shlokn/autogkb huggingface dataset:
Article: Association of variants in NEDD4L with blood pressure response and adverse cardiovascular outcomes in hypertensive patients treated with thiazide diuretics
Gene: NEDD4L
Variant/haplotype: rs1008899
Drug(s): hydrochlorothiazide
Phenotype category: Efficacy
Significant: no
Association: Genotypes AA + AG are associated with increased response to hydrochlorothiazide in people with Hypertension as compared to genotype GG.
Notes: (trend)
Article: The effect of rifampicin-based antitubercular therapy and cytochrome P450 2B6 genotype on efavirenz mid-dosing interval concentrations in a South African HIV-infected population
Gene: CYP2B6
Variant/haplotype: rs3745274
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotypes GT + TT are associated with increased concentrations of efavirenz as compared to genotype GG.
Article: SLCO1B1 genetic variation and hormone therapy in menopausal women
Gene: SLCO1B1
Variant/haplotype: rs4149056
Drug(s): conjugated estrogens
Phenotype category: Efficacy
Significant: no
Association: Genotype CT is not associated with response to conjugated estrogens in women with Menopause as compared to genotype TT.
Notes: No association between genotype and change in symptom scores for hot flashes, insomnia or total symptoms following hormonal therapy was observed.
Article: Targeted pharmacogenetic analysis of antipsychotic response in the CATIE study
Gene: CSMD1
Variant/haplotype: rs17070785
Drug(s): olanzapine
Phenotype category: Efficacy
Significant: yes
Association: Allele A 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: IL28B genetic variations are associated with high sustained virological response (SVR) of interferon-α plus ribavirin therapy in Taiwanese chronic HCV infection
Gene: IFNL3
Variant/haplotype: rs8099917
Drug(s): peginterferon alfa-2b, ribavirin
Phenotype category: Efficacy
Significant: yes
Association: Genotypes GG + GT is associated with decreased response to peginterferon alfa-2b and ribavirin in people with Hepatitis C, Chronic as compared to genotype TT.
Notes: This genotype has decreased association with sustained virological response (SVR).
Article: Genetic polymorphisms in key methotrexate pathway genes are associated with response to treatment in rheumatoid arthritis patients
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: Interaction between ABCG2 421C>A polymorphism and valproate in their effects on steady‐state disposition of lamotrigine in adults with epilepsy
Gene: UGT1A4
Variant/haplotype: rs6755571
Drug(s): lamotrigine
Phenotype category: Metabolism/PK
Significant: no
Association: Allele A is not associated with concentrations of lamotrigine in people with Epilepsy as compared to allele C.
Article: Monitoring of peripheral blood cluster of differentiation 4+ adenosine triphosphate activity and CYP3A5 genotype to determine the pharmacokinetics, clinical effects and complications of tacrolimus in patients with autoimmune diseases
Gene: CYP3A5
Variant/haplotype: CYP3A5*1, CYP3A5*3
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: no
Association: CYP3A5 *1/*1 + *1/*3 is not associated with dose of tacrolimus in people with Autoimmune Diseases as compared to CYP3A5 *3/*3.
Notes: No significant difference in dose was found between the genotypes.
Article: A Genome-wide Approach Validates that Thiopurine Methyltransferase Activity is a Monogenic Pharmacogenomic Trait
Gene: TPMT
Variant/haplotype: rs1142345
Drug(s): mercaptopurine
Phenotype category: Efficacy
Significant: yes
Association: Allele C is associated with exposure to mercaptopurine in children with Leukemia as compared to allele T.
Article: Genetic variants in CYP2B6 and CYP2A6 explain interindividual variation in efavirenz plasma concentrations of HIV-infected children with diverse ethnic origin
Gene: CYP2B6
Variant/haplotype: rs35303484
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype GG is associated with increased concentrations of efavirenz in children with HIV Infections.
Notes: Allele also known as CYP2B6*11.
Article: Genotypic variation in the SV2C gene impacts response to atypical antipsychotics the CATIE Study
Gene: SV2C
Variant/haplotype: rs2358531
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 AA + AG.
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. In significant LD (r2 > 0.95) with rs10514062 and rs7732173.
Article: Association of corticotropin releasing hormone receptor 2 (CRHR2) genetic variants with acute bronchodilator response in asthma
Gene: CRHR2
Variant/haplotype: rs2267715
Drug(s): salbutamol
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with decreased response to salbutamol in people with Asthma as compared to allele A.
Article: Predictors of clozapine concentration and psychiatric symptoms in patients with schizophrenia
Gene: CYP2C19
Variant/haplotype: CYP2C19*1, CYP2C19*2
Drug(s): clozapine, n-desmethylclozapine
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2C19 *2/*2 (assigned as poor metabolizer phenotype) is associated with increased concentrations of clozapine and n-desmethylclozapine in people with Schizophrenia or Psychotic Disorder as compared to CYP2C19 *1/*1 + *1/*2 (assigned as normal metabolizer and intermediate metabolizer phenotype) .
Notes: "CYP2C19 phenotypes were significantly associated with the metabolic ratio (p = 0.033, Kruskal–Wallis test) at visit 2, with a higher metabolic ratio in PMs (n = 6) than that in NMs and IMs (n = 38) (p = 0.013, Mann–Whitney U test) (S2 Fig)." "CYP2C19, 20 patients were NMs (*1/ * 1), 19 were intermediate metabolizers (*1/ * 2), and six were poor metabolizers (PMs) (*2/ * 2). CYP1A2 phenotypes were determined by a combination of two SNPs, namely rs2069514 (c.-3860G > A) and rs762551 (c.-9-154C > A)."
Article: S4646 polymorphism in CYP19A1 gene is associated with the efficacy of hormone therapy in early breast cancer
Gene: CYP19A1
Variant/haplotype: rs4646
Drug(s): tamoxifen
Phenotype category: Efficacy
Significant: yes
Association: Genotype AA is associated with decreased response to tamoxifen in women with Breast Neoplasms and Menopause as compared to genotypes AC + CC.
Notes: Women were on tamoxifen (n=250) or on unnamed aromatase inhibitors (n=37). Disease free survival was compared at 62.7 weeks and 55.6 weeks follow-up for all women for all women, though different week comparisons were used for each significant association that was found. This association was significant in all women combined and the pre-menopausal subset, but had different directions of association in post- and pre-menopausal women.
Article: Relevance of CYP2B6 and CYP2D6 genotypes to methadone pharmacokinetics and response in the OPAL study
Gene: CYP2B6
Variant/haplotype: rs3745274
Drug(s): methadone
Phenotype category: Dosage
Significant: no
Association: Allele G is not associated with dose of methadone in people with Opioid-Related Disorders as compared to allele T.
Article: Influence of the Cytochrome P450 2B6 Genotype on Population Pharmacokinetics of Efavirenz in Human Immunodeficiency Virus Patients
Gene: CYP2B6
Variant/haplotype: rs3745274
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: not stated
Association: Genotypes GT + TT are associated with decreased clearance of efavirenz in people with HIV Infections as compared to genotype GG.
Article: Genome-wide association analysis of anti-TNF drug response in rheumatoid arthritis patients
Variant/haplotype: rs1568885
Drug(s): Tumor necrosis factor alpha (TNF-alpha) inhibitors
Phenotype category: Efficacy
Significant: no
Association: Allele A is associated with response to Tumor necrosis factor alpha (TNF-alpha) inhibitors in people with Arthritis, Rheumatoid.
Notes: This is one of three SNPs that showed directional consistency of association in 4 cohorts studied, along with improved  p value in a 3 stage meta-analysis compared to the first GWAS stage.  Since this is an AT SNP which is not mapped to a gene, it is difficult to determine which allele was found to be associated with increased response. p did not reach genome-wide significance.
Article: A genome-wide scan for common genetic variants with a large influence on warfarin maintenance dose
Gene: STX4
Variant/haplotype: rs10871454
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Allele T is associated with decreased dose of warfarin.
Notes: This SNP accounted for ~25% of the variance in stabilized warfarin dose in a GWAS study. It was in perfect linkage disequilibrium (r2=1) with rs9923231 (VKORC1:-1639)
Article: Replication study of polymorphisms associated with response to methotrexate in patients with rheumatoid arthritis
Gene: DDRGK1
Variant/haplotype: rs2295553
Drug(s): methotrexate
Phenotype category: Efficacy
Significant: no
Association: Allele C is not associated with response to methotrexate in people with Arthritis, Rheumatoid as compared to allele T.
Notes: The allele was initially significant did not remain significant after multiple-testing corrections.
Article: Pharmacogenetic Predictors of Cannabidiol Response and Tolerability in Treatment‐Resistant Epilepsy
Gene: AOC1
Variant/haplotype: rs12539
Drug(s): cannabidiol
Phenotype category: Efficacy
Significant: yes
Association: Genotypes CT + TT are associated with increased response to cannabidiol in people with Epilepsy as compared to genotype CC.
Article: Targeted pharmacogenetic analysis of antipsychotic response in the CATIE study
Gene: CDH13
Variant/haplotype: rs2116971
Drug(s): perphenazine
Phenotype category: Efficacy
Significant: yes
Association: Allele G 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. Please note: the allele was reported as C (though this gene is found on the plus chromosomal strand). It was unclear whether the allele was associated with an increased or decreased response to drug.
Article: Effect of GATA3 rs3824662 gene polymorphism in Han Chinese children with pre-B-cell acute lymphoblastic leukemia with 10 years follow-up
Gene: GATA3
Variant/haplotype: rs3824662
Drug(s): prednisolone
Phenotype category: Efficacy
Significant: yes
Association: Genotype AA is associated with decreased clinical benefit to prednisolone in children with Precursor Cell Lymphoblastic Leukemia-Lymphoma as compared to genotypes AC + CC.
Article: Pharmacokinetics of lamotrigine and its metabolite N‐2‐glucuronide: Influence of polymorphism of UDP‐glucuronosyltransferases and drug transporters
Gene: UGT2B7
Variant/haplotype: rs28365063
Drug(s): lamotrigine
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype GG is associated with increased clearance of lamotrigine in people with Epilepsy as compared to genotypes AA + AG.
Notes: This study was conducted in 100 patients -- 54 receiving monotherapy for lamotrigine, and 46 receiving combination therapy with carbamazepine, oxcarbazepine, valproic acid, phenytoin, phenobarbital, levetiracetam, topiramate, lacosamide, zonisamide, pregabalin, clonazepam, or clobazam. All patients were on stable therapy for at least 2 months.
Article: Impact of SLCO1B1 Genetic Variation on Rosuvastatin Systemic Exposure in Pediatric Hypercholesterolemia
Gene: SLCO1B1
Variant/haplotype: rs4149056
Drug(s): rosuvastatin
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotypes CC + CT are associated with increased concentrations of rosuvastatin in children with Hypercholesterolemia as compared to genotype TT.
Article: Assessing the Contribution of Opioid- and Dopamine-Related Genetic Polymorphisms to the Abuse Liability of Oxycodone
Variant/haplotype: rs6848893
Drug(s): oxycodone
Phenotype category: Efficacy
Significant: yes
Association: Genotype CT is associated with decreased response to oxycodone as compared to genotype TT.
Notes: Subjects with the CT genotype had a decreased subjective 'High Quality' response to oxycodone than subjects with the TT genotype. Authors note that this was an interaction with rs581111.
Article: Functional characterization of novel rare CYP2A6 variants and potential implications for clinical outcomes
Gene: CYP2A6
Variant/haplotype: rs374515279
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: Pharmacokinetics, metabolism and bioavailability of the triazole antifungal agent voriconazole in relation to CYP2C19 genotype
Gene: CYP2C19
Variant/haplotype: CYP2C19*1, CYP2C19*2
Drug(s): voriconazole
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2C19 *1/*1 (assigned as poor metabolizer phenotype) is associated with increased metabolism of voriconazole in healthy individuals as compared to CYP2C19 *1/*2 + *2/*2.
Notes: Subjects with the *1/*1 genotype had significantly decreased area under the concentration-time curve (AUC) and mean residence time (MRT) and significantly increased clearance of voriconazole as compared to those with the *1/*2 or *2/*2 genotype. No significant differences between genotypes were seen when considering maximum plasma concentration (Cmax), time to Cmax (Tmax), terminal elimination half-life (t1/2) or bioavailability.
Article: Implications of OPRM1 and CYP2B6 variants on treatment outcomes in methadone-maintained patients in Ontario: Exploring sex differences
Gene: CYP2B6
Variant/haplotype: rs3745274
Drug(s): methadone
Phenotype category: Efficacy
Significant: no
Association: Allele T is associated with increased response to methadone in men with Opioid-Related Disorders as compared to allele G.
Notes: The T allele was associated with reduced odds of continued opioid use in male patients undergoing MMT. However, this was not significant. No association was found in female patients.
Article: Genetic Variants in CPA6 and PRPF31 Are Associated With Variation in Response to Metformin in Individuals With Type 2 Diabetes
Gene: NBEA
Variant/haplotype: rs57081354
Drug(s): metformin
Phenotype category: Efficacy
Significant: yes
Association: Allele C is associated with decreased response to metformin in people with Diabetes Mellitus, Type 2 as compared to allele T.
Notes: This SNP is associated with changes in HbA1C when all races are combined.
Article: Exploring joint effects of genes and the clinical efficacy of morphine for cancer pain: OPRM1 and COMT gene
Gene: OPRM1
Variant/haplotype: rs1799971
Drug(s): morphine
Phenotype category: Efficacy
Significant: yes
Association: Genotypes AG + GG are associated with increased dose of morphine as compared to genotype AA.
Article: An expanded pharmacogenomics warfarin dosing table with utility in generalised dosing guidance
Gene: CYP2C9
Variant/haplotype: rs9332131
Drug(s): warfarin
Phenotype category: Dosage
Significant: not stated
Association: Allele A is associated with dose of warfarin as compared to allele del.
Notes: This variant annotation is part of a dosing algorithm table based on 8 genetic variants.
Article: Genetic association of primary non-response to Anti-TNFα therapy in patients with Inflammatory Bowel Disease
Variant/haplotype: rs34767465
Drug(s): adalimumab, certolizumab pegol, infliximab
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with response to adalimumab, certolizumab pegol or infliximab in people with Inflammatory Bowel Diseases as compared to allele A.
Notes: rs34767465 associated with primary nonresponse to anti-TNFα biologics. odds ratio: 2.07, 95% CI: 1.46–2.94, P = 2.43 × 10-7 , replication odds ratio: 1.8,95% CI, 1.04–3.16, P = 0.03
Article: Independent and interactive effects of OPRM1 and DAT1 polymorphisms on alcohol consumption and subjective responses in social drinkers
Gene: SLC6A3
Variant/haplotype: rs28363170
Drug(s): ethanol
Phenotype category: Other
Significant: yes
Association: Allele del is associated with increased response to ethanol in healthy individuals as compared to allele GGGGGCCCTGCATGCGTCCTGGGGTAGTACACGCTCCAGT.
Notes: This variant is a VNTR; the 'del' allele represented the 9-repeat allele, while the 'GGG...' allele represents the 10-repeat allele. Subjects with the 9-repeat allele had higher Subjective High Assessment Scale (SHAS) scores and higher Drug Effect Questionnaire Visual Analog Scale (DEQ VAS) negative scores across all timepoints compared to subjects carrying the 10-repeat allele. The authors note an epistatic effect, where carriers of both of the 9-repeat allele and the rs1799971 G allele in OPRM1 had the highest SHAS and DEQ VAS negative scores. However, there was no significant association between this variant and BAES score, DEQ VAS positive score or POMS score.
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: rs2279343
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype GG is associated with decreased clearance of efavirenz in people with HIV Infections as compared to genotype AG.
Notes: As shown by increased plasma concentrations (units = mg/L) for those with the GG genotype compared to those with the AG genotype. Fasting plasma efavirenz concentrations were measured 12 hours after the last dose, and after 12 weeks of treatment.
Article: Association between ADAM33 Single-Nucleotide Polymorphisms and Treatment Response to Inhaled Corticosteroids and a Long-Acting Beta-Agonist in Asthma
Gene: ADAM33
Variant/haplotype: rs3918396
Drug(s): corticosteroids, selective beta-2-adrenoreceptor agonists
Phenotype category: Efficacy
Significant: no
Association: Genotype TT is associated with decreased clinical benefit to corticosteroids and selective beta-2-adrenoreceptor agonists in people with Asthma as compared to genotypes CC + CT.
Notes: as measured by FEV1 after three months of ICS+LABA. Alleles complemented to the plus chromosomal strand. "The SNP rs3918396 (AA genotype) also showed a lower improvement in FVC, but this was not statistically significant due to the fewer patients with that polymorphism."
Article: Pharmacokinetics and response to pravastatin in paediatric patients with familial hypercholesterolaemia and in paediatric cardiac transplant recipients in relation to polymorphisms of the SLCO1B1 and ABCB1 genes
Gene: ABCB1
Variant/haplotype: rs2032582
Drug(s): pravastatin
Phenotype category: Metabolism/PK
Significant: no
Association: Allele C is not associated with response to pravastatin in children with Hyperlipoproteinemia Type II as compared to allele A.
Notes: No significant association was found between changes in cholesterol levels or triglycerides and this SNP.
Article: Genome-wide Association Study of Virologic Response with Efavirenz- or Abacavir-containing Regimens in AIDS Clinical Trials Group Protocols
Gene: CYP2B6
Variant/haplotype: rs28399499
Drug(s): efavirenz
Phenotype category: Efficacy
Significant: no
Association: Allele C 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: Influence of OATP1B1 and BCRP polymorphisms on the pharmacokinetics and pharmacodynamics of rosuvastatin in elderly and young Korean subjects
Gene: ABCG2
Variant/haplotype: rs2231142
Drug(s): rosuvastatin
Phenotype category: Efficacy
Significant: no
Association: Genotypes GT + TT are not associated with response to rosuvastatin as compared to genotype GG.
Notes: ABCG2 421C>A did not significantly affect the lipid-lowering response of rosuvastatin.
Article: Association of Cytidine Deaminase Polymorphism with Capecitabine Effectiveness in Breast Cancer Patients
Gene: CDA
Variant/haplotype: rs532545
Drug(s): capecitabine
Phenotype category: Efficacy
Significant: yes
Association: Genotype CC is associated with decreased response to capecitabine in women with Breast Neoplasms as compared to genotypes CT + TT.
Notes: as measured by estradiol E2 levels, however table 4 and text are contradictory. Alleles complemented. "Concerning rs532545, the mutant (GG) has an; elevated estradiol level (mean +/- SD) of (37.98 ± 3), the; heterozygous (AG) has a value of (33.08 ± 3.72), and; the wild type (AA) has a value of (74.43 ± 14.86), with significant differences between the heterozygous and; mutant and homozygous genotypes."
Article: The Influence of CYP2B6 Variants and Administration of Propofol on Patient Outcomes after Traumatic Brain Injury
Gene: CYP2B6
Variant/haplotype: CYP2B6*1, CYP2B6*6
Drug(s): propofol
Phenotype category: Toxicity
Significant: yes
Association: CYP2B6 *6 is associated with decreased response to propofol in people with Brain Injuries as compared to CYP2B6 *1.
Notes: "No significant interaction between genotype and propofol on patient outcomes after sTBI was found; however, when controlling for propofol, *6 homozygotes had worse outcomes at 3-month GOS. " GOS = Glasgow Outcome Scale, 1 = death, 2 = persistent vegetative state, 3 = severe disability, 4 = moderate disability, and 5 = good recovery
Article: The International SSRI Pharmacogenomics Consortium (ISPC): a genome-wide association study of antidepressant treatment response
Gene: PTCHD1
Variant/haplotype: rs7051085
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 A.
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).
Article: CYP4F2 1347 G>A & GGCX 12970 C>G polymorphisms: frequency in north Indians & their effect on dosing of acenocoumarol oral anticoagulant
Gene: GGCX
Variant/haplotype: rs11676382
Drug(s): acenocoumarol
Phenotype category: Dosage
Significant: no
Association: Genotype CG is not associated with dose of acenocoumarol as compared to genotype CC.
Notes: No significant differences in mean weight normalized acenocoumarol doses were found for these GGCX genotypes.