shlokn/autogkb huggingface dataset:
Article: Targeted pharmacogenetic analysis of antipsychotic response in the CATIE study
Gene: MAML3
Variant/haplotype: rs11100483
Drug(s): perphenazine
Phenotype category: Efficacy
Significant: yes
Association: Allele A is associated with response to perphenazine 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. It was unclear whether the allele was associated with an increased or decreased response to drug.
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: rs2289105
Drug(s): hdl cholesterol
Phenotype category: Other
Significant: yes
Association: Allele T is associated with decreased 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 decreases in HDL-cholesterol of 6.2 mg/dL (SE 1.6).
Article: The impact of ABCB1, CYP3A4/5 and ABCG2 gene polymorphisms on rivaroxaban trough concentrations and bleeding events in patients with non-valvular atrial fibrillation
Gene: ABCB1
Variant/haplotype: rs4728709
Drug(s): rivaroxaban
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype GG is associated with increased dose-adjusted trough concentrations of rivaroxaban in people with Atrial Fibrillation as compared to genotype AG.
Notes: no AA homozygotes were observed.
Article: IGF2BP2 variations influence repaglinide response and risk of type 2 diabetes in Chinese population
Gene: IGF2BP2
Variant/haplotype: rs1470579
Drug(s): repaglinide
Phenotype category: Dosage, Efficacy
Significant: yes
Association: Genotypes AC + CC are associated with decreased response to repaglinide in people with Diabetes Mellitus, Type 2 as compared to genotype AA.
Notes: The parameters that showed decreased response were FPG(fasting plasma glucose) and PPG(postprandial plasma glucose).  The authors noted that the C allele frequency was higher in the Type 2 Diabetes patients than in the healthy controls when the entire trial population of 350 patients and 207 controls was assayed (C freq = 0.3029 vs 0.2464) .  The subset of patients treated with repaglinide all had the same CYP2C8 genotypes(with respect to *3- but exact genotypes not given) and SLCO1B1 genotypes(with respect to *1B,*5 and *15, but exact genotypes not given) .
Article: Pharmacogenetic Factors Influence Escitalopram Pharmacokinetics and Adverse Events in Youth with a Family History of Bipolar Disorder: A Preliminary Study
Gene: CYP2C19
Variant/haplotype: CYP2C19 intermediate metabolizer
Drug(s): escitalopram
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2C19 intermediate metabolizer is associated with increased dose-adjusted trough concentrations of escitalopram in children with Depression or Anxiety Disorders as compared to CYP2C19 normal metabolizer.
Notes: CPIC guidelines used to assign CYP2C19  metabolizer phenotypes based on CYP2C19: *1, *2,*3, *4, *5, *6, *7, *8, *17. "CYP2C19 metabolizer phenotype had a significant effect on the dose-normalized AUC0–24 (p = 0.025), Ctrough (p = 0.013), and t1/2 (p = 0.0008) of escitalopram (Fig. 1).” "CYP2C19 metabolizer phenotypes were almost exclusively rapid metabolizer (RM n = 17), normal metabolizer (NM n = 31), or intermediate metabolizer (IM n = 17), with only one ultrarapid metabolizer (UM) and no poor metabolizers (PMs)."
Article: CYP3A5, ABCB1 and SLCO1B1 Polymorphisms and Pharmacokinetics and Virologic Outcome of Lopinavir/Ritonavir in HIV-infected Children
Gene: CYP3A5
Variant/haplotype: rs776746
Drug(s): lopinavir, ritonavir
Phenotype category: Metabolism/PK
Significant: no
Association: Allele C is not associated with response to lopinavir or ritonavir in children with HIV Infections as compared to allele T.
Notes: No association between this variant and virologic suppression in patients treated with lopinavir/ritonavir. Variant referred to in the paper as A6986G.
Article: Pharmacogenetic analysis of high-dose methotrexate treatment in children with osteosarcoma
Gene: ABCC2
Variant/haplotype: rs3740066
Drug(s): methotrexate
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype TT is associated with decreased concentrations of methotrexate in children with Osteosarcoma as compared to genotypes CC + CT.
Notes: Concentrations refers to area under the concentration time curve (0-48hrs)
Article: The pharmacokinetics of ondansetron after intravenous injection in healthy volunteers phenotyped as poor or extensive metabolisers of debrisoquine
Gene: CYP2D6
Variant/haplotype: CYP2D6 poor metabolizer
Drug(s): ondansetron
Phenotype category: Metabolism/PK
Significant: no
Association: CYP2D6 poor metabolizer is not associated with decreased metabolism of ondansetron in healthy individuals as compared to CYP2D6 normal metabolizer.
Notes: Cmax, AUC, plasma clearance (calculated from Dose/AUC) and half-life were measured with no significant differences in any category between poor and extensive metabolizers.  Metabolizer status had been previously determined using oral debrisoquine as the substrate probe. No genotyping or genetics was used in this study.
Article: Genetic markers for the efficacy of tumour necrosis factor blocking therapy in rheumatoid arthritis
Gene: TNF
Variant/haplotype: rs1800629
Drug(s): etanercept
Phenotype category: Efficacy
Significant: yes
Association: Genotype GG is associated with increased response to etanercept in people with Arthritis, Rheumatoid as compared to genotypes AA + AG.
Notes: When this genotype is combined with the rs1800896 CC genotype. Those with the GG-CC combination genotype were more likely to be responders to treatment, as compared to those with any other combination of genotypes. However, no significant difference in genotype frequencies was seen between responders and non-responders when considering the rs1800629 or 1800896 SNPs alone. Responders defined using the American College of Rheumatology (ACR) response criteria and response criteria based on the modified disease activity score (DAS)28 index. Non-responders failed to fulfill both these criteria.
Article: Population pharmacokinetics of unbound mycophenolic acid in adult allogeneic haematopoietic cell transplantation: effect of pharmacogenetic factors
Gene: UGT1A9
Variant/haplotype: rs17868320
Drug(s): mycophenolic acid
Phenotype category: Metabolism/PK
Significant: no
Association: Genotype CC is not associated with metabolism of mycophenolic acid as compared to genotype TT.
Notes: Genotype CC is not associated with any pharmacokinetic parameters measured in the study when exposed to mycophenolic acid as compared to genotype TT.
Article: The Effect Of Alcohol Priming On Neural Markers Of Alcohol Cue-Reactivity
Gene: OPRM1
Variant/haplotype: rs1799971
Drug(s): ethanol
Phenotype category: Other
Significant: not stated
Association: Genotypes AG + GG are associated with increased response to ethanol in people with Alcoholism as compared to genotype AA.
Notes: MRI study. Subjects carrying the G allele showed increased pre- vs. post-priming alcohol cue reactivity activation in the left caudate, thalamus, putamen, and bilateral supramarginal gyrus and parietal operculum cortex compared to subjects with the AA genotype.
Article: Dosing equation for tacrolimus using genetic variants and clinical factors
Gene: CYP3A5
Variant/haplotype: rs776746
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: not stated
Association: Allele T is associated with increased metabolism of tacrolimus in people with Kidney Transplantation as compared to allele C.
Notes: Patients carrying at least one CYP3A5*1 allele had lower trough tacrolimus levels than CYP3A5*3/*3 carriers at 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22 and 24 week post-transplantation.  Compared to CYP3A5*3/*3 carriers, CL/F was increased by 69% in CYP3A5*1/*3 carriers, and increased by 100 in CYP3A5*1/*1 carriers.  Other factors affecting tacrolimus CL/F were days post transplant, transplantation at a steroid sparing center, recipient's age and the use of calcium channel blockers.
Article: Influence of CYP2C9 and VKORC1 on warfarin dose, anticoagulation attainment and maintenance among European American and African Americans
Gene: VKORC1
Variant/haplotype: rs8050894
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Genotypes CG + GG are associated with decreased dose of warfarin as compared to genotype CC.
Notes: in European Americans.
Article: Tell-Tale SNPs: The Role of CYP2B6 in Methadone Fatalities
Gene: CYP2B6
Variant/haplotype: rs8192709
Drug(s): S-EDDP
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype CT is associated with increased concentrations of (S)-EDDP as compared to genotype CC.
Article: Genome-Wide Association and Functional Studies Reveal Novel Pharmacological Mechanisms for Allopurinol
Gene: ABCG2
Variant/haplotype: rs76979899
Drug(s): allopurinol
Phenotype category: Efficacy
Significant: no
Association: Allele T is associated with decreased response to allopurinol as compared to allele C.
Notes: Response to allopurinol was determined by whether serum uric acid concentrations decreased following allopurinol treatment.
Article: Characterisation of the Clinical Pharmacokinetics of Actinomycin D and the Influence of ABCB1 Pharmacogenetic Variation on Actinomycin D Disposition in Children with Cancer
Gene: ABCB1
Variant/haplotype: rs1128503
Drug(s): dactinomycin
Phenotype category: Metabolism/PK
Significant: no
Association: Allele A is not associated with clearance of dactinomycin in children with Neoplasms as compared to allele G.
Notes: No significant difference in actinomycin D clearance was seen between the genotypes (AA, AG, GG). Please note that alleles have been complemented to the plus chromosomal strand.
Article: UGT1A1*28 genotype and irinotecan dosage in patients with metastatic colorectal cancer: a Dutch Colorectal Cancer Group study
Gene: UGT1A1
Variant/haplotype: UGT1A1*1, UGT1A1*28
Drug(s): irinotecan
Phenotype category: Dosage
Significant: no
Association: UGT1A1 *1/*28 + *28/*28 are not associated with dose of irinotecan in people with Colorectal Neoplasms as compared to UGT1A1 *1/*1.
Notes: No significant difference was seen in median total irinotecan dose received over all cycles (g/m2), or in frequency of reductions in irinotecan dose after treatment cycle 1 between the genotypes in patients were treated with irinotecan monotherapy or irinotecan plus capecitabine.
Article: The Association Between Clozapine Plasma Concentration, CYP2D6 (*10, *2) Polymorphisms and Risk of Adverse Reactions
Gene: CYP2D6
Variant/haplotype: rs1065852
Drug(s): clozapine
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype AA is associated with increased concentrations of clozapine in people with Schizophrenia as compared to genotypes AG + GG.
Notes: Alleles complemented. "Compared with the corresponding groups, the clozapine plasma concentrations of individuals with the *10TT genotype and individuals with the *2CC genotype were the highest (P < .05). "
Article: Targeted pharmacogenetic analysis of antipsychotic response in the CATIE study
Gene: MCPH1
Variant/haplotype: rs17570753
Drug(s): perphenazine
Phenotype category: Efficacy
Significant: yes
Association: Allele A is associated with response to perphenazine 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. It was unclear whether the allele was associated with an increased or decreased response to drug.
Article: Drug Metabolizing Enzyme and Transporter Gene Variation, Nicotine Metabolism, Prospective Abstinence, and Cigarette Consumption
Gene: CYP2A6
Variant/haplotype: rs4803381
Drug(s): nicotine
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele T is associated with decreased metabolism of nicotine as compared to allele C.
Notes: In the discovery stage: Participants derived from 1) the PKTWIN study and 2) the SMOFAM studyBoth were assessed for nicotine metabolite ratio (NMR) which was used as a biomarker of CYP2A6 activity. Nominally significant SNPs in the discovery stage were tested in the validation stage. Validation stage participants were self-identified White participants from 8 clinical trials of smoking cessation therapies conducted in six US sites.
Article: Association of Cytochrome P450 Genetic Variants with Clopidogrel Resistance and Outcomes in Acute Ischemic Stroke
Gene: CYP2C8
Variant/haplotype: rs17110453
Drug(s): clopidogrel
Phenotype category: Efficacy
Significant: no
Association: Genotypes AC + CC is not associated with resistance to clopidogrel in people with Stroke as compared to genotype AA.
Article: CYP2C9 Genotype and Pharmacodynamic Responses to Losartan in Patients with Primary and Secondary Kidney Diseases
Gene: CYP2C9
Variant/haplotype: CYP2C9*1, CYP2C9*2, CYP2C9*3
Drug(s): losartan
Phenotype category: Efficacy
Significant: yes
Association: CYP2C9 *1/*2 is associated with decreased response to losartan in people with Kidney Diseases as compared to CYP2C9 *1/*1.
Notes: Patients with secondary kidney diseases carrying CYP2C9 variant alleles (*2 or *3) showed increases in blood pressure (both systolic and diastolic) as compared to patients with the *1/*1 genotype. A nonsignificant trend towards improved urinary protein excretion was seen in patients with primary kidney diseases with the *1/*1 genotype as compared to patients carrying variant alleles (*2 or *3).
Article: Warfarin Anticoagulant Therapy: A Southern Italy Pharmacogenetics-Based Dosing Model
Gene: VKORC1
Variant/haplotype: rs9923231
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Genotype TT is associated with decreased dose of warfarin in people with Cardiovascular Diseases as compared to genotypes CC + CT.
Notes: A gene-dose effect was seen in that dose of warfarin decreased with the presence of the T allele: CC>CT>TT. When studied together with CYP2C9, patients carrying variants in both genes needed between 34.8% and 84% of the dose needed for patients wildtype for both genes.
Article: Population pharmacokinetics of voriconazole and CYP2C19 polymorphisms for optimizing dosing regimens in renal transplant recipients
Gene: CYP2C19
Variant/haplotype: CYP2C19*1, CYP2C19*2, CYP2C19*3
Drug(s): voriconazole
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2C19 *2 + *3 is associated with increased concentrations of voriconazole in people with Kidney Transplantation as compared to CYP2C19 *1.
Notes: 106 patients were prospectively included in a population PK analysis. Non-linear mixed effect models were used and dosing simulations were performed based on the final model. A one-compartment model with first-order absorption and elimination was used to characterize voriconazole pharmacokinetics. CYP2C19 genotype had a significant effect on the clearance. Voriconazole trough concentrations in poor metabolizers were significantly higher than in both intermediate metabolizers and extensive metabolizers.
Article: Population Pharmacokinetics, Pharmacodynamics, and Pharmacogenetics Modeling of Oxypurinol in Hmong Adults with Gout and/or Hyperuricemia
Gene: SLC22A12
Variant/haplotype: rs505802
Drug(s): allopurinol
Phenotype category: Dosage
Significant: not stated
Association: Allele T is associated with increased dose of allopurinol in people with Gout as compared to allele C.
Notes: "Most individuals with both PDZK1 rs12129861 AA and SLC22A12 rs505802 CC genotypes achieve target SU (with at least 75% success rate) with allopurinol below the maximum dose, regardless of renal function and body mass. In contrast, individuals with both PDZK1 rs12129861 GG and SLC22A12 rs505802 TT genotypes would require more than the maximum dose, thus selecting alternative medications."
Article: Influence of CYP2C9 and VKORC1 on warfarin dose, anticoagulation attainment and maintenance among European American and African Americans
Gene: VKORC1
Variant/haplotype: rs2359612
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 European Americans and African Americans.
Article: Genetic Variants Associated With Response to Platinum-Based Chemotherapy in Non-Small Cell Lung Cancer Patients: A Field Synopsis and Meta‐Analysis
Gene: CYP1A1
Variant/haplotype: rs1048943
Drug(s): Platinum compounds
Phenotype category: Efficacy
Significant: yes
Association: Genotypes CC + CT is associated with increased resistance to Platinum compounds in people with Carcinoma, Non-Small-Cell Lung as compared to genotype TT.
Notes: "Similarly, an increased risk of chemoresistance was observed ... as well as for CYP1A1 rs1048943 (dominant model, OR = 2.593, 95% CI = 1.535–4.381, p < 0.01; heterozygous model, OR = 2.512, 95% CI = 1.437–4.392, p < 0.01; allele model, OR = 1.851, 95% CI = 1.303–2.631, p < 0.01),"
Article: CYP2B6 Variants and Plasma Efavirenz Concentrations during Antiretroviral Therapy in Port-au-Prince, Haiti
Gene: CYP2B6
Variant/haplotype: rs28399499
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele C (assigned as poor metabolizer phenotype) is associated with decreased metabolism of efavirenz in people with HIV Infections as compared to allele T (assigned as normal metabolizer phenotype) .
Notes: As determined by significantly higher efavirenz plasma levels. This SNP was only significant in composite analysis with rs3745274: extensive metabolizers were defined as having no variant alleles at positions 516 (allele G) or (983 allele T), intermediate metabolizers had a single variant at one of the positions but not both, slow metabolizers (described as "poor" here) had 2 variant alleles (either genotype 516TT, 983CC, or 516 GT with 983 TC). Significant after Bonferroni correction for multiple comparisons.
Article: The role of candidate pharmacogenetic variants in determining valproic acid efficacy, toxicity and concentrations in patients with epilepsy
Gene: CYP2C9
Variant/haplotype: rs1057910
Drug(s): valproic acid
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype AC is associated with increased dose-adjusted trough concentrations of valproic acid in people with Epilepsy as compared to genotype AA.
Notes: "The rs1057910 variant (CYP2C9*3) was associated with increased ADC with a mean of 4.9 ± 1.75 [(ug/mL/day)/(mg/kg)] in carriers vs 4.15 ± 1.61 in wildtype individuals (p = 0.028). "
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: HMGCR
Variant/haplotype: rs3846662
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: Impact of efavirenz pharmacokinetics and pharmacogenomics on neuropsychological performance in older HIV-infected patients
Gene: CYP2B6
Variant/haplotype: rs3745274
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele T is associated with increased concentrations of efavirenz in people with HIV Infections as compared to allele G.
Notes: Significant association was seen at T=12 and 18 hours.
Article: Ethnic and genetic factors in methadone pharmacokinetics: A population pharmacokinetic study
Gene: ABCB1
Variant/haplotype: rs2032582
Drug(s): methadone
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype CC is associated with decreased clearance of methadone in people with Opioid-Related Disorders as compared to genotypes AC + CT.
Article: Genome-Wide Association Study of Serum Creatinine Levels during Vancomycin Therapy
Gene: MIA3
Variant/haplotype: rs75328711
Drug(s): vancomycin
Phenotype category: Metabolism/PK
Significant: no
Association: Allele C is not associated with trough concentration of vancomycin as compared to allele A.
Notes: The SNP was not associated with trough levels of vancomycin (first vancomycin trough documented in EMR after at least 3 doses vancomycin). Elimination constants were also calculated.
Article: Genetic Variation in CYP3A43 Explains Racial Difference in Olanzapine Clearance
Variant/haplotype: rs929087
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: An unequal cross-over event within the CYP2D gene cluster generates a chimeric CYP2D7/CYP2D6 gene which is associated with the poor metabolizer phenotype
Gene: CYP2D6
Variant/haplotype: CYP2D6*5, CYP2D6*13
Drug(s): dextromethorphan
Phenotype category: Metabolism/PK
Significant: not stated
Association: CYP2D6 *5/*13 (assigned as poor metabolizer phenotype) is associated with decreased metabolism of dextromethorphan.
Notes: Study identified *13 in a male with a dextromethorphan poor metabolizer phenotype (PM was defined with a log DEM/DOR higher -0.5.  All the exons were successfully amplified using except exon 1 which required a combination of CYP2D7 gene-specific 5' primer and a CYP2D6 gene-specific 3' primer. he chimeric gene is non-functional presumably due to an insertion in exon 1 (characteristic of the exon 1 of the CYP2D7 gene) which causes a shift in the reading frame with premature termination of translation.
Article: Pharmacogenetics of tenofovir clearance among Southern Africans living with HIV
Gene: DPYD
Variant/haplotype: rs1801159
Drug(s): tenofovir
Phenotype category: Metabolism/PK
Significant: no
Association: Allele C is not associated with clearance of tenofovir in people with HIV Infections as compared to allele T.
Notes: Significance threshold was set at 3.3E-3.
Article: A pharmacogenetic study of docetaxel and thalidomide in patients with castration-resistant prostate cancer using the DMET genotyping platform
Gene: CHST3
Variant/haplotype: rs4148945
Drug(s): docetaxel, thalidomide
Phenotype category: Efficacy
Significant: yes
Association: Allele C is associated with increased response to docetaxel and thalidomide in people with Prostatic Neoplasms as compared to allele T.
Notes: (allele inferred by frequency comparison with data in pgkb, actual base not listed in paper)
Article: Influence of cytochrome P450 and glutathione S transferase polymorphisms on response to nilotinib therapy among chronic myeloidleukemia patients from Pakistan
Gene: GSTP1
Variant/haplotype: rs1695
Drug(s): nilotinib
Phenotype category: Efficacy
Significant: yes
Association: Allele A is associated with increased response to nilotinib in people with Leukemia, Myelogenous, Chronic, BCR-ABL Positive as compared to allele G.
Notes: Rs number from PharmGKB, effects reported for GSTP1A313G. Excerpt "wild type CYP1A1, GSTP1 and GSTM1 deletion was significantly frequent in responders. The partial responders carried heterozygous mutant genotypes of CYP1A1, GSTP1 and wild type of GSTM1/GSTT1 whereas homozygous GSTP1genotype was significantly linked to treatment failure."