: no
Association: Genotype CC is not associated with metabolism of efavirenz in people with HIV Infections as compared to genotype TT.
Notes: Plasma levels of efavirenz were not statistically significantly different between the CC and TT genotypes of this SNP.
Article: Association studies of dopamine synthesis and metabolism genes with multiple phenotypes of heroin dependence
Gene: DDC
Variant/haplotype: rs12666409
Drug(s): methadone
Phenotype category: Dosage
Significant: no
Association: Allele A is not associated with dose of methadone in people with Heroin Dependence as compared to allele T.
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
Variant/haplotype: rs324899
Drug(s): lithium
Phenotype category: Efficacy
Significant: yes
Association: Allele A is associated with decreased response to lithium in people with Bipolar Disorder as compared to allele G.
Article: Differential role of sodium channels SCN1A and SCN2A gene polymorphisms with epilepsy and multiple drug resistance in the north Indian population
Gene: SCN2A
Variant/haplotype: rs17183814
Drug(s): carbamazepine, phenobarbital, phenytoin, valproic acid
Phenotype category: Efficacy
Significant: yes
Association: Allele A is associated with resistance to carbamazepine, phenobarbital, phenytoin or valproic acid as compared to allele G.
Notes: p value was above significance level after correction for multiple testing.  Authors note that association was found at the allele level but not at the genotype level, and that this may be due to a low number of AA individuals.