shlokn/autogkb huggingface dataset:
Article: Prediction of Methotrexate Clinical Response in Portuguese Rheumatoid Arthritis Patients: Implication of MTHFR rs1801133 and ATIC rs4673993 Polymorphisms
Gene: MTHFR
Variant/haplotype: rs1801133
Drug(s): methotrexate
Phenotype category: Efficacy
Significant: yes
Association: Genotypes AG + GG is associated with increased response to methotrexate in people with Arthritis, Rheumatoid as compared to genotype AA.
Notes: "MTHFR 677TT ... associated with over 4-fold increased risk for nonresponse. " Alleles complemented to plus chromosomal strand.
Article: APOE Polymorphisms Contribute to Reduced Atorvastatin Response in Chilean Amerindian Subjects
Gene: APOE
Variant/haplotype: rs429358
Drug(s): atorvastatin
Phenotype category: Efficacy
Significant: yes
Association: Genotype CT is associated with decreased response to atorvastatin in people with Hypercholesterolemia as compared to genotype TT.
Notes: Effect reported for E3/E4 compared to E3/E3 (there were no E4/E4 subjects in cohort).
Article: G Protein-Coupled Receptor Kinase 5 Gene Polymorphisms Are Associated with Postoperative Atrial Fibrillation Following Coronary Artery Bypass Graft Surgery in Patients Receiving Beta-Blockers
Gene: GRK5
Variant/haplotype: rs11198893
Drug(s): Beta Blocking Agents
Phenotype category: Efficacy
Significant: yes
Association: Allele A is associated with decreased response to Beta Blocking Agents in people with Coronary Artery Disease as compared to allele G.
Notes: Single-nucleotide polymorphisms in 10 candidate genes were tested for association with atrial fibrillation after coronary artery bypass grafting despite perioperative beta blocker therapy.
Article: Genome-wide association study of letrozole plasma concentrations identifies non-exonic variants that may affect CYP2A6 metabolic activity
Variant/haplotype: rs7937
Drug(s): letrozole
Significant: yes
Association: Allele C is associated with increased concentrations of letrozole in women with Breast Neoplasms as compared to allele T.
Notes: rs7937 was associated with age- and BMI-adjusted letrozole levels even after adjusting for genotype-predicted CYP2A6 metabolic phenotype (P = 3.86 × 10−10). Median (interquartile range) letrozole concentration in patients with genotypes CC, CT and TT were 107.9 (48.5), 90.5 (46.4) and 73.2 (33.4)ng/ml.
Article: Therapeutic efficacy of generic artemether–lumefantrine in the treatment of uncomplicated malaria in Ghana: assessing anti-malarial efficacy amidst pharmacogenetic variations
Gene: CYP3A5
Variant/haplotype: CYP3A5*1, CYP3A5*3, CYP3A5*6
Drug(s): desbutyl lumefantrine
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP3A5 *1/*3 is associated with decreased concentrations of desbutyl lumefantrine in people with Malaria, Falciparum as compared to CYP3A5 *1/*1 + *1/*6.
Notes: "Figure 5 shows the plasma lumefantrine and DBL for CYP3A5 expressor status. There were significant differences in plasma DBL concentrations on day 3 between *1/*1 versus *1/*6 (p = 0.002), *1/*3 versus *1/*6 (p = 0.006) and *1/*7 versus *1/*6 (p = 0.008). There was an observed significance on day 7 desbutyl plasma concentrations among *1/*6 and *1/*3 (p = 0.026) expressors."
Article: Impact of IL28B, APOH and ITPA Polymorphisms on Efficacy and Safety of TVR- or BOC-Based Triple Therapy in Treatment-Experienced HCV-1 Patients with Compensated Cirrhosis from the ANRS CO20-CUPIC Study
Gene: IFNL3, IFNL4
Variant/haplotype: rs12979860
Drug(s): boceprevir, peginterferon alfa-2a, peginterferon alfa-2b, ribavirin, telaprevir
Phenotype category: Efficacy
Significant: yes
Association: Allele C is associated with increased response to boceprevir, peginterferon alfa-2a, peginterferon alfa-2b, ribavirin or telaprevir in people with Hepatitis C, Chronic as compared to allele T.
Notes: The favorable allele C of rs12979860 was significantly associated with SVR to triple therapy including telaprevir or boceprevir in patients with compensated cirrhosis chronically infected with HCV-1.  The effect of rs12979860 on triple therapy-induced clearance in treatment-experienced patients is restricted to those who experienced prior PegIFN/RBV relapse.
Article: G-Protein-Coupled Receptor Kinase 4 Polymorphisms and Blood Pressure Response to Metoprolol Among African Americans: Sex-Specificity and Interactions
Gene: GRK4
Variant/haplotype: rs1801058
Drug(s): metoprolol
Phenotype category: Efficacy
Significant: yes
Association: Genotype CT is associated with decreased response to metoprolol in women with hypertensive nephrosclerosis as compared to genotype CC.
Notes: Note; there were no female TT (V486) homozygotes. Response was measured by time to reach a mean arterial pressure of < or = 107 mm Hg.
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): lansoprazole
Phenotype category: Efficacy
Significant: no
Association: CYP2C19 *1/*2 + *1/*3 is not associated with response to lansoprazole 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 9 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: Genetic variants in CYP2B6 and CYP2A6 explain interindividual variation in efavirenz plasma concentrations of HIV-infected children with diverse ethnic origin
Gene: CYP2A6
Variant/haplotype: rs28399433
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype AC is associated with increased concentrations of efavirenz in children with HIV Infections.
Notes: Allele also known as CYP2A6*9.
Article: Comparative efficacy and safety of sitagliptin or gliclazide combined with metformin in treatment-naive patients with type 2 diabetes: A single-center, prospective, randomized, controlled, noninferiority study with genetic polymorphism analysis
Gene: DPP4
Variant/haplotype: rs2909451
Drug(s): sitagliptin
Phenotype category: Efficacy
Significant: yes
Association: Genotype TT is associated with decreased response to sitagliptin in people with Diabetes Mellitus, Type 2.
Notes: "Patients with the rs2909451 TT genotype in the study group (treated with sitagliptin) exhibited a median HbA1c improvement of 0.57 (interquartile range [IQR], 0.18–0.85), whereas the control group (treated with gliclazide) showed a median improvement of 1.11 (IQR, 0.86–1.35; P < .001)."
Article: Effects of genetic polymorphisms on methotrexate levels and toxicity in Chinese patients with acute lymphoblastic leukemia
Gene: SLC19A1
Variant/haplotype: rs2838958
Drug(s): methotrexate
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotypes AA + AG is associated with increased concentrations of methotrexate in people with Precursor Cell Lymphoblastic Leukemia-Lymphoma as compared to genotype GG.
Notes: at 24 hours.
Article: Genotypic variation in the SV2C gene impacts response to atypical antipsychotics the CATIE Study
Gene: SV2C
Variant/haplotype: rs12522597
Drug(s): ziprasidone
Phenotype category: Efficacy
Significant: no
Association: Genotype GG is not associated with response to ziprasidone in people with Schizophrenia as compared to genotypes AA + AG.
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: Genetic Variation in CYP2D6, UGT1A4, SLC6A2 and SLCO1B1 Alters the Pharmacokinetics and Safety of Mirabegron
Gene: SLC6A2
Variant/haplotype: rs12708954
Drug(s): mirabegron
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype CC is associated with increased clearance of mirabegron in healthy individuals as compared to genotype AC.
Notes: "A lower AUC/DW and a higher CL/F were observed in the SLC6A2 rs12708954 C/C genotype compared to the C/A genotype (puv = 0.015 and puv = 0.016, respectively)."
Article: Low heritability in pharmacokinetics of talinolol: a pharmacogenetic twin study on the heritability of the pharmacokinetics of talinolol, a putative probe drug of MDR1 and other membrane transporters
Gene: ABCG2
Variant/haplotype: rs2231142
Drug(s): talinolol
Phenotype category: Metabolism/PK
Significant: no
Association: Allele G is not associated with clearance of talinolol in healthy individuals as compared to allele T.
Notes: This was a twin study of monozygotic and dizygotic twins.
Article: Exonuclease 1 genetic variant is associated with clinical outcomes of pemetrexed chemotherapy in lung adenocarcinoma
Gene: EXO1
Variant/haplotype: rs1047840
Drug(s): pemetrexed
Phenotype category: Efficacy
Significant: yes
Association: Genotypes AA + AG is associated with decreased clinical benefit to pemetrexed in people with Lung Neoplasms as compared to genotype GG.
Article: VKORC1 variants as significant predictors of warfarin dose in Emiratis
Gene: VKORC1
Variant/haplotype: rs188009042
Drug(s): warfarin
Phenotype category: Dosage
Significant: no
Association: Allele C is not associated with dose of warfarin as compared to allele T.
Notes: Please note that alleles have been complemented to the positive strand.
Article: A discordance between cytochrome P450 2D6 genotype and phenotype in patients undergoing methadone maintenance treatment
Gene: CYP2D6
Variant/haplotype: CYP2D6*1, CYP2D6*4
Drug(s): dextromethorphan
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2D6 *4 is associated with decreased metabolism of dextromethorphan in women as compared to CYP2D6 *1.
Notes: Multiple regression analysis indicated that CYP2D6*4 alleles and being female were associated with lower CYP2D6 activity as measured by the log (MR); (P < 0.001; r2 = 0.75).; Study only typed for CYP2D6*3, *4, and *6. Mix of genotyping and phenotyping with DEX/DOR MR (0.1 was used as the antimode separating NM and PM). 3 patients were *4/*4 (*3 and *6 were not detected); phenotyped *4/*4 subject had a MR of above 1 (fig1) . 16 out of the 28 phenotyped patients show a MR >0.1 and were classified as PM but did not align with genotype for the smaller subset that had genotype and phenotype data. Patients took methadone and other medications.
Article: Genetic variation in the Catechol-O-Methyltransferase (COMT) gene and morphine requirements in cancer patients with pain
Gene: COMT
Variant/haplotype: rs737866
Drug(s): morphine
Phenotype category: Dosage, Efficacy
Significant: yes
Association: Allele T is associated with decreased dose of morphine in people with Neoplasms as compared to allele C.
Notes: This was for alleviation of pain from cancer.  The association was as part of a haplotype consisting of 11 rsIDs (the other rsIDs are rs2075507,rs7287550, rs5746849, rs740603, rs6269, rs2239393, rs4818, rs4680, rs174699, rs165728).  The haplotype was associated with a dose reduction factor of 0.71 .  Authors state that because the SNPs are linked, a strict Bonferroni correction is too conservative; however, that is what has been done here for p value.  Also noted was that the carriers of haplotype 1 have had the cancer diagnosis longer than have carriers of other haplotypes, and so the true difference in morphine requirements may be even greater than observed here.
Article: Genetic Variation of VKORC1 and CYP4F2 Genes Related to Warfarin Maintenance Dose in Patients with Myocardial Infarction
Gene: VKORC1
Variant/haplotype: rs9934438
Drug(s): warfarin
Phenotype category: Dosage, Efficacy
Significant: yes
Association: Genotypes AA + AG is associated with decreased dose of warfarin in people with Myocardial Infarction as compared to genotype GG.
Notes: This is shown for *2/*2, *2/*3 and *2/*4 vs *3/*3, *3/*4 and *4/*4. Authors define *2 as VKORC1*2 (rs9934438/6484 C > T). Alleles complemented.
Article: An Expanded Analysis of Pharmacogenetics Determinants of Efavirenz Response that Includes 3′-UTR Single Nucleotide Polymorphisms among Black South African HIV/AIDS Patients
Gene: CYP2B6
Variant/haplotype: rs28399499
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype CC is associated with increased concentrations of efavirenz in people with HIV Infections as compared to genotypes CT + TT.
Article: Effect of eNOS polymorphisms on salbutamol evoked endothelium dependent vasodilation in South Indian healthy subjects
Gene: NOS3
Variant/haplotype: rs1799983
Drug(s): salbutamol
Phenotype category: Efficacy
Significant: no
Association: Genotype GG is not associated with response to salbutamol in healthy individuals as compared to genotypes GT + TT.
Notes: No significant differences in the change in digital volume pulse parameters - reflection index and stiffness index - before and after salbutamol administration were seen between the two genotype groups. This indicates that this SNP does not affect salbutamol-evoked endothelium-dependent vasodilation.
Article: Comparative performance of gene-based warfarin dosing algorithms in a multiethnic population
Gene: CYP2C9
Variant/haplotype: CYP2C9*1, CYP2C9*2, CYP2C9*3, CYP2C9*5
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: CYP2C9 *3 + *5 + *2 + *1 is associated with dose of warfarin.
Notes: Neither the addition of race, number of concurrent medications nor the number of concurrent medications interacting with warfarin enhanced algorithm performance. Similarly, consideration of CYP4F2, CALU or GGCX variant genotypes did not improve algorithms.
Article: Population pharmacokinetics and pharmacogenetics of once daily tacrolimus formulation in stable liver 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 are associated with increased clearance of tacrolimus in people with liver transplantation as compared to CYP3A5 *3/*3.
Notes: The *1A/*1A + *1A/*3A genotypes were associated with a significantly higher apparent clearance as compared to the *3A/*3A genotype. This was true when analyzing the effect of the genotypes of liver donors, liver recipients, as well as when genotypes were combined.
Article: COMT Val158Met, BDNF Val66Met, and OPRM1 Asn40Asp and Methamphetamine Dependence Treatment Response: Preliminary Investigation
Gene: COMT
Variant/haplotype: rs4680
Drug(s): modafinil
Phenotype category: Efficacy
Significant: no
Association: Genotype GG is not associated with response to modafinil in people with methamphetamine dependence as compared to allele A.
Notes: No significant association between this variant and Treatment Effectiveness Scores following modafinil treatment compared to placebo in Non-Hispanic Caucasian subjects.
Article: Population pharmacokinetic approach to evaluate the effect of CYP2D6, CYP3A, ABCB1, POR and NR1I2 genotypes on donepezil clearance
Gene: CYP3A4
Variant/haplotype: rs4646437
Drug(s): donepezil
Phenotype category: Metabolism/PK
Significant: no
Association: Genotype GG is not associated with clearance of donepezil in people with Alzheimer Disease as compared to genotype AA.
Notes: Genotypes of GG, AG and AA did not influence donepezil clearance in a covariate model. Alleles have been complemented to the plus chromosomal strand.
Article: VKORC1 variants as significant predictors of warfarin dose in Emiratis
Gene: VKORC1
Variant/haplotype: rs2359612
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Genotypes AG + GG are associated with increased dose of warfarin as compared to genotype AA.
Notes: Please note that alleles have been complemented to the positive strand.
Article: Relevance of CYP2B6 and CYP2D6 genotypes to methadone pharmacokinetics and response in the OPAL study
Gene: CYP2D6
Variant/haplotype: CYP2D6 poor and ultrarapid metabolizers
Drug(s): methadone
Phenotype category: Metabolism/PK
Significant: no
Association: CYP2D6 poor metabolizer and ultrarapid metabolizer are not associated with response to methadone in people with Opioid-Related Disorders as compared to CYP2D6 normal metabolizer.
Notes: There was no significant association between CYP2D6 phenotype and cessation of opioid use.
Article: Relationships of related genetic polymorphisms and individualized medication of tacrolimus in patients with renal transplantation
Gene: CYP3A4
Variant/haplotype: CYP3A4*1, CYP3A4*18
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP3A4 *18 is associated with decreased dose-adjusted trough concentrations of tacrolimus in people with Kidney Transplantation as compared to CYP3A4 *1.
Notes: CYP3A4*18B was negatively correlated with tacrolimus dose-adjusted trough concentrations (C/D). However, in the best multiple regression model, this allele no longer retained statistical significance. Factors that retained statistical significance were CYP3A5*3, hematocrit and albumin. PharmVar has consolidated CYP3A4*18B under CYP3A4*18 .001
Article: Genetic polymorphisms in key methotrexate pathway genes are associated with response to treatment in rheumatoid arthritis patients
Gene: TYMS
Variant/haplotype: rs11280056
Drug(s): methotrexate
Phenotype category: Efficacy
Significant: no
Association: Allele del is not associated with response to methotrexate in people with Arthritis, Rheumatoid.
Notes: Variant was originally mapped to TTAAAG allele of rs151264360, which has now been merged into rs11280056. This annotation replaces VA 827863352.
Article: OPRM1, OPRK1 and COMT Genetic Polymorphisms Associated with Opioid Effects on Experimental Pain: A Randomized, Double-Blind, Placebo-Controlled Study
Gene: OPRM1
Variant/haplotype: rs1799971
Drug(s): butorphanol
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with response to butorphanol in healthy individuals as compared to allele A.
Notes: Study-wide significance was set to p<0.017.
Article: The effects of OPRM1 118A>G on methadone response in pain management in advanced cancer at end of life
Gene: OPRM1
Variant/haplotype: rs1799971
Drug(s): methadone
Phenotype category: Dosage
Significant: no
Association: Genotypes AA + AG is not associated with increased dose of methadone in people with Neoplasms and Pain as compared to genotype GG.
Notes: "We did not find an association with methadone dose or pain scores for our study"
Article: Interplay of Genetic Risk Factors (CHRNA5-CHRNA3-CHRNB4) and Cessation Treatments in Smoking Cessation Success
Gene: CHRNA3, CHRNA5
Variant/haplotype: rs16969968
Drug(s): Drugs used in nicotine dependence
Phenotype category: Other
Significant: yes
Association: Allele A is associated with increased response to Drugs used in nicotine dependence in people with Tobacco Use Disorder.
Notes: in haplotype analysis; individuals with haplotype 3 (rs16969968 allele A - rs680244 allele C) were more likely to respond to active treatment/ had a lower risk of relapse (remain abstinent from smoking cigarettes) than those with haplotype 3 that were treated with placebo. The odds of abstinence from cigarette smoking were not significantly different in individuals with haplotype 1 (rs16969968 allele G - rs680244 allele C) that underwent active treatment or placebo.
Article: Genetic Variants Influencing Plasma Renin Activity in Hypertensive Patients from the Pharmacogenomic Evaluation of Antihypertensive Responses (PEAR) Study
Gene: XIRP2
Variant/haplotype: rs7606603
Drug(s): atenolol
Phenotype category: Dosage
Significant: no
Association: Allele C is not associated with dose of atenolol in people with Hypertension as compared to allele T.
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: rs1537416
Drug(s): antiepileptics
Phenotype category: Efficacy
Significant: no
Association: Allele C 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: Two Novel Loci of RELN Associated With Antipsychotics Response in Chinese Han Population
Gene: RELN
Variant/haplotype: rs362719
Drug(s): aripiprazole, olanzapine, perphenazine, quetiapine, risperidone
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to aripiprazole, olanzapine, perphenazine, quetiapine or risperidone in people with Schizophrenia as compared to allele C.
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: Analgesic therapy failure in a COMT HPS/HPS diplotype carrier heterozygous for the CYP2D6 *4 allele with fibromyalgia—a case report
Gene: CYP2D6
Variant/haplotype: CYP2D6*1, CYP2D6*4
Drug(s): acetaminophen, duloxetine, ibuprofen, oxycodone, pregabalin
Phenotype category: Efficacy
Significant: no
Association: CYP2D6 *1/*4 (assigned as intermediate metabolizer phenotype) is associated with decreased clinical benefit to acetaminophen, duloxetine, ibuprofen, oxycodone and pregabalin in women with Fibromyalgia and Low Back Pain.
Notes: "40-year-old female patient was diagnosed with chronic lumbalgia and fibromyalgia" " insufficient pain relief" "COMT HPS/HPS diplotype carrier implicating lower COMT activity and higher pain sensitivity" Genotypes from table 2: rs6269 AA, rs4633 CC, rs4818 CC, rs4680 GG and CYP2D6 *1/*4
Article: Analysis of Genetic and Clinical Factors Associated with Buprenorphine Response
Variant/haplotype: rs6973474
Drug(s): buprenorphine
Phenotype category: Efficacy
Significant: yes
Association: Allele T 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: Prediction of phenprocoumon maintenance dose and phenprocoumon plasma concentration by genetic and non-genetic parameters
Gene: PROC
Variant/haplotype: rs1799808
Drug(s): phenprocoumon
Phenotype category: Dosage, Metabolism/PK
Significant: yes
Association: Genotype CC is associated with increased dose of phenprocoumon as compared to genotypes CT + TT.
Notes: Patients with the CC genotype require significantly higher daily doses of phenprocoumon as compared to patients with the CT or TT genotype. While it seems that there may be a gene dose effect (CC>CT>TT), the paper did not specify whether or not this is the case. Daily dose is also 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 not associated with differences in phenprocoumon concentration.
Article: Discordant Associations between SLCO1B1 521T→C and Plasma Levels of Ritonavir-boosted Protease Inhibitors in AIDS Clinical Trials Group Study A5146
Gene: SLCO1B1
Variant/haplotype: rs4149056
Drug(s): lopinavir
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele C is associated with increased trough concentration of lopinavir in people with HIV Infections as compared to allele T.
Notes: Association was significant in white patients only. Only 1/31 black patients and 1/17 Hispanic patients carried the C allele, so statistical analysis could not be carried out. However, the authors note that these patients had amongst the highest trough concentrations of lopinavir.