shlokn/autogkb huggingface dataset:
Article: Methacholine PC20 In African Americans And Whites With Asthma With Homozygous Genotypes at ADRB2 Codon 16
Gene: ADRB2
Variant/haplotype: rs1042713
Drug(s): methacholine
Phenotype category: Efficacy
Significant: yes
Association: Genotype AA is associated with decreased response to methacholine in people with Asthma as compared to genotype GG.
Notes: Patients with the AA genotype had lower log PC20 (provocative concentration of methacholine that causes a 20% fall in FEV1) compared to those with the GG genotype, indicating increased airway reactivity and an increased risk of worse asthma outcomes. Please note that this genotype was compared within African Americans, and between African Americans (AA genotype) and Whites (GG genotype). However, allele frequencies were the same between the two ethnicities in this population. African Americans n=45, Whites n=43.
Article: The influence of CYP3A, PPARA, and POR genetic variants on the pharmacokinetics of tacrolimus and cyclosporine in renal transplant recipients
Gene: PPARA
Variant/haplotype: rs4823613
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele G is associated with decreased metabolism of tacrolimus in people with Kidney Transplantation as compared to allele A.
Notes: A single steady-state concentration of tacrolimus was collected for each patient 2-7 wks post-transplant and compared to dose of tacrolimus administered to patients at Oslo University Hospital. Reported concentrations are "steady-state dose-adjusted concentration" of tacrolimus. Steady-state is defined as at least 3 days after last dose adjustment for Tac and 4 days for cyclosporine.
Article: An Acenocoumarol Dosing Algorithm Using Clinical and Pharmacogenetic Data in Spanish Patients with Thromboembolic Disease
Gene: CYP2C9
Variant/haplotype: CYP2C9*2, CYP2C9*3
Drug(s): acenocoumarol
Phenotype category: Dosage
Significant: yes
Association: CYP2C9 *2 + *3 is associated with dose of acenocoumarol.
Notes: CYP2C9 variants were significantly associated with acenocoumarol dose, and explained 11.7% of the variability in dose. Clinical variables (Age, BMI, Enzyme inducers status and Amiodarone status) explained 22% of the variability in dose. This study developed an algorithm for acenocoumarol dosing using clinical and pharmacogenetic data.
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: rs3745274
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype TT is associated with decreased clearance of efavirenz in people with HIV Infections as compared to genotype GG.
Notes: As shown by increased plasma concentrations (units = mg/L) for those with the TT genotype compared to those with the GG genotype. Fasting plasma efavirenz concentrations were measured 12 hours after the last dose, and after 12 weeks of treatment.
Article: ERCC1 Cys8092Ala and XRCC1 Arg399Gln Polymorphisms Predict Progression-Free Survival after Curative Radiotherapy for Nasopharyngeal Carcinoma
Gene: XRCC1
Variant/haplotype: rs25487
Drug(s): cisplatin, radiotherapy
Phenotype category: Efficacy
Significant: yes
Association: Genotype TT is associated with decreased response to cisplatin and radiotherapy in people with Nasopharyngeal Neoplasms and Tobacco Use Disorder as compared to genotypes CC + CT.
Notes: All patients had stage II-IV nasopharyngeal cancer and progression free survival (PFS) was the primary endpoint.
Article: PDE4 Gene Family Variants Are Associated with Response to Apremilast Treatment in Psoriasis
Gene: EIF3G, P2RY11, PPAN-P2RY11
Variant/haplotype: rs2305795
Drug(s): apremilast
Phenotype category: Efficacy
Significant: yes
Association: Allele G is associated with increased clinical benefit to apremilast in people with Psoriasis as compared to allele A.
Notes: "Allele-based association tests detected 64 SNPs displaying nominal p values < 0.05 (Table 2) including 10 SNPs with p values ≤ 0.01. " Table 2 shows frequency of minor allele is responders and non-responders. Responder status maybe defined by PASI score improvement greater than 75% after 24–36 weeks of treatment.
Article: Gemcitabine Metabolic and Transporter Gene Polymorphisms Are Associated with Drug Toxicity and Efficacy in Patients with Locally Advanced Pancreatic Cancer
Gene: CDA
Variant/haplotype: rs2072671
Drug(s): gemcitabine
Phenotype category: Efficacy
Significant: yes
Association: Genotype AA is associated with increased response to gemcitabine in people with Pancreatic Neoplasms as compared to genotypes AC + CC.
Notes: Patients with the AA genotype had a better response to gemcitabine therapy than patients with either the AC or the CC genotype. However, progression free survival did not significantly differ between genotype groups. There were four SNPs in this study that, when taken together, affected progression free survival: rs183484, rs2072671, rs760370, and rs9937. Using patients with 0 or 1 variant as reference, patients with 2 variants had an increased HR of 1.79 (P = 0.004) and patients with 3-4 variants has an increased HR of 3.25 (P < 0.001). There were also two SNPs in this study that, when taken together, affected tumor response to therapy: rs2072671 and rs760370. Using patients with 0 variants as reference, patients with 1-2 variants had an increased OR of 3.40 (P = 0.004).
Article: Genetic Variation in CYP3A43 Explains Racial Difference in Olanzapine Clearance
Gene: CYP3A43
Variant/haplotype: rs651430
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: Association of ABCB1 Gene Polymorphisms with Efficacy and Adverse Reaction to Risperidone or Paliperidone in Han Chinese Schizophrenic Patients
Gene: ABCB1
Variant/haplotype: rs12535512
Drug(s): risperidone
Phenotype category: Efficacy
Significant: yes
Association: Genotypes CC + CT are not associated with response to risperidone in people with Schizophrenia as compared to genotype TT.
Notes: Efficacy measured with reduction in PANSS total score reduced rate.
Article: Impact of CYP3A4*22 on Pazopanib Pharmacokinetics in Cancer Patients
Gene: ABCG2
Variant/haplotype: rs2231137
Drug(s): pazopanib
Phenotype category: Metabolism/PK
Significant: no
Association: Genotype CT is not associated with decreased clearance of pazopanib in people with Neoplasms as compared to genotype CC.
Notes: No homozygous TT observed. Alleles complemented to plus chromosomal strand.
Article: Effect of Genotype-Guided Warfarin Dosing on Clinical Events and Anticoagulation Control Among Patients Undergoing Hip or Knee Arthroplasty: The GIFT Randomized Clinical Trial
Gene: CYP4F2
Variant/haplotype: rs2108622
Drug(s): warfarin
Phenotype category: Dosage
Significant: not stated
Association: Allele T is associated with dose of warfarin as compared to allele C.
Article: Efficacy of the pharmacologic chaperone migalastat in a subset of male patients with the classic phenotype of Fabry disease and migalastat-amenable variants: data from the phase 3 randomized, multicenter, double-blind clinical trial and extension study
Gene: GLA
Variant/haplotype: rs869312399
Drug(s): migalastat
Phenotype category: Efficacy
Significant: not stated
Association: Allele C is associated with increased response to migalastat in people with Fabry Disease.
Notes: Patients carrying the C allele showed improvements in renal function, cardiac geometry (specifically, reductions in left ventricular mass index) and gastrointestinal symptoms as well as reductions in GL-3 inclusions and plasma lyso-Gb3 and an increase in PBMC alpha-Gal A activity when treated with migalastat. Clinical benefit of migalastat was not substantially affected by disease severity. This variant was designated as an 'amenable variant' to migalastat treatment following an in vitro assay where migalastat increased the activity of alpha-Gal A by at least 3%. As all data were derived from post hoc analysis, statistical analyses were not carried out. Variant referred to as Pro259Arg in the paper.
Article: Attempted validation of 44 reported SNPs associated with tacrolimus troughs in a cohort of kidney allograft recipients
Gene: CYP2A7P1, CYP2B6
Variant/haplotype: rs3745274
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: no
Association: Allele T is not associated with trough concentration of tacrolimus in people with Kidney Transplantation and Transplantation as compared to allele G.
Notes: This study was attempting to validate reported variants and tacrolimus trough concentration in a large population of African American and European American kidney transplant patients.
Article: Gender-Specific Association of Galanin Polymorphisms with HPA-Axis Dysregulation, Symptom Severity, and Antidepressant Treatment Response
Gene: GAL
Variant/haplotype: rs948854
Drug(s): antidepressants, benzodiazepine derivatives, mirtazapine, Selective serotonin reuptake inhibitors
Phenotype category: Efficacy
Significant: yes
Association: Allele C is associated with decreased response to antidepressants, benzodiazepine derivatives, mirtazapine or Selective serotonin reuptake inhibitors in women Depressive Disorder, Major as compared to allele T.
Notes: This was specific to premenopausal women(not seen in postmenopausal women or in men).  The same allele was associated with more severe vegetative but not cognitive depressive symptoms.  Patients were on a variety of therapies, with the three largest groups being SSRIs,Tricyclics, and Mirtazapine.
Article: Impact of CYP2D6*2, CYP2D6*35, rs5758550, and related haplotypes on risperidone clearance in vivo
Gene: CYP2D6
Variant/haplotype: CYP2D6*1, CYP2D6*2, CYP2D6*9, CYP2D6*10, CYP2D6*35, CYP2D6*41
Drug(s): risperidone
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2D6 *2 + *9 + *10 + *35 + *41 is associated with decreased clearance of risperidone as compared to CYP2D6 *1.
Notes: "The clearances attributable to the alleles or haplotypes; of primary interest were estimated at 30% for CYP2D6*2-; rs5758550A, 66% for CYP2D6*2-rs5758550G, and 57% for CYP2D6*35, relative to the clearance for *1 (Fig. 1). For the; remaining decreased function alleles *9, *10, and *41, the; allele-specific clearances were estimated to be 39%, 32%, and; 15%, respectively, relative to the clearance for *1" "Each evaluated CYP2D6 allele was associated with significantly lower risperidone clearance than the reference normal function allele CYP2D6*1 (p < 0.001)."
Article: Characterizing variability in warfarin dose requirements in children using modelling and simulation
Gene: CYP4F2
Variant/haplotype: rs2108622
Drug(s): warfarin
Phenotype category: Dosage, Efficacy
Significant: no
Association: Allele T is not associated with increased dose of warfarin in children with Heart Diseases as compared to allele C.
Notes: A model was created to predict maintenance doses for children of different ages, all with a baseline INR of 1 and a target INR of 2.5, based on longitudinal data from children taking warfarin. Though there was a trend for a higher dose per T allele, CYP4F2 genotype was not retained in the final model. CYP2C9 genotype, VKORC1 genotype, bodyweight, age, baseline INR, target INR and time since initiation of therapy were all found to be significant causes of warfarin dose variability in children.
Article: A Pharmacogenetics-Based Warfarin Maintenance Dosing Algorithm from Northern Chinese Patients
Gene: CYP4F2
Variant/haplotype: rs2108622
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Allele C is associated with decreased dose of warfarin in people with heart valve replacement as compared to allele T.
Notes: Samples, genotypes and INRs from a cohort of 551 patients were used to derive an algorithm which was used to predict daily warfarin maintenance dose in a second cohort of 236 patients. Note: the authors state that "SNPs were tested for deviations from HWE using the chi-squared test, and for their association with the warfarin dose by Spearman correlation analysis using a *co-dominant* model." rs2108622 was not significantly associated with warfarin maintenance dose in the first cohort but was significant in the multivariate analysis.
Article: OPRM1 moderates daily associations of naltrexone adherence with alcohol consumption: Preliminary evidence from a mobile health trial
Gene: OPRM1
Variant/haplotype: rs1799971
Drug(s): naltrexone
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with response to naltrexone in people with Alcoholism as compared to allele A.
Notes: There was no significant main effect of rs1799971 genotype on alcohol craving or consumption during naltrexone treatment. However, the authors found that the G allele significantly moderated the interaction between adherence to naltrexone and same-day alcohol consumption.
Article: Genetic polymorphisms in the long noncoding RNA MIR2052HG offer a pharmacogenomic basis for the response of breast cancer patients to aromatase inhibitor therapy
Variant/haplotype: rs4735715
Drug(s): anastrozole, exemestane
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with increased response to anastrozole and exemestane in women with Breast Neoplasms as compared to allele G.
Notes: Patients included postmenopausal women with resected stage I–III breast cancer that was ERa and/or PgR positive and randomized to five years of anastrozole or exemestane. Did not reach statistical significance for GWAS (P<5 x 10^-8).
Article: IGF2BP2 variations influence repaglinide response and risk of type 2 diabetes in Chinese population
Gene: IGF2BP2
Variant/haplotype: rs4402960
Drug(s): repaglinide
Phenotype category: Dosage, Efficacy
Significant: yes
Association: Genotypes GT + TT are associated with increased response to repaglinide in people with Diabetes Mellitus, Type 2 as compared to genotype GG.
Notes: The parameter that showed enhanced response was PINS(postprandial serum insulin) .  The authors noted that the T 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 (T freq = 0.2714 vs 0.2126) .  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: Polymorphisms of the Proinflammatory Cytokine Genes Modulate the Response to NSAIDs but Not to Triptans in Migraine Attacks
Gene: TNF
Variant/haplotype: rs1800629
Drug(s): almotriptan, eletriptan, frovatriptan, rizatriptan, sumatriptan, zolmitriptan
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with clinical benefit to almotriptan, eletriptan, frovatriptan, rizatriptan, sumatriptan or zolmitriptan in people with Migraine without Aura as compared to allele G.
Article: VKORC1 and Novel CYP2C9 Variation Predict Warfarin Response in Alaska Native and American Indian People
Gene: VKORC1
Variant/haplotype: rs9923231
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Allele T is associated with decreased dose of warfarin as compared to allele C.
Notes: in Alaska Native and American Indian People. This variant -1639G>A is significantly associated with stable warfarin dose, decreasing the dose required to achieve therapeutic INR by 1.7 mg/day per allele (t-test of coefficients, unadjusted P = 1.4e-05, Bonferroni adjusted P = 7.0e-05).
Article: CYP2C19 genotype and sodium channel blockers in lacosamide-treated children with epilepsy: two major determinants of trough lacosamide concentration or clinical response
Gene: CYP2C19
Variant/haplotype: rs4244285
Drug(s): lacosamide
Phenotype category: Efficacy
Significant: no
Association: Genotypes AA + AG is associated with increased clinical benefit to lacosamide in children with Epilepsy as compared to genotype GG.
Notes: "Intriguingly, CYP2C19 *2 (rs4244285; G to A), but not *3 (rs4986893), was observed to be associated with the clinical response of LCM. Children carrying alleles GA or AA achieved better efficacy (Supplemental Table 4). Nevertheless, this association did not retain statistical significance after applying the Bonferroni correction for multiple comparisons. Moreover, the plasma trough concentration of LCM in nonresponders with wild GG genotypes was significantly lower than those responders with GA or AA genotypes (Figure 3). These findings suggest that individuals who have a better efficacy should have higher plasma concentrations, which was consistent with previous research.18,32 However, no statistical difference in concentration between responders and nonresponders was observed in our study."
Article: Genotypic variation in the SV2C gene impacts response to atypical antipsychotics the CATIE Study
Gene: SV2C
Variant/haplotype: rs6882321
Drug(s): risperidone
Phenotype category: Efficacy
Significant: no
Association: Genotype AA is not associated with response to risperidone in people with Schizophrenia as compared to genotypes AC + CC.
Notes: Not significant after correction for multiple testing using the False Discovery Rate. Response was assessed by change in the total Positive and Negative Syndrome Scale (PANSS) score.
Article: Effect of pharmacogenetics on plasma lumefantrine pharmacokinetics and malaria treatment outcome in pregnant women
Gene: ABCB1
Variant/haplotype: rs3842
Drug(s): lumefantrine
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with response to lumefantrine in women with Malaria and Pregnancy as compared to allele C.
Article: Beneficial effect of ezetimibe-atorvastatin combination therapy in patients with a mutation in ABCG5 or ABCG8 gene
Gene: ABCG8
Variant/haplotype: ABCG8 deficiency
Drug(s): ezetimibe
Phenotype category: Efficacy
Significant: yes
Association: ABCG8 deficiency is associated with increased clinical benefit to ezetimibe in people with Familial hypercholesterolemia.
Notes: "ezetimibe-atorvastatin combination therapy might be more beneficial in hypercholesterolemic patients with a mutation in ABCG5 or ABCG8 gene." Variants identified were c.55G > C (p.Asp19His) rs11887534, c.1226A > G (p.Asn409Ile) rs150977210,  c.1256 T > A (p.Ile419Asn) rs201659189, c.1285A > G (p.Met429Val) rs147194762, c.1763C > A (p.Ala588Glu) rs377433853, c.1798 T > G (p.Phe600Val) not found. Rs numbers for some variants mapped by manual curation of tables at ClinVar.
Article: Genetic and nongenetic factors associated with warfarin dose requirements in Egyptian patients
Gene: APOC1, APOE
Variant/haplotype: rs429358
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Allele T is associated with decreased dose of warfarin in people with haplotype epsilon2.
Article: Effects of FMO3 Polymorphisms on Pharmacokinetics of Sulindac in Chinese Healthy Male Volunteers
Gene: FMO3
Variant/haplotype: rs2266780
Drug(s): sulindac
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype GG is associated with increased exposure to sulindac in healthy individuals as compared to genotype AA.
Notes: Measures of exposure were AUC, Cmax, Tmax, and T1/2.
Article: The International SSRI Pharmacogenomics Consortium (ISPC): a genome-wide association study of antidepressant treatment response
Variant/haplotype: rs1596996
Drug(s): Selective serotonin reuptake inhibitors
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with response to Selective serotonin reuptake inhibitors in people with Depressive Disorder, Major as compared to allele C.
Notes: The allele did not reach genome wide significance in the discovery or replication cohorts. GWA analyses were performed for two phenotypes: ‘% change in HRSD-17 score’ (% HRSD defined as the change in HRSD-17 score divided by the baseline score) and ‘response’ (defined as greater than or equal to 50% reduction in HRSD-17 score from baseline to 4-week visit). Please note, alleles have been complemented to the + chromosomal strand.
Article: Measurements of Functional Responses in Human Primary Lung Cells as a Basis for Personalized Therapy for Cystic Fibrosis
Gene: CFTR
Variant/haplotype: rs121909047
Drug(s): lumacaftor
Phenotype category: Efficacy
Significant: yes
Association: Genotype AA is associated with response to lumacaftor.
Notes: A561E allele. Study carried out using primary bronchial epithelial cells from donors with cystic fibrosis. Secretion of chloride ions across the cell membrane was measured to determine CFTR activity.
Article: Gemcitabine Metabolic and Transporter Gene Polymorphisms Are Associated with Drug Toxicity and Efficacy in Patients with Locally Advanced Pancreatic Cancer
Gene: CDA
Variant/haplotype: rs1048977
Drug(s): gemcitabine
Phenotype category: Efficacy, Toxicity
Significant: no
Association: Genotype CC is not associated with increased response to gemcitabine in people with Pancreatic Neoplasms as compared to genotypes CT + TT.
Notes: Tumor response to therapy, progression free survival, and risk of neutropenia development did not significantly differ between genotype groups.
Article: Polymorphisms of MTHFR Associated with Higher Relapse/Death Ratio and Delayed Weekly MTX Administration in Pediatric Lymphoid Malignancies
Gene: SLCO1B1
Variant/haplotype: rs11045879
Drug(s): methotrexate
Phenotype category: Efficacy
Significant: no
Association: Allele C is not associated with response to methotrexate in children with Lymphoma, Non-Hodgkin or Precursor Cell Lymphoblastic Leukemia-Lymphoma as compared to allele T.
Notes: No significant difference in relapse-free survival between genotype groups.
Article: Genotypic variation in the SV2C gene impacts response to atypical antipsychotics the CATIE Study
Gene: SV2C
Variant/haplotype: rs1995380
Drug(s): risperidone
Phenotype category: Efficacy
Significant: no
Association: Genotype GG is not associated with response to risperidone in people with Schizophrenia as compared to genotypes CC + CG.
Notes: Not significant after correction for multiple testing using the False Discovery Rate. Response was assessed by change in the total Positive and Negative Syndrome Scale (PANSS) score.
Article: Effects of CYP2B6 G516T polymorphisms on plasma efavirenz and nevirapine levels when co-administered with rifampicin in HIV/TB co-infected Thai adults
Gene: CYP2B6
Variant/haplotype: rs3745274
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype TT is associated with decreased metabolism of efavirenz in people with HIV Infections and Tuberculosis as compared to genotypes GG + GT.
Notes: Association with significantly increased efavirenz plasma levels. Was significant at week 6, 12 of treatment and 1 month after rifampicin discontinuation.
Article: Clinical Impact of Cytochrome P450 2C19 Genotype on the Treatment of Invasive Aspergillosis under Routine Therapeutic Drug Monitoring of Voriconazole in a Korean Population
Gene: CYP2C19
Variant/haplotype: CYP2C19*1, CYP2C19*2, CYP2C19*3, CYP2C19*17
Drug(s): voriconazole
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2C19 *1/*1 + *1/*17 is associated with decreased trough concentration of voriconazole in people with Hematologic Diseases as compared to CYP2C19 *1/*2 + *1/*3 + *2/*2 + *3/*3.
Notes: The percentage of patients with an out-of-range (i.e. below-range) initial trough level differed significantly between extensive metabolizers (*1/*1, *1/*17), heterozygous extensive metabolizers (*1/*2, *1/*3) and poor metabolizers (*2/*2, *2/*3): 46% vs 26% vs 0% respectively. No significant difference was seen when considering above-range levels.