shlokn/autogkb huggingface dataset:
Article: Comparative performance of gene-based warfarin dosing algorithms in a multiethnic population
Gene: VKORC1
Variant/haplotype: rs2359612
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Allele A is associated with decreased dose of warfarin as compared to allele G.
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: Modifying Role of Serotonergic 5-HTTLPR & TPH2 Variants on Disulfiram Treatment of Cocaine Addiction: A Preliminary Study
Gene: TPH2
Variant/haplotype: rs4290270
Drug(s): disulfiram
Phenotype category: Efficacy
Significant: yes
Association: Genotypes AA + AT is associated with increased response to disulfiram in people with Cocaine-Related Disorders as compared to genotype TT (assigned as high activity phenotype) .
Notes: There was no difference between disulfiram treatment and placebo for the TT homozygotes but the AT/TT group had lower cocaine positive urines during treatment compared to placebo.
Article: A functional variant in the serotonin receptor 7 gene (HTR7), rs7905446, is associated with good response to SSRIs in bipolar and unipolar depression
Gene: HTR7
Variant/haplotype: rs7905446
Drug(s): escitalopram, nortriptyline
Phenotype category: Efficacy
Significant: no
Association: Genotype TT is not associated with response to escitalopram or nortriptyline in people with Depression as compared to genotypes GG + GT.
Notes: Although there was no significant association of this variant with treatment response in the combined group of patients treated with escitalopram or nortriptyline, there was a significant association in the group of escitalopram-treated patients.
Article: Targeted pharmacogenetic analysis of antipsychotic response in the CATIE study
Gene: PTPRN2
Variant/haplotype: rs221253
Drug(s): olanzapine
Phenotype category: Efficacy
Significant: yes
Association: Allele C is associated with response to olanzapine in people with Schizophrenia.
Notes: as measured by changes in PANSS-T (positive and negative syndrome scale total score), using a mixed model repeated measures approach. Examined 6789 SNPs - p-value of p< or equal to 5x10-4 was considered significant. It was unclear whether the allele was associated with an increased or decreased response to drug.
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: rs681243
Drug(s): ethanol
Phenotype category: Efficacy
Significant: yes
Association: Allele T is associated with increased response to ethanol as compared to allele C.
Notes: Please note that alleles have been complemented to the positive strand. The T allele was associated with increased scores in the buzzed, clumsy, dizzy and nausea traits as well as increased total score on the Subjective High Assessment Scale-Expectations (SHAS-E) questionnaire.
Article: Single nucleotide polymorphisms in the apolipoprotein B and low density lipoprotein receptor genes affect response to antihypertensive treatment
Gene: APOB
Variant/haplotype: rs1367117
Drug(s): irbesartan
Phenotype category: Efficacy, Metabolism/PK
Significant: yes
Association: Genotype AG is associated with response to irbesartan in people with Hypertension.
Notes: reduction in systolic blood pressure.  Treatment was with 150 mg/day for 12 weeks.  The dose was doubled; after six weeks if the diastolic blood pressure was >= 90; mm Hg.  Avg reduction in G carriers was 14 mm Hg.
Article: Association between UGT2B7 gene polymorphisms and fentanyl sensitivity in patients undergoing painful orthognathic surgery
Gene: UGT2B7
Variant/haplotype: rs7668282
Drug(s): fentanyl
Phenotype category: Efficacy
Significant: no
Association: Allele C is not associated with response to fentanyl in people with Pain, Postoperative as compared to allele T.
Notes: There was no significant difference in PPLpost-PPLpre between the genotype groups.
Article: Common polymorphisms of CYP2B6 influence stereoselective bupropion disposition
Gene: CYP2B6
Variant/haplotype: CYP2B6*1, CYP2B6*4, CYP2B6*6
Drug(s): bupropion
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2B6 *1/*4 + *4/*6 are associated with increased metabolism of bupropion in healthy individuals as compared to CYP2B6 *1/*1.
Notes: Carriers of CYP2B6*4 allele had increased hydroxylation of both bupropion enantiomers, assessed by plasma hydroxybupropion/bupropion AUC ratios and urine hydroxybupropion formation clearances. "Median hydroxybupropion/bupropion AUC ratios in CYP2B6*4/X and CYP2B6*1/*1 subjects were 53 (36, 71) and 21 (15, 25) for R,R-hydroxybupropion, 3.4 (2.7, 4.7) and 2.1 (1.6, 2.7) for S,S-hydroxybupropion, and 37 (24, 52) and 15 (10, 18) for total hydroxybupropion."
Article: Association of ABCB1 Gene Polymorphisms with Efficacy and Adverse Reaction to Risperidone or Paliperidone in Han Chinese Schizophrenic Patients
Gene: ABCB1
Variant/haplotype: rs2032582
Drug(s): risperidone
Phenotype category: Efficacy
Significant: no
Association: Genotype CC is not associated with response to risperidone in people with Schizophrenia as compared to genotype AA.
Notes: Alleles given as reverse strand G, A and T. Efficacy measured with reduction in PANSS total score reduced rate. No difference found in PANSS reduction in any genotype.
Article: Association between UGT2B7 gene polymorphisms and fentanyl sensitivity in patients undergoing painful orthognathic surgery
Gene: UGT2B7
Variant/haplotype: rs4235108
Drug(s): fentanyl
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to fentanyl in people with Pain, Postoperative as compared to allele G.
Notes: There was no significant difference in PPLpost-PPLpre between the genotype groups.
Article: Efficacy of the pharmacologic chaperone migalastat in a subset of male patients with the classic phenotype of Fabry disease and migalastat-amenable variants: data from the phase 3 randomized, multicenter, double-blind clinical trial and extension study
Gene: GLA
Variant/haplotype: rs398123212
Drug(s): migalastat
Phenotype category: Efficacy
Significant: not stated
Association: Allele T is associated with increased response to migalastat in people with Fabry Disease.
Notes: Patients carrying the T allele showed improvements in renal function, cardiac geometry (specifically, reductions in left ventricular mass index) and gastrointestinal symptoms as well as reductions in GL-3 inclusions and plasma lyso-Gb3 and an increase in PBMC alpha-Gal A activity when treated with migalastat. Clinical benefit of migalastat was not substantially affected by disease severity. This variant was designated as an 'amenable variant' to migalastat treatment following an in vitro assay where migalastat increased the activity of alpha-Gal A by at least 3%. As all data were derived from post hoc analysis, statistical analyses were not carried out. Variant referred to as Gly183Asp in the paper.
Article: Impact of UGT1A1 Gilbert Variant on Discontinuation of Ritonavir-Boosted Atazanavir in AIDS Clinical Trials Group Study A5202
Gene: UGT1A1
Variant/haplotype: UGT1A1*1, UGT1A1*28, UGT1A1*36
Drug(s): atazanavir / ritonavir
Phenotype category: Toxicity
Significant: yes
Association: UGT1A1 *28/*28 is associated with increased discontinuation of atazanavir / ritonavir in people with HIV Infections as compared to UGT1A1 *1/*1 + *1/*28 + *1/*36 + *36/*36.
Notes: There was an association between *28/*28 (TA7 and TA8 combined) and increased ritonavir-boosted atazanavir discontinuation among Hispanic participants (P = .005) but not among white or black participants (P = .79 and P = .46, respectively). "Genotyping of UGT1A1 rs8175347...*36 (TA)5, *1 (TA)6, *28 (TA)7, and *37 (TA)8." "On the basis of the low expected frequencies of UGT1A1*36 (TA)5 and *37 (TA)8 and their known effects on UGT1A1 expression, UGT1A1*36 (TA)5 and *37 (TA)8 were grouped with *1 (TA)6 and *28 (TA)7 alleles, respectively. This provided a 3-level ordered genotype based on (allele 1)/(allele 2): (*1 or *36)/(*1 or *36), (*1 or *36)/(*28* or *37), and (*28* or *37)/(*28* or *37). These are hereafter referred to as *1/*1, *1/*28*, and 28*/*28*, respectively." " Participants were randomly assigned to receive open-label 300-mg atazanavir plus 100-mg ritonavir or 600-mg efavirenz, with placebo controlled 600-mg abacavir 300-mg lamivudine or 300-mg tenofovir DF 200-mg emtricitabine." NCT00118898
Article: Genetic variants in CYP2A6 and UGT1A9 genes associated with urinary nicotine metabolites in young Mexican smokers
Gene: CYP2A6
Variant/haplotype: rs145014075
Drug(s): nicotine
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype GT is associated with increased concentrations of nicotine as compared to genotype GG.
Notes: Participants with the GT genotype had significantly higher creatinine-adjusted levels of nicotine.
Article: Novel variants in NUDT15 and thiopurine intolerance in children with acute lymphoblastic leukemia from diverse ancestry
Gene: NUDT15
Variant/haplotype: rs766023281
Drug(s): mercaptopurine
Phenotype category: Dosage, Toxicity
Significant: no
Association: Allele C is associated with decreased dose of mercaptopurine in children with Precursor Cell Lymphoblastic Leukemia-Lymphoma as compared to allele G.
Notes: The variant was recurrent in two patients: one from Taiwan and one from Singapore. Both patients tolerated very low doses of mercaptopurine (17.9 and16.4 mg/m /day). Nucleotide diphosphotase activity could not be detected in in vitro studies.
Article: Integrative genomic analysis of methylphenidate response in attention-deficit/hyperactivity disorder
Gene: SENP3
Variant/haplotype: rs11552708
Drug(s): methylphenidate
Phenotype category: Efficacy
Significant: no
Association: Allele A is associated with increased response to methylphenidate in people with Attention Deficit Disorder with Hyperactivity.
Notes: The authors carried out a GWAS in a Spanish cohort of pediatric patients, than performed a meta-analysis using data from the Spanish cohort and data from a Brazilian adult patient cohort.; This variant was not significant in the meta-analysis after Bonferroni correction had been applied, and was nominally significant (i.e did not reach genome-wide significance) in the initial GWAS in the Spanish cohort.; Response was measured on the Clinical Global Impression-Improvement scale (CGI-I). A CGI-I score of two points or less after eight weeks of treatment was considered a good response.
Article: Polymorphisms in STAT4, PTPN2, PSORS1C1 and TRAF3IP2 Genes Are Associated with the Response to TNF Inhibitors in Patients with Rheumatoid Arthritis
Gene: PSORS1C1
Variant/haplotype: rs2233945
Drug(s): adalimumab
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to adalimumab in people with Arthritis, Rheumatoid as compared to allele C.
Notes: No significant associations were seen at six months after the beginning of treatment when response was measured as number of patients in remission or with low disease activity or by EULAR score.; A significant association was seen at two years after treatment when response was measured by EULAR score however this significance was lost after correction for multiple variables. No significant association was seen at two years after treatment when response was measured as the number of patients in remission or with low disease activity.
Article: Variation in Maturity-Onset Diabetes of the Young Genes Influence Response to Interventions for Diabetes Prevention
Variant/haplotype: rs6719578
Drug(s): metformin
Phenotype category: Efficacy
Significant: yes
Association: Genotype CG is associated with increased response to metformin as compared to genotype GG.
Notes: Subjects were at high risk of diabetes and were recruited from Diabetes Prevention Program (DPP) and were followed for a year. The authors measured changes in response to insulin at baseline and one year after treatment. The C allele was significantly associated with response to Metformin (vs. Placebo).
Article: Lack of Associations of CHRNA5-A3-B4 Genetic Variants with Smoking Cessation Treatment Outcomes in Caucasian Smokers despite Associations with Baseline Smoking
Gene: CHRNA5
Variant/haplotype: rs588765
Drug(s): nicotine, varenicline
Phenotype category: Efficacy
Significant: no
Association: Genotype TT is not associated with response to nicotine or varenicline in people with Tobacco Use Disorder as compared to genotypes CC + CT.
Notes: Response here refers to smoking cessation outcomes at 7 days and nicotine refers to nicotine patches. Smoking cessation outcomes at 6 months and 12 months were also not significantly associated with genotype.
Article: Gene Variants in CYP2C19 Are Associated with Altered In Vivo Bupropion Pharmacokinetics but Not Bupropion-Assisted Smoking Cessation Outcomes
Gene: CYP2C19
Variant/haplotype: CYP2C19*1, CYP2C19*2, CYP2C19*17
Drug(s): bupropion
Phenotype category: Efficacy
Significant: no
Association: CYP2C19 *2 + *17 are not associated with response to bupropion in people with Tobacco Use Disorder as compared to CYP2C19 *1.
Notes: There was no association between CYP2C19 variants and the efficacy of bupropion to promote cessation of smoking in African-American smokers. 270 patients were treated with placebo and 270 patients were treated with bupropion. Patients in the treatment arm were given 150 mg once a day of bupropion for 3 days then 150mg twice a day for seven weeks.
Article: Apolipoprotein B genetic variants modify the response to fenofibrate: a GOLDN study
Gene: APOB
Variant/haplotype: rs676210
Drug(s): fenofibrate
Phenotype category: Efficacy
Significant: yes
Association: Genotype AA is associated with increased response to fenofibrate in people with Hypertriglyceridemia as compared to genotypes AG + GG.
Notes: AA genotype participants had greater lowering of triglycerides than did AG or GG individuals.
Article: Efficacy of the pharmacologic chaperone migalastat in a subset of male patients with the classic phenotype of Fabry disease and migalastat-amenable variants: data from the phase 3 randomized, multicenter, double-blind clinical trial and extension study
Gene: GLA
Variant/haplotype: rs190347120
Drug(s): migalastat
Phenotype category: Efficacy
Significant: not stated
Association: Allele A is associated with increased response to migalastat in people with Fabry Disease.
Notes: Patients carrying the A allele showed improvements in renal function, cardiac geometry (specifically, reductions in left ventricular mass index) and gastrointestinal symptoms as well as reductions in GL-3 inclusions and plasma lyso-Gb3 and an increase in PBMC alpha-Gal A activity when treated with migalastat. Clinical benefit of migalastat was not substantially affected by disease severity. This variant was designated as an 'amenable variant' to migalastat treatment following an in vitro assay where migalastat increased the activity of alpha-Gal A by at least 3%. As all data were derived from post hoc analysis, statistical analyses were not carried out. Variant referred to as Asp264Tyr in the paper.
Article: Polymorphism of Drug Transporters, Rather Than Metabolizing Enzymes, Conditions the Pharmacokinetics of Rasagiline
Gene: CYP1A2
Variant/haplotype: rs762551
Drug(s): rasagiline
Phenotype category: Metabolism/PK
Significant: no
Association: Genotype AA is not associated with clearance of rasagiline in healthy individuals.
Notes: "Rasagiline pharmacokinetic parameters based on CYP1A2 diplotypes are shown in Table 4. No significant associations were observed. " "The most prevalent allele was *1F (53%),the most prevalent diplotypes were *1F/*1F (33%) and *1B/*1F (31%)" *1F=*30=rs762551 (-163) C>A (PharmVar 2024). Article included diplotypes based on the following alleles *1B, *1C, *1E, *1F, *1G, *1J, *1K, *1L, *1N. After CYP1A2 full transition into PharmVar (12/2024) *1B is assigned under the *1 core allele. *1C, *1E, *1G, *1J, *1K were not transferred to the PharmVar CYP1A2 nomenclature and *1F, *1L, *1N are grouped under *30. Annotation done on rs762551. The -163C>A SNP by itself is the core allele definition for *30, however, -163C>A is included in several other core alleles (25 different CYP1A2 core alleles in addition to *30, as of 02/2025).
Article: Haplotypes of P2RX7 gene polymorphisms are associated with both cold pain sensitivity and analgesic effect of fentanyl
Gene: P2RX7
Variant/haplotype: rs7132846
Drug(s): fentanyl
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with dose of fentanyl in people with Pain, Postoperative as compared to allele C.
Notes: No significant association between this variant and 24-h postoperative fentanyl use or perioperative fentanyl use.
Article: The MAOA rs979605 Genetic Polymorphism Is Differentially Associated with Clinical Improvement Following Antidepressant Treatment between Male and Female Depressed Patients
Gene: MAOB
Variant/haplotype: rs1799836
Drug(s): 5-hydroxyindole-3-acetic acid, serotonin
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele T is associated with increased concentrations of 5-hydroxyindole-3-acetic acid and serotonin in men with Depressive Disorder, Major as compared to allele C.
Notes: "TT/T females/males had a significantly higher 5HIAA/5HT ratio (2.79 ± 0.27) compared to CC/C females/males (2.18 ± 0.28) following Bonferroni correction"
Article: Impact of CYP2B6, ABCB1 and CYP3A5 Polymorphisms on Efavirenz Pharmacokinetics and Treatment Response: An AIDS Clinical Trials Group Study
Gene: ABCB1
Variant/haplotype: rs1045642
Drug(s): efavirenz
Phenotype category: Other, Metabolism/PK
Significant: no
Association: Allele A is not associated with decreased response to efavirenz in people with Acquired Immunodeficiency Syndrome.
Notes: Analyses comprised 831 subjects (19% female, 48% white, 34% black, and 18% Hispanic)
Article: IFNL4 ss469415590 Variant Is Associated with Treatment Response in Japanese HCV Genotype 1 Infected Individuals Treated with IFN-Including Regimens
Gene: IFNL4
Variant/haplotype: rs11322783
Drug(s): peginterferon alfa-2a, peginterferon alfa-2b, ribavirin
Phenotype category: Efficacy
Significant: yes
Association: Genotype TT/TT is associated with increased response to peginterferon alfa-2a, peginterferon alfa-2b and ribavirin in people with Hepatitis C as compared to genotypes G/TT + GG.
Notes: in Japanese hepatitis C genotype 1 patients.
Article: Attempted validation of 44 reported SNPs associated with tacrolimus troughs in a cohort of kidney allograft recipients
Gene: SLCO1B1
Variant/haplotype: rs4149056
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: no
Association: Allele T is not associated with trough concentration of tacrolimus in people with Kidney Transplantation and Transplantation as compared to allele C.
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.
Article: Influences of an NR1I2 polymorphism on heterogeneous antiplatelet reactivity responses to clopidogrel and clinical outcomes in acute ischemic stroke patients
Gene: N6AMT1
Variant/haplotype: rs2254638
Drug(s): clopidogrel
Phenotype category: Efficacy
Significant: yes
Association: Allele G is associated with decreased response to clopidogrel in people with Coronary Artery Disease as compared to allele A.
Notes: This variant is associated with decreased H4 concentration, and decreased antiplatelet effects of clopidogrel with a higher PRU.
Article: Measurements of Functional Responses in Human Primary Lung Cells as a Basis for Personalized Therapy for Cystic Fibrosis
Gene: CFTR
Variant/haplotype: rs80034486
Drug(s): lumacaftor
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with response to lumacaftor.
Notes: N1303K allele. Study carried out using primary bronchial epithelial cells from donors with cystic fibrosis. Secretion of chloride ions across the cell membrane was measured to determine CFTR activity.; Cells had the CFTR genotype N1303K/G542X. As the G542X allele does not generate a protein molecule, these cells were used to assess the effects of lumacaftor on the N1303K allele only.
Article: Tacrolimus dose requirements in paediatric renal allograft recipients are characterized by a biphasic course determined by age and bone maturation
Gene: ABCB1
Variant/haplotype: rs2032582
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: no
Association: Genotype AA is not associated with concentrations of tacrolimus in children with Kidney Transplantation.
Notes: As compared to AC, CT and AT genotypes. Dose-corrected tacrolimus exposure (AUC0-12/doseBW). Please note that alleles have been complemented to the plus chromosomal strand.
Article: Population pharmacokinetics and pharmacogenomics of apixaban in Japanese adult patients with atrial fibrillation
Gene: CYP3A5
Variant/haplotype: rs776746
Drug(s): apixaban
Phenotype category: Metabolism/PK
Significant: not stated
Association: Genotypes CT + TT is associated with increased clearance of apixaban in people with Atrial Fibrillation as compared to genotype CC.
Article: Meta-Analysis on Pharmacogenetics of Platinum-Based Chemotherapy in Non Small Cell Lung Cancer (NSCLC) Patients
Gene: ERCC1
Variant/haplotype: rs11615
Drug(s): Platinum compounds
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with increased response to Platinum compounds in people with Carcinoma, Non-Small-Cell Lung as compared to allele A.
Notes: No significant relationship between genotype and drug response was detected.
Article: Polymorphisms in drug-metabolizing enzymes and steady-state exemestane concentration in post-menopausal patients with breast cancer
Gene: CYP4A11
Variant/haplotype: rs9332978
Drug(s): exemestane
Phenotype category: Metabolism/PK
Significant: no
Association: Genotype CT is not associated with concentrations of exemestane in women with Breast Neoplasms as compared to genotype TT.
Notes: No significant difference in exemestane concentrations were seen between the genotypes. Please note that alleles have been complemented to the plus chromosomal strand.
Article: CHRNB2 Promoter Region: Association with subjective effects to nicotine and expression differences
Gene: CHRNA4
Variant/haplotype: rs2229959
Drug(s): nicotine
Phenotype category: Other
Significant: yes
Association: Allele C is associated with increased response to nicotine in people with daily smoking as compared to allele A.
Notes: Response(sweating, heart pounding and nausea) to the first experimental cigarette was measured using the NEQ(nicotine effects scale).
Article: Genetic Polymorphism of Cytochrome P450 4F2, Vitamin E Level and Histological Response in Adults and Children with Nonalcoholic Fatty Liver Disease Who Participated in PIVENS and TONIC Clinical Trials
Gene: CYP4F2
Variant/haplotype: rs2108622
Drug(s): vitamin e
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with response to vitamin e in people with Fatty liver disease as compared to allele C.
Notes: The T allele is not significantly associated with improvement in liver histology in pediatric or adult patients receiving vitamin E (alpha-tocopherol) supplements at week 48 or at week 96.
Article: S-1 plus irinotecan and oxaliplatin for the first-line treatment of patients with metastatic colorectal cancer: a prospective phase II study and pharmacogenetic analysis
Gene: CYP2A6
Variant/haplotype: CYP2A6*1, CYP2A6*4, CYP2A6*7, CYP2A6*9
Drug(s): irinotecan, oxaliplatin, tegafur / gimeracil / oteracil
Phenotype category: Efficacy
Significant: yes
Association: CYP2A6 *4 + *7 + *9 are associated with decreased response to irinotecan, oxaliplatin and tegafur / gimeracil / oteracil in people with Colorectal Neoplasms as compared to CYP2A6 *1/*1.
Notes: The objective response rate was significantly lower in patients carrying CYP2A6 variant alleles compared to those with no variant alleles.