shlokn/autogkb huggingface dataset:
Article: Genetic coding variants in the niacin receptor, hydroxyl-carboxylic acid receptor 2 (HCAR2), and response to niacin therapy
Gene: HCAR2
Variant/haplotype: rs2454727
Drug(s): niacin
Phenotype category: Efficacy
Significant: no
Association: Genotypes CT + TT is not associated with response to niacin as compared to genotype CC.
Notes: The study compared statin + placebo treated patients with statin + extended release niacin treated patients from the from the Atherothrombosis Intervention in Metabolic Syndrome with Low HDL/High Triglycerides and Impact on Global Health Outcomes (AIM-HIGH) trial. No association of this variant (p.M317I) with changes in low-density lipoprotein cholesterol, triglycerides, or high-density lipoprotein cholesterol at 1 year were found.
Article: Identification of Candidate Single-Nucleotide Polymorphisms in NRXN1 Related to Antipsychotic Treatment Response in Patients with Schizophrenia
Gene: NRXN1
Variant/haplotype: rs12467557
Drug(s): antipsychotics
Phenotype category: Efficacy
Significant: yes
Association: Genotype AA is associated with increased response to antipsychotics in people with Schizophrenia as compared to genotypes AG + GG.
Notes: Patients homozygous for the A allele had significant improvement in positive symptoms (p=0.002), general psychopathology (p=0.005), thought disturbance (p=0.005), activation (p=0.005) and negative symptoms (p=0.005), while patients carrying the G allele showed no overall response. No significant results were seen for anergia (p=0.0505), paranoid belligerence (p=0.1212) or depression (p=0.1183). Additionally, no significant results were seen when the associations for positive and negative symptoms and general psychopathology were tested for replication in a different cohort (CATIE study).
Article: Population pharmacokinetic approach to evaluate the effect of CYP2D6, CYP3A, ABCB1, POR and NR1I2 genotypes on donepezil clearance
Gene: CYP2D6
Variant/haplotype: CYP2D6*1, CYP2D6*1xN
Drug(s): donepezil
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2D6 *1/*1xN + *1xN/*1xN (assigned as ultrarapid metabolizer phenotype) is associated with increased clearance of donepezil in people with Alzheimer Disease.
Notes: Please note; diplotypes were described as *1/*XN, *XN/*XN. Pharmacokinetic model: gender and CYP2D6 metabolizer status explained 11% of the overall variability in donepezil clearance. Model-based simulations were also performed to compared predicted average plasma concentrations with a 10mg once daily dosage regimen suggesting a 41% decrease in average plasma concentrations for ultrarapid metabolizers. Extensive metabolizers were grouped together (diplotypes *1/*3, *1/*4, *1/*5, *1/*6, *1/*1, *4/*1xN, *6/*1xN).
Article: Pharmacogenetics of tenofovir clearance among Southern Africans living with HIV
Variant/haplotype: rs2356369
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 6E-7.
Article: Measurements of 6-thioguanine nucleotide levels with TPMT and NUDT15 genotyping in patients with Crohn’s disease
Gene: TPMT
Variant/haplotype: TPMT*1, TPMT*3A, TPMT*3C
Drug(s): thioguanine
Phenotype category: Metabolism/PK
Significant: yes
Association: TPMT *1/*3A + *1/*3C are associated with increased concentrations of thioguanine in people with Crohn Disease as compared to TPMT *1/*1.
Notes: Study participants were genotyped at rs1142345 for the presence of the TPMT *3 allele. This SNP is found in the TPMT *3A, *3C, *3D and *3E haplotypes and it is not stated which of these haplotypes was found in the study cohort. All participants had either the *1/*1 or *1/*3 genotypes.
Article: Association of a Single-Nucleotide Polymorphism in the Pregnane X Receptor (PXR 63396C→T) with Reduced Concentrations of Unboosted Atazanavir
Gene: NR1I2
Variant/haplotype: rs1523130
Drug(s): atazanavir
Phenotype category: Metabolism/PK
Significant: no
Association: Allele C is not associated with concentrations of atazanavir in people with HIV Infections as compared to allele T.
Article: A Pharmacogenetics-Based Warfarin Maintenance Dosing Algorithm from Northern Chinese Patients
Gene: CYP2C19
Variant/haplotype: rs4244285
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 A.
Notes: Samples, genotypes and INRs from a cohort of 551 patients were used to derive an algorithm which was used to predict daily warfarin maintenance dose in a second cohort of 236 patients. Note: the authors state that "SNPs were tested for deviations from HWE using the chi-squared test, and for their association with the warfarin dose by Spearman correlation analysis using a *co-dominant* model."
Article: Role of TNFRSF1A and TNFRSF1B polymorphisms in susceptibility, severity, and therapeutic efficacy of etanercept in human leukocyte antigen-B27-positive Chinese Han patients with ankylosing spondylitis
Gene: TNFRSF1B
Variant/haplotype: rs1061622
Drug(s): etanercept
Phenotype category: Efficacy
Significant: yes
Association: Genotype GT is associated with decreased response to etanercept in people with Spondylitis, Ankylosing as compared to genotypes GG + TT.
Notes: Response to etanercept was determined using the Assessment in Ankylosing Spondylitis 20 (ASAS20) and Assessment in Ankylosing Spondylitis 40 (ASAS40). Patients with the GT genotype had a significantly decreased response to etanercept at 12 months after the initiation of etanercept treatment compared to patients with the GG or TT genotypes. However, there was no significant difference in response between the different genotypes at 3 months after initiation of treatment.
Article: Clinical Pharmacology of an Atrasentan and Docetaxel Regimen in Men with Hormone-Refractory Prostate Cancer
Gene: ORM2
Variant/haplotype: rs2250242
Drug(s): docetaxel
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype AA is associated with increased clearance of docetaxel in men with Prostatic Neoplasms as compared to genotypes AG + GG.
Notes: Systemic docetaxel clearance was 70.0 L/h in those with the AA genotype as compared to 44.5 L/h in those having at least one copy of the wild-type allele.
Article: Naltrexone Use in Treating Hypersexuality Induced by Dopamine Replacement Therapy: Impact of OPRM1 A/G Polymorphism on Its Effectiveness
Gene: OPRM1
Variant/haplotype: rs1799971
Drug(s): naltrexone
Phenotype category: Efficacy
Significant: not stated
Association: Genotype AG is associated with increased response to naltrexone in men with hypersexuality state and Parkinson Disease.
Notes: Case study of a patient with hypersexuality caused by dopamine replacement therapy who was successfully treated with naltrexone. The authors hypothesize that the response may be mediated by the patient's AG genotype.
Article: CHRNA4 rs1044396 is associated with smoking cessation in varenicline therapy
Gene: CHRNB2
Variant/haplotype: rs2072661
Drug(s): varenicline
Phenotype category: Efficacy
Significant: no
Association: Genotypes AA + AG are not associated with response to varenicline in people with Tobacco Use Disorder as compared to genotype GG.
Article: Genome-Wide Association Study Identifies Genetic Polymorphisms Associated with Estimated Minimum Effective Concentration of Fentanyl in Patients Undergoing Laparoscopic-Assisted Colectomy
Gene: DRD1
Variant/haplotype: rs966775
Drug(s): fentanyl
Phenotype category: Efficacy
Significant: yes
Association: Genotypes AG + GG is associated with increased concentrations of fentanyl in people with Pain, Postoperative as compared to genotype AA.
Notes: "Compared with non-carriers, G-allele carriers of this SNP were associated with higher plasma and/or effect-site MECs of fentanyl, suggesting that G allele carriers would feel pain at a higher plasma/effect-site fentanyl concentration and thus would require more frequent self-dosing of fentanyl for adequate pain control. "
Article: CYP3A4*22 and CYP3A5*3 are associated with increased levels of plasma simvastatin concentrations in the cholesterol and pharmacogenetics study cohort
Gene: CYP3A4
Variant/haplotype: CYP3A4*1, CYP3A4*22
Drug(s): simvastatin
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP3A4 *1/*22 + *22/*22 is associated with concentrations of simvastatin as compared to CYP3A4 *1/*1.
Notes: CYP3A4*22 carriers had 14% higher concentrations; of simvastatin acid (P = 0.04) and 20% higher concentrations of simvastatin lactone; (P= 0.06) compared with noncarriers.
Article: CYP2D6 GENOTYPE AND REDUCED CODEINE ANALGESIC EFFECT IN REAL-WORLD CLINICAL PRACTICE
Gene: CYP2D6
Variant/haplotype: CYP2D6 poor metabolizer and intermediate metabolizer genotypes
Drug(s): codeine
Phenotype category: Efficacy
Significant: not stated
Association: CYP2D6 poor metabolizer and intermediate metabolizer genotypes are associated with decreased response to codeine in people with Pain as compared to CYP2D6 normal metabolizer and ultrarapid metabolizer genotypes.
Notes: Fewer patients in the pooled PM/IM group were categorized as responders to codeine compared to the pooled NM/UM group. Authors tested for the following alleles: *2, *3, *4, *5, *6, *9, *10, *17, *29, *35, *41, and *42 as well as copy number variation. Diplotypes were mapped to phenotpye groups using the methods in the CPIC/DPWG CYP2D6 Standardization Project.
Article: PTPRD gene associated with blood pressure response to atenolol and resistant hypertension
Variant/haplotype: rs12346562
Drug(s): bisoprolol
Phenotype category: Efficacy
Significant: no
Association: Genotypes AA + AC is associated with increased response to bisoprolol in people with Hypertension as compared to genotype CC.
Notes: rs12346562 had a trend in association with response to bisoprolol in 207 Finnish men in the genetics of drug responsiveness in essential hypertension study.
Article: Contribution of Cytochrome P450 and ABCB1 Genetic Variability on Methadone Pharmacokinetics, Dose Requirements, and Response
Gene: CYP2D6
Variant/haplotype: CYP2D6*1, CYP2D6*2, CYP2D6*2xN
Drug(s): methadone
Phenotype category: Dosage
Significant: yes
Association: CYP2D6 *1/*2xN + *2/*2xN (assigned as ultrarapid metabolizer phenotype) are associated with increased dose of methadone in people with Opioid-Related Disorders as compared to CYP2D6 normal metabolizer.
Notes: CYP2D6 ultrarapid metabolizers had significantly higher doses of methadone compared to those classed as normal metabolizers. No details about which specific variants/alleles were tested for are given and it is not apparent how different genotypes were categorized into metabolizer phenotypes.
Article: Genome-wide association study of patient and clinician rated global impression severity during antipsychotic treatment
Gene: PDE4D
Variant/haplotype: rs17382202
Drug(s): quetiapine
Phenotype category: Efficacy
Significant: yes
Association: Allele T is associated with increased response to quetiapine in people with Schizophrenia as compared to allele C.
Notes: The number of T alleles present in a patient was negatively associated with PGI score. Please note that this variant is in high linkage disequilibrium with rs17742120 and rs2164660.
Article: Further evidence for an acetylator phenotype difference in the metabolism of hydralazine in man
Gene: NAT2
Variant/haplotype: NAT2 slow acetylator
Drug(s): hydralazine
Phenotype category: Metabolism/PK
Significant: not stated
Association: NAT2 slow acetylator is associated with decreased metabolism of hydralazine in people with Hypertension as compared to NAT2 rapid acetylator.
Notes: Note, NAT2 not specified just categorized in slow and rapid acetylator. Patients' acetylator status was determined by the sulphamethazine method. Subjects were undergoing maintenance therapy with hydralazine, twice daily 100 mg. Patients had been receiving in conjunction with hydralazine a number of other drugs: (numbers of patients indicated):chlorethiazole 1+; bendrofluazide 8; atenolol 7; clonidine 1+; glyceryltrinitrate 1*; propranolol 6; methyldopa 6; oxprenolo l2; digoxin 2+; frusemide 2; naproxen 1+; diazepam 1*; navidrex 2*, moduretic 4; SlowK 7; bethanidine 2 and hydrochlorothiazide 1* (+These drugs were only administered to rapid acetylators; *these drugs were only administered to slow acetylators). The level of the acetylated metabolites NAcHPZ and TP (terminal product of the primary acetylation pathway) are higher in the rapid compared with the slow acetylator phenotype. Conversely the level of PZ is significantly higher in slow compared with rapid acetylators.
Article: Association between UGT2B7 gene polymorphisms and fentanyl sensitivity in patients undergoing painful orthognathic surgery
Gene: UGT2B7
Variant/haplotype: rs12645107
Drug(s): fentanyl
Phenotype category: Dosage
Significant: no
Association: Allele A is not associated with dose of fentanyl in people with Pain, Postoperative as compared to allele G.
Notes: There was no significant difference in 24 hour fentanyl use between the genotype groups.
Article: ASSOCIATIONS OF ABCB1 3435C>T AND IL-10 -1082G>A POLYMORPHISMS WITH LONG-TERM SIROLIMUS DOSE REQUIREMENTS IN RENAL TRANSPLANT PATIENTS
Gene: CYP3A5
Variant/haplotype: CYP3A5*1, CYP3A5*3
Drug(s): sirolimus
Phenotype category: Metabolism/PK
Significant: no
Association: CYP3A5 *1 is not associated with dose-adjusted trough concentrations of sirolimus in people with Kidney Transplantation as compared to CYP3A5 *3.
Notes: No significant difference in log-transformed dose-adjusted trough concentrations was seen between any of the genotypes *1/*1, *1/*3 or *3/*3.
Article: Tacrolimus Concentration Is Effectively Predicted Using Combined Clinical and Genetic Factors in the Perioperative Period of Kidney Transplantation and Associated with Acute Rejection
Gene: ABCC2
Variant/haplotype: rs3740066
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype TT is associated with increased dose-adjusted trough concentrations of tacrolimus in people with Kidney Transplantation as compared to genotype CC.
Notes: heterozygote had increased C/D but not significantly so.
Article: CYP2D6 Genotyping as an alternative to phenotyping for determination of metabolic status in a clinical trial setting
Gene: CYP2D6
Variant/haplotype: CYP2D6*4
Drug(s): debrisoquine, dextromethorphan
Phenotype category: Metabolism/PK
Significant: not stated
Association: CYP2D6 *4/*4 is associated with decreased metabolism of debrisoquine or dextromethorphan.
Notes: Out of 558 subjects previously phenotyped for clinical studies and genotyped for this study, 46 PM were found.  30 of these 46 were *4/*4.  One *4/*4 had been phenotyped on dextromethorphan as EM.
Article: Roles of the m6A methyltransferases METTL3, METTL14, and WTAP in pulmonary tuberculosis
Gene: METTL3
Variant/haplotype: rs1139130
Drug(s): Drugs For Treatment Of Tuberculosis
Phenotype category: Efficacy
Significant: yes
Association: Genotype GG is associated with increased resistance to Drugs For Treatment Of Tuberculosis in people with Tuberculosis as compared to genotypes AA + AG.
Notes: drug regimen is not specified.
Article: OCT1 genetic variants influence the pharmacokinetics of morphine in children
Gene: SLC22A1
Variant/haplotype: rs72552763
Drug(s): morphine
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype del/del is associated with decreased clearance of morphine in children with adenotonsillectomy as compared to genotypes GAT/GAT + GAT/del.
Notes: Children with two loss of function SLC22A1 alleles (*2 rs72552763 GAT>del, *3 rs12208357C>T, *4 rs34130495 G>A, or *5 rs34059508 G>A) were grouped together and had significantly lower clearance compared to children with the *1/*1 or *1/variant genotype.
Article: Genotypic variation in the SV2C gene impacts response to atypical antipsychotics the CATIE Study
Gene: SV2C
Variant/haplotype: rs11960832
Drug(s): quetiapine
Phenotype category: Efficacy
Significant: no
Association: Genotype TT is not associated with response to quetiapine in people with Schizophrenia as compared to genotypes CC + CT.
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: Pharmacokinetics of Bupropion and Its Pharmacologically Active Metabolites in Pregnancy
Gene: CYP2B6
Variant/haplotype: CYP2B6*1, CYP2B6*6
Drug(s): bupropion
Phenotype category: Metabolism/PK
Significant: no
Association: CYP2B6 *6 is associated with decreased metabolism of bupropion in women with Pregnancy as compared to CYP2B6 *1.
Article: Therapeutic Dosing of Acenocoumarol: Proposal of a Population Specific Pharmacogenetic Dosing Algorithm and Its Validation in North Indians
Gene: VKORC1
Variant/haplotype: rs9923231
Drug(s): acenocoumarol
Phenotype category: Dosage
Significant: yes
Association: Genotype CC is associated with increased dose of acenocoumarol as compared to genotypes CT + TT.
Notes: Variants at this position in the VKORC1 gene were found to exhibit a gene-dose effect in the following manner: CC>CT>TT. This study also provides an algorithm for predicting the maintenance dose of acenocoumarol using genotypes as well as clinical factors as predictive variables.
Article: IL17RB genetic variants are associated with acamprosate treatment response in patients with alcohol use disorder: A proteomics-informed genomics study
Gene: CHDH, IL17RB
Variant/haplotype: rs6801605
Drug(s): acamprosate
Phenotype category: Efficacy
Significant: yes
Association: Allele A is associated with increased clinical benefit to acamprosate in people with Alcoholism as compared to allele G.
Notes: IL17RB SNPs were associated with acamprosate treatment outcomes. (A) The locus zoom plot shows the top SNPs of the GWAS for IL17RB on chromosome 3. "Our results indicated that the rs6801605 SNP was associated with time until relapse to alcohol use during the three months of acamprosate treatment (p: 0.038) (Fig. 3B).
Article: Correlation of the DRD2 gene polymorphism with psychopathology and predictive antimanic responses in patients with bipolar mania
Gene: DRD2
Variant/haplotype: rs1800497
Drug(s): lithium, olanzapine
Phenotype category: Efficacy
Significant: yes
Association: Genotype GG is associated with increased clinical benefit to lithium and olanzapine in people with Bipolar Disorder as compared to genotypes AA + AG.
Notes: "The early response in the 2nd week correlates with genotype GG (see Table 5). The higher early response in the 2nd week in patients with genotype GG of DRD2 gene polymorphism rs1800497 was found than that in patients with genotype AA + AG. Remission in the 8th week also correlates with genotyp GG (see Table 6). The higher remission in the 8th week in patients with genotype GG of DRD2 gene polymorphism rs1800497 was found than that in patients with genotype AA + AG." "Manic patients with genotype GG had a greater improvement in the YMRS score due to a greater early effective response and remission, which was not related to higher doses and serum concentrations of olanzapine and lithium."
Article: A Pharmacogenetic Investigation of Intravenous Furosemide in Decompensated Heart Failure: A Meta-Analysis of 3 Clinical Trials
Gene: ABCC4
Variant/haplotype: rs17268282
Drug(s): furosemide
Phenotype category: Efficacy
Significant: yes
Association: Allele T is associated with increased response to furosemide in people with Heart Failure as compared to allele G.
Notes: Decompensated heart failure. Meta-analysis of the DOSE, CARRESS and ROSE randomized trials. Carriers of the T allele experienced a greater amount of weight loss, and therefore an increased response to furosemide, as compared to those with the G allele. No association was seen between this variant and net fluid loss (p=0.12). Please note that alleles have been complemented to the plus chromosomal strand.
Article: Analysis of Genetic and Clinical Factors Associated with Buprenorphine Response
Variant/haplotype: rs11782370
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: A polymorphism in the OPRM1 3′ untranslated region is associated with methadone efficacy in treating opioid dependence
Gene: OPRM1
Variant/haplotype: rs10485058
Drug(s): buprenorphine
Phenotype category: Efficacy
Significant: no
Association: Genotype AA is not associated with response to buprenorphine in people with Opioid-Related Disorders as compared to genotypes AG + GG.
Notes: No significant difference in the percentage of opioid-positive urine drug screens over 24 weeks was seen between patients with the AA and AG+GG genotypes. This SNP was associated with response to methadone treatment.
Article: Genomic Association Analysis of Common Variants Influencing Antihypertensive Response to Hydrochlorothiazide
Gene: PRKCA
Variant/haplotype: rs4791040
Drug(s): "diuretics", "hydrochlorothiazide", "Thiazides, plain"
Phenotype category: Efficacy
Significant: yes
Association: Allele T is associated with decreased response to diuretics, hydrochlorothiazide or Thiazides, plain in people with Hypertension as compared to allele C.
Notes: The association was with diastolic blood pressure response.   It did not reach genome-wide significance when only PEAR + GERA were analyzed, but this SNP was selected for replication in NORDIL and this association was significant. Observations: 4.46 mm Hg decreased reduction of diastolic blood pressure per T allele in PEAR + GERA, 3.30 mm Hg decreased reduction of diastolic blood pressure per T allele in NORDIL, and 4.17 mm Hg decreased  reduction of diastolic blood pressure per T allele in PEAR + GERA + NORDIL.
Article: Genetic variation in OPRD1 and the response to treatment for opioid dependence with buprenorphine in European American females
Gene: OPRD1
Variant/haplotype: rs529520
Drug(s): buprenorphine, methadone
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to buprenorphine or methadone in men with Opioid-Related Disorders as compared to allele C.
Notes: Opioid dependence. This genetic variant did not have a significant effect on the percentage of opioid-positive urine drug screens or missing urine drug screens in males. Note that significant results were seen for females. Patients were treated with buprenorphine or methadone for 24 weeks.
Article: Impact of Gastric H+/K+-ATPase rs2733743 on the Intragastric pH-Values of Dexlansoprazole Injection in Chinese Subjects
Gene: ABCB1
Variant/haplotype: rs1045642
Drug(s): dexlansoprazole
Phenotype category: Metabolism/PK
Significant: no
Association: Allele A is not associated with metabolism of dexlansoprazole in healthy individuals as compared to allele G.
Article: Effect of TCF7L2 polymorphism on pancreatic hormones after exenatide in type 2 diabetes
Gene: TCF7L2
Variant/haplotype: rs7903146
Drug(s): exenatide
Phenotype category: Efficacy
Significant: yes
Association: Genotypes CT + TT is associated with increased response to exenatide in people with Diabetes Mellitus, Type 2 as compared to genotype CC.
Notes: "After treatment with exenatide, only CT/TT individuals demonstrated a significant insulin reduction at 30–180 min during the meal test compared with CC subjects (p < 0.05). Patients with the CC genotype presented no differences in insulin concentrations before and after treatment. The area under the insulin curve between 0 and 180 min was similar between groups before exenatide but decreased only in the CT/TT group after exenatide (p < 0.001) (Fig. 1b)."