shlokn/autogkb huggingface dataset:
Article: Pharmacogenetic analysis of opioid dependence treatment dose and dropout rate
Gene: HTR2A
Variant/haplotype: rs6311
Drug(s): buprenorphine, methadone
Phenotype category: Efficacy
Significant: no
Association: Genotype TT is not associated with response to buprenorphine or methadone in people with Opioid-Related Disorders as compared to genotypes CC + CT.
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 TT genotype compared to the CT genotype in the methadone group and the total cohort, but not in the buprenorphine group.
Article: Replication study of polymorphisms associated with response to methotrexate in patients with rheumatoid arthritis
Gene: TYMS
Variant/haplotype: rs699517
Drug(s): methotrexate
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with response to methotrexate in people with Arthritis, Rheumatoid as compared to allele C.
Article: Association of Variants in Candidate Genes with Lipid Profiles in Women with Early Breast Cancer on Adjuvant Aromatase Inhibitor Therapy
Gene: CYP19A1
Variant/haplotype: rs10046
Drug(s): triglycerides
Phenotype category: Other
Significant: yes
Association: Allele A is associated with decreased concentrations of triglycerides in women with Breast Neoplasms and Menopause as compared to allele G.
Notes: when taking letrozole alone or with lipid lowering agents (LLA), such as statins. Data are from a sub-analysis of the Exemestane and Letrozole Pharmacogenomics (ELPh) study, where post-menopausal women with early stage breast cancer were randomized to receive exemestane or letrozole. Of the 303 eligible women, 160 were randomized to the letrozole group, 52 of whom were also taking LLA. This SNP was associated with decreases in triglycerides of 36.4 mg/dL (SE 7.8).
Article: Deciphering the Interleukin 28B Variants That Better Predict Response to Pegylated Interferon-α and Ribavirin Therapy in HCV/HIV-1 Coinfected Patients
Gene: IFNL3
Variant/haplotype: rs4803217
Drug(s): peginterferon alfa-2b, ribavirin
Phenotype category: Efficacy
Significant: yes
Association: Genotype CC is associated with increased response to peginterferon alfa-2b and ribavirin in people with Hepatitis C and HIV Infections as compared to genotypes AA + AC.
Notes: This genotype is associated with sustained virological response (SVR).
Article: High imatinib dose overcomes insufficient response associated with ABCG2 haplotype in chronic myelogenous leukemia patients
Gene: ABCG2
Variant/haplotype: rs2725252
Drug(s): imatinib
Phenotype category: Efficacy
Significant: yes
Association: Allele C is associated with increased response to imatinib in people with Leukemia, Myelogenous, Chronic, BCR-ABL Positive as compared to allele A.
Notes: As part of a haplotype with rs12505410: those with the G-C haplotype (rs12505410-rs2725252) had a significantly higher cumulative incidence major molecular response (CI-MMR) as compared to those with any other haplotype (i.e. G-A, T-C, T-A). This study was done in an exploratory cohort (n=105) and a validation cohort (n=239); within the validation cohort, patients were either taking a 400mg/day dose of imatinib (n=132) or a 600mg/day dose (n=107). Results were NOT significant for those taking a 600mg/day dose. Please note that alleles have been complemented to the plus chromosomal strand.
Article: Childhood asthma exacerbations and the Arg-16 beta2 receptor polymorphism: a meta-analysis stratified by treatment
Gene: ADRB2
Variant/haplotype: rs1042713
Drug(s): corticosteroids, selective beta-2-adrenoreceptor agonists
Phenotype category: Efficacy
Significant: yes
Association: Allele A is associated with decreased response to corticosteroids and selective beta-2-adrenoreceptor agonists in children with Asthma as compared to genotype GG.
Article: CYP3A5*3 and CYP3A4*22 Cluster Polymorphism Effects on LCP-Tac Tacrolimus Exposure: Population Pharmacokinetic Approach
Gene: CYP3A4
Variant/haplotype: CYP3A4*1, CYP3A4*22
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP3A4 *1/*22 is associated with increased dose-adjusted trough concentrations of tacrolimus in people with Kidney Transplantation as compared to CYP3A4 *1/*1.
Notes: " CYP3A4*22 carriers vs. CYP3A4*22 non-carriers C0 normalized by dose showed significant differences when compared (p < 0.01)."
Article: Atomoxetine pharmacokinetics in healthy Chinese subjects and effect of the CYP2D6*10 allele
Gene: CYP2D6
Variant/haplotype: CYP2D6*1, CYP2D6*10
Drug(s): atomoxetine
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2D6 *10/*10 is associated with decreased clearance of atomoxetine in healthy individuals as compared to CYP2D6 *1/*1 + *1/*10.
Notes: Mean clearance was about 50% lower in *10/*10 compared to *1/*10 and *1/*1. Genotyped using AmpliChip for *2, *3, *4, *5, *6, *7, *8, *9,*10, *11, *14A, *14B, *15, *17, *19, *20, *25, *26, *29, *30, *31, *35, *36, *40 and *41. If subjects had two nonfunctional alleles in any combination of *3, *4, *5, *6, *7, *8, *11, *14A, *15, *19, *20 and *40 alleles, a PM genotype was assigned; otherwise, an EM genotype was assigned. Eight subjects identified as homozygous CYP2D6*10, 13 subjects as heterozygous CYP2D6*10 and three as homozygous CYP2D6*1. Each subject received atomoxetine, 40 mg once daily (qd) or placebo for 3 days (days 1, 2 and 3), followed by atomoxetine or placebo, 80 mg qd for 7 days (days 4–10).
Article: Influence of RGS2 on Sertraline Treatment for Social Anxiety Disorder
Gene: HTR2A
Variant/haplotype: rs3742278
Drug(s): sertraline
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with response to sertraline in people with Anxiety Disorders as compared to allele A.
Notes: rs3742278 was not associated with significant differences in change in LSAS score in patients receiving sertraline.
Article: Efficacy and Safety of Ivacaftor in Patients Aged 6 to 11 Years with Cystic Fibrosis with a G551D Mutation
Gene: CFTR
Variant/haplotype: rs75527207
Drug(s): ivacaftor
Phenotype category: Efficacy
Significant: yes
Association: Allele A is associated with response to ivacaftor in children with Cystic Fibrosis.
Notes: Patients aged 6-11 at time of screening who had at least one allele with the G551D mutation (allele A at position rs75527207) were recruited for this trial. Ivacaftor is only indicated in CF patients with this mutation. Significant improvements in lung function were seen in the ivacaftor treatment group compared to placebo.
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: rs2229571
Drug(s): carboplatin, docetaxel, trastuzumab
Phenotype category: Efficacy
Significant: no
Association: Allele C is not 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. As the paper gives the G allele as the reference allele for this SNP, it is assumed that the alleles are presented as being on the positive strand.
Article: Discordant Associations between SLCO1B1 521T→C and Plasma Levels of Ritonavir-boosted Protease Inhibitors in AIDS Clinical Trials Group Study A5146
Gene: CYP3A5
Variant/haplotype: rs776746
Drug(s): lopinavir
Phenotype category: Metabolism/PK
Significant: no
Association: Allele C is not associated with trough concentration of lopinavir in people with HIV Infections as compared to allele T.
Notes: No association between this variant and trough concentrations of lopinavir in black or Hispanic patients. Please note that alleles have been complemented to the positive strand.
Article: ARG1 Is a Novel Bronchodilator Response Gene: Screening and Replication in Four Asthma Cohorts
Gene: ARG1
Variant/haplotype: rs2781659
Drug(s): selective beta-2-adrenoreceptor agonists
Phenotype category: Efficacy
Significant: yes
Association: Allele A is associated with increased response to selective beta-2-adrenoreceptor agonists in people with Asthma as compared to allele G.
Article: Warfarin Dose Model for the Prediction of Stable Maintenance Dose in Indian Patients
Gene: VKORC1
Variant/haplotype: rs9923231
Drug(s): warfarin
Phenotype category: Dosage, Other
Significant: yes
Association: Allele T is associated with decreased dose of warfarin as compared to allele C.
Notes: Please note: alleles have been complemented to the + chromosomal strand.
Article: Atazanavir pharmacokinetics in genetically determined CYP3A5 expressors versus non-expressors
Gene: ABCB1
Variant/haplotype: rs1128503
Drug(s): ritonavir
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype AA is associated with increased clearance of ritonavir in healthy individuals as compared to genotypes AG + GG.
Notes: For the haplotype "1236C/2677G/3435C" "overall ritonavir CL/F was ∼1.9-fold faster in subjects with zero versus two CGC haplotype""and was 1.47-fold faster in subjects with zero versus one CGC copy". In this two-phase study, healthy participants were given atazanavir only for 7 days and then were co-administered ritonavir as a booster for days 8-14. The results here are for day 8-14 (atazanavir plus ritonavir).
Article: PTPRD gene associated with blood pressure response to atenolol and resistant hypertension
Variant/haplotype: rs10739150
Drug(s): atenolol
Phenotype category: Efficacy
Significant: yes
Association: Genotypes GG + GT are associated with increased response to atenolol in people with Hypertension as compared to genotype TT.
Notes: in black patients. Black participants with rs10739150 GG, TG, and TT genotypes had a BP response of -8.7/-7.2,-4.6/-4.8, and 1.4/-1.5 mmHg, respectively, after atenolol monotherapy.
Article: Common polymorphisms of CYP2B6 influence stereoselective bupropion disposition
Gene: POR
Variant/haplotype: rs1057868
Drug(s): bupropion
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotypes CT + TT are not associated with metabolism of bupropion in healthy individuals as compared to genotype CC.
Notes: There's no difference in plasma hydroxybupropion/bupropion AUC ratios, or urine R,R- or S,S hydroxybupropion formation clearances in carriers of POR*28 (A503V 1508C>T (rs1057868)) as compared to *1/*1.
Article: Combinational effect of intestinal and hepatic CYP3A5 genotypes on tacrolimus pharmacokinetics in recipients of living donor liver transplantation
Gene: CYP3A5
Variant/haplotype: rs776746
Drug(s): tacrolimus
Phenotype category: Dosage, Metabolism/PK
Significant: yes
Association: Genotypes CT + TT are associated with increased dose of tacrolimus in people with liver transplantation as compared to genotype CC.
Notes: After 4 months post-transplantation, C/D ratios of donor CYP3A5 expresser were lower than those of nonexpresser regardless of recipients' genotype.  Given the same donor genotype, C/D ratios of recipient CYP3A5 expresser were lower than those of nonexpresser. C/D is the ratio of blood concentration/dose.
Article: Population pharmacokinetic and pharmacogenetic analysis of tacrolimus in paediatric liver transplant patients
Gene: CYP3A5
Variant/haplotype: rs776746
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: not stated
Association: Genotypes CT + TT is associated with increased clearance of tacrolimus in children with liver transplantation as compared to genotype CC.
Notes: Population pharmacokinetic modeling showed time post transplantation and CYP3A5*1 as influential covariates on tacrolimus apparent clearance. Apparent clearance of tacrolimus increased 1.53 times in an individual with the *1/*1 or *1/*3 genotype as compared to those with the *3/*3 genotype.
Article: Germline genomic variations associated with childhood acute lymphoblastic leukemia
Gene: ARID5B
Variant/haplotype: rs10994982
Drug(s): methotrexate
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele A is associated with decreased clearance of methotrexate in children with Precursor Cell Lymphoblastic Leukemia-Lymphoma as compared to allele G.
Notes: A was associated with greater methotrexate polyglutamate accumulation in lymphoblasts from patients with B-hyperdiploid ALL.
Article: Association between opioid receptor mu 1 (OPRM1) gene polymorphisms and tobacco and alcohol consumption in a Spanish population
Gene: OPRM1
Variant/haplotype: rs510769
Drug(s): ethanol
Phenotype category: Dosage
Significant: no
Association: Allele T is not associated with dose of ethanol as compared to allele C.
Notes: No significant association between this variant and alcohol consumption.
Article: Avoiding Tacrolimus Underexposure and Overexposure with a Dosing Algorithm for Renal Transplant Recipients: A Single Arm Prospective Intervention Trial
Gene: CYP3A4
Variant/haplotype: CYP3A4*1, CYP3A4*22
Drug(s): tacrolimus
Phenotype category: Dosage
Significant: not stated
Association: CYP3A4 *22 is associated with decreased dose of tacrolimus in people with Kidney Transplantation as compared to CYP3A4 *1.
Notes: see Rx annotation for algorithm.
Article: Polymorphisms of GLP-1 Receptor Gene and Response to GLP-1 Analogue in Patients with Poorly Controlled Type 2 Diabetes
Gene: GLP1R
Variant/haplotype: rs761386
Drug(s): exenatide
Phenotype category: PD
Significant: no
Association: Genotypes CT + TT is associated with increased response to exenatide in people with Diabetes Mellitus, Type 2 as compared to genotype CC.
Notes: "The effects of GLP1R genotypes on glucose, insulin, and C-peptide concentrations during the 75 g OGTT after GLP-1 analogue treatment are shown in Figure 3." Figure 3 shows CC with increasing insulin while CT/TT has lower increases.  "Quantitative trait loci analysis of GLP1R gene variation with clinical response of GLP1 analogue showed the missense rs3765467 and rs761386 significantly associated with changes in the standard deviation of plasma glucose (SDPG(baseline) - SDPG(treatment with GLP-1 analogue)) (P = 0.041 and 0.019, resp.). The reported P values became insignificant after multiple testing adjustments."
Article: Association and cis-mQTL analysis of variants in CHRNA3-A5, CHRNA7, CHRNB2, and CHRNB4 in relation to nicotine dependence in a Chinese Han population
Gene: CHRNA4
Variant/haplotype: rs3827020
Drug(s): nicotine
Phenotype category: Other
Significant: no
Association: Allele C is not associated with exposure to nicotine in men as compared to allele T.
Notes: No significant association between this allele and status as a smoker or non-smoker.
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: rs4803219
Drug(s): peginterferon alfa-2b, ribavirin
Phenotype category: Efficacy
Significant: yes
Association: Genotype CT is associated with decreased response to peginterferon alfa-2b and ribavirin in people with Hepatitis C, Chronic as compared to genotype CC.
Notes: This genotype has decreased association with sustained virological response (SVR).
Article: Genetic Polymorphisms of Cytokines Might Affect Postoperative Sufentanil Dosage for Analgesia in Patients
Gene: IL1A
Variant/haplotype: rs1800587
Drug(s): sufentanil
Phenotype category: Dosage
Significant: no
Association: Allele A is not associated with dose of sufentanil in people with Pain, Postoperative as compared to allele G.
Article: CYP2B6*6 and CYP2B6*18 Predict Long-Term Efavirenz Exposure Measured in Hair Samples in HIV-Positive South African Women
Gene: CYP2B6
Variant/haplotype: CYP2B6*1, CYP2B6*2
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: no
Association: CYP2B6 *2 is not associated with concentrations of efavirenz in people with HIV as compared to CYP2B6 *1/*1.
Article: CYP3A5 and ABCB1 genotype influence tacrolimus and sirolimus pharmacokinetics in renal transplant recipients
Gene: CYP3A5
Variant/haplotype: CYP3A5*1, CYP3A5*3
Drug(s): sirolimus, tacrolimus
Phenotype category: Dosage
Significant: yes
Association: CYP3A5 *1/*1 + *1/*3 is associated with increased dose of sirolimus or tacrolimus in people with Kidney Transplantation as compared to CYP3A5 *3/*3.
Article: Genetic factors influencing warfarin dose in Black-African patients: a systematic review and meta-analysis
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: In this meta-analysis of warfarin Dose in Black-African Patients, this variant is associated with 12.7mg/week less warfarin dose requirement compared to wild-type homozygotes.
Article: GENOMIC ASSOCIATION ANALYSIS IDENTIFIES MULTIPLE LOCI INFLUENCING ANTIHYPERTENSIVE RESPONSE TO AN ANGIOTENSIN II RECEPTOR BLOCKER
Gene: GPR83
Variant/haplotype: rs3758785
Drug(s): candesartan
Phenotype category: Efficacy
Significant: yes
Association: Genotype GG is associated with increased response to candesartan in people with Essential hypertension as compared to genotype AA.
Notes: Heterozygotes had intermediate response and pattern was the same for both SBP and DBP.
Article: Pharmacogenetic Predictors of Adverse Events and Response to Chemotherapy in Metastatic Colorectal Cancer: Results From North American Gastrointestinal Intergroup Trial N9741
Gene: ERCC1
Variant/haplotype: rs11615
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, overall survival or time to progression 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: Combined study of genetic and epigenetic biomarker risperidone treatment efficacy in Chinese Han schizophrenia patients
Gene: HTT
Variant/haplotype: rs362267
Drug(s): risperidone
Phenotype category: Efficacy
Significant: no
Association: Allele T is associated with decreased response to risperidone in people with Schizophrenia as compared to allele C.
Notes: The T allele was initially significantly more frequent in patients designated as non-responders to risperidone (i.e. <50% reduction in PANSS score compared to the cohort average). However, significance was lost following correction for multiple testing.
Article: ABCC3 and OCT1 genotypes influence pharmacokinetics of morphine in children
Gene: ABCC3
Variant/haplotype: rs4793665
Drug(s): morphine
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype CC is associated with increased metabolism of morphine in children as compared to genotypes CT + TT.
Notes: Children with the CC genotype had higher levels of morphine-3-glucuronide and morphine-6-glucuronide metabolite formation compared to the CT and TT genotype.
Article: CYP2C9 polymorphism and warfarin dose requirements
Gene: CYP2C9
Variant/haplotype: rs1799853
Drug(s): warfarin
Phenotype category: Dosage
Significant: not stated
Association: Allele T is associated with decreased dose of warfarin as compared to allele C.
Article: Gemcitabine Metabolic and Transporter Gene Polymorphisms Are Associated with Drug Toxicity and Efficacy in Patients with Locally Advanced Pancreatic Cancer
Gene: DCTD
Variant/haplotype: rs4742
Drug(s): gemcitabine
Phenotype category: Efficacy, Toxicity
Significant: no
Association: Genotype GG is not associated with increased response to gemcitabine in people with Pancreatic Neoplasms as compared to genotypes AA + AG.
Notes: Tumor response to therapy, progression free survival, and risk of neutropenia development did not significantly differ between genotype groups. This study presented this SNP as rs7663494, but dbSNP has merged that rsID with rs4742.
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: Efficacy
Significant: no
Association: Allele G is not associated with response to methotrexate in children with Precursor Cell Lymphoblastic Leukemia-Lymphoma as compared to allele A.
Notes: However, the presence of the G  (5.92 days) allele was associated with a prolonged duration of hospitalization as compared to the A allele (5.51 days) (P = 0.006). Please note: alleles have been complemented to the + chromosomal strand.
Article: Correlation between Rs2108622 Locus of CYP4F2 Gene Single Nucleotide Polymorphism and Warfarin Dosage in Iranian Cardiovascular Patients
Gene: CYP4F2
Variant/haplotype: rs2108622
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Allele T is associated with increased dose of warfarin in people with Cardiovascular Diseases as compared to allele C.
Notes: Patients were divided into two groups: those who required more than 5 mg/day of warfarin (Group B) and those who required less than 5 mg/day of warfarin (Group A). Within Group B, the frequency of the T allele was 44% vs. 30% in Group A.
Article: Adiponectin Gene Polymorphism rs2241766 T/G Is Associated with Response to Pioglitazone Treatment in Type 2 Diabetic Patients from Southern China
Gene: ADIPOQ
Variant/haplotype: rs1501299
Drug(s): pioglitazone
Phenotype category: Efficacy
Significant: no
Association: Genotypes GT + TT are not associated with response to pioglitazone in people with Diabetes Mellitus as compared to genotype TT.
Notes: Response was defined as "any decrease greater than (or equal to) 15%" of glycated hemoglobin (HbA1C%).
Article: Potentially Functional SNPs (pfSNPs) as Novel Genomic Predictors of 5-FU Response in Metastatic Colorectal Cancer Patients
Gene: DLG5
Variant/haplotype: rs2289310
Drug(s): capecitabine, fluorouracil
Phenotype category: Efficacy
Significant: not stated
Association: Allele T is associated with increased response to capecitabine and fluorouracil in people with Neoplasm Metastasis as compared to allele G.
Notes: pfSNP identified 2800 SNPS associated with key-words: 5-FU, capecitabine and oxilaplatin and colorectal cancer. Various criteria were used to determine 1536 SNPs to genotype. These SNPs were genotyped in a discovery cohort (N=62) and tested in a validation cohort (N=27). Both cohorts consisted of patients with colorectal cancer metastasis in liver. Five SNPs (rs2289310 G>T; rs1047840 G>A; rs17431184 T>C; rs17160359 G>T; rs2236722 A>G) were identified to be more common in the "non-responder" phenotype using a logistic regression multivariate model. The AUC for the receiver operating characteristic curve of the 5 SNPs is 0.875. This logistic-based multivariate model is said to be able to identify 39.1% of non-responders.
Article: Serotonin transporter 5-HTTLPR polymorphism and escitalopram treatment response in patients with major depressive disorder
Gene: CYP2D6
Variant/haplotype: CYP2D6 poor metabolizer
Drug(s): escitalopram
Phenotype category: Efficacy
Significant: no
Association: CYP2D6 poor metabolizer is not associated with decreased response to escitalopram in people with Major Depressive Disorder as compared to CYP2D6 normal metabolizer.
Notes: "No significant differences were observed in the distribution of predicted CYP2C19 and CYP2D6 metabolizer phenotypes between responder and non-responder groups."