shlokn/autogkb huggingface dataset:
Article: A genetic risk score is associated with statin-induced low-density lipoprotein cholesterol lowering
Gene: LPA
Variant/haplotype: rs10455872
Drug(s): hmg coa reductase inhibitors
Phenotype category: Efficacy
Significant: yes
Association: Allele G is associated with decreased response to hmg coa reductase inhibitors as compared to allele A.
Notes: as part of a three SNP genetic risk score with rs2231142 in ABCG2 and rs2075650 in APOE. Associated allele not explicitly stated but methods reference Chasman et al., so used the associated allele from there [PMID:22331829].
Article: Pharmacokinetic and pharmacogenetic determinants of the activity and toxicity of irinotecan in metastatic colorectal cancer patients
Gene: UGT1A1
Variant/haplotype: UGT1A1*1, UGT1A1*28
Drug(s): SN-38
Phenotype category: Metabolism/PK
Significant: no
Association: UGT1A1 *1/*28 + *28/*28 are not associated with metabolism of SN-38 in people with Colorectal Neoplasms as compared to UGT1A1 *1/*1.
Notes: No association was seen between rs8175347 genotype and the area under the concentration curve (AUC) of SN-38G, the glucuronidated and inactive SN-38 metabolite. UGT1A1 is responsible for the glucuronidation of SN-38.
Article: Association of BDNF, HTR2A, TPH1, SLC6A4, and COMT polymorphisms with tDCS and escitalopram efficacy: ancillary analysis of a double-blind, placebo-controlled trial
Gene: HTR2A
Variant/haplotype: rs6311
Drug(s): escitalopram
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with response to escitalopram in people with Depression as compared to allele C.
Article: Association studies of dopamine synthesis and metabolism genes with multiple phenotypes of heroin dependence
Gene: TH
Variant/haplotype: rs10770141
Drug(s): heroin
Phenotype category: Dosage
Significant: no
Association: Allele G is not associated with dose of heroin in people with Heroin Dependence as compared to allele A.
Article: Germline Genetic Variants in TEK, ANGPT1, ANGPT2, MMP9, FGF2 and VEGFA Are Associated with Pathologic Complete Response to Bevacizumab in Breast Cancer Patients
Gene: ANGPT2
Variant/haplotype: rs2515409
Drug(s): bevacizumab
Phenotype category: Efficacy
Significant: no
Association: Allele C is not associated with response to bevacizumab in women with Breast Neoplasms as compared to allele T.
Article: Predictive factors for 24 weeks sustained virologic response (SVR24) and viral relapse in patients treated with simeprevir plus peginterferon and ribavirin
Gene: IFNL3
Variant/haplotype: rs8099917
Drug(s): peginterferon alfa-2a, peginterferon alfa-2b, ribavirin, simeprevir
Phenotype category: Efficacy
Significant: yes
Association: Genotype TT is associated with increased response to peginterferon alfa-2a, peginterferon alfa-2b, ribavirin or simeprevir in people with Hepatitis C as compared to genotypes GG + GT.
Notes: in treatment-naïve patients and relapsers.
Article: Genotypic variation in the SV2C gene impacts response to atypical antipsychotics the CATIE Study
Gene: SV2C
Variant/haplotype: rs10514062
Drug(s): risperidone
Phenotype category: Efficacy
Significant: no
Association: Genotype TT is not associated with response to risperidone in people with Schizophrenia as compared to genotypes AA + AT.
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. In significant LD (r2 > 0.95) with rs7732173 and rs2358531.
Article: Effect of CYP2C19*2 and *17 mutations on pharmacodynamics and kinetics of proton pump inhibitors in Caucasians
Gene: CYP2C19
Variant/haplotype: CYP2C19*1, CYP2C19*2, CYP2C19*17
Drug(s): omeprazole, pantoprazole
Phenotype category: Efficacy
Significant: no
Association: CYP2C19 *1/*1 is not associated with response to omeprazole or pantoprazole in healthy individuals as compared to CYP2C19 *1/*17.
Notes: No significant difference in the mean percentage of time with intragastric pH greater than 4.0 was seen between the genotypes in subjects taking omeprazole (20 mg/day) or pantoprazole (40 mg/day). Subjects were treated with either drug for 6 days, in a crossover fashion; mean percentage of time with intragastric pH greater than 4.0 was measured on day 1 and day 6 after initiation of treatment.
Article: Warfarin Dosage Response Related Pharmacogenetics in Chinese Population
Gene: CYP4F2
Variant/haplotype: rs2108622
Drug(s): warfarin
Phenotype category: Dosage
Significant: no
Association: Genotypes CT + TT are not associated with concentrations of warfarin in people with heart valve replacement as compared to genotype CC.
Notes: 130 plasma samples were obtained 12 hours after the last dose of warfarin. The plasma warfarin concentrations of these samples were comparing plasma concentration within the group of patients with INR between 1.5–2.5 (n = 92). Please note: alleles have been complemented to the + chromosomal strand.
Article: Polymorphisms in methotrexate transporters and their relationship to plasma methotrexate levels, toxicity of high-dose methotrexate, and outcome of pediatric acute lymphoblastic leukemia
Gene: SLC19A1
Variant/haplotype: rs1051266
Drug(s): methotrexate
Phenotype category: Efficacy
Significant: no
Association: Allele C is not associated with response to methotrexate in children with Precursor Cell Lymphoblastic Leukemia-Lymphoma as compared to allele T.
Notes: Please note: alleles have been complemented to the + chromosomal strand.
Article: Variant‐based heritability assessment of dexmedetomidine and fentanyl clearance in pediatric patients
Gene: KCNA3
Variant/haplotype: rs114087210
Drug(s): dexmedetomidine
Phenotype category: Metabolism/PK
Significant: no
Association: Allele A is associated with decreased clearance of dexmedetomidine in children with Pain, Postoperative as compared to allele G.
Notes: Data from Table S2, direction of effect and risk allele not clear. Minor allele and frequency stated. Mapped to dbSNP using genomic location 1:111239222:A:G on hg19/GRCh37. "GWAS failed to identify any variants meeting the genome-wide statistical significance threshold of 5 × 10−8" This is top scoring variant.
Article: VKORC1 variants as significant predictors of warfarin dose in Emiratis
Gene: VKORC1
Variant/haplotype: rs61742245
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Genotypes AA + AC are associated with increased dose of warfarin as compared to genotype CC.
Notes: Please note that alleles have been complemented to the positive strand.
Article: A genetic risk score is associated with statin-induced low-density lipoprotein cholesterol lowering
Gene: ABCG2
Variant/haplotype: rs2231142
Drug(s): hmg coa reductase inhibitors
Phenotype category: Efficacy
Significant: yes
Association: Allele G is associated with decreased response to hmg coa reductase inhibitors as compared to allele T.
Notes: as part of a three SNP genetic risk score with rs10455872 in LPA and rs2075650 in APOE. Associated allele not explicitly stated but methods reference Tomlinson et al. so used the associated allele from there [PMID:20130569].
Article: CYP2A6 and the plasma level of 5‐chloro‐2, 4‐dihydroxypyridine are determinants of the pharmacokinetic variability of tegafur and 5‐fluorouracil, respectively, in Japanese patients with cancer given S‐1
Gene: CYP2A6
Variant/haplotype: CYP2A6*1, CYP2A6*4, CYP2A6*7
Drug(s): tegafur
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2A6 *4/*4 + *4/*7 + *7/*7 are associated with decreased clearance of tegafur in people with Neoplasms as compared to CYP2A6 *1/*1.
Notes: Oral clearance. Please note; the allele was described in the study as *4, and here is represented as *4. Also, the 3' UTR conversion of the *7 allele was not mentioned in the study.
Article: Adiponectin Gene Polymorphism rs2241766 T/G Is Associated with Response to Pioglitazone Treatment in Type 2 Diabetic Patients from Southern China
Gene: ADIPOQ
Variant/haplotype: rs1063538
Drug(s): pioglitazone
Phenotype category: Efficacy
Significant: no
Association: Genotypes CC + CT are not associated with response to pioglitazone in people with Diabetes Mellitus as compared to genotype TT.
Notes: Response was defined as "any decrease greater than (or equal to) 15%" of glycated hemoglobin (HbA1C%).
Article: Genome-wide association scan identifies candidate polymorphisms associated with differential response to anti-TNF treatment in Rheumatoid Arthritis
Gene: PON1
Variant/haplotype: rs854547
Drug(s): Tumor necrosis factor alpha (TNF-alpha) inhibitors
Phenotype category: Efficacy
Significant: no
Association: Allele A is associated with decreased response to Tumor necrosis factor alpha (TNF-alpha) inhibitors in people with Arthritis, Rheumatoid as compared to allele G.
Notes: 54 subjects were treated with etanercept, 37 with infliximab, and 25 with adalimumab. Response to therapy was determined by the change in Disease Activity Score (DAS28) observed after 14 wks.
Article: Functional genetic variation in the Rev-Erbα pathway and lithium response in the treatment of bipolar disorder
Gene: CLOCK
Variant/haplotype: rs1801260
Drug(s): lithium
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with increased response to lithium in people with Bipolar Disorder as compared to allele A.
Article: The MAOA rs979605 Genetic Polymorphism Is Differentially Associated with Clinical Improvement Following Antidepressant Treatment between Male and Female Depressed Patients
Gene: MAOA
Variant/haplotype: rs979605
Drug(s): antidepressants
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype AA is associated with decreased clinical benefit to antidepressants in people with Depressive Disorder, Major as compared to allele A.
Notes: as measured by Hamilton score. "rs979605(G) allele was correlated with the rs6323(T) allele" "The rs979605 × sex interaction was significantly associated with the HDRS score, and after 6 months of treatment, a significantly higher HDRS score was observed in female rs979605 AA homozygotes compared to male A carriers."
Article: Prognostic Role of Human Leukocyte Antigen Alleles and Cytokine Single-Nucleotide Polymorphisms in Patients with Chronic Myeloid Leukemia Treated with Tyrosine Kinase Inhibitor Drugs
Gene: HLA-A
Variant/haplotype: HLA-A*03:01
Drug(s): BCR-ABL tyrosine kinase inhibitors
Phenotype category: Efficacy
Significant: yes
Association: HLA-A *03:01 is associated with decreased clinical benefit to BCR-ABL tyrosine kinase inhibitors in people with Leukemia, Myelogenous, Chronic, BCR-ABL Positive.
Notes: "The frequency of A*03 is increased by a factor of 2.3 in the unfavorable group (p-value = 0.0347). "
Article: Nuclear receptor gene polymorphisms and warfarin dose requirements in the Quebec Warfarin Cohort
Gene: VDR
Variant/haplotype: rs11168292
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Genotype GG is associated with increased dose of warfarin as compared to genotypes CC + CG.
Notes: This SNP is in very tight linkage disequilibrium with rs11168293 and rs4760658 (r2>0.97). Mean dose (in mg) of warfarin according to genotype was: GG>CG>CC. p-value adjusted for CYP2C9 metabolizer status and VKORC1 activity status phenotypes, among other factors. Warfarin dose requirement was defined as the reported daily dose at 3 months following treatment initiation.
Article: Combined study of genetic and epigenetic biomarker risperidone treatment efficacy in Chinese Han schizophrenia patients
Gene: CYP1B1
Variant/haplotype: rs1056827
Drug(s): risperidone
Phenotype category: Efficacy
Significant: no
Association: Allele A is associated with decreased response to risperidone in people with Schizophrenia as compared to allele C.
Notes: The A allele was initially significantly more frequent in patients designated as non-responders to risperidone (i.e. <50% reduction in PANSS score compared to the cohort average). However, significance was lost following correction for multiple testing.
Article: CYP2B6 SNPs are associated with methadone dose required for effective treatment of opioid addiction
Gene: CYP2B6
Variant/haplotype: rs3745274
Drug(s): methadone
Phenotype category: Dosage
Significant: yes
Association: Genotypes GG + GT are associated with increased dose of methadone in people with Heroin Dependence as compared to genotype TT.
Notes: Patients with the GG or GT genotype required an increased mean daily methadone dose (mg/day) as compared to those with the TT genotype. Please note that this SNP was found to be in strong LD (D' = 1 and r2 = 0.9) with rs2279343 in this sample population.
Article: An expanded pharmacogenomics warfarin dosing table with utility in generalised dosing guidance
Gene: CYP2C9
Variant/haplotype: rs1057910
Drug(s): warfarin
Phenotype category: Dosage
Significant: not stated
Association: Allele A is associated with dose of warfarin as compared to allele C.
Notes: This variant annotation is part of a dosing algorithm table based on 8 genetic variants.
Article: Association between imatinib transporters and metabolizing enzymes genotype and response in newly diagnosed chronic myeloid leukemia patients receiving imatinib therapy
Gene: ABCB1
Variant/haplotype: rs1045642
Drug(s): imatinib
Phenotype category: Efficacy
Significant: no
Association: Genotype GG is not associated with response to imatinib in people with Leukemia, Myelogenous, Chronic, BCR-ABL Positive as compared to genotypes AA + AG.
Notes: This genotype was not significantly with associated with likelihood of achieving major molecular response (MMR) within 12 months. MMR was classified based on BCR-ABL to control gene transcript ratios, expressed on the International Scale; MMR was a ratio <= 0.1%. Please note that alleles have been complemented to the plus chromosomal strand, and that this SNP was listed as rs60023214.
Article: IL-4 receptor polymorphisms predict reduction in asthma exacerbations during response to an anti–IL-4 receptor α antagonist
Gene: IL4R
Variant/haplotype: rs1029489
Drug(s): pitrakinra
Phenotype category: Efficacy
Significant: yes
Association: Genotype GG is associated with increased response to pitrakinra in people with Asthma as compared to genotypes AA + AG.
Notes: Subjects with the GG genotype have a reduced frequency of asthma exacerbations compared to those with the AA + AG genotypes. There is also a significant dose-response relationship for this phenotype in subjects with the GG genotype.
Article: Comprehensive Ara-C SNP score predicts leukemic cell intracellular ara-CTP levels in pediatric acute myeloid leukemia patients
Gene: DCK
Variant/haplotype: rs4643786
Drug(s): ara-CTP
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotypes CC + CT is associated with decreased concentrations of ara-CTP in children with Leukemia, Myeloid, Acute as compared to genotype TT.
Article: Association between UGT2B7 gene polymorphisms and fentanyl sensitivity in patients undergoing painful orthognathic surgery
Gene: UGT2B7
Variant/haplotype: rs6851533
Drug(s): fentanyl
Phenotype category: Dosage
Significant: no
Association: Allele T is not associated with dose of fentanyl in people with Pain, Postoperative as compared to allele C.
Notes: There was no significant difference in 24 hour fentanyl use between the genotype groups.
Article: The effects of CYP2D6 and CYP3A activities on the pharmacokinetics of immediate release oxycodone
Gene: CYP2D6
Variant/haplotype: CYP2D6 poor metabolizer genotype
Drug(s): oxycodone
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2D6 poor metabolizer is associated with increased exposure to oxycodone in healthy individuals as compared to CYP2D6 normal metabolizer.
Notes: The half-life of oxycodone was significantly increased in poor metabolizers compared to extensive metabolizers, but there was no significant difference in oxycodone half-life between poor metabolizers and ultrarapid metabolizers.
Article: Optimizing clopidogrel dose response: a new clinical algorithm comprising CYP2C19 pharmacogenetics and drug interactions
Gene: CYP2C19
Variant/haplotype: CYP2C19*2, CYP2C19*3, CYP2C19*17
Drug(s): clopidogrel
Phenotype category: Dosage
Significant: not stated
Association: CYP2C19 *2 + *3 + *17 are associated with dose of clopidogrel.
Notes: This study provided a table of dose adjustments for clopidogrel, based on CYP2C19 genotype and interacting drugs metabolized by CYP2C19. It was based on a clopidogrel dose of 75 mg.
Article: Genetic polymorphisms are associated with individual susceptibility to dexmedetomidine
Gene: KCNMA1
Variant/haplotype: rs16934182
Drug(s): dexmedetomidine
Phenotype category: Toxicity
Significant: yes
Association: Genotypes AA + AG is associated with increased response to dexmedetomidine in people with surgery as compared to genotype GG.
Notes: as measured by decreased in mean arterial pressure. "Concerning the hemodynamic effect, we discovered the patients with GA/AA had a greater percent change in MAP than those with GG (−23.07 ± 4.41 vs. −8.58 ± 9.36, p = 0.009). Therefore, heterozygosity or homozygosity for A allele of KCNMA1 rs16934182 was more sensitive to the cardiovascular effect of DXM."
Article: Novel CYP2A6 variants identified in African Americans are associated with slow nicotine metabolism in vitro and in vivo
Gene: CYP2A6
Variant/haplotype: CYP2A6*1, CYP2A6*39
Drug(s): nicotine
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2A6 *39 is associated with decreased metabolism of nicotine as compared to CYP2A6 *1.
Notes: Association with lower activity of the novel variant groups [CYP2A6*39 (V68M; rs143690364), CYP2A6*40 (I149M), CYP2A6*41 (R265Q; rs140471703), CYP2A6*42 (I268T), CYP2A6*43 (T303I), CYP2A6*44 (E390K; rs376817657), CYP2A6*44 (L462P)] was; tested using a one-way analysis of variance with Bonferroni tests used for post-hoc analysis, P<0.01. A comparison between CYP2A6*1/*1 and; the combined group was tested using an unpaired t-test, ***P<0.001
Article: The Relation Between CYP2C19 Genotype and Phenotype in Stented Patients on Maintenance Dual Antiplatelet Therapy
Gene: CYP2C19
Variant/haplotype: rs4244285
Drug(s): aspirin, clopidogrel
Phenotype category: Efficacy
Significant: yes
Association: Allele A is associated with decreased response to aspirin and clopidogrel in people with Coronary Artery Disease as compared to allele G.
Notes: The prevalence of High Platelet Reactivity (HPR) was higher in  (AA + AG) compared to GG, but the template doesn't accommodate this.  *2 SNP.  [stat_test: chi-square]
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: rs1045642
Drug(s): pravastatin
Phenotype category: Metabolism/PK
Significant: no
Association: Allele G is not associated with metabolism of pravastatin in children with Hyperlipoproteinemia Type II as compared to allele A.
Notes: No significant association was found between PK parameters and this SNP.
Article: ASSOCIATIONS OF ABCB1 3435C>T AND IL-10 -1082G>A POLYMORPHISMS WITH LONG-TERM SIROLIMUS DOSE REQUIREMENTS IN RENAL TRANSPLANT PATIENTS
Gene: TNF
Variant/haplotype: rs1800629
Drug(s): sirolimus
Phenotype category: Metabolism/PK
Significant: no
Association: Allele A is not associated with dose-adjusted trough concentrations of sirolimus in people with Kidney Transplantation as compared to allele G.
Notes: No significant difference in log-transformed dose-adjusted trough concentrations (C/D) were seen between the genotypes AA, AG or GG.
Article: Pharmacogenomic Next-Generation DNA Sequencing: Lessons from the Identification and Functional Characterization of Variants of Unknown Significance in CYP2C9 and CYP2C19
Gene: CYP2C9
Variant/haplotype: rs771237265
Drug(s): tolbutamide
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele C is associated with decreased clearance of tolbutamide as compared to allele A.
Notes: In vitro analysis showed that intrinsic clearance of tolbutamide by CYP2C9 protein containing the C allele was 9.6% of that of the WT protein. Variant referred to as 343A>C in the paper.
Article: Influence of genetic polymorphisms in P2Y12 receptor signaling pathway on antiplatelet response to clopidogrel in coronary heart disease
Gene: CYP2C19
Variant/haplotype: CYP2C19*1, CYP2C19*3
Drug(s): clopidogrel
Phenotype category: Efficacy
Significant: no
Association: CYP2C19 *1/*3 is associated with increased resistance to clopidogrel in people with Coronary Disease as compared to CYP2C19 *1/*1.
Notes: *3 was not significant alone, there were no *3/*3 individuals in the discovery sample set.
Article: A GRK5 Polymorphism that Inhibits β-Adrenergic Receptor Signaling is Protective in Heart Failure
Gene: GRK5
Variant/haplotype: rs2230345
Drug(s): Beta Blocking Agents
Phenotype category: Efficacy
Significant: not stated
Association: Genotypes AA + AT are associated with response to Beta Blocking Agents in people with Heart Failure as compared to genotype TT.
Notes: P value is comparing with and without drug, not genotypes. When not treated with beta blockers patients with GRK-Q41 have increased risk of death or transplantation compared to patients with GRK-L41. When treated with beta blockers patients with GRK-Q41 showed improvements with beta blockers that brought the Kaplan Meier curve up to the same as that for GRK-L41. When treated with beta blockers patients with the GRK-L41 (TT) did not show any change in outcome.
Article: Impact of the CYP2C19*17 Allele on the Pharmacokinetics of Omeprazole and Pantoprazole in Children: Evidence for a Differential Effect
Gene: CYP2C19
Variant/haplotype: CYP2C19*1, CYP2C19*2, CYP2C19*17
Drug(s): omeprazole
Phenotype category: Metabolism/PK
Significant: no
Association: CYP2C19 *17 is not associated with increased metabolism of omeprazole in children as compared to CYP2C19 *1 + *2.
Notes: There was no significant difference in PK parameters in pediatric subjects among those carrying *17, *1 and *2 (*1/*1, *1/*17, *17/*17, *1/*2, *2/*17).
Article: A genome-wide association study of plasma concentrations of warfarin enantiomers and metabolites in sub-Saharan black-African patients
Gene: CYP2C9
Variant/haplotype: rs28371685
Drug(s): warfarin
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele T is associated with decreased metabolism of warfarin in people with Atrial Fibrillation, venous thromboembolism or Heart Valve Diseases as compared to allele C.
Notes: for S-warfarin stereoisomer in particular, measured as increased S-warfarin/R-warfarin ratio and decreased S-7OH-warfarin/S-warfarin and using a Bonferroni-adjusted replication significance threshold p < 3.21 × 10−4. (CYP2C9*11)
Article: Association studies of dopamine synthesis and metabolism genes with multiple phenotypes of heroin dependence
Gene: SLC6A3
Variant/haplotype: rs6347
Drug(s): methadone
Phenotype category: Dosage
Significant: no
Association: Allele C is not associated with dose of methadone in people with Heroin Dependence as compared to allele T.
Article: ABC Transporter Polymorphisms are Associated with Irinotecan Pharmacokinetics and Neutropenia
Gene: ABCB1
Variant/haplotype: rs2373586
Drug(s): SN-38
Phenotype category: Metabolism/PK
Significant: no
Association: Genotypes AC + CC are not associated with exposure to SN-38 in people with Colorectal Neoplasms as compared to genotype AA.
Notes: AUC of SN-38 was adjusted for irinotecan dose.
Article: Race, Gender, and Genetic Polymorphism Contribute to Variability in Acetaminophen Pharmacokinetics, Metabolism, and Protein-Adduct Concentrations in Healthy African-American and European-American Volunteers
Gene: UGT2B15
Variant/haplotype: rs1902023
Drug(s): acetaminophen
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype AA is associated with increased metabolism of acetaminophen in healthy individuals as compared to genotypes AC + CC.
Notes: Metabolism here refers to concentration of acetaminophen protein adducts. The A allele is also referred to as the *2 allele. Please note: alleles have been complemented to the + chromosomal strand.