shlokn/autogkb huggingface dataset:
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: ABCB1
Variant/haplotype: rs1128503
Drug(s): methotrexate
Phenotype category: Metabolism/PK
Significant: no
Association: Genotypes AG + GG are not associated with concentrations of methotrexate in children with Precursor Cell Lymphoblastic Leukemia-Lymphoma as compared to genotype AA.
Notes: There is no association between selected SNPs and methotrexate plasma level at 48 h between the first dose of methotrexate infusion. med. MTX concentration: AG+GG 0.47 (0.09–19.88)) vs. AA 0.39 (0.12–41.63)). Please note: alleles have been complemented to the + chromosomal strand.
Article: ASSOCIATIONS OF ABCB1 3435C>T AND IL-10 -1082G>A POLYMORPHISMS WITH LONG-TERM SIROLIMUS DOSE REQUIREMENTS IN RENAL TRANSPLANT PATIENTS
Gene: IL10
Variant/haplotype: rs1800896
Drug(s): sirolimus
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype CC are associated with increased dose-adjusted trough concentrations of sirolimus in people with Kidney Transplantation as compared to genotypes CT + TT.
Notes: Patients with the CC genotype had a 24% higher mean sirolimus log-transformed dose-adjusted trough concentrations (C/D) as compared to those with the CT or TT genotype. Multivariate analysis. Please note that alleles have been complemented to the plus chromosomal strand.
Article: The Association of Transporter Genes Polymorphisms and Lung Cancer Chemotherapy Response
Gene: AQP9
Variant/haplotype: rs1516400
Drug(s): platinum
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to platinum in people with Lung Neoplasms as compared to allele G.
Notes: 26 SNPs were selected which satisfied the following criteria: 1) SNPs were from HapMap Project Phase II of the Han Chinese population 2) were haplotype tagger SNPs 3) SNP minor allele frequency was higher than 5% in Han Chinese 4) the pairwise linkage disequilibrium correlation coefficient (r-squared) was greater than 0.8. After Bonferroni corrections no SNPs remained significantly associated with platinum drug efficacy.
Article: CYP2B6 18492T→C Polymorphism Compromises Efavirenz Concentration in Coinfected HIV and Tuberculosis Patients Carrying CYP2B6 Haplotype *1/*1
Gene: CYP2B6
Variant/haplotype: rs2279345
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype CT is associated with increased metabolism of efavirenz in people with HIV Infections as compared to genotype TT.
Notes: Significantly lower efavirenz plasma levels were observed in patients with the CT genotype compared to TT only at 24 weeks (after rifampin discontinuation). All patients had the CYP2B6*1/*1 haplotype (as determined by 7 SNPs) before being assessed by this SNP. Please note; this SNP was described as 18492T>C (and previous studies by this group provided the rsID). Multivariate analysis of efavirenz plasma levels at weeks 12 and 24 of treatment showed that this SNP significantly contributed with the C allele was associated with decreased efavirenz plasma concentrations (P at 12 week=0.004 and p at 24 week = 0.007).
Article: Race influences warfarin dose changes associated with genetic factors
Variant/haplotype: rs12777823
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Genotypes AA + AG are associated with decreased dose of warfarin as compared to genotype GG.
Notes: only in African Americans, but not European Americans. However, the dose reduction per variant allele was higher among European Americans (2.3% vs 12.3%, interaction P value=0.006) compared with African Americans.
Article: Pharmacogenomic Next-Generation DNA Sequencing: Lessons from the Identification and Functional Characterization of Variants of Unknown Significance in CYP2C9 and CYP2C19
Gene: CYP2C19
Variant/haplotype: rs183701923
Drug(s): mephenytoin
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele T is associated with decreased clearance of mephenytoin as compared to allele C.
Notes: In vitro analysis showed that intrinsic clearance of S-mephenytoin by CYP2C19 protein containing the T allele was 1.6% of that of the WT protein. Variant referred to as 556C>T in the paper.
Article: N-acetyltransferase 1 polymorphism increases cotinine levels in Caucasian children exposed to secondhand smoke: the CCAAPS birth cohort
Gene: NAT1
Variant/haplotype: rs13253389
Drug(s): cotinine
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotypes AG + GG is associated with increased concentrations of cotinine in children as compared to genotype AA.
Notes: Cotinine is a proxy for secondhand smoke exposure. Children with the AG or GG genotypes who were exposed to secondhand smoke had two-fold higher hair cotinine as compared to those with the AA genotype. After adjustment for secondhand smoke dose. Using Bonferroni correction, associations were considered significant at p=0.000677.
Article: Lack of Association between Opioid-Receptor Genotypes and Smoking Cessation Outcomes in a Randomized, Controlled Naltrexone Trial
Gene: OPRD1
Variant/haplotype: rs2298896
Drug(s): naltrexone
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with response to naltrexone in people with Tobacco Use Disorder as compared to allele T.
Notes: No significant association between this variant and smoking quit rate when naltrexone was used as augmentation to nicotine patch therapy. Please note that alleles have been complemented to the positive strand.
Article: Association of variants in NEDD4L with blood pressure response and adverse cardiovascular outcomes in hypertensive patients treated with thiazide diuretics
Gene: NEDD4L
Variant/haplotype: rs1008899
Drug(s): atenolol
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to atenolol in people with Hypertension as compared to allele G.
Article: A genome-wide association study of plasma concentrations of warfarin enantiomers and metabolites in sub-Saharan black-African patients
Gene: PARP14
Variant/haplotype: rs10433340
Drug(s): 6-hydroxy s-warfarin
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele A is associated with increased concentrations of 6-hydroxy s-warfarin in people with Atrial Fibrillation, venous thromboembolism or Heart Valve Diseases as compared to allele G.
Notes: measured as increased S-6OH-warfarin and using a genome wide significance threshold of < 3.846 × 10−9.
Article: Gene Variations of Sixth Complement Component Affecting Tacrolimus Metabolism in Patients with Liver Transplantation for Hepatocellular Carcinoma
Gene: C6
Variant/haplotype: rs3805715
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: no
Association: Genotype AA is not associated with dose-adjusted trough concentrations of tacrolimus in people with liver transplantation as compared to genotypes AG + GG.
Notes: No significant difference was seen when considering RECIPIENT genotype at week 4 of treatment. Patients with hepatocellular carcinoma.
Article: A pharmacogenetic pilot study reveals MTHFR, DRD3, and MDR1 polymorphisms as biomarker candidates for slow atorvastatin metabolizers
Gene: DRD3
Variant/haplotype: rs6280
Drug(s): atorvastatin
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype TT are associated with increased concentrations of atorvastatin in healthy individuals as compared to genotypes CC + CT.
Article: Association of Cytidine Deaminase Polymorphism with Capecitabine Effectiveness in Breast Cancer Patients
Gene: CDA
Variant/haplotype: rs2072671
Drug(s): capecitabine
Phenotype category: Efficacy
Significant: yes
Association: Genotypes AA + AC is associated with decreased response to capecitabine in women with Breast Neoplasms as compared to genotype CC.
Notes: as measured by estradiol E2 levels. "Specifically, for rs2072671, the mutant (CC) has an; elevated estradiol level (mean +/- SD) of (41.01 ± 10.78),; the heterozygous (AC) has a value of (53.98 ± 10.96),; and the wild type (AA) has a value of (51.89 ± 10.42),; with a statistically significant difference between the; three groups."
Article: Genetic variants of ABCB1 and CES1 genes on dabigatran metabolism in the Kazakh population
Gene: CES1
Variant/haplotype: rs8192935
Drug(s): dabigatran
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype GG is associated with increased concentrations of dabigatran in people with Atrial Fibrillation as compared to genotypes AA + AG.
Notes: " Individuals with the rs8192935 AA genotype had lower concentrations than those with the GG genotype (P = 0.001). " "Genetic variants of CES1 (rs8192935 and rs8192935) were significantly associated with minimal dabigatran concentrations in the additive and recessive models. "
Article: Functional characterization of novel rare CYP2A6 variants and potential implications for clinical outcomes
Gene: CYP2A6
Variant/haplotype: rs138978736
Drug(s): nicotine
Phenotype category: Metabolism/PK
Significant: not stated
Association: Allele T is not associated with metabolism of nicotine as compared to allele G.
Notes: Assigned as neutral function following in vitro assessments, in vivo associations and variant construct functional assignments.
Article: Genetic Polymorphisms of Cytokines Might Affect Postoperative Sufentanil Dosage for Analgesia in Patients
Gene: IL10
Variant/haplotype: rs1800872
Drug(s): sufentanil
Phenotype category: Dosage
Significant: no
Association: Allele G is not associated with dose of sufentanil in people with Pain, Postoperative as compared to allele T.
Article: Assessing the Contribution of Opioid- and Dopamine-Related Genetic Polymorphisms to the Abuse Liability of Oxycodone
Gene: OPRD1
Variant/haplotype: rs581111
Drug(s): oxycodone
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to oxycodone as compared to allele G.
Notes: No association between this variant and analgesic response to oxycodone, as assessed by cold pressor test. Please note that alleles have been complemented to the positive strand.
Article: A multi-factorial analysis of response to warfarin in a UK prospective cohort
Gene: CYP2C9
Variant/haplotype: CYP2C9*1, CYP2C9*2, CYP2C9*3
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: CYP2C9 *2 + *3 are associated with decreased dose of warfarin as compared to CYP2C9 *1/*1.
Article: Genetic variation of CYP2C19 affects both pharmacokinetic and pharmacodynamic responses to clopidogrel but not prasugrel in aspirin-treated patients with coronary artery disease
Gene: CYP2C19
Variant/haplotype: CYP2C19*1, CYP2C19*2, CYP2C19*8, CYP2C19*17
Drug(s): prasugrel
Phenotype category: Efficacy, Metabolism/PK
Significant: no
Association: CYP2C19 *1/*2 + *1/*8 + *2/*2 (assigned as poor metabolizer phenotype) is not associated with metabolism of prasugrel in people with Coronary Artery Disease as compared to CYP2C19 *1/*1 + *1/*17 + *17/*17 (assigned as normal metabolizer phenotype) .
Notes: Patients were also treated with aspirin.  There were 35 EM (by genotype) and 15 PM (by genotype).  Dosage was 60 mg loading/10 mg maintenance.
Article: Effect of CYP4F2, VKORC1, and CYP2C9 in Influencing Coumarin Dose: A Single-Patient Data Meta-Analysis in More Than 15,000 Individuals
Gene: CYP4F2
Variant/haplotype: rs2108622
Drug(s): acenocoumarol, warfarin
Phenotype category: Dosage
Significant: yes
Association: Genotypes CT + TT are associated with increased dose of acenocoumarol or warfarin as compared to genotype CC.
Notes: The meta-analysis showed that  this variant (CYP4F2*3) was consistently associated with an increase in mean coumarin dose (+9% (95%CI 7-10%), with a higher effect in females, in patients taking acenocoumarol and in Whites and Asians, but with a low effect size and not in Blacks or other ethnic groups.
Article: Factors Associated with Variability in Rifampin Plasma Pharmacokinetics and the Relationship between Rifampin Concentrations and Induction of Efavirenz Clearance
Gene: SLCO1B1
Variant/haplotype: rs11045819
Drug(s): rifampin
Phenotype category: Metabolism/PK
Significant: not stated
Association: Genotype AC is associated with increased clearance of rifampin in healthy individuals as compared to genotype CC.
Notes: Lower Cmax concentrations of rifampin were observed in individuals with the AC genotype.
Article: Population pharmacokinetics and pharmacogenomics of apixaban in Japanese adult patients with atrial fibrillation
Gene: ABCB1
Variant/haplotype: rs2032582
Drug(s): apixaban
Phenotype category: Metabolism/PK
Significant: no
Association: Allele A is not associated with clearance of apixaban in people with Atrial Fibrillation as compared to allele C.
Article: Cytochrome P450 Genetic Variation Associated with Tamoxifen Biotransformation in American Indian and Alaska Native People
Gene: CYP2C9
Variant/haplotype: CYP2C9 poor metabolizer and intermediate metabolizer genotypes
Drug(s): N-desmethyltamoxifen
Phenotype category: Metabolism/PK
Significant: no
Association: CYP2C9 poor metabolizer and intermediate metabolizer genotypes are not associated with concentrations of n-desmethyltamoxifen in women with Breast Neoplasms.
Article: Genome-Wide Association Study of Serum Creatinine Levels during Vancomycin Therapy
Variant/haplotype: rs62360865
Drug(s): vancomycin
Phenotype category: Metabolism/PK
Significant: no
Association: Allele A is not associated with trough concentration of vancomycin as compared to allele G.
Notes: The SNP was not associated with trough levels of vancomycin (first vancomycin trough documented in EMR after at least 3 doses vancomycin). Elimination constants were also calculated.
Article: Race/ethnicity difference in the pharmacogenetics of bilirubin-related atazanavir discontinuation
Gene: UGT1A1
Variant/haplotype: rs887829
Drug(s): atazanavir
Phenotype category: Toxicity
Significant: no
Association: Genotype CT is not associated with increased discontinuation of atazanavir as compared to genotype CC.
Notes: Risk to for bilirubin-related atazanavir discontinuation.
Article: Association studies of dopamine synthesis and metabolism genes with multiple phenotypes of heroin dependence
Gene: SLC6A3
Variant/haplotype: rs27072
Drug(s): heroin
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with response to heroin as compared to allele C.
Notes: No significant association between this variant and strength of euphoria on first heroin use.
Article: A genome-wide association study identifies a candidate gene associated with atazanavir exposure measured in hair
Gene: SORCS2
Variant/haplotype: rs73208473
Drug(s): atazanavir
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele A is associated with decreased exposure to atazanavir in women with HIV Infections as compared to allele C.
Notes: "each copy of the rs73208473 minor “A” allele was associated with a 46%; decrease in ATV levels (95% confidence interval (CI) 0.35–0.61)." rs73208473 is relatively common, with allele frequencies of 0.118, 0.319, and 0.119 in the AA, WT, and HIS participants. The association with ATV exposure is stronger in white patients as compared to African American and Hispanic patients.
Article: Warfarin Dosage Response Related Pharmacogenetics in Chinese Population
Gene: VKORC1
Variant/haplotype: rs7294
Drug(s): warfarin
Phenotype category: Dosage
Significant: no
Association: Genotype CC is not associated with dose of warfarin in people with heart valve replacement as compared to genotypes CT + TT.
Notes: 158/220 patients had the target INR (1.5–2.5). The comparison of weekly warfarin maintenance dose was significantly different among patients of different genotypes: GGCX rs7294 (CC 19.40±5.75 mg/w vs CT 27.87±8.80 mg/w p < 0.001 ANOVA). The allele was not significantly associated with weekly maintenance dose when analyzed in multiple linear regression analysis, however.
Article: Effect of gene polymorphisms on the levels of calcineurin inhibitors in Indian renal transplant recipients
Gene: CYP3A5
Variant/haplotype: rs776746
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele C is associated with decreased metabolism of tacrolimus in people with Kidney Transplantation as compared to allele T.
Notes: Median L/D ratio for tacrolimus was higher in subjects with CYP3A5*3/*3 than in subjects with CYP3A5*1 carriers at 6th day post-transplantation..
Article: Multigene predictors of tacrolimus exposure in kidney 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 is associated with decreased trough concentration of tacrolimus in people with Kidney Transplantation.
Notes: One CYP3A5*1 allele reduced trough concentrations of tacrolimus by 34.8%, and two *1 alleles were associated with a 57.5% reduction. n=35,043 tacrolimus trough concentrations were available for analysis.
Article: Association studies of dopamine synthesis and metabolism genes with multiple phenotypes of heroin dependence
Gene: SLC6A3
Variant/haplotype: rs27072
Drug(s): heroin
Phenotype category: Dosage
Significant: no
Association: Allele T is not associated with dose of heroin in people with Heroin Dependence as compared to allele C.
Article: APOE Polymorphisms Contribute to Reduced Atorvastatin Response in Chilean Amerindian Subjects
Gene: LDLR
Variant/haplotype: rs5925
Drug(s): atorvastatin
Phenotype category: Efficacy
Significant: no
Association: Genotype CC is not associated with response to atorvastatin in people with Hypercholesterolemia as compared to genotypes CT + TT.
Article: Association between Polymorphisms in Vascular Endothelial Growth Factor Gene and Response to Chemotherapies in Colorectal Cancer: A Meta-Analysis
Gene: VEGFA
Variant/haplotype: rs3025039
Drug(s): bevacizumab, capecitabine, fluorouracil, irinotecan, leucovorin, oxaliplatin
Phenotype category: Efficacy
Significant: yes
Association: Genotype TT is associated with decreased response to bevacizumab, capecitabine, fluorouracil, irinotecan, leucovorin and oxaliplatin in people with Colorectal Neoplasms as compared to genotypes CC + CT.
Notes: Response to treatment was determined by RECIST criteria.
Article: Pharmacogenomics of platinum-based chemotherapy response in NSCLC: a genotyping study and a pooled analysis
Gene: XRCC3
Variant/haplotype: rs861539
Drug(s): Platinum compounds
Phenotype category: Efficacy
Significant: yes
Association: Genotypes AA + AG are associated with increased response to Platinum compounds in people with Carcinoma, Non-Small-Cell Lung as compared to genotype GG.
Notes: "CC genotype of XRCC3 C18067T carriers showed more resistance to platinum-based chemotherapy when compared to those with CT or TT genotypes."
Article: CYP2D6 Genotyping as an alternative to phenotyping for determination of metabolic status in a clinical trial setting
Gene: CYP2D6
Variant/haplotype: CYP2D6*4, CYP2D6*5
Drug(s): debrisoquine, dextromethorphan
Phenotype category: Metabolism/PK
Significant: not stated
Association: CYP2D6 *4/*5 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.  8 of these 46 were *4/*5.
Article: Pharmacogenomics of celiprolol – evidence for a role of P‐glycoprotein and organic anion transporting polypeptide 1A2 in celiprolol pharmacokinetics
Gene: SLCO1A2
Variant/haplotype: rs11568563
Drug(s): celiprolol
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele G is associated with decreased concentrations of Celiprolol in healthy individuals as compared to allele T.
Notes: "the AUC0-infinity values were 25% smaller (p < 5 × 10−4) per copy of the SLCO1A2 c.516A>C minor allele". Alleles complemented to plus chromosomal strand.
Article: Role of UGT1A1*6, UGT1A1*28 and ABCG2 c.421C>A polymorphisms in irinotecan‐induced neutropenia in Asian cancer patients
Gene: UGT1A1
Variant/haplotype: rs4148323
Drug(s): SN-38
Phenotype category: Dosage
Significant: yes
Association: Genotype AA is associated with decreased metabolism of SN-38 in people with Neoplasms as compared to genotype GG.
Notes: This refers to reduced metabolism of the SN-38 metabolite into the inactive SN-38G form by UGT1A1. Patients homozygous for the A allele had increased exposure to SN-38, increased biliary index values and decreased relative extent of glucuronidation (please see study parameters for further description of these measurements). Irinotecan was given once every three weeks in a 375 mg/m2 dose, and neoplasms included nasopharyngeal carcinoma (n=1), gastrointestinal (n=35), genitourinary (n=2), non-small-cell lung cancer (n=5) and miscellaneous (n=2).
Article: Association between UGT2B7 gene polymorphisms and fentanyl sensitivity in patients undergoing painful orthognathic surgery
Gene: UGT2B7
Variant/haplotype: rs7439366
Drug(s): fentanyl
Phenotype category: Efficacy
Significant: yes
Association: Genotype TT is associated with decreased response to fentanyl in people with Pain, Postoperative as compared to genotypes CC + CT.
Notes: There was a significant difference in PPLpost-PPLpre between the genotype groups.
Article: UGT2B15 single nucleotide polymorphism reduces dabigatran acylglucuronide formation in humans
Gene: UGT2B15
Variant/haplotype: rs1902023
Drug(s): dabigatran glucuronide
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype AA is associated with decreased concentrations of dabigatran glucuronide in healthy individuals as compared to genotypes AC + CC.
Notes: Alleles complemented. "The m/p ratios for both Cmax and AUCall were significantly higher in the GG and GT genotypes than in the TT genotype (Table 2; Figure 3), indicating more efficient conversion of DAB to its acylglucuronide form in the GG and GT genotypes. Conversely, the reduced m/p ratio among individuals with the TT genotype suggests that this polymorphism impairs the conversion of DAB to its acylglucuronide form, further confirming the role of UGT2B15 in DAB metabolism."
Article: Polymorphism of Drug Transporters, Rather Than Metabolizing Enzymes, Conditions the Pharmacokinetics of Rasagiline
Gene: SLC22A1
Variant/haplotype: rs34059508
Drug(s): rasagiline
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype AG is associated with increased clearance of rasagiline in healthy individuals as compared to genotype GG.
Notes: and lower Cmax and higher tmax were significant and Cmax remained significant after Bonferroni. Authors state "SLC22A1 rs34059508 genotype (*1/*1 equals to G/G, *1/*5 equals to G/A).
Article: Functional genetic variation in the Rev-Erbα pathway and lithium response in the treatment of bipolar disorder
Gene: NR1D1, THRA
Variant/haplotype: rs2071427
Drug(s): lithium
Phenotype category: Efficacy
Significant: yes
Association: Genotype TT is associated with increased response to lithium in people with Bipolar Disorder.
Notes: This result is for the combination of this SNP with; rs6438552 GG.  People with this genotype combination had a 75% chance of being in the Li-responsive group.  People with rs2071427 CC/rs6438552 AA had a 44% response rate.  Those with 2 or 3 favorable alleles had responses on a gradient between these two results.
Article: VKORC1 variants as significant predictors of warfarin dose in Emiratis
Gene: VKORC1
Variant/haplotype: rs17708472
Drug(s): warfarin
Phenotype category: Dosage
Significant: no
Association: Allele A is not associated with dose of warfarin as compared to allele G.
Notes: Please note that alleles have been complemented to the positive strand.