shlokn/autogkb huggingface dataset:
Article: Genetic factors influencing warfarin dose in Black-African patients: a systematic review and meta-analysis
Gene: VKORC1
Variant/haplotype: rs9934438
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Genotypes AA + AG are associated with decreased dose of warfarin as compared to genotype GG.
Notes: In this meta-analysis of warfarin Dose in Black-African Patients, this variant is associated with 21.6mg/week less warfarin dose requirement compared to wild-type homozygotes.
Article: Influence of Genetic Variants on Steady-State Etonogestrel Concentrations Among Contraceptive Implant Users
Gene: CYP3A7
Variant/haplotype: CYP3A7*1A, CYP3A7*1C
Drug(s): etonogestrel
Phenotype category: Efficacy, Metabolism/PK
Significant: no
Association: CYP3A7 *1C is associated with decreased steady-state concentration of etonogestrel in women as compared to CYP3A7 *1A/*1A.
Notes: "Carriers of CYP3A7*1C had, on average, 23% lower etonogestrel concentrations; than participants with the wild-type genotype"  in contraceptive; implant users which may theoretically put them at risk for contraceptive failure. Corrected P-value cutoff of 5.0E-4 was not met.
Article: Polymorphic Variants of SCN1A and EPHX1 Influence Plasma Carbamazepine Concentration, Metabolism and Pharmacoresistance in a Population of Kosovar Albanian Epileptic Patients
Gene: ABCB1
Variant/haplotype: rs1045642
Drug(s): carbamazepine
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype AG is associated with increased dose of carbamazepine in people with Epilepsy as compared to genotypes AA + GG.
Notes: The authors evaluated daily dose and maintenance dose and calculated the means for each genotype. The AG genotype is associated with a higher mean daily dose of carbamazepine (CBZ). Mean CBZ daily dose (mg/day) for the AG genotype was 594.4 vs. 440.4-525.4 for the GG and CC genotypes, respectively. There were no significant differences in maintenance dose, however. Please note: alleles have been complemented to the + chromosomal strand.
Article: Pharmacogenetics of Naltrexone And Disulfiram in Alcohol Dependent, Dually Diagnosed Veterans
Gene: DBH
Variant/haplotype: rs1611115
Drug(s): disulfiram
Phenotype category: Efficacy
Significant: yes
Association: Genotype CC is associated with increased response to disulfiram in men with Alcoholism as compared to genotypes CT + TT.
Notes: Veterans. Two-thirds had a lifetime history of major depressive disorder, 37% had a lifetime history of post-traumatic stress disorder. 65% took SSRIs and 39% took anticonvulsants. 84-day treatment period. "DBH genotype interacted with disulfram (p=0.01) on drinks per drinking day with less drinking for subjects with the “CC” genotype than for T allele carriers on disulfiram."
Article: A polymorphism in the histone deacetylase 1 gene is associated with the response to corticosteroids in asthmatics
Gene: HDAC1
Variant/haplotype: rs1741981
Drug(s): Corticosteroids For Systemic Use
Phenotype category: Efficacy
Significant: yes
Association: Genotype CC is associated with decreased response to Corticosteroids For Systemic Use in people with Asthma as compared to genotypes CT + TT.
Notes: Adults with the CC genotype showed significantly lower percent forced expiratory volume in 1 second (%FEV1) increases in response to systemic corticosteroids, as compared to those with the CT or TT genotype. Patients were treated for 7 days. Note that this allele was significantly related to asthma severity (same direction of association; corrected p=0.036).
Article: Association studies of dopamine synthesis and metabolism genes with multiple phenotypes of heroin dependence
Gene: SLC6A3
Variant/haplotype: rs1042098
Drug(s): methadone
Phenotype category: Dosage
Significant: no
Association: Allele G is not associated with dose of methadone in people with Heroin Dependence as compared to allele A.
Article: Genome-wide Association Study of Virologic Response with Efavirenz- or Abacavir-containing Regimens in AIDS Clinical Trials Group Protocols
Variant/haplotype: rs374527
Drug(s): efavirenz
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with response to efavirenz in people with HIV Infections as compared to allele T.
Notes: No significant association with virologic failure is found for the combinations of CYP2B6 polymorphisms (rs3745274, rs28399499, and rs4803419).
Article: Replication study of polymorphisms associated with response to methotrexate in patients with rheumatoid arthritis
Gene: MTHFD1
Variant/haplotype: rs2236225
Drug(s): methotrexate
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to methotrexate in people with Arthritis, Rheumatoid as compared to allele G.
Article: Race, Gender, and Genetic Polymorphism Contribute to Variability in Acetaminophen Pharmacokinetics, Metabolism, and Protein-Adduct Concentrations in Healthy African-American and European-American Volunteers
Gene: UGT2B15
Variant/haplotype: rs1902023
Drug(s): acetaminophen
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele A is associated with decreased clearance of acetaminophen in healthy individuals as compared to allele C.
Notes: Clearance refers to apparent oral plasma clearance of acetaminophen and clearance of acetaminophen glucuronide. The A allele is also referred to as the *2 allele. Please note: alleles have been complemented to the + chromosomal strand.
Article: Polymorphism of the dopamine transporter type 1 gene modifies the treatment response in Parkinson’s disease
Gene: SLC6A3
Variant/haplotype: rs3836790
Drug(s): levodopa, methylphenidate
Phenotype category: Efficacy
Significant: yes
Association: Genotype ACATACACACTCAGACACACATACCATGCA/ACATACACACTCAGACACACATACCATGCA is associated with increased response to levodopa and methylphenidate in people with Parkinson Disease as compared to genotypes ACATACACACTCAGACACACATACCATGCA/del + del/del.
Notes: In a multivariate analysis adjusted for the dose of l-DOPA, the SLC6A3 rs3836790 genotype was strongly correlated with the motor UPDRS score ON l-DOPA (P = 0.002) the number of steps ON l-DOPA (P = 0.0003), the completion time OFF l-DOPA (P = 0.027), the completion time ON l-DOPA (P = 0.0009) and the number of freezing of gait episodes ON l-DOPA (P = 0.017).
Article: Polymorphic Variants of SCN1A and EPHX1 Influence Plasma Carbamazepine Concentration, Metabolism and Pharmacoresistance in a Population of Kosovar Albanian Epileptic Patients
Gene: ABCB1
Variant/haplotype: rs1045642
Drug(s): carbamazepine
Phenotype category: Efficacy
Significant: no
Association: Genotype GG is not associated with resistance to carbamazepine in people with Epilepsy as compared to genotypes AA + AG.
Notes: The authors evaluated the distribution of genotypes between individuals who developed resistance to carbamazepine (CBZ) and those who did not. There were no significant differences in genotype distributions between the two groups. Please note: alleles have been complemented to the + chromosomal strand.
Article: IL-3 and CTLA4 gene polymorphisms may influence the tacrolimus dose requirement in Chinese kidney transplant recipients
Gene: IL3
Variant/haplotype: rs181781
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype AA is associated with increased exposure to tacrolimus in people with Kidney Transplantation as compared to genotypes AG + GG.
Notes: This association was significant in CYP3A5 nonexpressors but not in CYP3A5 expressers, although the trend is similar. The time of measurement was 30 and 90 days after transplantation. Day 7 after transplantation did not show a significant association.
Article: Effect of ADRA2A gene polymorphisms on the anesthetic and analgesic effects of dexmedetomidine in Chinese Han women with cesarean section
Gene: ADRA2A
Variant/haplotype: rs201376588
Drug(s): dexmedetomidine
Phenotype category: Efficacy
Significant: yes
Association: Genotypes CT + TT are associated with decreased response to dexmedetomidine in women with Pain, Postoperative as compared to genotype CC.
Notes: Patients with the CC genotype had significantly increased pain thresholds and significantly reduced VAS pain scores post-surgery than women with the CT or TT genotypes. There was no significant difference in pain thresholds between genotype group pre-surgery.
Article: Characterizing variability in warfarin dose requirements in children using modelling and simulation
Gene: CYP2C9
Variant/haplotype: CYP2C9*1, CYP2C9*3
Drug(s): warfarin
Phenotype category: Dosage, Efficacy
Significant: yes
Association: CYP2C9 *3/*3 is associated with decreased dose of warfarin in children with Heart Diseases as compared to CYP2C9 *1/*1.
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. Due to the nature of the model, the quantitative CYP2C9 allele effects on clearance were assumed to be the same as for adults - no children had the *3/*3 genotype in the data cohort. 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. This association is based on a table presenting results from the model predicting warfarin dose for children of 2, 8 and 14 years old with different rs9923231 genotype and CYP2C9 genotype presented in the paper. CYP2C9*2 was defined as rs1799853 and CYP2C9*3 as rs1057910.
Article: A Nanopore Sequencing-based Pharmacogenomic Panel to Personalize Tuberculosis Drug Dosing
Gene: AADAC
Variant/haplotype: rs1803155
Drug(s): rifampin
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype AA is associated with decreased clearance of rifampin in people with Tuberculosis as compared to genotypes AG + GG.
Notes: "RIF clearance was 16.5% (1.30-29.3) lower in individuals who were homozygous alternate for AADACrs1803155 G>A substitutions (p=0.0015; Figure 4, Figure  E3)."
Article: Pharmacogenetics of Antiepileptic Drug Efficacy in Childhood Absence Epilepsy
Gene: CACNA1I
Variant/haplotype: rs3747178
Drug(s): ethosuximide
Phenotype category: Efficacy
Significant: yes
Association: Allele T is associated with decreased clinical benefit to ethosuximide in children with Epilepsy as compared to allele C.
Notes: as measured by minor allele (T) frequency in not–seizure‐free vs seizure-free children.
Article: Association of Polygenic Score for Schizophrenia and HLA Antigen and Inflammation Genes With Response to Lithium in Bipolar Affective Disorder: A Genome-Wide Association Study
Variant/haplotype: rs1611259
Drug(s): lithium
Phenotype category: Efficacy
Significant: yes
Association: Allele T is associated with decreased response to lithium in people with Bipolar Disorder as compared to allele C.
Notes: Please note that this SNP is given the ID rs142425863 in the paper.
Article: TCF7L2 Genetic Variation Augments Incretin Resistance and Influences Response to a Sulfonylurea and Metformin: The Study to Understand the Genetics of the Acute Response to Metformin and Glipizide in Humans (SUGAR-MGH)
Gene: TCF7L2
Variant/haplotype: rs7903146
Drug(s): metformin
Phenotype category: Efficacy
Significant: yes
Association: Allele T is associated with increased response to metformin as compared to allele C.
Notes: as measured by decreases in fasting glucose compared to pre-treatment in people with risk factors for type 2 diabetes.
Article: Genetic variants in combination with early partial improvement as a clinical utility predictor of treatment outcome in major depressive disorder: the result of two pooled RCTs
Gene: ADRA2A
Variant/haplotype: rs1800544
Drug(s): milnacipran
Phenotype category: Efficacy
Significant: yes
Association: Genotypes CC + CG are associated with increased response to milnacipran in people with Depressive Disorder as compared to genotype GG.
Notes: depressive symptoms measured on Hamilton Rating Scale for Depression and outcome as change in symptoms, as measured 6 weeks after drug, following 10 days washout.
Article: Pharmacogenetic-Based Efavirenz Dose Modification: Suggestions for an African Population and the Different CYP2B6 Genotypes
Gene: CYP2B6
Variant/haplotype: CYP2B6*6
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2B6 *6 is associated with metabolism of efavirenz in people with HIV.
Notes: Steady-state plasma concentration from HIV infected patients treated with EFV were used to calculate baseline biochemistries, CD4 counts, and viral load. The authors used non-linear mixed effect modeling to create a PK model of efavirenz. Significant covariates predicted to affect PK of efavirenz were included in the final model.; CYP2B6*6 haplotype was considered a significant factors in covariate analysis and included in the final pharmacokinetic model.
Article: Assessing the clinical impact of CYP2C9 pharmacogenetic variation on phenytoin prescribing practice and patient response in an integrated health system
Gene: CYP2C9
Variant/haplotype: CYP2C9*1, CYP2C9*2
Drug(s): phenytoin
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2C9 *1/*2 is associated with increased concentrations of phenytoin as compared to CYP2C9 *1/*1.
Notes: Compared to CYP2C9 extensive metabolizers (*1/*1 by the absence of *2 or *3), high-intermediate metabolizers (*1/*2) had an 8.6 pg/mL increase in mean dose-ad- justed phenytoin blood concentrations [95% confidence interval (CI): 2.3–14.8pg/mL; P<0.01]
Article: The CYP2D6 polymorphism in relation to the metabolism of amitriptyline and nortriptyline in the Faroese population
Gene: CYP2D6
Variant/haplotype: CYP2D6*4
Drug(s): amitriptyline
Phenotype category: Metabolism/PK
Significant: no
Association: CYP2D6 *4/*4 is not associated with metabolism of amitriptyline as compared to CYP2D6 normal metabolizer.
Notes: Parameter: amitriptyline + nortriptyline/ dose or AT/dose or NT/dose. The study reports on CYP2D6PM (5) compared to EM (18) but diplotype was only reported for PM. 5 PMs (genotype as *4/*4) were included in the study.
Article: Pharmacogenetic guidance: individualized medicine promotes enhanced pain outcomes
Gene: MTHFR
Variant/haplotype: rs1801131
Drug(s): folic acid
Phenotype category: Metabolism/PK
Significant: not stated
Association: Allele G is associated with decreased metabolism of folic acid.
Notes: Please note that alleles have been complemented to the positive stand.; Case study of a patient with the A allele at rs1801133 and the G allele at rs1801131 who subsequently responded to folate supplementation.
Article: The International SSRI Pharmacogenomics Consortium (ISPC): a genome-wide association study of antidepressant treatment response
Gene: BRD2
Variant/haplotype: rs17220479
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: Prediction of tacrolimus metabolism and dosage requirements based on CYP3A4 phenotype and CYP3A5*3 genotype in Chinese renal transplant recipients
Gene: CYP3A5
Variant/haplotype: CYP3A5*1, CYP3A5*3
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP3A5 *3/*3 is associated with increased dose-adjusted trough concentrations of tacrolimus in people with Kidney Transplantation as compared to CYP3A5 *1/*1 + *1/*3.
Notes: The study also provided a regression equation to predict trough concentration and dose of tacrolimus based on CYP3A5 genotype, among other factors.
Article: Potentially Functional SNPs (pfSNPs) as Novel Genomic Predictors of 5-FU Response in Metastatic Colorectal Cancer Patients
Gene: CYP19A1
Variant/haplotype: rs2236722
Drug(s): capecitabine, fluorouracil
Phenotype category: Efficacy
Significant: not stated
Association: Allele G is associated with decreased response to capecitabine and fluorouracil in people with Neoplasm Metastasis as compared to allele A.
Notes: pfSNP identified 2800 SNPS associated with key-words: 5-FU, capecitabine and oxilaplatin and colorectal cancer. Various criteria were used to determine 1536 SNPs to genotype. These SNPs were genotyped in a discovery cohort (N=62) and tested in a validation cohort (N=27). Both cohorts consisted of patients with colorectal cancer metastasis in liver. Five SNPs (rs2289310 G>T; rs1047840 G>A;  rs17431184 T>C; rs17160359 G>T; rs2236722 A>G)  were identified as distinguishing the "non-responder" phenotype from the "responder" phenotype when using a logistic regression multivariate model. The AUC for the receiver operating characteristic curve of the 5 SNPs is 0.875. This logistic-based multivariate model is said to be able to identify 39.1% of non-responders.
Article: IL28B genetic variations are associated with high sustained virological response (SVR) of interferon-α plus ribavirin therapy in Taiwanese chronic HCV infection
Variant/haplotype: rs10853728
Drug(s): peginterferon alfa-2b, ribavirin
Phenotype category: Efficacy
Significant: yes
Association: Genotypes CG + GG is associated with decreased response to peginterferon alfa-2b and ribavirin in people with Hepatitis C, Chronic as compared to genotype CC.
Notes: This genotype has decreased association with sustained virological response (SVR).
Article: Pharmacogenetics for Genes Associated with Age-Related Macular Degeneration (AMD) in the Comparison of AMD Treatments Trials (CATT)
Gene: ARMS2
Variant/haplotype: rs10490924
Drug(s): bevacizumab, ranibizumab
Phenotype category: Efficacy
Significant: no
Association: Genotype TT is not associated with response to bevacizumab or ranibizumab in people with Macular Degeneration as compared to genotypes GG + GT.
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: Effects of CYP2C19 Loss-of-Function Variants on the Eradication of H. pylori Infection in Patients Treated with Proton Pump Inhibitor-Based Triple Therapy Regimens: A Meta-Analysis of Randomized Clinical Trials
Gene: CYP2C19
Variant/haplotype: CYP2C19*1, CYP2C19*2, CYP2C19*3
Drug(s): lansoprazole
Phenotype category: Efficacy
Significant: yes
Association: CYP2C19 *1/*1 is associated with decreased response to lansoprazole in people with Helicobacter Infections as compared to CYP2C19 *1/*2 + *1/*3.
Notes: Subjects with the *1/*1 genotype had a significantly lower eradication rate of Helicobacter pylori (H. pylori), as compared to those with the *1/*2 or *1/*3 genotype. This was a meta-analysis and included 9 studies. Patients were treated with the drugs anywhere from 7-14 days, and also received the antibiotics amoxicillin and clarithromycin as part of triple therapy.
Article: Replication study of polymorphisms associated with response to methotrexate in patients with rheumatoid arthritis
Gene: ITPA
Variant/haplotype: rs1127354
Drug(s): methotrexate
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to methotrexate in people with Arthritis, Rheumatoid as compared to allele C.
Article: Influence of genetic polymorphisms in P2Y12 receptor signaling pathway on antiplatelet response to clopidogrel in coronary heart disease
Gene: TLN1
Variant/haplotype: rs2295795
Drug(s): clopidogrel
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with increased resistance to clopidogrel in people with Coronary Disease as compared to allele G.
Article: Identification of Cytochrome P450 Polymorphisms in Burn Patients and Impact on Fentanyl Pharmacokinetics: A Pilot Study
Gene: CYP2D6
Variant/haplotype: CYP2D6*1, CYP2D6*29
Drug(s): fentanyl
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2D6 *29 is associated with decreased clearance of fentanyl in people with Burns as compared to CYP2D6 *1.
Notes: Single patient identified with the CYP2D6*29 allele. Clearance of fentanyl in this patient was significantly lower than in WT patients.
Article: Lack of Associations of CHRNA5-A3-B4 Genetic Variants with Smoking Cessation Treatment Outcomes in Caucasian Smokers despite Associations with Baseline Smoking
Gene: CHRNA5
Variant/haplotype: rs16969968
Drug(s): nicotine
Phenotype category: Dosage
Significant: yes
Association: Allele A is associated with increased dose of nicotine in people with Tobacco Use Disorder as compared to allele G.
Notes: The A allele of rs16969968 was significantly associated with 10% higher cotinine levels, however it was not significantly with self-reported number of cigarettes per day (P = 0.30). Smokers carrying an ‘A’ allele of rs16969968 had significantly higher cotinine per cigarette (P = 0.002).
Article: Targeted pharmacogenetic analysis of antipsychotic response in the CATIE study
Gene: PLAGL1
Variant/haplotype: rs2247408
Drug(s): olanzapine
Phenotype category: Efficacy
Significant: yes
Association: Allele C is associated with response to olanzapine 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: A Longitudinal HbA1c Model Elucidates Genes Linked to Disease Progression on Metformin
Gene: SLC22A2
Variant/haplotype: rs316009
Drug(s): metformin
Phenotype category: Efficacy
Significant: yes
Association: Genotype TT is associated with increased response to metformin in people with Diabetes Mellitus as compared to genotypes CC + CT.
Notes: using computational model-based approaches and genetic, demographic, and long-term HbA1c data from 1,056 patients.
Article: Novel and replicated clinical and genetic risk factors for toxicity from high-dose methotrexate in pediatric acute lymphoblastic leukemia
Gene: SLC19A1
Variant/haplotype: rs2838958
Drug(s): methotrexate
Phenotype category: Metabolism/PK
Significant: not stated
Association: Allele A is associated with decreased clearance of methotrexate in children with Precursor Cell Lymphoblastic Leukemia-Lymphoma as compared to allele G.
Notes: "We identified one SNP associated with delayed MTX clearance and likely associated with; increased creatinine. Each additional A allele of rs2838958, an intronic variant of SLC19A1,; demonstrated an OR of 1.73 (95% CI 1.24-2.38) for prolonged MTX clearance and 1.35 (95% CI; 0.99-1.81) for increased creatinine (Table 5 and Figures 2)."
Article: Genetic variability of three common NK and γδ T cell receptor genes (FCγ3R, NCR3, and DNAM-1) and their role in Polish patients with rheumatoid arthritis and ankylosing spondylitis
Gene: NCR3
Variant/haplotype: rs1052248
Drug(s): adalimumab, certolizumab pegol, etanercept, infliximab, Tumor necrosis factor alpha (TNF-alpha) inhibitors
Phenotype category: Efficacy
Significant: yes
Association: Genotypes AT + TT is associated with increased clinical benefit to adalimumab, certolizumab pegol, etanercept, infliximab or Tumor necrosis factor alpha (TNF-alpha) inhibitors in people with Arthritis, Rheumatoid as compared to genotype AA.
Notes: " a more favorable impact of the rs1052248 T allele was also seen in; RA patients concerning the anti-TNF treatment outcome"