shlokn/autogkb huggingface dataset:
Article: CGRP 4218T/C polymorphism correlated with postoperative analgesic effect of fentanyl
Gene: CALCA
Variant/haplotype: rs145837941
Drug(s): fentanyl
Phenotype category: Dosage
Significant: yes
Association: Genotype GG is associated with increased dose of fentanyl in people with Pain, Postoperative as compared to genotypes AA + AG.
Notes: "At the 12th hour and the 24th hour after the surgery, the fentanyl consumption for PCA of the C/C group was significantly higher than the T/T group (P=0.013, 0.004). At the 24th hour after the surgery, the fentanyl consumption for PCA of the C/C group was significantly higher than the T/C group (P=0.021) " Alleles complemented. Mapped CGRP 4218T/C to rs145837941 in the CALCA gene using PMID:23237777.
Article: Effect of Concomitant Artesunate Administration and Cytochrome P4502C8 Polymorphisms on the Pharmacokinetics of Amodiaquine in Ghanaian Children with Uncomplicated Malaria
Gene: CYP2C8
Variant/haplotype: rs11572103
Drug(s): amodiaquine, artesunate
Phenotype category: Efficacy, Metabolism/PK
Significant: no
Association: Genotype AA is not associated with metabolism of amodiaquine and artesunate in children with Malaria as compared to genotypes AT + TT.
Notes: Plasma DEAQ concentrations were slightly but insignificantly lower in subjects with mutant CYP2C8 genotypes than in those with wild-type alleles or heterozygotes. No difference was seen in adverse events or efficacy. NOTE: this gene is on the minus strand, *2 represents T on coding strand and shown here as A on plus strand.
Article: IL28B polymorphisms associated with therapy response in Chilean chronic hepatitis C patients
Gene: IFNL3
Variant/haplotype: rs12980275
Drug(s): peginterferon alfa-2a, ribavirin
Phenotype category: Efficacy
Significant: yes
Association: Genotype AA is associated with increased response to peginterferon alfa-2a and ribavirin in people with Hepatitis C, Chronic as compared to genotypes AG + GG.
Notes: This genotype is associated with sustained virological response (SVR).
Article: CALCA and TRPV1 genes polymorphisms are related to a good outcome in female chronic migraine patients treated with OnabotulinumtoxinA
Gene: KCNS1
Variant/haplotype: rs734784
Drug(s): botulinum toxin type a
Phenotype category: Efficacy
Significant: no
Association: Allele C 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. Please note that alleles have been complemented to the positive strand.
Article: Effect of pharmacogenetics on plasma lumefantrine pharmacokinetics and malaria treatment outcome in pregnant women
Gene: CYP2B6
Variant/haplotype: rs3745274
Drug(s): lumefantrine
Phenotype category: Metabolism/PK
Significant: no
Association: Allele T is not associated with concentrations of lumefantrine in women with Malaria and Pregnancy as compared to allele G.
Notes: Median concentrations of lumefantrine 7 days after beginning treatment with artemether-lumefantrine were not significantly different and no more likely to have median concentrations of lumefantrine  >600 ng/ml between genotypes.
Article: Evaluation of TS and ENOSF1 Variants as a Biomarker in Response to Neoadjuvant Chemotherapy based on 5FU in Gastric Cancer Patients
Gene: ENOSF1
Variant/haplotype: rs2612091
Drug(s): fluorouracil
Phenotype category: Efficacy
Significant: yes
Association: Genotype CC is associated with increased response to fluorouracil in people with Stomach Neoplasms as compared to genotypes CT + TT.
Notes: Alleles complemented to plus chromosomal strand. The authors describe the effect as "Patients with genotype AG did not respond to treatment. " however in table 3 it shows GG as over represented in the responders.
Article: The Distribution of the Genotypes of ABCB1 and CES1 Polymorphisms in Kazakhstani Patients with Atrial Fibrillation Treated with DOAC
Gene: ABCB1
Variant/haplotype: rs1128503
Drug(s): dabigatran
Phenotype category: Metabolism/PK
Significant: no
Association: Allele A is not associated with decreased dose-adjusted trough concentrations of dabigatran in people with Atrial Fibrillation as compared to allele G.
Article: Role of the HPA Axis and the A118G Polymorphism of the μ-Opioid Receptor in Stress-Induced Drinking Behavior
Gene: OPRM1
Variant/haplotype: rs1799971
Drug(s): ethanol
Phenotype category: Dosage
Significant: no
Association: Genotype AG is not associated with dose of ethanol in people with Alcoholism and Stress as compared to genotype AA.
Notes: There was no significant difference in alcohol intake, craving or latency to access alcohol between the genotype groups in alcoholic subjects subjected to stress.
Article: Functional characterization of novel rare CYP2A6 variants and potential implications for clinical outcomes
Gene: CYP2A6
Variant/haplotype: rs145308399
Drug(s): nicotine
Phenotype category: Metabolism/PK
Significant: not stated
Association: Allele T is associated with decreased metabolism of nicotine as compared to allele C.
Notes: Assigned as decreased function following in vitro assessments, in vivo associations and variant construct functional assignments.
Article: The influence of COMT and ABCB1 gene polymorphisms on sufentanil analgesic effect for postoperative pain in children with fracture
Gene: COMT
Variant/haplotype: rs4680
Drug(s): sufentanil
Phenotype category: Dosage
Significant: yes
Association: Genotype AA is associated with increased dose of sufentanil in children with Pain, Postoperative as compared to genotypes AG + GG.
Notes: "Pediatric patients in the AA group of COMT had higher pain scores and total consumption of sufentanil at awakening, as well as at 2, 6, 12, and 24 hours postoperatively, compared to the AG and GG groups (P < .05). There was no statistically significant difference between the AG and GG groups (P > .05)."
Article: Effect of race and glucuronidation rates on the relationship between nicotine metabolite ratio and nicotine clearance
Gene: UGT2B10
Variant/haplotype: rs11726322
Drug(s): nicotine
Phenotype category: Metabolism/PK
Significant: no
Association: Allele G is not associated with clearance of nicotine as compared to allele C.
Notes: No effect of the UGT2B10 variant genotypes on the ability of plasma nicotine metabolite ratio to predict nicotine clearance.
Article: STOP Pain Project—Opioid Response in Pediatric Cancer Patients and Gene Polymorphisms of Cytokine Pathways
Gene: TNF
Variant/haplotype: rs1800629
Drug(s): opioids
Phenotype category: Dosage
Significant: yes
Association: Genotype GG is associated with increased dose of opioids in children with Neoplasms and Pain as compared to genotype AG.
Notes: no AA homozygotes were observed.
Article: The Effect of CYP2D6 polymorphisms on the Response to Pain Treatment for Pediatric Sickle Cell Pain Crisis
Gene: CYP2D6
Variant/haplotype: CYP2D6*1, CYP2D6*6
Drug(s): codeine
Phenotype category: Efficacy
Significant: yes
Association: CYP2D6 *6 is associated with decreased response to codeine in children with Anemia, Sickle Cell as compared to CYP2D6 *1.
Notes: Pediatric patients with severe sickle cell disease who have failed codeine therapy for a pain crisis while taking hydroxyurea were found to be more likely to have a reduced function allele (including *4, *5, *6, *17, *40) as compared to those with mild disease, likely due to a decreased conversion of codeine to morphine. Allele frequencies were not reported. Reduced function alleles were grouped for analysis.
Article: Prognostic Role of Human Leukocyte Antigen Alleles and Cytokine Single-Nucleotide Polymorphisms in Patients with Chronic Myeloid Leukemia Treated with Tyrosine Kinase Inhibitor Drugs
Gene: HLA-B
Variant/haplotype: HLA-B*57:03
Drug(s): BCR-ABL tyrosine kinase inhibitors
Phenotype category: Efficacy
Significant: yes
Association: HLA-B *57:03 is associated with increased clinical benefit to BCR-ABL tyrosine kinase inhibitors in people with Leukemia, Myelogenous, Chronic, BCR-ABL Positive.
Notes: "B*57:03:01 showed a higher frequency of 7.3% in the favorable group compared to the unfavorable group (2.4%) (p = 0.0451)."
Article: Influence of genetic polymorphisms in the folate pathway on toxicity after high-dose methotrexate treatment in pediatric osteosarcoma
Gene: C1orf167, CLCN6, MTHFR
Variant/haplotype: rs1801131
Drug(s): methotrexate
Phenotype category: Metabolism/PK
Significant: no
Association: Allele G is not associated with concentrations of methotrexate in children with Osteosarcoma as compared to allele T.
Notes: Please note that alleles have been complemented to the positive strand.
Article: Effects of cytochrome P450 2B6 and constitutive androstane receptor genetic variation on Efavirenz plasma concentrations among HIV patients in Kenya
Gene: CYP2B6
Variant/haplotype: rs2279345
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: no
Association: Allele C is associated with increased concentrations of efavirenz in people with HIV Infections as compared to allele T.
Notes: this was significant in preliminary analysis but not in the multivariate analysis. Described in tables as 18492C>T.
Article: G PROTEIN RECEPTOR KINASE 4 (GRK4) POLYMORPHISMS: BETA-BLOCKER PHARMACOGENETICS AND TREATMENT RELATED OUTCOMES IN HYPERTENSION
Gene: GRK4
Variant/haplotype: rs1024323
Drug(s): atenolol
Phenotype category: Efficacy
Significant: yes
Association: Allele T is associated with decreased response to atenolol in people with Hypertension as compared to allele C.
Notes: This decrease in response was only significant* when considered as part of a haplotype with rs2960306. The finding was that increasing copies of rs2960306T-rs1024323T haplotype were associated with significantly reduced atenolol-induced diastolic blood pressure lowering (-9.1±6.8 versus -6.8±7.1 versus -5.3±6.4 mm Hg in participants with 0, 1, and 2 copies respectively).  Analysis of the SNP alone showed a trend towards decreased response with the T allele. The association of the haplotype was only observed in rs1801253 CC genotypes in Whites.; *= authors state that the data are statistically significant when Bonferroni-corrected for the number of SNPs tested in the analysis but that they do not meet chip-wide Bonferroni-corrected significance.
Article: Lumacaftor/Ivacaftor Treatment of Patients with Cystic Fibrosis Heterozygous for F508del‐CFTR
Gene: CFTR
Variant/haplotype: rs113993960
Drug(s): ivacaftor, lumacaftor
Phenotype category: Efficacy
Significant: no
Association: Genotype CTT/del is not associated with response to ivacaftor and lumacaftor in people with Cystic Fibrosis.
Notes: F508del allele. All study participants had the F508del allele on one allele and a second that was predicted to not respond to ivacaftor/lumacaftor treatment. Three out of five outcomes did not show a significant improvement following 56 days of ivacaftor/lumacaftor treatment.
Article: Effect of the VKORC1 D36Y variant on warfarin dose requirement and pharmacogenetic dose prediction
Gene: VKORC1
Variant/haplotype: rs61742245
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Genotype AC is associated with increased dose of warfarin in people with warfarin maintenance treatment as compared to genotype CC.
Notes: In carriers of allele A, the weekly warfarin dose was increased by a median of 43.7 mg (IQR, 40.5-47.2 mg) compared to non-carriers.  Median weekly dose overall = 35 mg (interquartile range [IQR], 24.5 to 52.5 mg).; Also, refinement of the IWPC prediction model to include this variant resulted in significantly better model performance.
Article: Warfarin Dose Model for the Prediction of Stable Maintenance Dose in Indian Patients
Gene: GGCX
Variant/haplotype: rs12714145
Drug(s): warfarin
Phenotype category: Dosage
Significant: no
Association: Allele T is not associated with dose of warfarin as compared to allele C.
Article: Donor CYP3A5 genotype influences tacrolimus disposition on the first day after paediatric liver transplantation
Gene: CYP3A5
Variant/haplotype: CYP3A5*1, CYP3A5*3
Drug(s): tacrolimus
Phenotype category: Dosage, Metabolism/PK
Significant: yes
Association: CYP3A5 *3/*3 is associated with decreased metabolism of tacrolimus in children with liver transplantation as compared to CYP3A5 *1/*1 + *1/*3.
Notes: Children whose DONOR liver had the *3/*3 genotype had increased trough concentrations and dose-adjusted trough concentrations as compared to those with the *1/*1 or *1/*3 genotypes.
Article: Impact of Single Nucleotide Polymorphisms on Plasma Concentrations of Efavirenz and Lopinavir/ritonavir in Chinese Children Infected with the Human Immunodeficiency Virus
Gene: ABCB1
Variant/haplotype: rs1045642
Drug(s): ritonavir
Phenotype category: Metabolism/PK
Significant: no
Association: Genotypes AA + AG are not associated with concentrations of ritonavir in children with HIV Infections as compared to genotype GG.
Article: Meta-analysis of genome-wide association studies of HDL cholesterol response to statins
Variant/haplotype: rs247616
Drug(s): hmg coa reductase inhibitors
Phenotype category: Efficacy
Significant: yes
Association: Allele T is associated with increased response to hmg coa reductase inhibitors as compared to allele C.
Notes: GWAS study.
Article: Nifedipine pharmacokinetics are influenced by CYP3A5 genotype when used as a preterm labor tocolytic
Gene: CYP3A5
Variant/haplotype: rs776746
Drug(s): nifedipine
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotypes CT + TT are associated with increased clearance of nifedipine in women with Pregnancy as compared to genotype CC.
Notes: Women homozygous or heterozygous for the T allele (CYP3A5 *1/*1 or *1/*3) had increased apparent oral clearance (Cl/F; units = L/h), increased apparent volume of distribution (Vd/F; units = L) and decreased average concentration of nifedipine (Cave; units = ug/L) compared to those homozygous for the C allele (CYP3A5 *3/*3).
Article: Germline Polymorphisms as Biomarkers of Tumor Response in Colorectal Cancer Patients Treated with Anti-EGFR Monoclonal Antibodies: A Systematic Review and Meta-Analysis
Gene: VEGFA
Variant/haplotype: rs3025039
Drug(s): cetuximab, panitumumab
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with response to cetuximab or panitumumab in people with Colorectal Neoplasms as compared to allele C.
Notes: Meta-analysis with 3 studies. The authors did not provide the exact number of patients but stated that "the median number of patients per analysis was 110 (range 50 - 740)". Most definitions of response were variations of the RECIST criteria.
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: rs869312138
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 Leu36Trp in the paper.
Article: CYP2D6 polymorphisms and endoxifen concentration in Chinese patients with breast cancer
Gene: CYP2D6
Variant/haplotype: CYP2D6*1, CYP2D6*2, CYP2D6*10
Drug(s): endoxifen
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2D6 *10/*10 + *2/*10 is associated with decreased concentrations of endoxifen in women with Breast Neoplasms as compared to CYP2D6 *1/*10.
Notes: "The median endoxifen concentration was highest in CYP2D6 genotype *1/*2 (24ng/ml, 95%CI 18–27 ng/ml) and *1/*10 (23ng/ml, 95%CI 21–31 ng/ml, Fig. 1). Patients with genotype *1/*10 were with higher median endoxifen concentrations when compared with patients with *10/*10 (p = 0.0144) and with *2/*10 (p = 0.0337)."
Article: Impact of the novel CYP2C:TG haplotype and CYP2B6 variants on sertraline exposure in a large patient population
Gene: CYP2B6
Variant/haplotype: CYP2B6*1, CYP2B6*6, CYP2B6*9
Drug(s): sertraline
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2B6 *6 + *9 are associated with increased concentrations of sertraline as compared to CYP2B6 *1/*1.
Notes: Compared to the reference group, patients homozygous or heterozygous for the CYP2B6*6 or *9 allele had a 25% (n = 40, p = 0.008) and 15% (n = 261, p<0.001) in- creased serum concentration of sertraline, respectively.
Article: The Pharmacogenetics of Tacrolimus in Corticosteroid-Sparse Pediatric and Adult Kidney Transplant Recipients
Gene: CYP3A4
Variant/haplotype: CYP3A4*1, CYP3A4*22
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: no
Association: CYP3A4 *1/*22 is not associated with trough concentration of tacrolimus in people with Kidney Transplantation as compared to CYP3A4 *1/*1.
Article: The impact of age and CYP2C9 and VKORC1 variants on stable warfarin dose in the paediatric population
Gene: CYP2C9
Variant/haplotype: CYP2C9*1, CYP2C9*2, CYP2C9*3
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: CYP2C9 *1/*2 + *1/*3 + *2/*3 is associated with decreased dose of warfarin in children as compared to CYP2C9 *1/*1.
Notes: Patients who carried the CYP2C9 *2 or *3 variant alleles required 71% the dose of warfarin as compared to those with the wild-type genotype. CYP2C9 genotype was found to account for 6% of the variability in stable warfarin dose (mg/day).
Article: Genetic predictors of the maximum doses patients receive during clinical use of the anti-epileptic drugs carbamazepine and phenytoin
Gene: ABCB1
Variant/haplotype: rs1045642
Drug(s): phenytoin
Phenotype category: Dosage, Metabolism/PK
Significant: no
Association: Allele A is not associated with increased dose of phenytoin in people with Epilepsy as compared to allele G.
Article: Genetic factors influencing warfarin dose in Black-African patients: a systematic review and meta-analysis
Gene: CYP2C9
Variant/haplotype: CYP2C9*1, CYP2C9*11
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: CYP2C9 *1/*11 is associated with decreased dose of warfarin as compared to CYP2C9 *1/*1.
Notes: In this meta-analysis of warfarin Dose in Black-African Patients, CYP2C9*11 allele is associated with 5.4mg/week less warfarin dose requirement compared to wild-type homozygotes.
Article: Effect of APOE and CHRNA7 Genotypes on the Cognitive Response to Cholinesterase Inhibitor Treatment at Different Stages of Alzheimer’s Disease
Gene: CHRNA7
Variant/haplotype: rs6494223
Drug(s): donepezil, galantamine, rivastigmine
Phenotype category: Efficacy
Significant: yes
Association: Allele T is associated with increased response to donepezil, galantamine and rivastigmine in people with Alzheimer Disease as compared to allele C.
Notes: In patients with mild Alzheimer's disease only (baseline Mini-Mental State Examination (MMSE) score >= 20); in patients with moderate to severe Alzheimer's (MMSE <20) no significant results were seen (p=0.73). Adjusted for gender, age, baseline MMSE, and presence of the APOE E4 allele. After 6 months of treatment with cholinesterase inhibitors, those with the T allele were more likely to be a responder to treatment, as compared to those without the T allele. A responder was defined as a patient who showed improvement or no deterioration in cognition comparing MMSE scores at baseline with MMSE scores after 6 months. The authors note in the Discussion section that after 24 months of treatment, no significant association was seen.
Article: Deciphering the Interleukin 28B Variants That Better Predict Response to Pegylated Interferon-α and Ribavirin Therapy in HCV/HIV-1 Coinfected Patients
Variant/haplotype: rs8113007
Drug(s): peginterferon alfa-2b, ribavirin
Phenotype category: Efficacy
Significant: yes
Association: Genotype AA is associated with increased response to peginterferon alfa-2b and ribavirin in people with Hepatitis C and HIV Infections as compared to genotypes AT + TT.
Notes: This genotype is associated with sustained virological response (SVR).
Article: Functional genetic variation in the Rev-Erbα pathway and lithium response in the treatment of bipolar disorder
Gene: CRY1
Variant/haplotype: rs8192440
Drug(s): lithium
Phenotype category: Efficacy
Significant: no
Association: Allele G is associated with increased response to lithium in people with Bipolar Disorder as compared to allele A.
Notes: The authors describe this as a nominal association which did not survive correction for multiple testing.
Article: Influence of ABCB1 polymorphisms on aripiprazole and dehydroaripiprazole plasma concentrations
Gene: ABCB1
Variant/haplotype: rs1128503
Drug(s): aripiprazole, dehydroaripiprazole
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype GG is associated with increased concentrations of aripiprazole and dehydroaripiprazole as compared to genotype AA.
Notes: Alleles complemented. "Regarding ARI/DHA ratio, significant differences between the different variants were observed in the three SNPs analyzed. Specifically, for C3434T it was obtained an ARI/DHA ratio 37.4% higher for CC (2.35) compared to the TT variant (1.71), for G2677T 93% higher for GG (3.27) vs TT (1.69) and for C1236T 64.2% higher for CC (2.93) vs TT (1.78) (Fig. 1A). Comparing Non-T carriers vs. T carriers variants as a whole, yielded 22.3%, 70.07% and 47.43% more respectively, maintaining statistical significance (Fig. 1B)." "For ABCB1, the following variants were analyzed: C3435T (rs1045642), C2677 T/A (rs2032582) and C1236T (rs1128503)."
Article: Effect of pharmacogenetics on plasma lumefantrine pharmacokinetics and malaria treatment outcome in pregnant women
Gene: CYP3A4
Variant/haplotype: rs2740574
Drug(s): lumefantrine
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele C is associated with increased concentrations of lumefantrine in women with Malaria and Pregnancy as compared to allele T.
Notes: Median concentrations of lumefantrine 7 days after beginning treatment with artemether-lumefantrine were not significantly higher in carriers of the C allele as compared to non-carriers.
Article: The Impact of CYP2C9*11 Allelic Variant on the Pharmacokinetics of Phenytoin and (S)‐Warfarin
Gene: CYP2C9
Variant/haplotype: CYP2C9*1, CYP2C9*2, CYP2C9*11
Drug(s): hydroxyphenytoin
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2C9 *1/*11 + *2/*11 is associated with decreased concentrations of hydroxyphenytoin in healthy individuals as compared to CYP2C9 *1/*1.
Notes: Effect was for Urinary excretion of p‐HPPH (hydroxyphenytoin) in 24‐hour urine collection.
Article: Effect of CYP2C19 polymorphisms on antidepressant prescription patterns and treatment emergent mania in bipolar disorder
Gene: CYP2C19
Variant/haplotype: CYP2C19*1, CYP2C19*17
Drug(s): amitriptyline, clomipramine
Phenotype category: Other
Significant: yes
Association: CYP2C19 *17/*17 is associated with increased discontinuation of amitriptyline or clomipramine in people with Bipolar Disorder as compared to CYP2C19 *1/*1.
Notes: Patients with the CYP2C19 ultrarapid metabolizer phenotype (*17/*17) showed higher risk for discontinuation of amitriptyline or clomipramine treatment than extensive metabolizers (*1/*1). Only rs4244285 and rs12248560 were used to define the phenotype.
Article: ABCB1, CYP2B6, and CYP3A4 Genetic Polymorphisms do not Affect Methadone Maintenance Treatment in HCV-positive Patients
Gene: ABCB1
Variant/haplotype: rs1045642
Drug(s): methadone
Phenotype category: Metabolism/PK
Significant: no
Association: Allele G is not associated with metabolism of methadone in men with Heroin Dependence as compared to allele A.