shlokn/autogkb huggingface dataset:
Article: Association between single nucleotide polymorphisms in the mu opioid receptor gene (OPRM1) and self-reported responses to alcohol in American Indians
Gene: OPRM1
Variant/haplotype: rs553202
Drug(s): ethanol
Phenotype category: Efficacy
Significant: yes
Association: Allele T is associated with increased response to ethanol as compared to allele C.
Notes: Please note that alleles have been complemented to the positive strand. The T allele was associated with increased scores in the dizzy, drunk, high, nausea, terrible and uncomfortable traits on the Subjective High Assessment Scale-Expectations (SHAS-E) questionnaire.
Article: Characterization of the human cytochrome P450 enzymes involved in the metabolism of dihydrocodeine
Gene: CYP2D6
Variant/haplotype: CYP2D6*1, CYP2D6*4
Drug(s): dihydrocodeine
Phenotype category: Metabolism/PK
Significant: not stated
Association: CYP2D6 *4/*4 is associated with decreased metabolism of dihydrocodeine as compared to CYP2D6 *1/*1 + *1/*4.
Notes: Study of dihydrocodeine metabolism in liver microsomes from three subjects identified as *1/*1, two *1/*4, one phenotyped as a normal metabolizer but no genotype given and one with the *4/*4 genotype, who was designated the only poor metabolizer in the group.CLint of the poor metabolizer was found to be <10% of that in the group of six normal metabolizers.
Article: Polymorphisms in the ABCB1 gene and effect on outcome and toxicity in childhood acute lymphoblastic leukemia
Gene: ABCB1
Variant/haplotype: rs1128503
Drug(s): doxorubicin, methotrexate, prednisolone, vincristine
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with resistance to doxorubicin, methotrexate, prednisolone and vincristine in children with Precursor Cell Lymphoblastic Leukemia-Lymphoma as compared to allele G.
Notes: No statistically significant differences in relapse risk were found between the alleles or genotypes of rs1128503. Please note that alleles have been complemented to the plus chromosomal strand.
Article: Influence of SLCO1B1 polymorphisms on lopinavir C trough in Serbian HIV/AIDS patients
Gene: SLCO1B1
Variant/haplotype: rs4149056
Drug(s): lopinavir
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele C is associated with increased trough concentration of lopinavir in people with HIV Infections as compared to allele T.
Article: The pharmacokinetic and pharmacodynamic interaction of clopidogrel and cilostazol in relation to CYP2C19 and CYP3A5 genotypes
Gene: CYP3A5
Variant/haplotype: CYP3A5*1, CYP3A5*3
Drug(s): clopidogrel
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP3A5 *1/*3 (assigned as intermediate metabolizer phenotype) is associated with metabolism of clopidogrel in healthy individuals.
Notes: when clopidogrel is administered in combination with cilostazole. The authors observed no differences in AUC (ng*hr/ml) or Cmax (ng/ml) values of clopidogrel thiol metabolite when comparing between *1/*3 and *3/*3 diplotypes within the same treatment group. Differences in clopidogrel thiol metabolite concentrations were observed when comparing between treatment groups. When clopidogrel and cilostazole were co-administered, this caused a decrease in Cmax (ng/ml) and AUC (ng*hr/ml) within the CYP3A5 *1/*3 group as compared to when clopidogrel was administered alone.
Article: Genomewide Association Study Identifies Novel Genetic Loci That Modify Antiplatelet Effects and Pharmacokinetics of Clopidogrel
Gene: SLC14A2
Variant/haplotype: rs12456693
Drug(s): clopidogrel
Phenotype category: Metabolism/PK
Significant: no
Association: Genotype CT is associated with increased metabolism of clopidogrel as compared to genotype CC.
Notes: The CT genotype was associated with increased active metabolite H4 concentration. However, it was not statistically significant.
Article: DRD2, DRD3, and HTR2A Single-Nucleotide Polymorphisms Involvement in High Treatment Resistance to Atypical Antipsychotic Drugs
Gene: HTR2A
Variant/haplotype: rs7997012
Drug(s): antipsychotics
Phenotype category: Efficacy
Significant: yes
Association: Genotype AG is associated with increased resistance to antipsychotics in people with Mood Disorders or Schizophrenia as compared to genotypes AA + GG.
Notes: "The HTR2A rs7997012 A|G vs. A|A genotype (OR = 6.859; B = 1.926; p = 0.046), and; A|G vs. G|G genotype (OR = 2.879; B = 1.057; p = 0.041) significantly predicted the HTR; group membership."
Article: TSPAN5, ERICH3 and selective serotonin reuptake inhibitors in major depressive disorder: pharmacometabolomics-informed pharmacogenomics
Gene: TSPAN5
Variant/haplotype: rs11947402
Drug(s): serotonin
Phenotype category: Other
Significant: yes
Association: Allele G is associated with decreased concentrations of serotonin in people with Depressive Disorder as compared to allele A.
Notes: in patients taking citalopram or escitalopram. Baseline plasma serotonin concentrations before SSRI therapy, as well as changes in serotonin were used as a biomarker for response to SSRIs and GWAS was done w/respect to changes in plasma serotonin concentration. The G allele was associated with higher baseline plasma serotonin concentrations, as well as greater decreases in plasma serotonin concentrations at 4 and 8 weeks after beginning SSRI therapy.
Article: Effects of CYP2B6 and CYP1A2 Genetic Variation on Nevirapine Plasma Concentration and Pharmacodynamics as Measured by CD4 Cell Count in Zimbabwean HIV-Infected Patients
Gene: CYP1A2
Variant/haplotype: rs762551
Drug(s): nevirapine
Phenotype category: Efficacy
Significant: yes
Association: Genotype CC is associated with increased response to nevirapine in people with HIV Infections as compared to genotypes AA + AC.
Notes: Nevirapine was given as part of HAART therapy. Efficacy was determined based on CD4 count.
Article: Predictive Value of Interferon-Lambda Gene Polymorphisms for Treatment Response in Chronic Hepatitis C
Gene: IFNL4
Variant/haplotype: rs11322783
Drug(s): peginterferon alfa-2a, peginterferon alfa-2b, ribavirin, telaprevir
Phenotype category: Efficacy
Significant: yes
Association: Genotype TT/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 G/TT + GG.
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.; rs368234815 TT/TT was the only single SNP significant predictor of SVR in patients with HCV genotype 3.  Although rs368234815 TT/TT was significantly associated with SVR in univariate analysis, in a multivariate analysis of predictive factors of SVR within all genotype 1 infected patients the TT/TT genotype was not found to be significant. The TT/TT genotype was also associated with increases ALT levels in patients with HCV genotype 2 (p=0.018),3 (p=0.035) and 2/3 (p=0.006) as well as a higher HCV RNA concentration at baseline in GT1 (d) (p<0.001) and GT(t) patients (p=0.007). *Note: TT is a single allele whereas the other allele substitutes TT for a single G so the WT genotype is TT/TT.
Article: CYP2C8*3 predicts benefit/risk profile in breast cancer patients receiving neoadjuvant paclitaxel
Gene: ABCB1
Variant/haplotype: rs2032582
Drug(s): paclitaxel
Phenotype category: Efficacy
Significant: no
Association: Allele C is not associated with increased response to paclitaxel in women with Breast Neoplasms.
Notes: This is a C>T/A SNP(positive strand alleles).  The OR is given for variant carriers vs. wild-type homozygous patients, without stating which genotypes were found.  Response = complete clinical response (cCR). Some patients who had HER2 overexpressing tumors received trastuzumab at the same time as the paclitaxel.
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: HTR1A
Variant/haplotype: rs6295
Drug(s): escitalopram
Phenotype category: Efficacy
Significant: no
Association: Allele C is not associated with response to escitalopram Depressive Disorder, Major as compared to allele G.
Article: Brain/blood ratios of methadone and ABCB1 polymorphisms in methadone-related deaths
Gene: ABCB1
Variant/haplotype: rs1128503
Drug(s): methadone
Phenotype category: Metabolism/PK
Significant: no
Association: Allele G is not associated with concentrations of methadone as compared to allele A.
Notes: No significant association between this variant and medulla/blood concentration ratios of methadone. Please note that alleles have been complemented to the positive strand.
Article: The International SSRI Pharmacogenomics Consortium (ISPC): a genome-wide association study of antidepressant treatment response
Gene: REPS1
Variant/haplotype: rs17068112
Drug(s): Selective serotonin reuptake inhibitors
Phenotype category: Efficacy
Significant: no
Association: Allele G 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).
Article: Influence of genetic variants on renal uric acid handling in response to frusemide: an acute intervention study
Gene: SLC22A11
Variant/haplotype: rs2078267
Drug(s): furosemide
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with response to furosemide in healthy individuals as compared to allele C.
Notes: There was no difference in the absolute values of serum urate over the study period between those carrying the C allele versus those that did not.
Article: Association between single nucleotide polymorphisms in DNA repair genes and the efficacy of radiotherapy in nasopharyngeal carcinoma patients
Gene: XRCC1
Variant/haplotype: rs25487
Drug(s): radiotherapy
Phenotype category: Efficacy
Significant: no
Association: Allele C is not associated with response to radiotherapy in people with Nasopharyngeal Neoplasms as compared to allele T.
Notes: alleles complemented.
Article: Tell-Tale SNPs: The Role of CYP2B6 in Methadone Fatalities
Gene: CYP2B6
Variant/haplotype: rs3745274
Drug(s): S-EDDP
Phenotype category: Metabolism/PK
Significant: no
Association: Allele T is not associated with concentrations of (S)-EDDP as compared to allele G.
Article: A multi-factorial analysis of response to warfarin in a UK prospective cohort
Gene: VKORC1
Variant/haplotype: rs9923231
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Genotypes CT + TT are associated with decreased dose of warfarin as compared to genotype CC.
Article: Two Novel Loci of RELN Associated With Antipsychotics Response in Chinese Han Population
Gene: RELN
Variant/haplotype: rs362731
Drug(s): aripiprazole, olanzapine, perphenazine, quetiapine, risperidone
Phenotype category: Efficacy
Significant: no
Association: Allele C is not associated with response to aripiprazole, olanzapine, perphenazine, quetiapine or risperidone in people with Schizophrenia as compared to allele T.
Notes: Response was assessed by changes in PANSS score. A reduction of 50% or more in PANSS score was classified as a good response.
Article: Bleeding Events Associated with Rivaroxaban Therapy in Naive Patients with Nonvalvular Atrial Fibrillation: A Longitudinal Study from a Genetic Perspective with INR Follow-Up
Gene: ABCB1
Variant/haplotype: rs4148738
Drug(s): rivaroxaban
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele T is associated with decreased concentrations of rivaroxaban in people with Atrial Fibrillation as compared to allele C.
Notes: "In our study, we found that for ABCB1-related rs4148738 and rs2032582, there was a statistically significant difference between the wild and mutant genotypes and a decrease in the CDR max values of rivaroxaban, while CDRss was statistically significant between the wild and homozygous mutant genotypes. For rs1045642 and rs1128503 of ABCB1, the decreased CDR max and Css levels of rivaroxaban were statistically significant between the wild (AA) and mutant (AG, GG) genotypes. Our findings suggest that polymorphism in the P-glycoprotein expressed by the ABCB1 gene can affect the peak plasma levels of rivaroxaban." Was significant for TT v CC not CT v CC
Article: Enantioselective pharmacokinetics of tramadol and its three main metabolites; impact of CYP2D6, CYP2B6, and CYP3A4 genotype
Gene: CYP2D6
Variant/haplotype: CYP2D6*1, CYP2D6*2, CYP2D6*3, CYP2D6*4, CYP2D6*5, CYP2D6*9, CYP2D6*35, CYP2D6*41
Drug(s): "n,o-didesmethyltramadol", "o-desmethyltramadol"
Phenotype category: Metabolism/PK
Significant: not stated
Association: CYP2D6 *4/*4 + *4/*5 (assigned as poor metabolizer phenotype) are associated with decreased exposure to n,o-didesmethyltramadol or o-desmethyltramadol in healthy individuals as compared to CYP2D6 *1/*1 + *1/*2 + *1/*3 + *1/*4 + *1/*5 + *1/*9 + *1/*35 + *1/*41 + *2/*5 + *2/*35 + *2/*41 + *4/*35 + *4/*41 (assigned as intermediate metabolizer and normal metabolizer phenotype) .
Notes: The two subjects identified as PMs had smaller AUCs of O-desmethyltramadol and N,O-didesmethyltramadol compared to the other subjects in the cohort. Note that no statistical analysis appears to have been carried out.
Article: SLC28A3 genotype and gemcitabine rate of infusion affect dFdCTP metabolite disposition in patients with solid tumours
Gene: NT5C2
Variant/haplotype: rs11598702
Drug(s): gemcitabine
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype TT is associated with decreased clearance of gemcitabine as compared to genotypes CC + CT.
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. Pharmacokinetics of gemcitabine were described by a two-compartment model. NT5C2 rs11598702 genotype and body surface area of the patient, were significant co-variates in the final pharmacokinetic model to predict rate of gemcitabine clearance in patients.
Article: Clinical Impact of Cytochrome P450 2C19 Genotype on the Treatment of Invasive Aspergillosis under Routine Therapeutic Drug Monitoring of Voriconazole in a Korean Population
Gene: CYP2C19
Variant/haplotype: CYP2C19*1, CYP2C19*2, CYP2C19*3, CYP2C19*17
Drug(s): voriconazole
Phenotype category: Metabolism/PK
Significant: no
Association: CYP2C19 *2/*2 + *3/*3 (assigned as poor metabolizer phenotype) is not associated with trough concentration of voriconazole in people with Hematologic Diseases and Infection as compared to CYP2C19 *1/*1 + *1/*17 + *1/*2 + *1/*3.
Notes: No significant difference was seen when comparing poor metabolizers with extensive (*1/*1, *1/*17; p=0.062) or heterozygous extensive (*1/*2, *1/*3; p=0.779) metabolizers. The initial voriconazole trough concentrations were 1.8, 2.7, and 3.2 mg/L in EM, HEM, and PM, respectively. There was no significant difference when comparing all 3 groups either (p=0.068).
Article: An expanded pharmacogenomics warfarin dosing table with utility in generalised dosing guidance
Gene: CYP2C9
Variant/haplotype: rs28371686
Drug(s): warfarin
Phenotype category: Dosage
Significant: not stated
Association: Allele C is associated with dose of warfarin as compared to allele G.
Notes: This variant annotation is part of a dosing algorithm table based on 8 genetic variants.
Article: TOLLIP, MUC5B, and the Response to N-Acetylcysteine among Individuals with Idiopathic Pulmonary Fibrosis
Gene: MUC5B
Variant/haplotype: rs35705950
Drug(s): acetylcysteine
Phenotype category: Efficacy
Significant: no
Association: Genotype TT is not associated with response to acetylcysteine in people with Pulmonary Fibrosis as compared to genotypes GG + GT.
Notes: Clinical endpoints included death, transplant, hospitalization, or FVC decline,  and risk was adjusted for age, sex, prednisone use, azathioprine use, FVC, diffusion capacity of the lung, and trial/center. Alleles given on reverse strand A and G.
Article: Population pharmacokinetic analyses for belzutifan to inform dosing considerations and labeling
Gene: CYP2C19
Variant/haplotype: CYP2C19 poor metabolizer
Drug(s): belzutifan
Phenotype category: Metabolism/PK
Significant: not stated
Association: CYP2C19 poor metabolizer is associated with increased concentrations of belzutifan in people with von Hippel-Lindau Disease or Carcinoma, Renal Cell.
Notes: variants genotyped are not specified, nor are which variants are considered PM. "A population pharmacokinetic (PK) model was built, using NONMEM® v7.3, based on demographics/PK data from 3 clinical pharmacology (food effect, formulation bridging, genotype/race effect) and 2 clinical (phase 1 dose escalation/expansion in RCC and other solid tumors; phase 2 in VHL patients) studies." "UGT2B17 and CYP2C19 poor metabolizers (PM) were estimated to have a 3.2-fold higher area under the plasma concentration-time curve (AUC) compared to UGT2B17 extensive metabolizer and CYP2C19 non-PM patients."
Article: Haplotypes of P2RX7 gene polymorphisms are associated with both cold pain sensitivity and analgesic effect of fentanyl
Gene: P2RX7
Variant/haplotype: rs1180012
Drug(s): fentanyl
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with dose of fentanyl in people with Pain, Postoperative as compared to allele C.
Notes: No significant association between this variant and 24-h postoperative fentanyl use or perioperative fentanyl use.
Article: Effects of various factors on steady-state plasma concentrations of risperidone and 9-hydroxyrisperidone: lack of impact of MDR-1 genotypes
Gene: CYP2D6
Variant/haplotype: CYP2D6*1, CYP2D6*4, CYP2D6*5, CYP2D6*10, CYP2D6*14
Drug(s): risperidone
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2D6 *4 + *5 + *10 +*14 is associated with decreased metabolism of risperidone in people with Schizophrenia as compared to CYP2D6 *1.
Notes: This study evaluated patients with *1, *4, *5, *10, and *14 alleles. A gene dose effect was observed in that with increasing numbers of variant alleles, higher concentrations of risperidone were seen. Concentrations of the major metabolite, 9-OH-risperidone, and active moiety, risperidone + 9-OH-risperidone, correlated with age, but not with CYP2D6 genotype.
Article: Adiponectin Gene Polymorphism rs2241766 T/G Is Associated with Response to Pioglitazone Treatment in Type 2 Diabetic Patients from Southern China
Gene: ADIPOQ
Variant/haplotype: rs266729
Drug(s): pioglitazone
Phenotype category: Efficacy
Significant: no
Association: Genotype CC are not associated with response to pioglitazone in people with Diabetes Mellitus as compared to genotypes CG + GG.
Notes: Response was defined as "any decrease greater than (or equal to) 15%" of glycated hemoglobin (HbA1C%).
Article: Effect of age, weight and CYP2C19 genotype on escitalopram exposure
Gene: CYP2C19
Variant/haplotype: CYP2C19*1, CYP2C19*2, CYP2C19*3, CYP2C19*17
Drug(s): escitalopram
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2C19 *1/*2 + *1/*3 + *17/*2 + *17/*3 + *2/*2 + *2/*3 + *3/*3 are associated with decreased clearance of escitalopram in people with Depressive Disorder, Major as compared to CYP2C19 *1/*1 + *1/*17 + *17/*17.
Article: Effect of Fenofibrate Therapy and ABCA1 Polymorphisms on High Density Lipoprotein Subclasses in the Genetics of Lipid Lowering Drugs and Diet Network
Gene: ABCA1
Variant/haplotype: rs2230806
Drug(s): fenofibrate
Phenotype category: Efficacy
Significant: yes
Association: Genotype TT is associated with increased response to fenofibrate in people with Hypertriglyceridemia as compared to genotype CC.
Notes: Patients with the TT genotype had a greater total high-density lipoprotein (HDL) particle concentration (units = umol/L) after fenofibrate treatment for 3 weeks, as compared to patients with the CC genotype.
Article: Gene‐Wide Tagging Study of the Association Between KCNT1 Polymorphisms and the Susceptibility and Efficacy of Genetic Generalized Epilepsy in Chinese Population
Gene: KCNT1
Variant/haplotype: rs1318383
Drug(s): antiepileptics
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to antiepileptics in people with Epilepsy, Generalized as compared to allele G.
Notes: No significant differences in genotype frequencies were seen between patients who were responsive to antiepileptic drugs (n=279; those who had not experienced any type of seizure for a minimum of 1 year after receiving antiepileptic drugs) and patients who were resistant to antiepileptic drugs (n=204; those who had at least four seizures during the previous year while trying at least three antiepileptic medications at the maximal tolerated doses). Please note 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: rs758479488
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 loss-of-function following in vitro assessments, in vivo associations and variant construct functional assignments.
Article: Ivacaftor in severe cystic fibrosis lung disease and a G551D mutation
Gene: CFTR
Variant/haplotype: rs75527207
Drug(s): ivacaftor
Phenotype category: Efficacy
Significant: not stated
Association: Allele A is associated with response to ivacaftor in people with Cystic Fibrosis.
Notes: G551D allele. Case report of three patients with the F508del/G551D genotype. Reported improvements in FEV1, body weight, sweat chloride levels and scores in the respiratory domain of the CFQ-R.
Article: Relevance of CYP2B6 and CYP2D6 genotypes to methadone pharmacokinetics and response in the OPAL study
Gene: CYP2D6
Variant/haplotype: CYP2D6 poor and ultrarapid metabolizers
Drug(s): (S)-methadone
Phenotype category: Metabolism/PK
Significant: no
Association: CYP2D6 poor metabolizer and ultrarapid metabolizer are not associated with concentrations of (S)-methadone in people with Opioid-Related Disorders as compared to CYP2D6 normal metabolizer.
Article: OPRM1, OPRK1 and COMT Genetic Polymorphisms Associated with Opioid Effects on Experimental Pain: A Randomized, Double-Blind, Placebo-Controlled Study
Gene: COMT
Variant/haplotype: rs6269
Drug(s): morphine
Phenotype category: Efficacy
Significant: not stated
Association: Genotypes AG + GG are associated with increased response to morphine in healthy individuals as compared to genotype AA.
Notes: Nominally significant difference in ischemic pain threshold between genotype groups, but this association was not seen in other pain modalities. Study-wide significance was set to p<0.017.