shlokn/autogkb huggingface dataset:
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 response to prasugrel in people with Coronary Artery Disease as compared to CYP2C19 *1/*1 + *1/*17 + *17/*17 (assigned as normal metabolizer phenotype) .
Notes: VASP platelet reactivity index and VerifyNow(TM) P2Y12 reaction unit values were not significantly different in PM than in EM patients.  Patients were also treated with aspirin.   There were 35 EM (by genotype) and 15 PM (by genotype).  Dosage was 600 mg loading/75 mg maintenance.
Article: Associations Between the Polymorphisms in the Coding Sequence of SLCO1B1 and Blood Lipid Levels Before and After Treatment by Atorvastatin in the Chinese Han Adults with Dyslipidemia
Gene: SLCO1B1
Variant/haplotype: rs2306283
Drug(s): atorvastatin
Phenotype category: Efficacy
Significant: yes
Association: Genotype GG is associated with decreased clinical benefit to atorvastatin in people with Hyperlipidemias as compared to genotype AA.
Notes: "The effects of different genotypes of rs2306283 on the normalized differences in TC and TG levels before and after treatment were assessed after adjusting for other factors, with results shown in Figure 4. As shown in Figure 4, the therapeutic effect was worse in individuals with the rs2306283 GG genotype compared to those with the AA genotype in terms of TC and TG reduction."
Article: Association between the rs7583431 single nucleotide polymorphism close to the activating transcription factor 2 gene and the analgesic effect of fentanyl in the cold pain test
Gene: ATF2
Variant/haplotype: rs3845744
Drug(s): fentanyl
Phenotype category: Dosage
Significant: no
Association: Allele C is not associated with dose of fentanyl in people with Pain, Postoperative as compared to allele T.
Article: Pharmacogenetic analysis of opioid dependence treatment dose and dropout rate
Gene: COMT
Variant/haplotype: rs4680
Drug(s): buprenorphine, methadone
Phenotype category: Efficacy
Significant: no
Association: Genotype AA is not associated with response to buprenorphine or methadone in people with Opioid-Related Disorders as compared to genotypes AG + GG.
Notes: Response defined by changes in the rate of dropout from treatment between genotypes. Subsequent pairwise analysis resulted in a nominally significant association for the GG genotype compared to the AA genotype in the methadone group and the total cohort, but not in the buprenorphine group.
Article: Association of Pharmacogenetic Markers With Atazanavir Exposure in HIV-Infected Women
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: This variant had a statistically significant association with decrease in atazanavir exposure in plasma in African American (AA) participants (fold effect:0.54). The median oral clearances in AA participants’ homozygous and heterozygous for the reference allele of rs73208473 were 8.73 and 14.3 L/hour, respectively.
Article: The effect of the OPRM1 and DRD4 polymorphisms on the relation between attentional bias and alcohol use in adolescence and young adulthood
Gene: OPRM1
Variant/haplotype: rs1799971
Drug(s): ethanol
Phenotype category: Dosage
Significant: yes
Association: Allele G is associated with increased dose of ethanol in children as compared to allele A.
Notes: The G allele was significantly associated with increased frequency and quantity of alcohol use in adolescents.
Article: Genetic markers in CYP2C19 and CYP2B6 for prediction of cyclophosphamide's 4‐hydroxylation, efficacy and side effects in Chinese patients with systemic lupus erythematosus
Gene: CYP2B6
Variant/haplotype: rs2279343
Drug(s): cyclophosphamide
Phenotype category: Metabolism/PK
Significant: no
Association: Allele G is not associated with metabolism of cyclophosphamide in people with as compared to allele A.
Article: Hypertension Susceptibility Loci and Blood Pressure Response to Antihypertensives – Results from the Pharmacogenomic Evaluation of Antihypertensive Responses (PEAR) Study
Gene: EBF1
Variant/haplotype: rs4551053
Drug(s): hydrochlorothiazide
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with response to hydrochlorothiazide in people with Hypertension as compared to allele A.
Notes: Proxy for rs11953630. Not significant when using Bonferroni-corrected alpha of 0.0014. Response was assessed by change in systolic blood pressure (SBP) and diastolic blood pressure (DBP) after 9 weeks of treatment.
Article: Attempted validation of 44 reported SNPs associated with tacrolimus troughs in a cohort of kidney allograft recipients
Gene: IL6
Variant/haplotype: rs1524107
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: no
Association: Allele C is not associated with trough concentration of tacrolimus in people with Kidney Transplantation and Transplantation.
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.  Authors described association as suggestive in the EA population but it did not survive multiple testing correction. Direction of effect not stated. This is a proxy for rs1800796.
Article: Association of Genetic Polymorphisms with Warfarin Dose Requirements in Chinese Patients
Gene: CYP2C9
Variant/haplotype: rs1057910
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Genotypes AA + AC is associated with increased dose of warfarin as compared to genotype CC.
Notes: "The mean warfarin dose in patients with the CYP2C9 rs1057910AA genotype was 3.34 mg/day, which was higher than that in patients with the CYP2C9 rs1057910CC genotype (0.81 mg/day)."
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*6
Drug(s): debrisoquine, dextromethorphan
Phenotype category: Metabolism/PK
Significant: not stated
Association: CYP2D6 *4/*6 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.  2 of these 46 were *4/*6.
Article: Association between rs1799971 in the mu opioid receptor gene and methadone maintenance treatment response
Gene: OPRM1
Variant/haplotype: rs1799971
Drug(s): methadone
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with increased clinical benefit to methadone in people with Heroin Dependence as compared to allele G.
Notes: not significant in any model (recessive/dominant/additive/allelic) in primary study nor in meta-analysis.
Article: The use of ivacaftor in CFTR mutations resulting in residual functioning protein
Gene: CFTR
Variant/haplotype: rs77932196
Drug(s): ivacaftor
Phenotype category: Efficacy
Significant: yes
Association: Allele A is associated with increased response to ivacaftor in people with Cystic Fibrosis as compared to allele G.
Notes: Investigation of ivacaftor treatment in patients with CFTR variants conferring residual CFTR function, comparing patients with ivacaftor treatment to those without. Genotypes of the patients receiving ivacaftor were R347P/L1065P, 2789+5G/R1066C, S912X/D579G, S912X/D579G, del F508/R352Q, G542X/D1152H, and W1282W/D1152H. The outcomes measured were FEV1 %predicted, increase in BMI, CFQ-R, and number of exacerbations.
Article: Clinical and genetic factors associated with warfarin maintenance dose in northern Chinese patients with mechanical heart valve replacement
Gene: APOE
Variant/haplotype: rs7412
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Genotype CC is associated with decreased dose of warfarin in people with heart valve replacement as compared to genotype CT.
Article: ABCB1 (MDR1) genetic variants are associated with methadone doses required for effective treatment of heroin dependence
Gene: ABCB1
Variant/haplotype: rs2032583
Drug(s): methadone
Phenotype category: Dosage
Significant: no
Association: Allele G is not associated with dose of methadone in people with Heroin Dependence as compared to allele A.
Notes: Please note that alleles have been complemented to the positive strand. Alleles were not associated with the need for a higher (>150mg) or lower (<150 mg) dose of methadone.
Article: Association of Genetic Polymorphisms with Warfarin Dose Requirements in Chinese Patients
Gene: GGCX
Variant/haplotype: rs699664
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Genotypes CT + TT is associated with increased dose of warfarin as compared to genotype CC.
Notes: The mean warfarin dose in patients with the GGCX rs699664 TT genotype was 3.51mg/day, which was higher than that in patients with the GGCX rs699664 CC genotype (3.09 mg/day).
Article: Weight-loss response to naltrexone/bupropion is modulated by the Taq1A genetic variant near DRD2 (rs1800497): A pilot study
Gene: ANKK1, DRD2
Variant/haplotype: rs1800497
Drug(s): bupropion, naltrexone
Phenotype category: Efficacy
Significant: yes
Association: Genotypes AA + AG are associated with increased response to bupropion and naltrexone in people with Obesity as compared to genotype GG.
Notes: Patients with a baseline body mass index (BMI) of 27-45 were recruited. Those carrying the A allele had a greater mean weight-loss percentage and were more likely to be classed as responders to buproprion/naltrexone.
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: rs761895497
Drug(s): tolbutamide
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele C is associated with decreased clearance of tolbutamide as compared to allele T.
Notes: In vitro analysis showed that intrinsic clearance of tolbutamide by CYP2C9 protein containing the C allele was 43.6% of that of the WT protein. Variant referred to as 791T>C in the paper.
Article: Effect of UGT1A1, UGT1A3, DIO1 and DIO2 polymorphisms on L-thyroxine doses required for TSH suppression in patients with differentiated thyroid cancer
Gene: DIO1
Variant/haplotype: rs11206244
Drug(s): levothyroxine
Phenotype category: Dosage
Significant: no
Association: Allele T is not associated with dose of levothyroxine in people with Thyroid Neoplasms as compared to allele C.
Notes: This SNP was not associated with dose in univariate  regression.
Article: The C Allele of ATM rs11212617 Does Not Associate With Metformin Response in the Diabetes Prevention Program
Gene: C11orf65
Variant/haplotype: rs11212617
Drug(s): metformin
Phenotype category: Efficacy, Metabolism/PK
Significant: no
Association: Allele C is not associated with increased response to metformin as compared to allele A.
Notes: in people with impaired glucose tolerance. No significant differences found in metformin's effects on insulin sensitivity, fasting glucose,glycated hemoglobin or disposition index.
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 170% higher concentrations of simvastatin lactone than did; noncarriers (P< 0.01), but no significant difference was; detected for concentrations of simvastatin acid.
Article: CHRNA4 rs1044396 is associated with smoking cessation in varenicline therapy
Gene: CHRNA4
Variant/haplotype: rs1044396
Drug(s): varenicline
Phenotype category: Efficacy
Significant: yes
Association: Genotype GG is associated with decreased response to varenicline in people with Tobacco Use Disorder as compared to genotypes AA + AG.
Notes: CC genotype had lower success rate when in treatment with varenicline (29.5%) compared with patients with CT or TT genotypes.
Article: IL28B Polymorphism Cannot Predict Response to Interferon Alpha Treatment in Patients with Melanoma
Gene: IFNL3
Variant/haplotype: rs12979860
Drug(s): interferon alfa-2b, recombinant
Phenotype category: Efficacy
Significant: no
Association: Genotype CC is not associated with response to interferon alfa-2b, recombinant in people with Melanoma as compared to genotypes CT + TT.
Notes: The CC genotype at rs12979860 was not associated with either overall or progression free survival (PFS).
Article: Functional genetic variation in the Rev-Erbα pathway and lithium response in the treatment of bipolar disorder
Gene: PER3
Variant/haplotype: rs228729
Drug(s): lithium
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with increased response to lithium in people with Bipolar Disorder as compared to allele C.
Article: The pharmacokinetic and pharmacodynamic interaction of clopidogrel and cilostazol in relation to CYP2C19 and CYP3A5 genotypes
Gene: CYP2C19
Variant/haplotype: CYP2C19*1, CYP2C19*2, CYP2C19*3
Drug(s): clopidogrel
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2C19 *2 + *3 are associated with decreased metabolism of clopidogrel in healthy individuals as compared to CYP2C19 *1.
Notes: either when clopidogrel was administered alone or in combination with cilostazole. The authors observed no differences in AUC (ng*hr/ml) or Cmax (ng/ml) values of clopidogrel thiol metabolite when comparing within the same metabolizer group [extensive (CYP2C19 *1/*1), intermediate (CYP2C19 *1/*2, *1/*3), and poor (CYP2C19 *2/*2, *2/*3, *3/*3)] but between treatment groups. Differences in clopidogrel thiol metabolite concentrations were only observed when comparing between CYP2C19 metabolizer groups.
Article: Haplotypes of P2RX7 gene polymorphisms are associated with both cold pain sensitivity and analgesic effect of fentanyl
Gene: P2RX7
Variant/haplotype: rs1718136
Drug(s): fentanyl
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with dose of fentanyl in people with Pain, Postoperative as compared to allele A.
Notes: No significant association between this variant and 24-h postoperative fentanyl use or perioperative fentanyl use.
Article: Serum Calretinin and Genetic Variability as a Prognostic and Predictive Factor in Malignant Mesothelioma
Gene: MIR335
Variant/haplotype: rs3807348
Drug(s): cisplatin
Phenotype category: Efficacy
Significant: yes
Association: Genotypes AA + AG is associated with increased response to cisplatin in people with Mesothelioma as compared to genotype GG.
Notes: "When analyzing the effect of selected polymorphisms on the treatment response rate (Table 4), carriers of at least one MIR335 rs3807348 polymorphic allele had a significantly better response (OR = 2.41, 95% CI = 1.19–4.87, p = 0.015), even after adjusting for clinical factors (OR = 2.69, 95% CI = 1.17–6.18, p = 0.020)."
Article: A Pharmacogenetics-Based Warfarin Maintenance Dosing Algorithm from Northern Chinese Patients
Gene: MPZ
Variant/haplotype: rs12065184
Drug(s): warfarin
Phenotype category: Dosage
Significant: no
Association: Allele C 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: Measurements of Functional Responses in Human Primary Lung Cells as a Basis for Personalized Therapy for Cystic Fibrosis
Gene: CFTR
Variant/haplotype: rs113993960
Drug(s): lumacaftor
Phenotype category: Efficacy
Significant: yes
Association: Genotype del/del is associated with response to lumacaftor.
Notes: F508del 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.
Article: Pharmacogenetic association of the APOA1/C3/A4/A5 gene cluster and lipid responses to fenofibrate: the Genetics of Lipid-Lowering Drugs and Diet Network study
Gene: APOA4
Variant/haplotype: rs1263177
Drug(s): fenofibrate
Phenotype category: Efficacy
Significant: no
Association: Genotypes CC + CT are not associated with response to fenofibrate in people with Hypertriglyceridemia as compared to genotype TT.
Notes: No significant difference in the change in plasma triglyceride (TG) or high-density lipoprotein (HDL) levels between genotypes was seen, after three weeks of treatment with fenofibrate.
Article: Folate metabolic pathway single nucleotide polymorphisms: a predictive pharmacogenetic marker of methotrexate response in Indian (Asian) patients with rheumatoid arthritis
Gene: MTHFR
Variant/haplotype: rs1801131
Drug(s): methotrexate
Phenotype category: Efficacy
Significant: yes
Association: Genotypes GT + TT is associated with increased response to methotrexate in people with Arthritis, Rheumatoid as compared to genotype GG.
Article: Patients with CYP3A4∗1G genetic polymorphism consumed significantly lower amount of sufentanil in general anesthesia during lung resection
Gene: CYP3A4
Variant/haplotype: rs2242480
Drug(s): sufentanil
Phenotype category: Dosage
Significant: no
Association: Genotypes C/T + T/T is associated with decreased dose of sufentanil in people with Pain, Postoperative as compared to genotype C/C.
Notes: The publication reports the finding for CYP3A4*1G. PharmVar re-assigned CYP3A4*1G to CYP3A4*36. Previously, this annotation used CYP3A4*36 which has been retired by PharmVar. All references to *36 have been replaced by rs2242480 alleles.
Article: Pharmacogenetics of Antiepileptic Drug Efficacy in Childhood Absence Epilepsy
Gene: CACNA1H
Variant/haplotype: rs2753326
Drug(s): lamotrigine
Phenotype category: Efficacy
Significant: yes
Association: Allele A is associated with increased clinical benefit to lamotrigine in children with Epilepsy as compared to allele G.
Notes: as measured by minor allele frequency in not–seizure‐free vs seizure-free children. Authors do not specify which allele is minor allele but state "Two synonymous CACNA1H variants, located essentially next to each other (rs2753326 and rs2753325), were associated with greater seizure freedom in the lamotrigine group. Both have global minor allele frequency reported as 0.29 compared to 0.36 in the lamotrigine cohort." This does not seem to match with frequencies in Table 2. Assumed minor allele as same as dbSNP which was A and major allele as G.
Article: Disposition of debrisoquine and nortriptyline in Korean subjects in relation to CYP2D6 genotypes, and comparison with Caucasians
Gene: CYP2D6
Variant/haplotype: CYP2D6*1, CYP2D6*10
Drug(s): nortriptyline
Phenotype category: Metabolism/PK
Significant: no
Association: CYP2D6 *1/*10 is not associated with decreased metabolism of nortriptyline in healthy individuals as compared to CYP2D6 *1/*1.
Notes: There was a difference found between AUC (0-8) of 4-hydroxydebrisoquine, which was significantly lower in *1/*10 than in *1/*1, but no other differences were found for debrisoquine and none were found for nortriptyline in this sample.
Article: Impact of cytochrome P450 2C19 polymorphisms on the pharmacokinetics of tacrolimus when coadministered with voriconazole
Gene: CYP2C19
Variant/haplotype: CYP2C19*1, CYP2C19*2, CYP2C19*3
Drug(s): voriconazole
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2C19 *2/*2 + *2/*3 + *3/*3 is associated with increased concentrations of voriconazole in healthy individuals as compared to CYP2C19 *1/*1.
Notes: The maximum plasma concentration (Cmax) and area under the plasma concentration time curve from 0 to 12 hours (AUC0-12) was higher in poor metabolizers (*2/*2 n=2; *2/*3 n=3; *3/*3 n=1) as compared to extensive metabolizers (*1/*1 n=6).
Article: Thiopurine dose intensity and treatment outcome in childhood lymphoblastic leukaemia: the influence of thiopurine methyltransferase pharmacogenetics
Gene: TPMT
Variant/haplotype: TPMT*1, TPMT*3A
Drug(s): mercaptopurine, thioguanine
Phenotype category: Dosage
Significant: yes
Association: TPMT *1/*3A is associated with decreased dose of mercaptopurine or thioguanine in children with Precursor Cell Lymphoblastic Leukemia-Lymphoma as compared to TPMT *1/*1.
Notes: As compared to those with the wild-type genotype (*1/*1), those patients with the *1/*3A genotype had a 1) a lower average dose (70.1% vs 78.0%, where dose given as the % of standard protocol dose), 2) a greater percentage of time spent at no dose (21.3% vs 15.5%) and 3) a smaller percentage of time where the dose was escalated (1.5% vs 5.8%).
Article: Association studies of dopamine synthesis and metabolism genes with multiple phenotypes of heroin dependence
Gene: SLC6A3
Variant/haplotype: rs10064525
Drug(s): methadone
Phenotype category: Dosage
Significant: no
Association: Allele G is not associated with dose of methadone in people with Heroin Dependence as compared to allele T.
Article: Warfarin Dose Model for the Prediction of Stable Maintenance Dose in Indian Patients
Gene: EPHX1
Variant/haplotype: rs1051740
Drug(s): warfarin
Phenotype category: Dosage
Significant: no
Association: Allele C is not associated with dose of warfarin as compared to allele T.
Article: Pharmacogenetic Predictors of Adverse Events and Response to Chemotherapy in Metastatic Colorectal Cancer: Results From North American Gastrointestinal Intergroup Trial N9741
Gene: GSTP1
Variant/haplotype: rs1695
Drug(s): fluorouracil, irinotecan, oxaliplatin
Phenotype category: Efficacy
Significant: no
Association: Genotype GG is not associated with response to fluorouracil, irinotecan or oxaliplatin in people with Colorectal Neoplasms as compared to genotypes AA + AG.
Notes: Patients were taking either IFL (irinotecan + fluorouracil + leucovorin; n=114), FOLFOX (fluorouracil + oxaliplatin + leucovorin; n=299) or IROX (irinotecan + oxaliplatin; n=107). No significant association was seen between this variant and confirmed response rate in any of the treatment groups OR all treatment groups considered together. Significance level was set at 0.01. Please note that alleles have been complemented to the plus chromosomal strand.
Article: The International SSRI Pharmacogenomics Consortium (ISPC): a genome-wide association study of antidepressant treatment response
Variant/haplotype: rs7485210
Drug(s): Selective serotonin reuptake inhibitors
Phenotype category: Efficacy
Significant: no
Association: Allele C is not associated with response to Selective serotonin reuptake inhibitors in people with Depressive Disorder, Major as compared to allele A.
Notes: The allele did not reach genome wide significance in the discovery or replication cohorts. GWA analyses were performed for two phenotypes: ‘% change in HRSD-17 score’ (% HRSD defined as the change in HRSD-17 score divided by the baseline score) and ‘response’ (defined as greater than or equal to 50% reduction in HRSD-17 score from baseline to 4-week visit).
Article: Assessing the Contribution of Opioid- and Dopamine-Related Genetic Polymorphisms to the Abuse Liability of Oxycodone
Gene: COMT
Variant/haplotype: rs165599
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, subjective effects of oxycodone.