shlokn/autogkb huggingface dataset:
Article: Warfarin Dose Model for the Prediction of Stable Maintenance Dose in Indian Patients
Gene: CYP2C9
Variant/haplotype: rs1799853
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Genotype CT is associated with decreased dose of warfarin as compared to genotype CC.
Article: Impact of Pharmacogenetic Markers of CYP2B6, Clinical Factors, and Drug-Drug Interaction on Efavirenz Concentrations in HIV/Tuberculosis-Coinfected Patients
Gene: CYP2B6
Variant/haplotype: rs3211371
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: no
Association: Genotype CC is not associated with clearance of efavirenz in people with HIV Infections as compared to genotype CT.
Notes: No significant difference in plasma concentrations of efavirenz (units = mg/L) were seen between the two genotypes. Fasting plasma efavirenz concentrations were measured 12 hours after the last dose, and after 12 weeks of treatment. p-value from univariate analysis with plasma concentration as the dependent variable.
Article: G Protein-Coupled Receptor Kinase 5 Gene Polymorphisms Are Associated with Postoperative Atrial Fibrillation Following Coronary Artery Bypass Graft Surgery in Patients Receiving Beta-Blockers
Gene: GRK5
Variant/haplotype: rs10787959
Drug(s): Beta Blocking Agents
Phenotype category: Efficacy
Significant: yes
Association: Allele A is associated with decreased response to Beta Blocking Agents in people with Coronary Artery Disease as compared to allele G.
Notes: Single-nucleotide polymorphisms in 10 candidate genes were tested for association with atrial fibrillation after coronary artery bypass grafting despite perioperative beta blocker therapy.
Article: Association of serotonin transporter (SLC6A4) & receptor (5HTR1A, 5HTR2A) polymorphisms with response to treatment with escitalopram in patients with major depressive disorder: A preliminary study
Gene: SLC6A4
Variant/haplotype: SLC6A4 HTTLPR long form (L allele), SLC6A4 HTTLPR short form (S allele)
Drug(s): escitalopram
Phenotype category: Efficacy
Significant: no
Association: SLC6A4 HTTLPR long form (L allele) is not associated with response to escitalopram Depressive Disorder, Major as compared to SLC6A4 HTTLPR short form (S allele).
Article: Pharmacogenetic meta-analysis of genome-wide association studies of LDL cholesterol response to statins
Gene: CELSR2
Variant/haplotype: rs646776
Drug(s): hmg coa reductase inhibitors
Phenotype category: Efficacy
Significant: yes
Association: Allele C is associated with increased response to hmg coa reductase inhibitors as compared to allele T.
Notes: Carriers of this SNP respond to statins with an additional 1.5% increase per allele in LDL-C lowering effect compared with non-carriers.
Article: The role of CYP3A5 polymorphism and dose adjustments following conversion of twice-daily to once-daily tacrolimus in renal transplant recipients
Gene: CYP3A5
Variant/haplotype: CYP3A5*1, CYP3A5*3
Drug(s): tacrolimus
Phenotype category: Dosage
Significant: yes
Association: CYP3A5 *1/*1 + *1/*3 is associated with increased dose of tacrolimus in people with Kidney Transplantation as compared to CYP3A5 *3/*3.
Notes: Patients converting from tacrolimus 2X daily (BID) to once daily (OD). A greater percentage of patients with the *1/*1 or *1/*3 genotype required some increase in dose following conversion as compared to those with the *3/*3 genotype (69% vs 47%). Additionally, the mean dose increase for those with the *1/*1 or *1/*3 genotype was higher as compared to those with the *3/*3 genotype (45.3% vs 26.6%).
Article: Pharmacogenomic Study of Selected Genes Affecting Amlodipine Blood Pressure Response in Patients with Hypertension
Gene: CACNA1C
Variant/haplotype: rs2239050
Drug(s): amlodipine
Phenotype category: Efficacy
Significant: yes
Association: Genotype GG is associated with increased clinical benefit to amlodipine in people with Hypertension as compared to genotypes CC + CG.
Notes: "A strong association between amlodipine response and the SNP rs2239050/CACNA1C was observed in the study participants. Participants carrying the GG genotype had better response/outcomes (P=0.004) when treated with amlodipine than carriers of CC or CG genotypes. After adjusting for confounding factors (age, sex, drug and diet compliance, etc)., no observable changes were noticed in the degree, level, or magnitude of the association. "
Article: Impact of Promoter Polymorphisms on the Transcriptional Regulation of the Organic Cation Transporter OCT1 (SLC22A1)
Gene: SLC22A1
Variant/haplotype: rs6935207
Drug(s): metformin
Phenotype category: Metabolism/PK
Significant: no
Association: Allele A is not associated with clearance of metformin in healthy individuals as compared to allele G.
Article: A GENOME-WIDE ASSOCIATION STUDY OF BRONCHODILATOR RESPONSE IN LATINOS IMPLICATES RARE VARIANTS
Gene: SPATS2L
Variant/haplotype: rs295137
Drug(s): salbutamol
Phenotype category: Efficacy
Significant: no
Association: Allele C is not associated with response to salbutamol in children with Asthma as compared to allele T.
Notes: GALAII genotyping was done using the Affymetrix LAT1 Array, which was designed to capture Latino population variation.  This was assessed as a replication attempt for a previously reported association of a different SPATS2L SNP with response to bronchodilators.  Bonferroni correction was performed according to the number of SNPs included that are within 50 kb up and downstream of SPATS2L.
Article: The population pharmacokinetics of R- and S-warfarin: effect of genetic and clinical factors
Gene: CYP2C9
Variant/haplotype: CYP2C9*1, CYP2C9*3
Drug(s): warfarin
Phenotype category: Other, Metabolism/PK
Significant: not stated
Association: CYP2C9 *3 is associated with decreased clearance of warfarin as compared to CYP2C9 *1.
Notes: For S-Warfarin in a model that included bodyweight, age and sex.
Article: Personalizing initial calcineurin inhibitor dosing by adjusting to donor CYP3A‐status in liver transplant patients
Gene: CYP3A5
Variant/haplotype: rs776746
Drug(s): cyclosporine, tacrolimus
Phenotype category: Dosage, Metabolism/PK
Significant: yes
Association: Genotype CC is associated with decreased dose of cyclosporine or tacrolimus in people with liver transplantation as compared to genotypes CT + TT.
Notes: The genotype refers to the genotype of the donor liver. Patients who were recipients of a liver transplantation from a donor with the CC genotype AND low or intermediate CYP3A4 mRNA levels needed a significantly decreased dose of cyclosporine or tacrolimus as compared to patients who whose liver donors had the rs776746 CC genotype AND high CYP3A4 mRNA levels, or rs776746 CT/TT genotypes regardless of CYP3A4 mRNA levels.
Article: Impact of IL28B, APOH and ITPA Polymorphisms on Efficacy and Safety of TVR- or BOC-Based Triple Therapy in Treatment-Experienced HCV-1 Patients with Compensated Cirrhosis from the ANRS CO20-CUPIC Study
Gene: APOH
Variant/haplotype: rs1801690
Drug(s): boceprevir, peginterferon alfa-2a, peginterferon alfa-2b, ribavirin, telaprevir
Phenotype category: Efficacy
Significant: no
Association: Allele C is not associated with increased response to boceprevir, peginterferon alfa-2a, peginterferon alfa-2b, ribavirin or telaprevir in people with Hepatitis C, Chronic as compared to allele G.
Notes: This variant was not significantly associated with SVR to triple therapy including telaprevir or boceprevir in patients with compensated cirrhosis chronically infected with HCV-1.
Article: Genomic Association Analysis of Common Variants Influencing Antihypertensive Response to Hydrochlorothiazide
Gene: CNTNAP2
Variant/haplotype: rs13223171
Drug(s): "diuretics", "hydrochlorothiazide", "Thiazides, plain"
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with response to diuretics, hydrochlorothiazide or Thiazides, plain in people with Hypertension as compared to allele C.
Notes: Significance was not attained. Observations: 2.89 mm Hg increased reduction of systolic blood pressure per T allele in PEAR + GERA, 1.12 mm Hg decreased reduction of systolic blood pressure per T allele in NORDIL, and 1.59 mm Hg increased reduction of systolic blood pressure per T allele in PEAR + GERA + NORDIL.
Article: Genetic Variation in CYP3A43 Explains Racial Difference in Olanzapine Clearance
Variant/haplotype: rs11631682
Drug(s): olanzapine
Phenotype category: Metabolism/PK
Significant: no
Association: Allele A is not associated with clearance of olanzapine in people with Schizophrenia as compared to allele G.
Article: Influence of APOA5 Locus on the Treatment Efficacy of Three Statins: Evidence From a Randomized Pilot Study in Chinese Subjects
Gene: APOA5
Variant/haplotype: rs662799
Drug(s): atorvastatin, rosuvastatin, simvastatin
Phenotype category: Other
Significant: yes
Association: Genotype AA is associated with response to atorvastatin, rosuvastatin and simvastatin in people with Dyslipidaemia as compared to genotypes AG + GG.
Notes: The correlation between APoB concentration and LDL cholesterol before and after treatment changed only slightly for the AG+GG genotypes (before rho = 0.55 p <0.001; after rho = 0.50 p<0.001) but decreased significantly for the AA genotype (before rho = 0.78 p<0.001; after rho 0.44 p<0.001) showing that the absolute reduction of ApoB was much smaller than the statin-induced reduction of LDLc. Please note: alleles have been complemented to the + chromosomal strand.
Article: The influence of NUDT15 variants on 6-mercaptopurine-induced neutropenia in Vietnamese pediatric acute lymphoblastic leukemia
Gene: NUDT15
Variant/haplotype: NUDT15*1, NUDT15*2, NUDT15*3, NUDT15*5, NUDT15*6
Drug(s): mercaptopurine
Phenotype category: Dosage
Significant: yes
Association: NUDT15 *1/*2 + *1/*3 + *1/*5 + *1/*6 (assigned as intermediate metabolizer phenotype) is associated with decreased dose of mercaptopurine in children with Precursor Cell Lymphoblastic Leukemia-Lymphoma as compared to NUDT15 *1/*1 (assigned as normal metabolizer phenotype) .
Notes: Median 6-MP adjusted dose (mg/m2/day)  for IM was 48.7 and NM was 64.3
Article: Polymorphisms of SLC19A1 80 G>A, MTHFR 677 C>T, and Tandem TS Repeats Influence Pharmacokinetics, Acute Liver Toxicity, and Vomiting in Children With Acute Lymphoblastic Leukemia Treated With High Doses of Methotrexate
Gene: MTHFR
Variant/haplotype: rs1801133
Drug(s): methotrexate
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotypes AG + GG are associated with increased steady-state concentration of methotrexate in children with Precursor Cell Lymphoblastic Leukemia-Lymphoma as compared to genotype AA.
Notes: SNP is referred to in the paper as 677 C>T and was mapped to rs1801133 by PharmGKB. Please note that alleles have been complemented to the positive strand.
Article: Functional genetic variation in the Rev-Erbα pathway and lithium response in the treatment of bipolar disorder
Gene: NR1D1, THRA
Variant/haplotype: rs2071427
Drug(s): lithium
Phenotype category: Efficacy
Significant: no
Association: Allele T is associated with increased response to lithium in people with Bipolar Disorder as compared to allele C.
Notes: The authors describe this as a nominal association which did not survive correction for multiple testing.
Article: A Candidate Gene Analysis of Methylphenidate Response in Attention-Deficit/Hyperactivity Disorder
Gene: COMT
Variant/haplotype: rs4680
Drug(s): methylphenidate
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with response to methylphenidate in children with Attention Deficit Disorder with Hyperactivity as compared to allele A.
Notes: Scales used to assess response: ADHD-RS-IV, SWAN, and Permanent product Measure of Performance (PERMP). A trend of effect was detected for the COMT variant. significance = p<0.025
Article: Reduced 5-FU clearance in a patient with low DPD activity due to heterozygosity for a mutant allele of the DPYD gene
Gene: DPYD
Variant/haplotype: rs3918290
Drug(s): fluorouracil
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype CT is associated with decreased clearance of fluorouracil in people with Colorectal Neoplasms as compared to genotype CC.
Notes: 5-fluorouracil activity and DPD activity were compared between one patient with severe fluorouracil-induced toxicity and six control patients with normal 5-fluorouracil-related symptoms. All patients were being treated for colorectal cancer. The index patient was a 60-year-old white female who experienced leukopenia, thrombocytopenia, nausea, diarrhea, stomatitis, fever, hair loss. The control patients experienced mild nausea, vomiting, or grade 1 stomatitis. The clearance was 520 ml/min in the index patient vs 980-1780 mg/min in controls. The area under the curve from 0-3 hours in the index patient was 24.1 mgh/l vs 15.3 mgh/l as the highest value in controls. Sequence analysis revealed the index patient was heterozygous for the *2A (IVS14+1G>A) mutation. Sequence analysis of the six control patients revealed no mutations.
Article: Pharmacogenetics of tenofovir clearance among Southern Africans living with HIV
Gene: RPE
Variant/haplotype: rs7570090
Drug(s): tenofovir
Phenotype category: Metabolism/PK
Significant: no
Association: Allele T is not associated with clearance of tenofovir in people with HIV Infections as compared to allele C.
Notes: Significance threshold was set at 6E-7.
Article: A novel mutant variant of the CYP2D6 gene (CYP2D6 17) common in a black African population: association with diminished debrisoquine hydroxylase activity
Gene: CYP2D6
Variant/haplotype: CYP2D6*1, CYP2D6*2
Drug(s): debrisoquine
Phenotype category: Metabolism/PK
Significant: no
Association: CYP2D6 *1/*2 is not associated with decreased metabolism of debrisoquine in healthy individuals as compared to CYP2D6 *1/*1.
Notes: MR of both diplotypes were similar, *1/*1(n=12) =0.56 and *1/*2 (n=13)=0.59.
Article: A Candidate Gene Analysis of Methylphenidate Response in Attention-Deficit/Hyperactivity Disorder
Gene: SLC6A2
Variant/haplotype: rs5569
Drug(s): methylphenidate
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with response to methylphenidate in children with Attention Deficit Disorder with Hyperactivity as compared to allele A.
Notes: Scales used to assess response: ADHD-RS-IV, SWAN, and Permanent productMeasure of Performance (PERMP).
Article: Relevance of CYP2B6 and CYP2D6 genotypes to methadone pharmacokinetics and response in the OPAL study
Gene: CYP2B6
Variant/haplotype: rs3745274
Drug(s): (R)-methadone
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotypes GT + TT are associated with increased concentrations of (R)-methadone in people with Opioid-Related Disorders as compared to genotype GG.
Notes: Significance was lost following multivariate analysis.
Article: The Pharmacokinetics and Pharmacogenomics of Efavirenz and Lopinavir/Ritonavir in HIV-Infected Persons Requiring Hemodialysis
Gene: CYP2B6
Variant/haplotype: rs3745274
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotypes GT + TT are associated with increased concentrations of efavirenz in people with HIV Infections as compared to genotype GG.
Article: Meta-Analysis on Pharmacogenetics of Platinum-Based Chemotherapy in Non Small Cell Lung Cancer (NSCLC) Patients
Gene: ABCB1
Variant/haplotype: rs1045642
Drug(s): Platinum compounds
Phenotype category: Efficacy
Significant: no
Association: Genotype GG is associated with increased response to Platinum compounds in people with Carcinoma, Non-Small-Cell Lung as compared to genotypes AA + AG.
Notes: When stratified by race, this association was only significant in the Asian population, not in the Caucasian population.
Article: Physiologically based pharmacokinetic model for 6-mercpatopurine: exploring the role of genetic polymorphism in TPMT enzyme activity
Gene: TPMT
Variant/haplotype: TPMT poor metabolizer
Drug(s): mercaptopurine
Phenotype category: Metabolism/PK
Significant: not stated
Association: TPMT poor metabolizer is associated with increased concentrations of mercaptopurine as compared to TPMT normal metabolizer.
Notes: The PK model predicted plasma and tissue concentrations of mercaptopurine and its metabolites, including 6-thioguanine nucleotide, which is responsible for its activity and toxicity, with the use of various factors, including TPMT phenotypes.
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: APOC3
Variant/haplotype: rs2854116
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. Please note alleles have been complemented to the plus chromosomal strand.
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: rs1062033
Drug(s): hdl cholesterol
Phenotype category: Other
Significant: yes
Association: Allele G is associated with increased concentrations of hdl cholesterol in women with Breast Neoplasms and Menopause as compared to allele C.
Notes: when taking letrozole and 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 increases in HDL-cholesterol of 6.9 mg/dL (SE 1.5).
Article: CYP3A4 and CYP3A5 Polymorphisms and Blood Pressure Response to Amlodipine among African-American Men and Women with Early Hypertensive Renal Disease
Gene: CYP3A4
Variant/haplotype: rs2740574
Drug(s): amlodipine
Phenotype category: Efficacy
Significant: no
Association: Genotypes CT + TT are not associated with response to amlodipine in people with Hypertension as compared to genotype CC.
Notes: No significant change in the likelihood of a patient reaching a target mean arterial pressure concentration of <= 92 mmHg or <= 107 mmHg was seen between genotypes. Please note alleles have been complemented to the plus chromosomal strand.
Article: Pharmacogenetics for Genes Associated with Age-Related Macular Degeneration (AMD) in the Comparison of AMD Treatments Trials (CATT)
Gene: CFH
Variant/haplotype: rs1061170
Drug(s): bevacizumab, ranibizumab
Phenotype category: Efficacy
Significant: no
Association: Genotype CC is not associated with response to bevacizumab or ranibizumab in people with Macular Degeneration as compared to genotypes CT + TT.
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: CALCA and TRPV1 genes polymorphisms are related to a good outcome in female chronic migraine patients treated with OnabotulinumtoxinA
Gene: SLC1A2
Variant/haplotype: rs4354668
Drug(s): botulinum toxin type a
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with response to botulinum toxin type a in women with Migraine NOS as compared to allele T.
Notes: No significant difference in allele frequency between responders and non-responders.
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: rs268214
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: Pharmacokinetics of Bupropion and Its Pharmacologically Active Metabolites in Pregnancy
Gene: CYP2B6
Variant/haplotype: CYP2B6*1, CYP2B6*6
Drug(s): bupropion
Phenotype category: Metabolism/PK
Significant: no
Association: CYP2B6 *6 is associated with increased steady-state concentration of bupropion in women with Pregnancy as compared to CYP2B6 *1.
Notes: The AUC of steady state was compared.
Article: Effect of CYP4F2 Polymorphisms on Ticagrelor Pharmacokinetics in Healthy Chinese Volunteers
Gene: CYP2C9
Variant/haplotype: rs17847029
Drug(s): AR-C124910XX, ticagrelor
Phenotype category: Metabolism/PK
Significant: no
Association: Genotype CT is not associated with decreased concentrations of AR-C124910XX or ticagrelor in healthy individuals as compared to genotype CC.
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
Article: Influence of Genetic Variants on Steady-State Etonogestrel Concentrations Among Contraceptive Implant Users
Gene: NR1I2
Variant/haplotype: rs2461817
Drug(s): etonogestrel
Phenotype category: Efficacy, Metabolism/PK
Significant: no
Association: Allele C is associated with increased steady-state concentration of etonogestrel in women as compared to allele A.
Notes: Corrected P-value cutoff of 5.0E-4 was not met.
Article: Pharmacogenetic Pathway Analysis of Docetaxel Elimination
Gene: CYP3A5
Variant/haplotype: rs776746
Drug(s): docetaxel
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele T is associated with increased clearance of docetaxel in people with Neoplasms as compared to allele C.
Notes: The T allele corresponds with CYP3A5*1.  The presence of the CYP3A5*1A allele was associated with a 49% (P = 0.020) increase in docetaxel clearance.
Article: Polymorphic Variants of SCN1A and EPHX1 Influence Plasma Carbamazepine Concentration, Metabolism and Pharmacoresistance in a Population of Kosovar Albanian Epileptic Patients
Gene: SCN1A
Variant/haplotype: rs2298771
Drug(s): carbamazepine
Phenotype category: Metabolism/PK
Significant: no
Association: Genotype CC is not associated with metabolism of carbamazepine in people with Epilepsy as compared to genotypes CT + TT.
Notes: In none of the measures that the authors used to measure exposure showed any association with the genotype. Please note: alleles have been complemented to the + chromosomal strand.
Article: A published pharmacogenetic algorithm was poorly predictive of tacrolimus clearance in an independent cohort of renal transplant recipients
Gene: CYP3A5
Variant/haplotype: CYP3A5*1, CYP3A5*3
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP3A5 *1/*3 is associated with increased clearance of tacrolimus in people with Kidney Transplantation as compared to CYP3A5 *3/*3.
Notes: Genotype *1/*3 vs *3/*3 was reported. Clearance was estimated using the dose-normalized whole-blood trough concentration. The DeKAF algorithm was tested but it failed to predict tacrolimus clearance in this cohort.
Article: Association of HLA-DRB1 Haplotypes With Rheumatoid Arthritis Severity, Mortality, and Treatment Response
Gene: HLA-DRB1
Variant/haplotype: HLA-DRB1*04:01
Drug(s): adalimumab, etanercept, infliximab
Phenotype category: Efficacy
Significant: yes
Association: HLA-DRB1 *04:01 is associated with increased response to adalimumab, etanercept or infliximab in people with Arthritis, Rheumatoid.
Notes: Valine at position 11 (VKA haplotype is *04:01 based on table 1 in 22286218 with His at position 13 - position 13 not considered in this publication) was associated with better European League Against Rheumatism (EULAR) response to TNF inhibitor therapy (OR, 1.23 [95% CI, 1.06- 1.43]) 0.007.