shlokn/autogkb huggingface dataset:
Article: Thymidylate Synthase Genotype-Directed Chemotherapy for Patients with Gastric and Gastroesophageal Junction Cancers
Gene: XRCC1
Variant/haplotype: rs25487
Drug(s): fluorouracil, leucovorin, oxaliplatin
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with response to fluorouracil, leucovorin and oxaliplatin in people with Esophageal Neoplasms and Stomach Neoplasms as compared to allele C.
Article: Formation of omeprazole sulphone but not 5-hydroxyomeprazole is inhibited by grapefruit juice
Gene: CYP2C19
Variant/haplotype: CYP2C19 poor metabolizers
Drug(s): omeprazole
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2C19 poor metabolizer is associated with decreased metabolism of omeprazole in healthy individuals as compared to CYP2C19 normal metabolizer.
Notes: Patients who were poor metabolizers (n=2) had a mean AUC that was ~5X higher as compared to extensive metabolizers (n=11).
Article: Population Pharmacokinetic/Pharmacogenetic Model for Optimization of Efavirenz Therapy in Caucasian HIV-Infected Patients
Gene: CYP2B6
Variant/haplotype: CYP2B6*1, CYP2B6*6
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2B6 *1/*6 + *6/*6 are associated with increased concentrations of efavirenz in people with HIV as compared to CYP2B6 *1/*1.
Article: Influence of CYP450 Enzymes and ABCB1 Polymorphisms on Clopidogrel Response in Moroccan Patients with Acute Coronary Syndromes
Gene: ABCB1
Variant/haplotype: rs1045642
Drug(s): clopidogrel
Phenotype category: Efficacy
Significant: yes
Association: Allele A is associated with increased response to clopidogrel in people with Acute coronary syndrome as compared to allele G.
Notes: "Genotype distribution of the ABCB1 C3435T variant was marginally significant between the two groups of patients (P = 0.057), the frequency of the T allele in Clopidogrel non-responders was higher than in the responders (15/19; 78.9%) and (19/36; 52.8%) respectively." "Patients were subdivided into clopidogrel responder (PRU≤208) and clopidogrel non-responder group (PRU>208), 19 patients (34.55%) were clopidogrel non-responders, whereas 36 patients (65.45%) were clopidogrel responders. "
Article: RRM1 single nucleotide polymorphism -37C→A correlates with progression-free survival in NSCLC patients after gemcitabine-based chemotherapy
Gene: RRM1
Variant/haplotype: rs12806698
Drug(s): carboplatin, gemcitabine
Phenotype category: Efficacy
Significant: yes
Association: Genotype AC is associated with increased response to carboplatin and gemcitabine in people with Carcinoma, Non-Small-Cell Lung as compared to genotypes AA + CC.
Notes: Patients with the AC genotype had the longest duration of progression free survival (30.7 weeks) compared to patients with the AA (24.7 weeks) or CC (23.3 weeks) genotypes. There was no difference in "chemotherapy response" between groups. Chemotherapy response was classified as either partial response (PD), stable disease (SD), or progressive disease (PD).
Article: Interleukin-6 (IL-6) haplotypes and the response to therapy of chronic hepatitis C virus infection
Gene: IL6
Variant/haplotype: rs1800795
Drug(s): peginterferon alfa-2a
Phenotype category: Efficacy
Significant: yes
Association: Allele G is associated with decreased response to peginterferon alfa-2a in people with Hepatitis C, Chronic as compared to allele C.
Notes: This association is as part of a haplotype which also includes rs1800797G and rs1800796G.  This is a GC SNP so the listed associated allele may be incorrect.
Article: Targeted pharmacogenetic analysis of antipsychotic response in the CATIE study
Gene: TMEFF2
Variant/haplotype: rs3738883
Drug(s): risperidone
Phenotype category: Efficacy
Significant: yes
Association: Allele G is associated with response to risperidone 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. Please note: reported allele was C, this has been complemented to the plus chromosomal strand. It was unclear whether the allele was associated with an increased or decreased response to drug.
Article: Impact of IL6R genetic variants on treatment efficacy and toxicity response to sarilumab in rheumatoid arthritis
Gene: IL6R
Variant/haplotype: rs4329505
Drug(s): sarilumab
Phenotype category: Efficacy
Significant: yes
Association: Genotype TT is associated with increased response to sarilumab in people with Arthritis, Rheumatoid as compared to genotypes CC + CT.
Notes: "For rs4329505 and rs11265618, the genetic model that best fit the data was the dominant model, as patients homozygous for the wild-type allele (TT for rs4329505 and CC for rs11265618) showed better remission rates than the other patients; specifically, remission rates (CDAI-LDA) were 73.5% vs. 44.4% (p = 0.039) and the quantitative improvement in DAS28 was 2.9 vs. 2.0 (p = 0.048). No significant differences were found for DAS28 LDA, CDAI improvement, and/or EULAR response rates." "A linked inheritance was observed between rs4329505 and rs11265618, as all individuals carrying the T allele for rs4329505 also had the C allele for rs11265618, and vice versa. "
Article: The Distribution of the Genotypes of ABCB1 and CES1 Polymorphisms in Kazakhstani Patients with Atrial Fibrillation Treated with DOAC
Gene: ABCB1
Variant/haplotype: rs2032582
Drug(s): dabigatran
Phenotype category: Metabolism/PK
Significant: no
Association: Allele A is not associated with decreased dose-adjusted trough concentrations of dabigatran in people with Atrial Fibrillation as compared to allele C.
Article: Pharmacogenetics-based area-under-curve model can predict efficacy and adverse events from axitinib in individual patients with advanced renal cell carcinoma
Gene: UGT1A10, UGT1A8, UGT1A9
Variant/haplotype: rs3832043
Drug(s): axitinib
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele del is associated with concentrations of axitinib in people with Carcinoma, Renal Cell as compared to allele T.
Notes: The authors develop a prediction model and calculated area under the concentration curve (AUC) using 6 SNPs (rs17868323, rs3832043, rs2231142, rs2032582, rs1045642, rs35305980) was compared with actual AUC in 16 patients prospectively which significantly correlated with the objective response rate (P = 0.0002), hand-foot syndrome, P = 0.0055 and hypothyroidism, P = 0.0381, and correlated with actual AUC (P < 0.0001) - the validation study, calculated AUC prior to axitinib treatment precisely predicted actual AUC after axitinib treatment (P = 0.0066).
Article: An Intronic Variant in OPRD1 Predicts Treatment Outcome for Opioid Dependence in African-Americans
Gene: OPRD1
Variant/haplotype: rs678849
Drug(s): buprenorphine
Phenotype category: Efficacy
Significant: no
Association: Allele C is not associated with response to buprenorphine in people with Opioid-Related Disorders as compared to allele T.
Notes: Efficacy was determined based on the number of opioid-positive drug screens that each patient had during treatment.
Article: Population pharmacokinetic approach to evaluate the effect of CYP2D6, CYP3A, ABCB1, POR and NR1I2 genotypes on donepezil clearance
Gene: ABCB1
Variant/haplotype: rs1045642
Drug(s): donepezil
Phenotype category: Metabolism/PK
Significant: no
Association: Genotype GG is not associated with clearance of donepezil in people with Alzheimer Disease as compared to genotype AA.
Notes: Genotypes of GG, AG and AA did not influence donepezil clearance in a covariate model. Alleles have been complemented to the plus chromosomal strand.
Article: IL28B genetic variations are associated with high sustained virological response (SVR) of interferon-α plus ribavirin therapy in Taiwanese chronic HCV infection
Gene: IFNL3
Variant/haplotype: rs8105790
Drug(s): peginterferon alfa-2b, ribavirin
Phenotype category: Efficacy
Significant: yes
Association: Genotypes CC + CT is associated with decreased response to peginterferon alfa-2b and ribavirin in people with Hepatitis C, Chronic as compared to genotype TT.
Notes: This genotype has decreased association with sustained virological response (SVR).
Article: Effects of CYP3A4*22 and POR*28 variations on the pharmacokinetics of tacrolimus in renal transplant recipients: a meta-analysis of 18 observational studies
Gene: CYP3A4
Variant/haplotype: CYP3A4*1, CYP3A4*22
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP3A4 *22 is associated with increased dose-adjusted trough concentrations of tacrolimus in people with Kidney Transplantation as compared to CYP3A4 *1/*1.
Notes: "Similarly, for recipients at 3 days (SMD = -0.35, 95% CI: -0.65 to -0.06, I2 = 0.0%), 1 month (SMD = -0.67, 95% CI: -1.16 to -0.18, I2 = 57.8%), 3 months (SMD = -0.60, 95% CI: -0.89 to -0.31, I2 = 0.4%), 6 months (SMD = -0.76, 95% CI: -1.49 to -0.04, I2 = 78.7%), or 12 months (SMD = -0.69, 95% CI: -1.37 to 0.00, I2 = 76.8%) post-transplantation, a significantly lower C0/Dose was observed in CYP3A4*1/*1 carriers compared to CYP3A4*22 carriers (Fig. 2B)."
Article: Oxidative Stress-Related Genetic Polymorphisms Are Associated with the Prognosis of Metastatic Gastric Cancer Patients Treated with Epirubicin, Oxaliplatin and 5-Fluorouracil Combination Chemotherapy
Gene: GSTT1
Variant/haplotype: rs2266637
Drug(s): epirubicin, fluorouracil, oxaliplatin
Phenotype category: Efficacy
Significant: not stated
Association: Allele C is not associated with response to epirubicin, fluorouracil and oxaliplatin in people with Neoplasm Metastasis and Stomach Neoplasms.
Notes: Please note: the alleles reported here are complemented to the + chromosomal strand.
Article: Genetic Polymorphisms in ERCC1 Gene and Their Association with Response to Radiotherapy in Moroccan Patients with Nasopharyngeal Carcinoma
Gene: ERCC1
Variant/haplotype: rs11615
Drug(s): radiotherapy
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with resistance to radiotherapy in people with Nasopharyngeal Neoplasms as compared to allele G.
Notes: "For C118T SNP, CT genotype prevails in radioresistant cases (60.4%, 32/53) and TT in radiosensitive; cases (62.5%, 5/8). A borderline significance was obtained between ERCC1 C118T polymorphism genotypes and; radio-resistance status (p=0.07). Similarly, a borderline; association was found between radio-resistance status; and allelic frequency (p=0.091), as T allele prevails in; radiosensitive cases." Alleles complemented.
Article: Germline Variation in Colorectal Risk Loci Does Not Influence Treatment Effect or Survival in Metastatic Colorectal Cancer
Variant/haplotype: rs7013278
Drug(s): fluorouracil, irinotecan, oxaliplatin
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with response to fluorouracil, irinotecan and oxaliplatin in people with Colorectal Neoplasms and Neoplasm Metastasis as compared to allele C.
Notes: SNPs were investigated for their effects on response rate, time to progression and overall survival. After accounting for multiple testing there was no association with any SNPs and outcomes of patients with metastatic colorectal cancer.
Article: Germline single nucleotide polymorphisms in ERBB3 and BARD1 genes result in a worse relapse free survival response for HER2-positive breast cancer patients treated with adjuvant based docetaxel, carboplatin and trastuzumab (TCH)
Gene: BARD1
Variant/haplotype: rs2070096
Drug(s): carboplatin, docetaxel, trastuzumab
Phenotype category: Efficacy
Significant: yes
Association: Allele A is associated with decreased response to carboplatin, docetaxel and trastuzumab in women with Breast Neoplasms.
Notes: When compared to women who received different treatment regimens. Response was defined as likelihood of achieving relapse-free survival. The paper uses the G allele as the reference allele for this SNP, therefore we have assumed that the authors are referring to the negative strand. As a result, we have complemented the alleles to the positive strand.
Article: Effect of pharmacogenetics on plasma lumefantrine pharmacokinetics and malaria treatment outcome in pregnant women
Gene: CYP2B6
Variant/haplotype: rs28399499
Drug(s): lumefantrine
Phenotype category: Efficacy
Significant: no
Association: Allele C is not associated with response to lumefantrine in women with Malaria and Pregnancy as compared to allele T.
Article: Pharmacogenetics for Genes Associated with Age-Related Macular Degeneration (AMD) in the Comparison of AMD Treatments Trials (CATT)
Gene: C3
Variant/haplotype: rs2230199
Drug(s): bevacizumab, ranibizumab
Phenotype category: Efficacy
Significant: no
Association: Genotype GG is not associated with response to bevacizumab or ranibizumab in people with Macular Degeneration as compared to genotypes CC + CG.
Notes: No significant differences in mean visual acuity (units = letters), mean visual acuity change from baseline (units = letters), >= 15-letter increase from baseline (%), mean number of injections, retinal thickness (%, units = um), mean change in total foveal thickness from baseline (units = um), dry on optical coherence tomography (%), leakage on fluorescein angiography (%) or mean change in lesion size from baseline (units = disc area) after 1 year of treatment were seen between genotypes. p <= 0.01 was considered statistically significant to adjust for multiple comparisons.
Article: A functional polymorphism in the ABCB1 transporter predicts pharmacologic response to combination of nortriptyline and morphine in neuropathic pain patients
Gene: HTR2A
Variant/haplotype: rs6313
Drug(s): morphine, nortriptyline
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to morphine and nortriptyline in people with Pain as compared to allele G.
Notes: No significant difference in improvement in pain scores between genotype groups.
Article: Cyclophosphamide pharmacokinetics and pharmacogenetics in children with B-cell non-Hodgkin's lymphoma
Gene: CYP2B6
Variant/haplotype: CYP2B6*1, CYP2B6*6
Drug(s): cyclophosphamide
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2B6 *6 is associated with decreased clearance of cyclophosphamide in children with Lymphoma, B-Cell as compared to CYP2B6 *1/*1.
Notes: but there was no effect on progression-free survival.
Article: Impact of SLCO1B3 Polymorphisms on Clinical Outcomes in Lung Allograft Recipients Receiving Mycophenolic Acid
Gene: UGT1A9
Variant/haplotype: rs2741049
Drug(s): azathioprine, mycophenolic acid
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with response to azathioprine or mycophenolic acid in people with lung transplantation as compared to allele C.
Notes: No significant association between this variant and survival post-transplantation or development of acute cellular rejection, lymphocytic bronchiolitis or chronic lung allograft dysfunction (CLAD).
Article: Novel Sequence Variations in the Brain-Derived Neurotrophic Factor Gene and Association with Major Depression and Antidepressant Treatment Response
Gene: BDNF
Variant/haplotype: rs61888800
Drug(s): antidepressants, desipramine, fluoxetine
Phenotype category: Efficacy
Significant: not stated
Association: Genotype GG is associated with increased response to antidepressants, desipramine and fluoxetine in people with Depressive Disorder, Major.
Notes: Outcome with the two drugs was combined for analysis.  Not found to be associated with remission vs non-remission.  Found to be associated with reduction in HAM-D21 score after adjusting for age, sex, medication, and; baseline HAM-D21 score.
Article: Genetic Variation in CYP2D6, UGT1A4, SLC6A2 and SLCO1B1 Alters the Pharmacokinetics and Safety of Mirabegron
Gene: UGT1A3
Variant/haplotype: rs2008584
Drug(s): mirabegron
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype AA is associated with decreased half-life time of mirabegron in healthy individuals as compared to genotype AG.
Notes: " The UGT1A3 rs2008584 A/A genotype was associated with lower tmax than the UGT1A3 rs2008584 A/G genotype (puv = 0.014). "
Article: Influence of IL-18 and IL-10 Polymorphisms on Tacrolimus Elimination in Chinese Lung Transplant Patients
Gene: IL10
Variant/haplotype: rs1800896
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype TT is associated with increased dose-adjusted trough concentrations of tacrolimus in people with lung transplantation as compared to genotype CT.
Notes: Patients with the TT genotype had higher dose-adjusted trough concentrations of tacrolimus at weeks 1 (p=0.027) and 2 (p=0.034) post-transplant as compared to the CT genotype; no significant results were seen at weeks 3 (p=0.24) or 4 (p=0.24). Please note that alleles have been complemented to the plus chromosomal strand.
Article: An expanded pharmacogenomics warfarin dosing table with utility in generalised dosing guidance
Gene: CYP2C9
Variant/haplotype: rs28371685
Drug(s): warfarin
Phenotype category: Dosage
Significant: not stated
Association: Allele C is associated with dose of warfarin as compared to allele T.
Notes: This variant annotation is part of a dosing algorithm table based on 8 genetic variants.
Article: Impact of CYP3A5 genetic polymorphism on pharmacokinetics of tacrolimus in healthy Japanese subjects
Gene: CYP3A5
Variant/haplotype: rs776746
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype CC is associated with decreased clearance of tacrolimus in healthy individuals as compared to genotypes CT + TT.
Notes: Subjects with the CYP3A5*3/*3 genotype had a 1.8 times higher AUC than subjects who were carriers of the CYP3A5*1 allele. Of note, this study did not determine the proportion of CYP3A5*1/*3 or CYP3A5*1/*1 genotypes.  These were referred collectively as "CYP3A5*1 carriers".  In addition, subjects who were CYP3A5*1 carriers had 1.5 times higher clearance (Cl/F) than subjects with the CYP3A5*3/*3 genotype.
Article: Pharmacogenetics of Interaction between Depot Medroxyprogesterone Acetate and Efavirenz, Rifampicin and Isoniazid during Treatment of HIV and Tuberculosis
Gene: CYP2B6
Variant/haplotype: CYP2B6 poor metabolizer
Drug(s): medroxyprogesterone
Phenotype category: Metabolism/PK
Significant: no
Association: CYP2B6 poor metabolizer is not associated with metabolism of medroxyprogesterone in women with HIV Infections and Tuberculosis as compared to CYP2B6 normal metabolizer.
Notes: No significant associations between CYP2B6 metabolizer status and any primary pharmacokinetic parameter for medroxyprogesterone acetate. Patients also receiving efavirenz-based ART and rifampicin plus isoniazid for treatment. CYP2B6 phenotype determine based on 516G→T (rs3745274), 983T→C (rs28399499), and 15582C→T (rs4803419) with normal metabolizer (1: 15582CC-516GG-983TT or 2: 15582CT-516GG-983TT); intermediate metabolizer (3: 15582TT-516GG-983TT; 4: 15582CC-516GT-983TT; 5: 15582CC-516GG-983CT; 6: 15582CT-516GT-983TT; or 7: 15582CT-516GG-983CT); and poor metabolizer (8: 15582CC-516TT-983TT; 9: 15582CC-516GT-983CT; 10: 15582CC-516GG-983CC
Article: Comprehensive assessment of cytochromes P450 and transporter genetics with endoxifen concentration during tamoxifen treatment
Gene: CYP2C9
Variant/haplotype: CYP2C9 poor metabolizers
Drug(s): endoxifen
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2C9 poor metabolizer is associated with decreased concentrations of endoxifen as compared to CYP2C9 normal metabolizer.
Notes: An increase the steady-state endoxifen concentration was found for patients with increased CYP2C9 phenotype activity. After adjustment for CYP2D6 diplotype, weight, and season the association remained significant. Endoxifen concentration 2C9 PM: 6.26 ng/ml, 2C9 IM: 7.18 ng/ml, 2C9 NM: 8.29 ng/ml.
Article: Pharmacokinetic– pharmacodynamic analysis of the role of CYP2C19 genotypes in short-term rabeprazole-based triple therapy against Helicobacter pylori
Gene: CYP2C19
Variant/haplotype: CYP2C19*1, CYP2C19*2, CYP2C19*3
Drug(s): rabeprazole
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2C19 *2/*2 + *2/*3 is associated with decreased clearance of rabeprazole in people with Helicobacter Infections as compared to CYP2C19 *1/*1 + *1/*2 + *1/*3.
Notes: Subjects were treated with rabeprazole for 7 days, and also received amoxicillin and clarithromycin.
Article: Carfilzomib and lenalidomide response related to VEGF and VEGFR2 germline polymorphisms
Gene: KDR
Variant/haplotype: rs2305948
Drug(s): carfilzomib, dexamethasone, lenalidomide
Phenotype category: Efficacy
Significant: yes
Association: Genotypes CT + TT is associated with increased response to carfilzomib, dexamethasone and lenalidomide in people with Multiple Myeloma as compared to genotype CC.
Notes: Authors indicate repose as CR/nCR/sCR but do not define these and non-response as VGPR and PR/SD (which assume to mean progression/stable disease). There was only one TT individual who had sCR.
Article: CYP2B6 516G>T Minor Allele Protective of Late Virologic Failure in Efavirenz-treated HIV-Infected Patients in Botswana
Gene: CYP2B6
Variant/haplotype: rs3745274
Drug(s): efavirenz
Phenotype category: Efficacy
Significant: yes
Association: Genotypes GT + TT are associated with decreased resistance to efavirenz in people with HIV Infections as compared to genotype GG.
Notes: CYPB2B6 516 T-allele was protective against late virologic failure in patients with initial (6 month) HIV RNA suppression on EFV-based ART.
Article: Integrative genomic analysis of methylphenidate response in attention-deficit/hyperactivity disorder
Gene: CDH23
Variant/haplotype: rs17712523
Drug(s): methylphenidate
Phenotype category: Efficacy
Significant: no
Association: Allele G 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: The International SSRI Pharmacogenomics Consortium (ISPC): a genome-wide association study of antidepressant treatment response
Variant/haplotype: rs4236420
Drug(s): Selective serotonin reuptake inhibitors
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to Selective serotonin reuptake inhibitors in people with Depressive Disorder, Major as compared to allele G.
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: Effect of CYP4F2 Polymorphisms on Ticagrelor Pharmacokinetics in Healthy Chinese Volunteers
Gene: CYP2B6
Variant/haplotype: rs56156262
Drug(s): AR-C124910XX, ticagrelor
Phenotype category: Metabolism/PK
Significant: no
Association: Genotypes AA + AG is not associated with decreased concentrations of AR-C124910XX or ticagrelor in healthy individuals as compared to genotype GG.
Notes: from TABLE 4 Ticagrelor pharmacokinetic parameters based on genotypes without statistical significance and TABLE 5; AR-C124910XX pharmacokinetic parameters based on genotypes without statistical significance