shlokn/autogkb huggingface dataset:
Article: Exploring Genetic Variants and Platinum Chemotherapy Response in Indonesian Non-Small Cell Lung Cancer Patients: Insights from ERCC2 rs13181
Gene: ERCC2
Variant/haplotype: rs13181
Drug(s): Platinum compounds
Phenotype category: Efficacy
Significant: no
Association: Genotypes GG + GT is not associated with increased response to Platinum compounds in people with Carcinoma, Non-Small-Cell Lung as compared to genotype TT.
Notes: Alleles complemented. "Based on the statistical analysis results, no significant association was found with chemotherapy response (P>0,05) (Table 4)."
Article: Effect of race and glucuronidation rates on the relationship between nicotine metabolite ratio and nicotine clearance
Gene: UGT2B10
Variant/haplotype: rs835309
Drug(s): nicotine
Phenotype category: Metabolism/PK
Significant: no
Association: Allele G is not associated with clearance of nicotine as compared to allele T.
Notes: No effect of the UGT2B10 variant genotypes on the ability of plasma nicotine metabolite ratio to predict nicotine clearance.
Article: The Association of Transporter Genes Polymorphisms and Lung Cancer Chemotherapy Response
Gene: AQP9
Variant/haplotype: rs1867380
Drug(s): platinum
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to platinum in people with Lung Neoplasms as compared to allele G.
Notes: 26 SNPs were selected which satisfied the following criteria: 1) SNPs were from HapMap Project Phase II of the Han Chinese population 2) were haplotype tagger SNPs 3) SNP minor allele frequency was higher than 5% in Han Chinese 4) the pairwise linkage disequilibrium correlation coefficient (r-squared) was greater than 0.8. After Bonferroni corrections no SNPs remained significantly associated with platinum drug efficacy.
Article: CYP3A5, ABCB1 and SLCO1B1 Polymorphisms and Pharmacokinetics and Virologic Outcome of Lopinavir/Ritonavir in HIV-infected Children
Gene: CYP3A5
Variant/haplotype: rs776746
Drug(s): lopinavir, ritonavir
Phenotype category: Metabolism/PK
Significant: no
Association: Allele C is not associated with clearance of lopinavir or ritonavir in children with HIV Infections as compared to allele T.
Notes: No association between this variant and clearance of lopinavir or ritonavir in patients treated with lopinavir/ritonavir. Variant referred to in the paper as A6986G.
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: rs3919583
Drug(s): lithium
Phenotype category: Efficacy
Significant: yes
Association: Allele A is associated with decreased response to lithium in people with Bipolar Disorder as compared to allele C.
Article: Functional genetic variation in the Rev-Erbα pathway and lithium response in the treatment of bipolar disorder
Gene: CLOCK
Variant/haplotype: rs34897046
Drug(s): lithium
Phenotype category: Efficacy
Significant: no
Association: Allele C is not associated with increased response to lithium in people with Bipolar Disorder as compared to allele G.
Article: CHRNA4 rs1044396 is associated with smoking cessation in varenicline therapy
Gene: CHRNA4
Variant/haplotype: rs2236196
Drug(s): varenicline
Phenotype category: Efficacy
Significant: no
Association: Genotypes AA + AG is not associated with response to varenicline in people with Tobacco Use Disorder as compared to genotype GG.
Article: Pharmacogenetics of tenofovir clearance among Southern Africans living with HIV
Gene: SLC28A2
Variant/haplotype: rs11854484
Drug(s): tenofovir
Phenotype category: Metabolism/PK
Significant: no
Association: Allele T is not associated with clearance of tenofovir in people with HIV Infections as compared to allele C.
Article: Methadone Dosage and Plasma Levels, SNPs of OPRM1 Gene and Age of First Drug Use Were Associated With Outcomes of Methadone Maintenance Treatment
Gene: OPRM1
Variant/haplotype: rs562859
Drug(s): methadone
Phenotype category: Efficacy
Significant: no
Association: Genotype TT is not associated with response to methadone in people with Heroin Dependence as compared to genotypes CC + CT.
Notes: Although this SNP initially showed a significant association with both MMT compliance and 'negative rate of morphine urine test', significance in both associations was lost following adjusting for age, sex and methadone dosage.; Note that although this variant is located in MTRF1L, it is discussed in the paper as being an OPRM1 SNP.; Please note that alleles have been complemented to the positive strand.
Article: Hypertension Susceptibility Loci and Blood Pressure Response to Antihypertensives – Results from the Pharmacogenomic Evaluation of Antihypertensive Responses (PEAR) Study
Gene: MOV10
Variant/haplotype: rs12069113
Drug(s): atenolol
Phenotype category: Efficacy
Significant: no
Association: Allele C is not associated with response to atenolol in people with Hypertension as compared to allele T.
Notes: Not significant when using Bonferroni-corrected alpha of 0.0014. Response was assessed by change in diastolic blood pressure (DBP) after 9 weeks of treatment.
Article: ASSOCIATIONS OF ABCB1 3435C>T AND IL-10 -1082G>A POLYMORPHISMS WITH LONG-TERM SIROLIMUS DOSE REQUIREMENTS IN RENAL TRANSPLANT PATIENTS
Gene: CYP3A4
Variant/haplotype: rs2740574
Drug(s): sirolimus
Phenotype category: Metabolism/PK
Significant: no
Association: Allele C is not associated with dose-adjusted trough concentrations of sirolimus in people with Kidney Transplantation as compared to allele T.
Notes: No significant difference in log-transformed dose-adjusted trough concentrations (C/D) was seen between any of the genotypes CC, CT or TT. Please note that alleles have been complemented to the plus chromosomal strand.
Article: Functional characterization of novel rare CYP2A6 variants and potential implications for clinical outcomes
Gene: CYP2A6
Variant/haplotype: rs772964366
Drug(s): nicotine
Phenotype category: Metabolism/PK
Significant: not stated
Association: Allele G 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 Pharmacogenetics of Cannabis in the Treatment of Chronic Pain
Gene: TRPV1
Variant/haplotype: rs8065080
Drug(s): cannabinoids
Phenotype category: Efficacy
Significant: yes
Association: Genotype CC is associated with increased clinical benefit to cannabinoids in people with Pain as compared to genotypes CT + TT.
Notes: "CC homozygous patients for the TRPV1 gene obtained an average pain decrease of 2 VAS points, compared to the 1.3 VAS points of TT homozygotes or CT heterozygotes."
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: rs1569304898
Drug(s): migalastat
Phenotype category: Efficacy
Significant: not stated
Association: Allele T is associated with increased response to migalastat in people with Fabry Disease.
Notes: Patients carrying the T 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 Gly85Asp in the paper.
Article: TET2 and CSMD1genes affect SBP response to hydrochlorothiazide in never-treated essential hypertensives
Gene: FBXL17
Variant/haplotype: rs7706429
Drug(s): hydrochlorothiazide
Phenotype category: Efficacy
Significant: no
Association: Allele G is associated with decreased response to hydrochlorothiazide in people with Essential hypertension as compared to allele A.
Notes: The SNP was discovered in two independent cohorts, although no SNPs reached genome wide significance. The authors then considered P<1 x10^-5 as a threshold for significance (based on the results from a Q-Q plot distribution reference line). Using this revised threshold the authors reported that this SNP was associated with a lower decrease in diastolic blood pressure after hydrochlorothiazide treatment.
Article: Pharmacogenetics of Asthma Controller Treatment
Gene: CRHR1
Variant/haplotype: rs1876828
Drug(s): fluticasone propionate
Phenotype category: Efficacy
Significant: yes
Association: Allele T is associated with increased response to fluticasone propionate in people with Asthma as compared to allele C.
Notes: The minor  allele is reported to be associated with increased response.  dbSNP lists A as the minor allele in a CEU panel. Please note alleles have been complemented to the plus chromosomal strand.
Article: Genetic Variation in CYP3A43 Explains Racial Difference in Olanzapine Clearance
Gene: CYP1A2
Variant/haplotype: rs2472300
Drug(s): olanzapine
Phenotype category: Metabolism/PK
Significant: no
Association: Allele A is not associated with clearance of olanzapine in people with Schizophrenia as compared to allele G.
Article: Genome-wide association study of paliperidone efficacy
Gene: ADCK1
Variant/haplotype: rs56240334
Drug(s): paliperidone
Phenotype category: Efficacy
Significant: no
Association: Allele G is associated with increased response to paliperidone in people with as compared to allele A.
Notes: Authors suggest this SNP has "suggestive signals" since trend in response was seen by reduction in PANSS scores, Marder positive and Marder negative scores and CGI scores although it was not at genome wise significance level and was consistent across all three cohort used in meta-analysis.
Article: Genotype-Guided Tamoxifen Dosing Increases Active Metabolite Exposure in Women With Reduced CYP2D6 Metabolism: A Multicenter Study
Gene: CYP2D6
Variant/haplotype: CYP2D6 poor metabolizers and intermediate metabolizers
Drug(s): endoxifen
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotypes *3 + *4 + *5 + *6 + *9 + *10 + *17 + *29 + *41 (assigned as intermediate metabolizer and poor metabolizer phenotype) are associated with decreased concentrations of endoxifen in women with Breast Neoplasms as compared to genotypes *1 + *2 + *35 (assigned as normal metabolizer phenotype) .
Notes: Median baseline endoxifen concentrations are significantly higher in patients with the extensive metabolizer genotype as compared to those with the intermediate metabolizer (46% higher, p=0.0045) or poor metabolizer (88% higher, p<0.001) genotypes. Additionally, the median endoxifen concentration was 77% lower in poor metabolizers than intermediate metabolizers (p=0.0006). This study looked at whether giving poor and intermediate metabolizers a higher tamoxifen dose resulted in more similar endoxifen concentrations as compared to extensive metabolizers.
Article: Genetic factors influencing warfarin dose in Black-African patients: a systematic review and meta-analysis
Gene: VKORC1
Variant/haplotype: rs8050894
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Genotypes CG + GG are associated with decreased dose of warfarin as compared to genotype CC.
Notes: In this meta-analysis of warfarin Dose in Black-African Patients, this variant is associated with 11.7mg/week less warfarin dose requirement compared to wild-type homozygotes.
Article: Comparative efficacy and safety of sitagliptin or gliclazide combined with metformin in treatment-naive patients with type 2 diabetes: A single-center, prospective, randomized, controlled, noninferiority study with genetic polymorphism analysis
Gene: GLP1R
Variant/haplotype: rs3765467
Drug(s): sitagliptin
Phenotype category: Efficacy
Significant: yes
Association: Genotype AG is associated with increased response to sitagliptin in people with Diabetes Mellitus, Type 2.
Notes: "Conversely, patients with the rs3765467 AG genotype in the study group demonstrated a median HbA1c improvement of 1.42 (IQR, 1.22–1.68) compared with 1.08 (IQR, 0.97–1.15) in the control group (P = .023), indicating favorable responses to both treatments."
Article: Associations between CES1 variants and dosing and adverse effects in children taking methylphenidate
Gene: CES1
Variant/haplotype: rs74019272
Drug(s): methylphenidate
Phenotype category: Dosage
Significant: no
Association: Genotypes AA + AG is associated with decreased dose of methylphenidate in children with Attention Deficit Disorder with Hyperactivity as compared to genotype GG.
Notes: Authors never explicitly state which allele is associated with lower dose but do show that it is minor allele in figure 6. The frequencies in gnomAD for all populations show G as major allele and A as minor allele.  This was not significant after Benjamini-Hochberg correction for multiple hypothesis testing which the authors state "may be too stringent".
Article: Dual single‑nucleotide polymorphism biomarker combination for opioid selection to treat cancer pain
Gene: IL16
Variant/haplotype: rs4778889
Drug(s): morphine
Phenotype category: Efficacy
Significant: yes
Association: Genotype TT is associated with increased clinical benefit to morphine in people with Neoplasms and Pain as compared to genotypes CC + CT.
Notes: "Morphine tended to provide superior analgesic effect over oxycodone in patients with the IL-16 rs4778889 TT genotype and the CCL11 rs17809012 AG/GG genotype (n=45), while a trend towards a greater analgesic effect of oxycodone was observed in patients with other genotype combinations of these SNPs (n=93) (P=0.0012 for the interaction)"
Article: Tacrolimus dose requirements in paediatric renal allograft recipients are characterized by a biphasic course determined by age and bone maturation
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 concentrations of tacrolimus in children with Kidney Transplantation as compared to CYP3A5 *1/*1 + *1/*3.
Notes: Dose-corrected tacrolimus exposure (AUC0-12/doseBW).
Article: Association of Genetic Variants With Response to Anti–Vascular Endothelial Growth Factor Therapy in Age-Related Macular Degeneration
Gene: FHIT
Variant/haplotype: rs241692
Drug(s): bevacizumab, ranibizumab
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with response to bevacizumab and ranibizumab in people with as compared to allele A.
Notes: The authors performed GWAS in a discovery cohort, and did a replication analysis.
Article: Identification of sex-specific genetic associations in response to opioid analgesics in a White, non-Hispanic cohort from Southeast Minnesota
Gene: MACROD2
Variant/haplotype: rs76026520
Drug(s): hydrocodone, oxycodone
Phenotype category: Efficacy
Significant: yes
Association: Allele G is associated with increased clinical benefit to hydrocodone or oxycodone in people with Pain as compared to allele A.
Notes: variant is described as"protective" against poor pain control.
Article: Genetic Variants in CPA6 and PRPF31 Are Associated With Variation in Response to Metformin in Individuals With Type 2 Diabetes
Gene: CPA6
Variant/haplotype: rs2162145
Drug(s): metformin
Phenotype category: Efficacy
Significant: yes
Association: Allele T is associated with increased response to metformin in people with Diabetes Mellitus, Type 2 as compared to allele C.
Notes: This SNP is associated with changes in HbA1C in white patients.
Article: A genome-wide approach to identify genetic variants that contribute to etoposide-induced cytotoxicity
Variant/haplotype: rs446112
Drug(s): etoposide
Phenotype category: Other
Significant: yes
Association: Genotype AA is associated with increased resistance to etoposide as compared to genotypes AG + GG.
Article: Association of genetic variation in pharmacodynamic factors with methadone dose required for effective treatment of opioid addiction
Gene: NTRK2
Variant/haplotype: rs2289658
Drug(s): methadone
Phenotype category: Dosage
Significant: no
Association: Genotypes CC + CT are associated with increased dose of methadone in people with Heroin Dependence as compared to genotype TT.
Notes: This association was statistically significant after permutation analysis based on 40,000 replicates, but not statistically significant after adjusting for testing for multiple SNPs (Bonferroni correction).
Article: The atorvastatin metabolite pattern in muscle tissue and blood plasma is associated with statin muscle side effects in patients with coronary heart disease; An exploratory case-control study
Gene: SLCO2B1
Variant/haplotype: rs12422149
Drug(s): 4-hydroxyatorvastatin, 4-hydroxyatorvastatin lactone
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype AG is associated with increased concentrations of 4-hydroxyatorvastatin and 4-hydroxyatorvastatin lactone in people with Coronary Disease as compared to genotype GG.
Notes: Comparison was for "4-OH-ATV lactone/acid" vs "SLCO2B1 c.935 GA" vs "No variant" (SLCO1B1 c.521 TT and SLCO2B1 c.935GG) Supplementary 2-Table 1.
Article: Effects of SLCO1B1 and GATM gene variants on rosuvastatin-induced myopathy are unrelated to high plasma exposure of rosuvastatin and its metabolites
Gene: SLCO1B1
Variant/haplotype: rs4149056
Drug(s): rosuvastatin
Phenotype category: Metabolism/PK
Significant: no
Association: Genotypes CC + CT are associated with increased concentrations of rosuvastatin as compared to genotype TT.
Notes: SLCO1B1 521T>C (rs4149056) in patients with one or two copies of the variant allele had a significantly high plasma exposure to RST, whereas the significance was not found after multiple testing (Padj = 0.0247, FDR = 0.0988),
Article: Relationship between Lipid Phenotypes, Overweight, Lipid Lowering Drug Response and KIF6 and HMG-CoA Genotypes in a Subset of the Brisighella Heart Study Population
Gene: KIF6
Variant/haplotype: rs9471077
Drug(s): hmg coa reductase inhibitors
Phenotype category: Efficacy
Significant: no
Association: Genotypes AA + AG are not associated with response to hmg coa reductase inhibitors as compared to genotype GG.
Notes: With regard to lipid-lowering therapy with statins, the authors did not find any association between HMG-CoA or KIF6 genotypes and achievement of <130 mg/dL LDL-C level.
Article: ABCB1 Genotype is Associated with Fentanyl Requirements in Critically Ill Children
Gene: ABCB1
Variant/haplotype: rs1045642
Drug(s): fentanyl
Phenotype category: Metabolism/PK
Significant: no
Association: Genotype AA is not associated with concentrations of fentanyl in children as compared to genotypes AG + GG.
Notes: No significant difference in fentanyl blood levels between genotype groups.
Article: Genome-Wide Association Study and Gene Expression Analysis Identifies CD84 as a Predictor of Response to Etanercept Therapy in Rheumatoid Arthritis
Gene: CD84
Variant/haplotype: rs6427528
Drug(s): etanercept
Phenotype category: Efficacy
Significant: no
Association: Genotypes AA + AG are associated with increased response to etanercept in people with Arthritis, Rheumatoid as compared to genotype GG.
Notes: This association was not significant after correction for multiple testing.  p = 8 x 10 (-8); more than 2 x 10(6) SNPs were used.
Article: Genetic variants in CYP2A6 and UGT1A9 genes associated with urinary nicotine metabolites in young Mexican smokers
Gene: UGT1A9
Variant/haplotype: rs12471326
Drug(s): cotinine glucuronide
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype CT is associated with increased concentrations of cotinine glucuronide as compared to genotype TT.
Article: SLC28A3 genotype and gemcitabine rate of infusion affect dFdCTP metabolite disposition in patients with solid tumours
Gene: SLC29A1
Variant/haplotype: rs747199
Drug(s): gemcitabine
Phenotype category: Metabolism/PK
Significant: no
Association: Genotype GG is not associated with metabolism of gemcitabine as compared to genotypes CC + CG.
Notes: Gemcitabine, dFdCTP, and dFdU plasma concentrations were measured before (5, 15, 30, 45 min) and after gemcitabine infusion (1, 1.25, 1.5, 2, 6, 24, 48, 72 hrs). Population pharmacokinetic analysis of gemcitabine and metabolites (dFdU, dFdCTP) were performed by non-linear mixed effects modeling. No association was found between rs747199 and metabolism of gemcitabine.
Article: Comprehensive Pharmacogenomic Study Reveals an Important Role of UGT1A3 in Montelukast Pharmacokinetics
Gene: CYP2C8
Variant/haplotype: CYP2C8*1, CYP2C8*4
Drug(s): montelukast
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2C8 *4 is associated with increased concentrations of montelukast in healthy individuals as compared to CYP2C8 *1/*1.
Notes: The allele is associated with increased area under the plasma concentration-time curve (AUC) of montelukast (12.7% increase per copy of each allele, P=0.0184) from the candidate gene study.
Article: Predictive Value of Interferon-Lambda Gene Polymorphisms for Treatment Response in Chronic Hepatitis C
Gene: IFNL3
Variant/haplotype: rs8099917
Drug(s): peginterferon alfa-2a, peginterferon alfa-2b, ribavirin, telaprevir
Phenotype category: Efficacy
Significant: yes
Association: Genotype TT is associated with increased response to peginterferon alfa-2a, peginterferon alfa-2b, ribavirin or telaprevir in people with Hepatitis C, Chronic as compared to genotypes GG + GT.
Notes: Patients were analyzed by HCV genotype (1,2,3,4). Patients with HCV genotype 1 were divided into groups receiving dual therapy (GT1 (d); peg-intron alpha 2a/b, ribavirn) or triple therapy (GT1 (t); peg-intron alpha 2a/b, ribavirn, telaprevir). Sustained virological response (SVR) is a measure of therapeutic efficacy. Variables that were significant in univariate analysis were included in the multivariate analysis. The authors designated three "beneficial" genotypes that were found at higher frequencies in patients who achieved SVR: rs12979860 CC, rs8099917 TT, rs368234815 TT/TT. These genotypes were often found together. 98% of patients with GT1 (d), 100% of patients with GT1(t), 96% of patients with HCV genotype 2, 92% of patients with HCV genotype 3 and 98% of patients with HCV genotype 4 had those genotype combinations.; rs8099917 TT was the strongest predictor of SVR in GT1(t) patients (p=0.026) and was strongly correlated with SVR in patients infected with HCV genotype 4 (P<0.001).  In univariate analysis, the TT genotype was a significant predictor of SVR in GT1(d) (p<0.01) and GT1(t) (p=0.02). The TT genotype was found to be significant in a multivariate analysis of predictive factors of SVR within all HCV genotype 1 infected patients. The CC genotype was also associated with higher HCV RNA concentration at baseline in patients with HCV genotype 3 (p=0.005), 2/3 (p=0.017) and GT1(d) (p<0.001) as well as increased ALT levels in HCV genotype 2/3 (p=0.077).
Article: Association of NR1I2 Polymorphism with Midazolam Clearance in Mechanically Ventilated ICU Patients: A Population Pharmacokinetic and Pharmacogenetic Study
Gene: NR1I2
Variant/haplotype: rs2461817
Drug(s): midazolam
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype CC is associated with increased concentrations of midazolam in people with respiratory failure requiring assisted ventilation as compared to genotypes AA + AC.
Notes: "Patients with the rs2461817 mutant homozygous genotype had higher MDZ plasma concentrations compared to those with wild-type homozygous or mutant heterozygous genotypes. In addition, the CL value decreases from 22.6 L/h to 13.4 L/h in these patients (Figure 6)." Its unclear if "wild-type" means reference allele on GRCh38 (which is A) or major allele in the population (likely C), assumed reference allele in this annotation.