shlokn/autogkb huggingface dataset:
Article: The KCNH2 Genetic Polymorphism (1956, C>T) Is a Novel Biomarker That Is Associated with CCB and α,β-ADR Blocker Response in EH Patients in China
Gene: KCNH2
Variant/haplotype: rs1137617
Drug(s): candesartan, imidapril, irbesartan
Phenotype category: Efficacy
Significant: not stated
Association: Genotype GG is not associated with response to candesartan, imidapril or irbesartan in people with Essential hypertension as compared to genotypes AA + AG.
Article: Association between Genetic Polymorphisms in Cav2.3 (R-type) Ca2+ Channels and Fentanyl Sensitivity in Patients Undergoing Painful Cosmetic Surgery
Gene: CACNA1E
Variant/haplotype: rs3845446
Drug(s): fentanyl
Phenotype category: Dosage
Significant: yes
Association: Genotypes CC + CT are associated with decreased dose of fentanyl in people with Pain, Postoperative as compared to genotype TT.
Notes: Subjects carrying the C allele required significantly less intrapoperative and perioperative fentanyl than those not carrying the C allele. However, there was no significant difference in analgesic response to fentanyl between the genotype groups. Please note that alleles have been complemented to the positive strand.
Article: CYP2C8*3 predicts benefit/risk profile in breast cancer patients receiving neoadjuvant paclitaxel
Gene: ABCB1
Variant/haplotype: rs1045642
Drug(s): paclitaxel
Phenotype category: Efficacy
Significant: no
Association: Genotypes AA + AG are not associated with increased response to paclitaxel in women with Breast Neoplasms as compared to genotype GG.
Notes: Response = complete clinical response (cCR). Some patients who had HER2 overexpressing tumors received trastuzumab at the same time as the paclitaxel.
Article: Associations of the SLCO1B1 Polymorphisms With Hepatic Function, Baseline Lipid Levels, and Lipid-lowering Response to Simvastatin in Patients With Hyperlipidemia
Gene: SLCO1B1
Variant/haplotype: rs2306283
Drug(s): simvastatin
Phenotype category: Efficacy
Significant: no
Association: Genotypes AG + GG are not associated with increased response to simvastatin in people with Hypercholesterolemia as compared to genotype AA.
Notes: Patients carrying 388G allele alone is not significantly associated with greater TC and LDL-C reduction in response to simvastatin after 4 weeks of treatment. no significant associations were found between the 521T>C and 388A>G polymorphisms and the lipid-lowering effects of simvastatin treatment after 8 weeks.
Article: CYP2D6 Genotyping as an alternative to phenotyping for determination of metabolic status in a clinical trial setting
Gene: CYP2D6
Variant/haplotype: CYP2D6*3, CYP2D6*5
Drug(s): debrisoquine, dextromethorphan
Phenotype category: Metabolism/PK
Significant: not stated
Association: CYP2D6 *3/*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.  3 of these 46 were *3/*5.
Article: Effect of CYP4F2 Polymorphisms on Ticagrelor Pharmacokinetics in Healthy Chinese Volunteers
Gene: CYP4F2
Variant/haplotype: rs2074900
Drug(s): ticagrelor
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype AA is associated with decreased clearance of ticagrelor in healthy individuals as compared to genotypes AG + GG.
Article: Relationship between Lipid Phenotypes, Overweight, Lipid Lowering Drug Response and KIF6 and HMG-CoA Genotypes in a Subset of the Brisighella Heart Study Population
Gene: KIF6
Variant/haplotype: rs20455
Drug(s): hmg coa reductase inhibitors
Phenotype category: Efficacy
Significant: no
Association: Genotypes AG + GG are not associated with response to hmg coa reductase inhibitors as compared to genotype AA.
Notes: With regard to lipid-lowering therapy with statins, the authors did not find any association between HMG-CoA or KIF6 genotypes and achievement of <130 mg/dL LDL-C level.
Article: Verification of Pharmacogenetics-Based Warfarin Dosing Algorithms in Han-Chinese Patients Undertaking Mechanic Heart Valve Replacement
Gene: CYP2C9
Variant/haplotype: rs1057910
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Genotype AA is associated with increased dose of warfarin in people with Heart Valve Diseases as compared to genotype AC.
Notes: The goal of this study was to compare the accuracy of 8 different warfarin dosing algorithms, including the IWPC, and 6 Han Chinese PGx warfarin dosing algorithms, in Han Chinese patients taking warfarin scheduled to undergo mechanic heart valve replacement surgery. The authors concluded that the mean absolute error (MAE) of all algorithms was less than 0.6mg/day in initial and stable doses, and the percentage of patients whose actual doses were within 20% of their predicted dose was 45% for all algorithms.  Predictive power of algorithms was highest for patients in the ideal-dose range and lowest for patients in the low and high dose range.; The most accurate predictions came from three Han-Chinese PGx warfarin dosing algorithms (Du et al. 2010, Huang et al. 2009, Miao et al. 2007).
Article: Influence of FMO3 and CYP3A4 Polymorphisms on the Pharmacokinetics of Teneligliptin in Humans
Gene: FMO3
Variant/haplotype: rs909530
Drug(s): teneligliptin
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotypes CT + TT is associated with decreased clearance of teneligliptin in men as compared to genotype CC.
Notes: Alleles complemented to plus chromosomal strand. Significant for clearance, Cmax, and AUC.
Article: Genome-Wide Association Study Identifies Novel Pharmacogenomic Loci For Therapeutic Response to Montelukast in Asthma
Gene: GALNT17
Variant/haplotype: rs7794356
Drug(s): montelukast
Phenotype category: Efficacy
Significant: no
Association: Allele A is associated with increased response to montelukast in people with Asthma as compared to allele G.
Notes: This allele showed a trend toward association but not at the genome wide significance level. Study Cohort: Discovery cohort (N=133): American Lung Association Asthma Clinical Research Center (ALA-ACRC)-supported trials, the Leukotriene Modifier Or Corticosteroid or Corticosteroid-Salmeterol Trial (LOCCS) and Effectiveness of Low Dose Theophylline as Add On Therapy for the Treatment of Asthma (LODO) trials. Replication cohort (N=184): Childhood Asthma Research and Education (CARE) Network- Characterizing the Response to a LT Receptor Antagonist and an Inhaled Corticosteroid and Pediatric Asthma Controller Trial (CLIC and PACT).
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: ERBB3
Variant/haplotype: rs2229046
Drug(s): carboplatin, docetaxel, trastuzumab
Phenotype category: Efficacy
Significant: yes
Association: Allele C 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.
Article: Gene Variations of Sixth Complement Component Affecting Tacrolimus Metabolism in Patients with Liver Transplantation for Hepatocellular Carcinoma
Gene: C6
Variant/haplotype: rs10052999
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotypes CC + TT are associated with decreased dose-adjusted trough concentrations of tacrolimus in people with liver transplantation as compared to genotype CT.
Notes: When considering DONOR genotype - those with the CC or TT genotype had decreased concentration/dose ratios as compared to those with the CT genotype at weeks 2-4 of treatment. No significant difference was seen at week 1. In multiple linear regression analysis, donor rs10052999 genotype was significantly associated with concentration/dose ratio at week 4 (p=0.001) of treatment. Patients with hepatocellular carcinoma.
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: rs292449
Drug(s): hydrochlorothiazide
Phenotype category: Efficacy
Significant: no
Association: Allele C is not associated with response to hydrochlorothiazide in people with Hypertension as compared to allele G.
Notes: Minor allele in the Black patients is opposite to minor allele in Whites.
Article: Pharmacodynamics of PEG-IFN alpha-2a and HCV response as a function of IL28B polymorphism in HIV/HCV co-infected patients
Gene: IFNL3, IFNL4
Variant/haplotype: rs12979860
Drug(s): peginterferon alfa-2a, ribavirin
Phenotype category: Efficacy
Significant: yes
Association: Genotype CC is associated with increased response to peginterferon alfa-2a and ribavirin in people with Hepatitis C, Chronic as compared to genotypes CT + TT.
Notes: Patients were co-infected with HIV.  p listed is for RVR.
Article: PHARMACOGENOMIC GENOME-WIDE META-ANALYSIS OF BLOOD PRESSURE RESPONSE TO BETA-BLOCKERS IN HYPERTENSIVE AFRICAN AMERICANS
Gene: LRRC15
Variant/haplotype: rs11313667
Drug(s): atenolol, hydrochlorothiazide, metoprolol
Phenotype category: Efficacy
Significant: yes
Association: Allele del is associated with increased response to atenolol, hydrochlorothiazide or metoprolol in people with Hypertension as compared to allele C.
Notes: Study in African Americans
Article: Combined study of genetic and epigenetic biomarker risperidone treatment efficacy in Chinese Han schizophrenia patients
Gene: ABCB1
Variant/haplotype: rs1128503
Drug(s): risperidone
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with response to risperidone in people with Schizophrenia as compared to allele A.
Notes: Please note that alleles have been complemented to the positive strand.
Article: Polymorphisms within methotrexate pathway genes: Relationship between plasma methotrexate levels, toxicity experienced and outcome in pediatric acute lymphoblastic leukemia
Gene: ABCB1
Variant/haplotype: rs1045642
Drug(s): methotrexate
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype AG is associated with increased concentrations of methotrexate in children with Precursor Cell Lymphoblastic Leukemia-Lymphoma as compared to genotype GG.
Notes: Please note that alleles have been complemented to the positive strand. Patients with the AA genotype did not have significantly different methotrexate plasma levels compared to those with the GG genotype.
Article: Effect of the Polymorphism of Folylpolyglutamate Synthetase on Treatment of High-Dose Methotrexate in Pediatric Patients with Acute Lymphocytic Leukemia
Gene: FPGS
Variant/haplotype: rs1544105
Drug(s): methotrexate
Phenotype category: Efficacy
Significant: yes
Association: Genotype TT is associated with increased response to methotrexate in children with Precursor Cell Lymphoblastic Leukemia-Lymphoma as compared to genotypes CC + CT.
Notes: Patients with the TT genotype had an increased survival time compared to the other genotypes. Please note that alleles have been complemented to the positive strand.
Article: Impact of CYP2D6, CYP3A5, CYP2C9 and CYP2C19 polymorphisms on tamoxifen pharmacokinetics in Asian breast cancer patients
Gene: CYP2C19
Variant/haplotype: CYP2C19*1, CYP2C19*2, CYP2C19*3, CYP2C19*17
Drug(s): 4-hydroxytamoxifen, endoxifen, N-desmethyltamoxifen, tamoxifen
Phenotype category: Metabolism/PK
Significant: no
Association: CYP2C19 *2 + *3 + *17 is not associated with concentrations of 4-hydroxytamoxifen, endoxifen, n-desmethyltamoxifen and tamoxifen in women with Breast Neoplasms as compared to CYP2C19 *1.
Notes: Patients (pre- (83%) and postmenopausal (17%)) with ER and/or PR positive breast tumors, which received 20 mg tamoxifen daily. Patients taking CYP2D6 inhibitors were excluded. DNA extracted from blood.
Article: Association study between clinical response to rizatriptan and some candidate genes
Gene: HTR1B
Variant/haplotype: rs6296
Drug(s): rizatriptan
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with response to rizatriptan in people with Migraine without Aura as compared to allele C.
Notes: No significant difference in allele frequency between responders and non-responders to rizatriptan. Variant referred to in the paper as 5-HT1D-beta and mapped to rs6296 by PharmGKB.
Article: ADH single nucleotide polymorphism associations with alcohol metabolism in vivo
Gene: ADH1A
Variant/haplotype: rs931635
Drug(s): ethanol
Phenotype category: Toxicity, Metabolism/PK
Significant: yes
Association: Allele A is associated with metabolism of ethanol.
Notes: The authors did not report p-value correction for multiple hypotheses (103 snps tested).  Though they report multiple snps are significantly associated with alcohol metabolism (early or late) tested on blood or breath alcohol concentrations, this snp is NOT significant after Bonferroni correction (<0.00049).  Also, the authors did not state which alleles are associated with increased or decreased metabolism.  Instead, they simply report an association with the snp in general.  Note that this gene is on the minus strand.
Article: Effect of Multidrug-Resistant 1 (MDR1) and CYP3A4*1B Polymorphisms on Cyclosporine-Based Immunosuppressive Therapy in Renal Transplant Patients
Gene: CYP3A4
Variant/haplotype: rs2740574
Drug(s): cyclosporine
Phenotype category: Metabolism/PK
Significant: no
Association: Allele T is associated with increased concentrations of cyclosporine in people with Kidney Transplantation as compared to allele C.
Notes: Patients with the *1/*1 genotype had higher average blood concentrations of cyclosporine A than patients with the *1/*1B genotype. However, this was not a significant association. rs number is given but not which allele corresponded to *1B, mapping *1B as C and *1 as T. PharmVAR now considers *1B as the core allele CYP3A4*1.001
Article: A GENOME-WIDE ASSOCIATION STUDY OF BRONCHODILATOR RESPONSE IN LATINOS IMPLICATES RARE VARIANTS
Variant/haplotype: rs74973995
Drug(s): salbutamol
Phenotype category: Efficacy
Significant: yes
Association: Genotype AG is associated with increased response to salbutamol in children with Asthma as compared to genotype AA.
Notes: The allele associated with increased response and low frequency is not explicitly stated.  Response is increased for carriers of the rare, minor allele.  GALAII genotyping was done using the Affymetrix LAT1 Array, which was designed to capture Latino population variation.
Article: No association between IFNL3 (IL28B) genotype and response to peginterferon alfa-2a in HBeAg-positive or -negative chronic hepatitis B
Gene: IFNL3, IFNL4
Variant/haplotype: rs8099917
Drug(s): peginterferon alfa-2a
Phenotype category: Efficacy
Significant: no
Association: Genotype TT is not associated with response to peginterferon alfa-2a in people with Hepatitis B, Chronic as compared to genotypes GG + GT.
Notes: The authors found no association between IFNL3 genotype and peginterferon 2a response in either HBeAg-positive or HBeAg-negative chronic hepatitis B patients, in both Asian and White patients.
Article: Diversity of Opioid Requirements for Postoperative Pain Control Following Oral Surgery—Is It Affected by Polymorphism of the μ-Opioid Receptor?
Gene: OPRM1
Variant/haplotype: rs1799971
Drug(s): fentanyl
Phenotype category: Dosage, Efficacy
Significant: yes
Association: Genotype GG is associated with increased dose of fentanyl in people with Pain, Postoperative as compared to genotype AA.
Notes: Patients with the GG genotype required almost twice as much fentanyl in the first 24 hours following surgery than patients with the AA genotype.
Article: Nonspecific sarcolemmal cation channels are critical for the pathogenesis of malignant hyperthermia
Gene: RYR1
Variant/haplotype: rs118192161
Drug(s): halothane
Phenotype category: Other
Significant: yes
Association: Allele T is associated with increased response to halothane as compared to allele C.
Notes: Wild-type (WT) or mice with a knock in of the malignant hyperthermia causative variant (Arg163Cys; c.487C>T) were exposed to 1.5% halothane. Mice with the Arg163Cys variant had much greater elevations in calcium and sodium in "vastus lateralis" muscle when exposed to halothane in vivo as compared to the WT mice.
Article: GENE AND GENE BY SEX ASSOCIATIONS WITH INITIAL SENSITIVITY TO NICOTINE IN NONSMOKERS
Gene: OPRM1
Variant/haplotype: rs1799971
Drug(s): nicotine
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with response to nicotine in healthy individuals as compared to allele A.
Notes: No significant association between this variant and nicotine reward, perception, mood or reinforcement or physiological responses to nicotine.
Article: Common polymorphisms of CYP2B6 influence stereoselective bupropion disposition
Gene: CYP2B6
Variant/haplotype: CYP2B6*1, CYP2B6*6
Drug(s): bupropion
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2B6 *6/*6 is associated with decreased metabolism of bupropion in healthy individuals as compared to CYP2B6 *1/*1.
Notes: Carriers of CYP2B6*6/*6 had lower hydroxylation of both bupropion enantiomers, assessed by plasma hydroxybupropion/bupropion AUC ratios and urine hydroxybupropion formation clearances. Carriers of CYP2B6*1/*6 did not differ statistically as compared to *1/*1.
Article: HLA-DQA1*05 correlates with increased risk of anti-drug antibody development and reduced response to infliximab in Chinese patients with Crohn’s disease
Gene: HLA-DQA1
Variant/haplotype: HLA-DQA1*05
Drug(s): infliximab
Phenotype category: Efficacy
Significant: yes
Association: HLA-DQA1 *05 is associated with decreased response to infliximab in people with Crohn Disease.
Notes: "Furthermore, HLA-DQA1*05 G carriage was significantly associated with an elevated risk of loss response to IFX treatment (adjusted HR = 2.55, 95% CI 1.78–3.68, P < 0.001; Figure 3B and Supplementary Table 2)." Authors describe locus as HLADQ A1*05A>G (rs2097432)
Article: Leveraging an Electronic Health Record-Linked Biorepository to Generate a Metformin Pharmacogenomics Hypothesis
Gene: FMO5
Variant/haplotype: rs7541245
Drug(s): metformin
Phenotype category: Efficacy
Significant: yes
Association: Allele A is associated with decreased response to metformin in people with Diabetes Mellitus as compared to allele C.
Notes: EHR-linked and EHR-based phenotyping methods were used to study common variants within FMO5. Efficacy was assessed by A1c levels extracted from EHR records.
Article: Pharmacogenetics of unboosted atazanavir in HIV-infected individuals in resource-limited settings: a sub-study of the AIDS Clinical Trials Group (ACTG) PEARLS study (NWCS 342)
Gene: NR1I2
Variant/haplotype: rs2472677
Drug(s): atazanavir
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype CT (assigned as deficiency phenotype) is associated with decreased concentrations of atazanavir in people with HIV Infections as compared to genotypes CC + TT.
Notes: Looked at CL/F, concentration at 24 hours, and ratios of metabolites M1 and M2 to atazanavir.  Only concentration 24 hours post-dose was significantly lower in subjects with the CT genotype as compared to the CC or TT genotypes.
Article: Association of carbamazepine major metabolism and transport pathway gene polymorphisms and pharmacokinetics in patients with epilepsy
Gene: NR1I2
Variant/haplotype: rs7643645
Drug(s): carbamazepine
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele G is associated with increased metabolism of carbamazepine in people with Epilepsy as compared to allele A.
Notes: This association was significant in the whole cohort. As measured by a higher carbamazepine-10-11 epoxide: carbamazepine ratio.
Article: TSPYL Family Regulates CYP17A1 and CYP3A4 Expression: Potential Mechanism Contributing to Abiraterone Response in Metastatic Castration‐Resistant Prostate Cancer
Gene: TSPYL1
Variant/haplotype: rs3828743
Drug(s): abiraterone, prednisolone
Phenotype category: Efficacy
Significant: yes
Association: Allele A is associated with decreased response to abiraterone and prednisolone in people with Prostatic Neoplasms as compared to allele G.
Notes: in a prospective clinical trial of 87 metastatic castration-resistant prostate cancer patients treated with abiraterone acetate/prednisone. The variant allele (A) was more frequently presented in nonresponders (P=0.013), with an odds ratio of 2.47 (1.23, 4.96). This variant abolishes TSPYL1's ability to suppress CYP3A4 expression, resulting in reduced abiraterone concentrations and increased cell proliferation in vitro.
Article: S-1 plus irinotecan and oxaliplatin for the first-line treatment of patients with metastatic colorectal cancer: a prospective phase II study and pharmacogenetic analysis
Gene: UGT1A7
Variant/haplotype: UGT1A7*3
Drug(s): irinotecan, oxaliplatin, tegafur / gimeracil / oteracil
Phenotype category: Efficacy
Significant: no
Association: UGT1A7 *3 is not associated with response to irinotecan, oxaliplatin and s 1 (combination) in people with Colorectal Neoplasms.
Notes: No significant difference in the objective response rate was seen between those with the *3 allele (82% responders) and those without one (63%).
Article: Population pharmacokinetics of voriconazole and the role of CYP2C19 genotype on treatment optimization in pediatric patients
Gene: CYP2C19
Variant/haplotype: CYP2C19*1, CYP2C19*2, CYP2C19*3
Drug(s): voriconazole
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2C19 *1/*2 + *1/*3 + *2/*2 + *2/*3 + *3/*3 (assigned as intermediate metabolizer and poor metabolizer phenotype) is associated with increased dose-adjusted trough concentrations of voriconazole in children with Leukemia as compared to CYP2C19 *1/*1 (assigned as normal metabolizer phenotype) .
Notes: "The VRC trough concentrations of NMs were lower than in IMs (P = 0.001) and PMs (P = 0.001). In addition, 43.4%, 58.7% and 60.9% of VRC trough concentrations were within the target range in NMs, IMs and PMs, respectively. Furthermore, 53.0%, 34.6% and 26.1% of VRC trough concentrations were subtherapeutic in NMs, IMs and PMs, respectively." "The VRC trough concentrations of NMs were lower than in IMs (P = 0.001) and PMs (P = 0.001). In addition, 43.4%, 58.7% and 60.9% of VRC trough concentrations were within the target range in NMs, IMs and PMs, respectively. Furthermore, 53.0%, 34.6% and 26.1% of VRC trough concentrations were subtherapeutic in NMs, IMs and PMs, respectively."
Article: CYP2A6 genetic variation and dexmedetomidine disposition
Gene: CYP2A6
Variant/haplotype: CYP2A6*1, CYP2A6*4, CYP2A6*9
Drug(s): dexmedetomidine
Phenotype category: Metabolism/PK
Significant: no
Association: CYP2A6 *1/*4 + *1/*4 + *9/*9 are not associated with clearance of dexmedetomidine in ICU patients as compared to CYP2A6 *1/*1.
Notes: Comparison was between 33 normal metabolizers (*1/*1), 5 intermediate metabolizers (*1/*9), and 2 slow metabolizers (one *1/*4 and one *9/*9).
Article: Association of Cytochrome P450 Genetic Variants with Clopidogrel Resistance and Outcomes in Acute Ischemic Stroke
Gene: CYP2C8
Variant/haplotype: rs1934980
Drug(s): clopidogrel
Phenotype category: Efficacy
Significant: no
Association: Genotypes AA + AG is not associated with resistance to clopidogrel in people with Stroke as compared to genotype GG.
Article: Population pharmacokinetics and pharmacogenomics of apixaban in Japanese adult patients with atrial fibrillation
Gene: ABCG2
Variant/haplotype: rs2231142
Drug(s): apixaban
Phenotype category: Metabolism/PK
Significant: not stated
Association: Genotypes GG + GT is associated with increased clearance of apixaban in people with Atrial Fibrillation as compared to genotype TT.