shlokn/autogkb huggingface dataset:
Article: RAD51 and RAD50 genetic polymorphisms from homologous recombination repair pathway are associated with disease outcomes and organ toxicities in AML
Gene: RAD50
Variant/haplotype: rs2299014
Drug(s): cytarabine, daunorubicin
Phenotype category: Efficacy
Significant: yes
Association: Genotypes AA + AC is associated with increased resistance to cytarabine and daunorubicin in people with Leukemia, Myeloid, Acute as compared to genotype CC.
Notes: Alleles complemented. "All patients received remission induction chemotherapy with daunorubicin (45 mg/m2 per day for 3 days) and standard-dose cytosine arabinoside (200 mg/m2 per day for 7 days) with or without recombinant human granulocyte colony-stimulating factor." "As demonstrated in Table 2, RAD50 rs2299014 (p < 0.01) and RAD51 rs1801320 (p = 0.012) variant alleles were associated with resistant disease."
Article: Attempted validation of 44 reported SNPs associated with tacrolimus troughs in a cohort of kidney allograft recipients
Gene: CYP3A4
Variant/haplotype: rs2740574
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele T is associated with trough concentration of tacrolimus in people with Kidney Transplantation and Transplantation as compared to allele C.
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, this variant passed validation in the EA cohort. Direction of effect was not stated.
Article: Precision Dosing for Tacrolimus Using Genotypes and Clinical Factors in Kidney Transplant Recipients of European Ancestry
Gene: CYP3A4
Variant/haplotype: rs35599367
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotypes AA + AG are associated with decreased clearance of tacrolimus in people with Kidney Transplantation as compared to genotype GG.
Notes: The A allele is equivalent to the CYP3A4*22 allele.
Article: CYP3A5 and UGT1A9 Polymorphisms Influence Immunosuppressive Therapy in Pediatric Kidney Transplant Recipients
Gene: CYP3A5
Variant/haplotype: CYP3A5*1, CYP3A5*3
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP3A5 *1/*1 + *1/*3 is associated with decreased dose-adjusted trough concentrations of tacrolimus in children with Kidney Transplantation as compared to CYP3A5 *3/*3.
Article: A Low Fixed Tacrolimus Starting Dose Is Effective and Safe in Chinese Renal Transplantation Recipients
Gene: CYP3A5
Variant/haplotype: CYP3A5*1, CYP3A5*3
Drug(s): tacrolimus
Phenotype category: Efficacy
Significant: no
Association: CYP3A5 *3/*3 is not associated with response to tacrolimus in people with Kidney Transplantation as compared to CYP3A5 *1/*1 + *1/*3.
Notes: No significant difference in renal function after transplantation, rate of delayed graft function, or rate of acute rejection within 30 days after transplant was found between the two genotype groups.
Article: Pharmacodynamic and kinetic effect of rabeprazole on serum gastrin level in relation to CYP2C19 polymorphism in Chinese Hans
Gene: CYP2C19
Variant/haplotype: CYP2C19*1, CYP2C19*2
Drug(s): rabeprazole
Phenotype category: Efficacy
Significant: no
Association: CYP2C19 *1/*1 is not associated with response to rabeprazole in healthy individuals as compared to CYP2C19 *2/*2.
Notes: No significant differences in median 24 hour intragastric pH or serum gastrin area under the concentration-time curve from 0-24 hours (AUC0-24) were seen between genotypes. Subjects were given rabeprazole for 8 days; 24 hour intragastric pH and serum gastrin AUC were measured on day 1 and day 8 after rabeprazole administration. Please note that the *2 allele was referred to by its previous designation (CYP2C19*m1).
Article: Functional characterization of novel rare CYP2A6 variants and potential implications for clinical outcomes
Gene: CYP2A6
Variant/haplotype: rs148693084
Drug(s): nicotine
Phenotype category: Metabolism/PK
Significant: not stated
Association: Allele G is associated with decreased metabolism of nicotine as compared to allele A.
Notes: Assigned as loss-of-function following in vitro assessments, in vivo associations and variant construct functional assignments. Please note that alleles have been complemented to the positive strand.
Article: Individual and combined associations of genetic variants in CYP3A4, CYP3A5, and SLCO1B1 with simvastatin and simvastatin acid plasma concentrations
Gene: SLCO1B1
Variant/haplotype: rs4149056
Drug(s): simvastatin, simvastatin acid
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele C is associated with increased concentrations of simvastatin and simvastatin acid in people with Hypercholesterolemia as compared to allele T.
Notes: Patients were followed for 6 weeks (40 mg simvastatin at bedtime) and seen at the clinic at 2 week intervals. Patients with the CT and CC genotypes had 71% and 248% higher plasma simvastatin acid at 12 hours, respectively, as compared to those with the TT genotypes.; In a separate analysis, the authors combined patients into groups based on their expected simvastatin acid/ simvastatin ratios (SVA/SV). The groups were low, intermediate, or high. The high and medium SVA/SV group included carriers of the C allele. There was a significant difference in 12 hr plasma SVA/SV ratios between the low, intermediate, and high SVA/SV ratio genotype groups
Article: Genome-wide association analysis of anti-TNF drug response in rheumatoid arthritis patients
Variant/haplotype: rs4411591
Drug(s): Tumor necrosis factor alpha (TNF-alpha) inhibitors
Phenotype category: Efficacy
Significant: no
Association: Allele C is associated with response to Tumor necrosis factor alpha (TNF-alpha) inhibitors in people with Arthritis, Rheumatoid as compared to allele T.
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. p did not reach genome-wide significance.
Article: Pharmacogenomics of Hypertension: A Genome‐Wide, Placebo‐Controlled Cross‐Over Study, Using Four Classes of Antihypertensive Drugs
Gene: NPHS1
Variant/haplotype: rs3814995
Drug(s): losartan
Phenotype category: Efficacy
Significant: no
Association: Allele T is associated with increased response to losartan in men with Hypertension as compared to allele C.
Notes: Because of the GWAS design, these p-values are suggestive, not significant. Each participant received losartan 50 mg, bisoprolol 5 mg, hydrochlorothiazide 25 mg, and amlodipine 5 mg daily, each as a monotherapy in randomized order for 4 weeks. The study started with a 4-week run-in placebo period, and all 4 drug treatments were separated by 4-week placebo periods. 24-hour ABP readings were recorded at the end of each treatment period.
Article: Association of serotonin transporter (SLC6A4) & receptor (5HTR1A, 5HTR2A) polymorphisms with response to treatment with escitalopram in patients with major depressive disorder: A preliminary study
Gene: HTR2A
Variant/haplotype: rs6313
Drug(s): escitalopram
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to escitalopram Depressive Disorder, Major as compared to allele G.
Article: Polymorphisms in the Drug Transporter Gene ABCB1 Are Associated with Drug Response in Saudi Epileptic Pediatric Patients
Gene: ABCB1
Variant/haplotype: rs1045642
Drug(s): antiepileptics
Phenotype category: Efficacy
Significant: yes
Association: Genotype AA is associated with increased clinical benefit to antiepileptics in children with Epilepsy as compared to genotypes AG + GG.
Notes: Alleles complemented to plus chromosomal strand. "good responders were classified as those who were totally free from seizures for at least 1 year during treatment with ASMs as a monotherapy or in combination at optimal tolerated therapeutic doses." "good responders were significantly more likely to have the TT genotypes at rs1045642 and rs2032582 SNPs compared to poor responders." Specific antiseizure medications not mentioned.
Article: Influence of pharmacogenetic polymorphisms and demographic variables on metformin pharmacokinetics in an admixed Brazilian cohort
Gene: SLC22A1
Variant/haplotype: rs622342
Drug(s): metformin
Phenotype category: Metabolism/PK
Significant: no
Association: Allele A is not associated with exposure to metformin as compared to allele C.
Article: Pharmacogenetic association of the APOA1/C3/A4/A5 gene cluster and lipid responses to fenofibrate: the Genetics of Lipid-Lowering Drugs and Diet Network study
Gene: APOC3
Variant/haplotype: rs5128
Drug(s): fenofibrate
Phenotype category: Efficacy
Significant: no
Association: Genotypes CC + CG are not associated with response to fenofibrate in people with Hypertriglyceridemia as compared to genotype GG.
Notes: No significant difference in the change in plasma triglyceride (TG) or high-density lipoprotein (HDL) levels between genotypes was seen, after three weeks of treatment with fenofibrate.
Article: Attempted validation of 44 reported SNPs associated with tacrolimus troughs in a cohort of kidney allograft recipients
Gene: NR1I3
Variant/haplotype: rs11265572
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: Genome-Wide Association Study of Serum Creatinine Levels during Vancomycin Therapy
Gene: MIA3
Variant/haplotype: rs3002145
Drug(s): vancomycin
Phenotype category: Metabolism/PK
Significant: no
Association: Allele T is not associated with trough concentration of vancomycin.
Notes: The SNP was not associated with trough levels of vancomycin (first vancomycin trough documented in EMR after at least 3 doses vancomycin). Elimination constants were also calculated.
Article: Influence of genetic, biological and pharmacological factors on warfarin dose in a Southern Brazilian population of European ancestry
Gene: VKORC1
Variant/haplotype: rs9923231
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Genotypes CT + TT is associated with decreased dose of warfarin as compared to genotype CC.
Notes: in a Southern Brazilian population of European ancestry.
Article: The MTHFR C677T Variant is Associated with Responsiveness to Disulfiram Treatment for Cocaine Dependency
Gene: MTHFR
Variant/haplotype: rs1801133
Drug(s): disulfiram
Phenotype category: Efficacy
Significant: yes
Association: Genotypes AA + AG are associated with increased response to disulfiram in people with Cocaine-Related Disorders as compared to genotype GG.
Notes: The drop in percentage of cocaine-positive urines for patients with the CT and TT genotypes over the 10 weeks of disulfiram treatment was significantly greater compared to those with the CC genotype. Please note alleles have been complemented to the positive chromosomal strand.
Article: Pharmacogenetic role of dopamine transporter (SLC6A3) variation on response to disulfiram treatment for cocaine addiction
Gene: SLC6A3
Variant/haplotype: rs28363170
Drug(s): disulfiram
Phenotype category: Efficacy
Significant: yes
Association: Genotype GGGGGCCCTGCATGCGTCCTGGGGTAGTACACGCTCCAGT/GGGGGCCCTGCATGCGTCCTGGGGTAGTACACGCTCCAGT is associated with increased response to disulfiram in people with Cocaine-Related Disorders as compared to genotypes GGGGGCCCTGCATGCGTCCTGGGGTAGTACACGCTCCAGT/del + del/del.
Notes: GGGGGCCCTGCATGCGTCCTGGGGTAGTACACGCTCCAGT allele referred to in the paper as the 10-repeat allele. Patients with the 10,10-repeat genotype showed a significantly greater decrease in the number of cocaine-positive urine tests and a significantly greater increase in the number of cocaine-negative urine tests than patients with either the 9,9-repeat or 9,10-repeat genotypes. This association was not seen in genotyped patients treated with placebo.
Article: Genome-Wide Association Study Identifies Novel Pharmacogenomic Loci For Therapeutic Response to Montelukast in Asthma
Gene: MLLT3
Variant/haplotype: rs6475448
Drug(s): montelukast
Phenotype category: Efficacy
Significant: yes
Association: Genotype AA is associated with increased response to montelukast in people with Asthma as compared to genotype GG.
Notes: Patients who were homozygous for rs6475448 showed markedly increased mean d forced expiratory volume (FEV1) from baseline after 8 weeks of montelukast. The largest increase was observed for Leukotriene Modifier or Corticosteroid or Corticosteroid-Salmeterol (LOCCS); the rs6475448-AA genotype was associated with a LS-mean delta FEV1 of 344 mL vs. -4.66 mL for rs6475448-GG genotype. Study Cohort: Discovery cohort (N=133): American Lung Association Asthma Clinical Research Center (ALA-ACRC)-supported trials, the Leukotriene Modifier Or Corticosteroid or Corticosteroid-Salmeterol Trial (LOCCS) and Effectiveness of Low Dose Theophylline as Add On Therapy for the Treatment of Asthma (LODO) trials. Replication cohort (N=184): Childhood Asthma Research and Education (CARE) Network- Characterizing the Response to a LT Receptor Antagonist and an Inhaled Corticosteroid and Pediatric Asthma Controller Trial (CLIC and PACT)
Article: A novel polymorphism in ABCB1 gene, CYP2B6*6 and sex predict single-dose efavirenz population pharmacokinetics in Ugandans
Gene: CYP2B6
Variant/haplotype: CYP2B6*1, CYP2B6*6
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2B6 *6 is associated with decreased clearance of efavirenz in healthy individuals as compared to CYP2B6 *1/*1.
Notes: Subjects homozygous for CYP2B6*6 (G516T, A785G) displayed 21% lower apparent oral clearance.
Article: Influence of SLCO1B1 polymorphisms on lopinavir C trough in Serbian HIV/AIDS patients
Gene: SLCO1B1
Variant/haplotype: rs4149032
Drug(s): lopinavir
Phenotype category: Metabolism/PK
Significant: no
Association: Allele T is not associated with trough concentration of lopinavir in people with HIV Infections as compared to allele C.
Notes: Although the T allele was initially found to be significantly associated with decreased trough concentrations of lopinavir, this significance was lost following multivariate regression analysis.
Article: Genotypic variation in the SV2C gene impacts response to atypical antipsychotics the CATIE Study
Gene: SV2C
Variant/haplotype: rs10214163
Drug(s): olanzapine
Phenotype category: Efficacy
Significant: no
Association: Genotype TT is not associated with response to olanzapine in people with Schizophrenia as compared to genotypes CC + CT.
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: Oxidative Stress-Related Genetic Polymorphisms Are Associated with the Prognosis of Metastatic Gastric Cancer Patients Treated with Epirubicin, Oxaliplatin and 5-Fluorouracil Combination Chemotherapy
Gene: SOD3
Variant/haplotype: rs1799895
Drug(s): epirubicin, fluorouracil, oxaliplatin
Phenotype category: Efficacy
Significant: not stated
Association: Allele G is not associated with response to epirubicin, fluorouracil and oxaliplatin in people with Neoplasm Metastasis and Stomach Neoplasms.
Article: Assessing the Contribution of Opioid- and Dopamine-Related Genetic Polymorphisms to the Abuse Liability of Oxycodone
Gene: COMT
Variant/haplotype: rs4680
Drug(s): oxycodone
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to oxycodone as compared to allele G.
Notes: No association between this variant and analgesic response to oxycodone, as assessed by cold pressor test.
Article: Genetic variation in OPRD1 and the response to treatment for opioid dependence with buprenorphine in European American females
Gene: OPRD1
Variant/haplotype: rs581111
Drug(s): buprenorphine
Phenotype category: Efficacy
Significant: yes
Association: Genotypes AA + AG is associated with decreased response to buprenorphine in women with Opioid-Related Disorders as compared to genotype GG.
Notes: Opioid dependence. Four cohorts were analyzed. The first three were women taking buprenorphine or methadone, women taking only buprenorphine and women taking only methadone, where opiod-positive urine drug screens or missing urine drug screens were both considered a "positive" drug screen. The fourth was women taking only buprenorphine were missing urine drug screens were coded as "missing" and not as "positive". No significant results were seen when considering women only taking methadone, but significant results were seen for all other cohorts: women with the AA and AG genotypes were more likely to have opioid-; "positive" urine drug screens, as compared to those with the GG genotype. Patients were treated with buprenorphine or methadone for 24 weeks.
Article: Childhood asthma exacerbations and the Arg-16 beta2 receptor polymorphism: a meta-analysis stratified by treatment
Gene: ADRB2
Variant/haplotype: rs1042713
Drug(s): corticosteroids, Leukotriene receptor antagonists, selective beta-2-adrenoreceptor agonists
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to corticosteroids, Leukotriene receptor antagonists and selective beta-2-adrenoreceptor agonists in children with Asthma as compared to genotype GG.
Article: Potentially Functional SNPs (pfSNPs) as Novel Genomic Predictors of 5-FU Response in Metastatic Colorectal Cancer Patients
Gene: REV3L
Variant/haplotype: rs3218592
Drug(s): capecitabine, fluorouracil
Phenotype category: Efficacy
Significant: no
Association: Allele T is associated with decreased response to capecitabine and fluorouracil in people with Neoplasm Metastasis as compared to allele C.
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. Three non-responder SNPs combined with any one of three SNPs in LD in the UMPS gene (rs2291078 A, rs3772809 G, rs3772810 G) account for 37.5% of all patients that were classified as non-responders to capecitabine/fluorouracil therapy. Combined multivariate collapsing analyses revealed a statistical significance between those SNPs and the "non-responder" phenotype.
Article: Metabolic capacity of CYP2D6 within an Iranian population (Mazandaran Province)
Gene: CYP2D6
Variant/haplotype: CYP2D6 poor metabolizer
Drug(s): dextromethorphan
Phenotype category: Metabolism/PK
Significant: not stated
Association: CYP2D6 poor metabolizer is associated with decreased metabolism of dextromethorphan in healthy individuals as compared to CYP2D6 normal metabolizer.
Notes: Subjects with metabolic ratio > 0.3 in log scale were classified as PMs and the remaining subjects with metabolic ratios ≤ 0.3 were classified as extensive metabolizers. Metabolic ratio of dextromethorphan/dextrorphan.
Article: OPRM1, OPRK1 and COMT Genetic Polymorphisms Associated with Opioid Effects on Experimental Pain: A Randomized, Double-Blind, Placebo-Controlled Study
Gene: OPRK1
Variant/haplotype: rs1051660
Drug(s): butorphanol
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to butorphanol in healthy individuals as compared to allele C.
Notes: Study-wide significance was set to p<0.017.
Article: Population Pharmacokinetics and Pharmacogenetics Analysis of Rilpivirine in HIV-1-Infected Individuals
Gene: CYP3A4
Variant/haplotype: rs35599367
Drug(s): rilpivirine
Phenotype category: Metabolism/PK
Significant: no
Association: Allele A is not associated with clearance of rilpivirine in people with HIV Infections as compared to allele G.
Article: Influence of CYP2B6 and CYP3A4 polymorphisms on the virologic and immunological responses of patients treated with efavirenz containing regimen
Gene: CYP2B6
Variant/haplotype: rs2279343
Drug(s): efavirenz, lamivudine, tenofovir
Phenotype category: Efficacy
Significant: yes
Association: Genotypes AG + GG is associated with increased clinical benefit to efavirenz, lamivudine and tenofovir in people with HIV Infections as compared to genotype AA.
Notes: Cases = VLS: viral load suppression (HIV-1 RNA copies ml-1less than 50 copies), controls = No VLS (HIV-1 RNA copies ml-1higher than 50 copies) at 6 months treatment. GG v AA was not significant but AG v AA was.
Article: ADH single nucleotide polymorphism associations with alcohol metabolism in vivo
Gene: ADH1A
Variant/haplotype: rs1229976
Drug(s): ethanol
Phenotype category: Toxicity, Metabolism/PK
Significant: yes
Association: Allele C is associated with metabolism of ethanol.
Notes: The authors did not report p-value correction for multiple hypotheses (103 snps tested).  Though they report multiple snps are significantly associated with alcohol metabolism (early or late) tested on blood or breath alcohol concentrations, this snp is NOT significant after Bonferroni correction (<0.00049).  Also, the authors did not state which alleles are associated with increased or decreased metabolism.  Instead, they simply report an association with the snp in general.  Note that this gene is on the minus strand.
Article: Pharmacogenetics of tenofovir clearance among Southern Africans living with HIV
Gene: SLC19A1
Variant/haplotype: rs1051266
Drug(s): tenofovir
Phenotype category: Metabolism/PK
Significant: no
Association: Allele C is not associated with clearance of tenofovir in people with HIV Infections as compared to allele T.
Notes: Significance threshold was set at 3.3E-3.
Article: PDE4 Gene Family Variants Are Associated with Response to Apremilast Treatment in Psoriasis
Gene: CDKN2B, CDKN2B-AS1
Variant/haplotype: rs1063192
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: 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): aspirin, diclofenac, ibuprofen, indomethacin, ketorolac, naproxen
Phenotype category: Efficacy
Significant: yes
Association: Allele A is associated with decreased clinical benefit to aspirin, diclofenac, ibuprofen, indomethacin, ketorolac or naproxen in people with Migraine without Aura as compared to allele G.
Notes: "episodic migraine patients carrying the A allele of the TNF-α promoter −308 A/G polymorphism showed a significant association with a lack of efficacy after NSAID administration in migraine attacks compared to the G allele"
Article: Association between opioid receptor mu 1 (OPRM1) gene polymorphisms and tobacco and alcohol consumption in a Spanish population
Gene: OPRM1
Variant/haplotype: rs510769
Drug(s): nicotine
Phenotype category: Dosage
Significant: no
Association: Allele T is not associated with dose of nicotine as compared to allele C.
Notes: No significant association between this variant and tobacco consumption.