shlokn/autogkb huggingface dataset:
Article: Association of DRD2, DRD4 and COMT genes variants and their gene-gene interactions with antipsychotic treatment response in patients with schizophrenia
Gene: DRD2
Variant/haplotype: rs1799978
Drug(s): haloperidol, olanzapine, perphenazine, quetiapine, risperidone
Phenotype category: Efficacy
Significant: yes
Association: Allele C is associated with increased resistance to haloperidol, olanzapine, perphenazine, quetiapine or risperidone in people with Schizophrenia as compared to allele T.
Notes: Alleles complemented. "The G allele of DRD2 A-241G was associated with increased risk of resistant to treatment when compared to A allele (OR(95%CI): 3.661,P = 0.02,Table 2)."
Article: Association study between clinical response to rizatriptan and some candidate genes
Gene: MAOA
Variant/haplotype: rs1137070
Drug(s): rizatriptan
Phenotype category: Efficacy
Significant: no
Association: Allele C is not associated with response to rizatriptan in people with Migraine without Aura as compared to allele T.
Notes: No significant difference in allele frequency between responders and non-responders to rizatriptan. Variant referred to in the paper as MAO-A EcoRV and mapped to rs1137070 by PharmGKB.
Article: Comparison of Functional Variants in IFNL4 and IFNL3 for Association with Hepatitis C Virus Clearance
Gene: IFNL3
Variant/haplotype: rs4803217
Drug(s): peginterferon alfa-2a, ribavirin
Phenotype category: Efficacy
Significant: yes
Association: Genotypes AC + CC are associated with increased response to peginterferon alfa-2a and ribavirin in people with Hepatitis C, Chronic as compared to genotype AA.
Notes: in African-American patients.  The associations were stronger for IFNL4-rs368234815 than rs4803217 for undetectable HCV RNA at week 24 in Virahep C (p=0.03) trial and week 20 in HALT-C (p=0.03) trial.
Article: Genetic variation in the Catechol-O-Methyltransferase (COMT) gene and morphine requirements in cancer patients with pain
Gene: COMT
Variant/haplotype: rs2075507
Drug(s): morphine
Phenotype category: Dosage, Efficacy
Significant: yes
Association: Allele G is associated with decreased dose of morphine in people with Neoplasms as compared to allele A.
Notes: This was for alleviation of pain from cancer.  The association was as part of a haplotype consisting of 11 rsIDs (the other rsIDs are rs737866,rs7287550, rs5746849, rs740603, rs6269, rs2239393, rs4818, rs4680, rs174699, rs165728).  The haplotype was associated with a dose reduction factor of 0.71 .  Authors state that because the SNPs are linked, a strict Bonferroni correction is too conservative; however, that is what has been done here for p value.  Also noted was that the carriers of haplotype 1 have had the cancer diagnosis longer than have carriers of other haplotypes, and so the true difference in morphine requirements may be even greater than observed here.
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: rs869312136
Drug(s): migalastat
Phenotype category: Efficacy
Significant: not stated
Association: Allele C is associated with increased response to migalastat in people with Fabry Disease.
Notes: Patients carrying the C 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 Asp33Gly in the paper.
Article: The effects of CYP2D6 and CYP3A activities on the pharmacokinetics of immediate release oxycodone
Gene: CYP2D6
Variant/haplotype: CYP2D6 poor metabolizer genotype
Drug(s): noroxymorphone
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2D6 poor metabolizer is associated with decreased concentrations of noroxymorphone in healthy individuals as compared to CYP2D6 ultrarapid metabolizer.
Notes: Cmax and AUC for noroxymorphone were significantly lower in poor metabolizers than in ultrarapid metabolizers.
Article: CYP2C19 Genotyping May Provide a Better Treatment Strategy when Administering Escitalopram in Chinese Population
Gene: CYP2C19
Variant/haplotype: CYP2C19*1, CYP2C19*2, CYP2C19*3
Drug(s): escitalopram
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2C19 *2/*2 +*3/*3 + *2/*3 (assigned as poor metabolizer phenotype) is associated with increased exposure to escitalopram in healthy individuals as compared to CYP2C19 *1/*1 + *1/*2 + *1/*3 (assigned as intermediate metabolizer and normal metabolizer phenotype) .
Notes: Per Table 2: PM (N = 13), IM (N = 47), EM (N = 27)
Article: Genetic variants in CYP2B6 and CYP2A6 explain interindividual variation in efavirenz plasma concentrations of HIV-infected children with diverse ethnic origin
Gene: CYP3A5
Variant/haplotype: rs10264272
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: no
Association: Allele C is not associated with concentrations of efavirenz in children with HIV Infections as compared to allele T.
Notes: This is stated in the paper, but supporting data is not shown.; Allele also known as CYP3A5*6.
Article: Association of OPRM1 A118G variant with risk of morphine-induced respiratory depression following spine fusion in adolescents
Gene: OPRM1
Variant/haplotype: rs1799971
Drug(s): morphine
Phenotype category: Efficacy
Significant: yes
Association: Genotypes AG + GG is associated with decreased response to morphine in children as compared to genotype AA.
Notes: Presence of the G allele was associated with higher pain scores in patients taking morphine. Otherwise healthy adolescents undergoing spinal fusion for scoliosis.
Article: The International SSRI Pharmacogenomics Consortium (ISPC): a genome-wide association study of antidepressant treatment response
Gene: MTCL1
Variant/haplotype: rs2377898
Drug(s): Selective serotonin reuptake inhibitors
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to Selective serotonin reuptake inhibitors in people with Depressive Disorder, Major as compared to allele G.
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: Drug response is related to NR3C1 and FAAH polymorphism in Chinese pediatric epilepsy patients
Gene: NR3C1
Variant/haplotype: rs41423247
Drug(s): antiepileptics
Phenotype category: Efficacy
Significant: yes
Association: Genotype GG is associated with decreased clinical benefit to antiepileptics in children with Epilepsy as compared to genotypes CC + CG.
Notes: From table 4. "The frequency of the C allele was significantly higher in the good response group than in the poor response group (P < 0.001, Table 4). "In genetic model analysis, the dominant model of rs41423247 showed a difference between the good response group and the poor response group (P < 0.001, Table 5)" "In our study, we found a correlation between NR3C1 and drug response to ASM treatment in Chinese pediatric epilepsy patients, mainly in the form of CG genotype, and C allele is associated with a good response to the drug, suggesting that the NR3C1 rs41423247 polymorphism may affect the therapeutic effect of ASM in epilepsy patients." Drugs not specified.
Article: Genetic Variation in CYP3A43 Explains Racial Difference in Olanzapine Clearance
Variant/haplotype: rs2213712
Drug(s): olanzapine
Phenotype category: Metabolism/PK
Significant: no
Association: Allele C is not associated with clearance of olanzapine in people with Schizophrenia as compared to allele G.
Article: Pharmacokinetics and pharmacogenetics of the MEK1/2 inhibitor, selumetinib, in Asian and Western healthy subjects: a pooled analysis
Gene: ABCG2
Variant/haplotype: rs2231142
Drug(s): selumetinib
Phenotype category: Metabolism/PK
Significant: no
Association: Allele T is not associated with dose of selumetinib in healthy individuals as compared to allele G.
Notes: Not associated with normalized dose when allele was assessed within ethnic groups (Asian, White, Black) and when all ethnic groups were pooled together.
Article: Lack of effect of genetic polymorphisms of SLCO1B1 on the lipid-lowering response to pitavastatin in Chinese patients
Gene: SLCO1B1
Variant/haplotype: rs4149056
Drug(s): pitavastatin
Phenotype category: Efficacy
Significant: no
Association: Genotypes CC + CT are not associated with response to pitavastatin in people with Hyperlipidemias as compared to genotype TT.
Notes: There was no statistical difference among patients with wild type, SLCO1B1 388A>G or SLCO1B1 521T>C in the lipid-lowering efficacy of pitavastatin in Chinese patients with essential hyperlipidemia.
Article: Pharmacogenetic interactions of efavirenz or rifampin and isoniazid with levonorgestrel emergency contraception during treatment of HIV or tuberculosis
Gene: UGT1A1
Variant/haplotype: rs887829
Drug(s): levonorgestrel
Phenotype category: Metabolism/PK
Significant: no
Association: Genotypes CT + TT (assigned as intermediate metabolizer and poor metabolizer phenotype) is not associated with clearance of levonorgestrel in women with HIV Infections as compared to genotype CC (assigned as normal metabolizer phenotype) .
Notes: Study investigated the effect on steady-state drugs used to treat HIV or tuberculosis on the pharmacokinetics of single dose levonorgestrel. Association found in the cohort treated with dolutegravir.
Article: Effect of race and glucuronidation rates on the relationship between nicotine metabolite ratio and nicotine clearance
Variant/haplotype: rs2331559
Drug(s): nicotine
Phenotype category: Metabolism/PK
Significant: no
Association: Allele C is not associated with clearance of nicotine as compared to allele G.
Notes: No effect of the UGT2B10 variant genotypes on the ability of plasma nicotine metabolite ratio to predict nicotine clearance.
Article: Characterization of Statin Dose-response within Electronic Medical Records
Gene: PRDM16
Variant/haplotype: rs11807862
Drug(s): atorvastatin, hmg coa reductase inhibitors, simvastatin
Phenotype category: Efficacy
Significant: no
Association: Genotype AA is associated with decreased response to atorvastatin, hmg coa reductase inhibitors or simvastatin as compared to genotype TT.
Notes: There could be strand confusion with this A/T SNP.  The result is reported as max effect with simvastatin = 51.7 +/- 33.87 mg/dl in subjects homozygous for the minor allele vs. 74.96 +/- 29.71 mg/dl in those homozygous for the major allele, and 71.66 +/- 32.43 mg/dl for heterozygotes.  The gene is on the positive chromosomal strand and dbSNP lists T>A.  This SNP was also found to be associated with simvastatin max effect, also not significantly so after correction for multiple testing.
Article: Association of HTR1A Gene Polymorphisms with Efficacy and Plasma Concentrations of Atypical Antipsychotics in the Treatment of Male Patients with Schizophrenia
Gene: HTR1A
Variant/haplotype: rs6295
Drug(s): quetiapine
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype GG is associated with increased concentrations of quetiapine in men with Schizophrenia as compared to genotype CG.
Notes: At 6 weeks, "the rs6295 locus GG genotype had significantly higher plasma concentrations than the CG genotype (t = 2.877, P = 0.008). However, there were no statistically significant differences between the genotypes at weeks 3 and 12 of treatment."
Article: Effects of CYP3A4*22 and POR*28 variations on the pharmacokinetics of tacrolimus in renal transplant recipients: a meta-analysis of 18 observational studies
Gene: POR
Variant/haplotype: rs1057868
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype CC is associated with increased dose-adjusted trough concentrations of tacrolimus in people with Kidney Transplantation as compared to genotypes CT + TT.
Notes: "A significantly higher C0/Dose was observed in POR*1/*1 carriers compared to POR*28 carriers for recipients at 7 days post-transplantation (SMD = 0.34, 95% CI: 0.02 to 0.65, I2 = 84.0%). However, no significant difference was observed for the other time courses of post-transplantation (Fig. 3A). In the subgroup analysis stratified by CYP3A5 genotype, for CYP3A5 expressers (CYP3A5*1 carriers), C0/Dose of POR*1/*1 carriers was 22.64 (WMD = 22.64, 95% CI: 2.54 to 42.74, I2 = 47.2%) or 19.41 (ng/ml)/(mg/kg/day) (WMD = 19.41, 95% CI: 9.58 to 29.24, I2 = 73.5%) higher compared to POR*28 carriers for recipients at 3 days or 7 days post-transplantation (Fig. 3B). However, for CYP3A5 non-expressers (CYP3A5*3/*3 carriers), no significant difference was observed between POR*1/*1 and POR*28 carriers at any time course of post-transplantations (Fig. 3C). "
Article: Interactive Modeling for Ongoing Utility of Pharmacogenetic Diagnostic Testing: Application for Warfarin Therapy
Gene: VKORC1
Variant/haplotype: rs9923231
Drug(s): warfarin
Phenotype category: Dosage, Efficacy
Significant: yes
Association: Allele C is associated with increased dose of warfarin as compared to allele T.
Notes: CC individuals required a daily maintenance dose of S-warfarin of 5.2 mg/day; TC individuals required 4.1 mg/day, and TT individuals required 2.4 mg/day.
Article: Genetic variants associated with response to lithium treatment in bipolar disorder: a genome-wide association study
Variant/haplotype: rs74795342
Drug(s): lithium
Phenotype category: Efficacy
Significant: yes
Association: Allele G is associated with increased response to lithium in people with Bipolar Disorder as compared to allele A.
Notes: Patients had been taking lithium for at least 6 mo. Response to lithium was assayed using the Alda scale, which quantifies symptom improvement over time. The scale is from 0-10, with 10 being the highest response score and 0 being the lowest. The authors evaluated response using a dichotomous (=7 is "responder" and < 7 is "non-responder") and a continuous phenotype (0-10). This SNP was found to be associated with improved response to lithium using the continuous phenotype but not the dichotomous phenotype measure. The same alleles had a lower rate of relapse of symptoms in an independent prospective study of 73 patients. The AG genotype was also associated with a greater risk of relapse as compared to the GG genotype. This is one of four SNPs in LD that show association (rs79663003, rs78015114, rs74795342, rs75222709).
Article: Influence of IL-18 and IL-10 Polymorphisms on Tacrolimus Elimination in Chinese Lung Transplant Patients
Gene: IL18
Variant/haplotype: rs1946518
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotypes GG + GT is associated with increased dose-adjusted trough concentrations of tacrolimus in people with lung transplantation as compared to genotype TT.
Notes: Dose-adjusted trough concentrations of tacrolimus were GG>GT>TT at weeks 1 (p=0.007), 2 (p=0.018) and 3 (p=0.019) post-transplant. No significant results were seen at week 4 (p=0.079). This variant was also analyzed in combination with rs5744247 - patients with <=1 allele (Group 1), patients with 2 alleles (Group 2) and patients with >= 3 alleles (Group 3) were compared. Group 3 had lower dose-adjusted trough concentrations as compared to Groups 1 + 2 (p<0.05); no significant difference was seen between Groups 1 and 2. Additionally, note that this polymorphism had a significant impact among CYP3A5 expressers (rs776746 CT+TT) but NOT among nonexpressers (CC). Please note that alleles have been complemented to the plus chromosomal strand.
Article: CYP3A4*1B and CYP3A5*3 SNPs significantly impact the response of Egyptian candidates to high-intensity statin therapy to atorvastatin
Gene: CYP3A5
Variant/haplotype: rs776746
Drug(s): atorvastatin
Phenotype category: Efficacy
Significant: yes
Association: Genotype CC is associated with increased response to atorvastatin in people with Cardiovascular Disease or Hyperlipidemias as compared to genotype CT.
Notes: as measured by decreased triglycerides. "The serum TG concentration was greater in the C/C genotype carriers (50.53 ± 43.61) than in the C/T genotype carriers (38.01 ± 16.64) (P value < 0.05) (Table 5)." CC genotype had higher triglycerides at start of study compared to CT and still higher levels post-treatment but had greater reductions, although percentage change was not significant.
Article: A genome-wide association study of plasma concentrations of warfarin enantiomers and metabolites in sub-Saharan black-African patients
Gene: CYP2C9
Variant/haplotype: rs2256871
Drug(s): warfarin
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele G is associated with decreased metabolism of warfarin in people with Atrial Fibrillation, venous thromboembolism or Heart Valve Diseases as compared to allele A.
Notes: for S-warfarin stereoisomer in particular, measured as increased S-warfarin/R-warfarin ratio and using a Bonferroni-adjusted replication significance threshold p < 3.21 × 10−4. (CYP2C9*9)
Article: Functional genetic variation in the Rev-Erbα pathway and lithium response in the treatment of bipolar disorder
Gene: BMAL1
Variant/haplotype: rs2278749
Drug(s): lithium
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with increased response to lithium in people with Bipolar Disorder as compared to allele C.
Article: Familial deficiency of dihydropyrimidine dehydrogenase. Biochemical basis for familial pyrimidinemia and severe 5-fluorouracil-induced toxicity
Gene: DPYD
Variant/haplotype: DPYD deficiency
Drug(s): fluorouracil
Phenotype category: Metabolism/PK
Significant: not stated
Association: DPYD deficiency is associated with decreased metabolism of fluorouracil in women with Breast Neoplasms.
Notes: Case report. This patient was later genotyped in PMID 11895907. A 40-year-old white woman was diagnosed with breast cancer. She was treated with fluorouracil and developed neurotoxicity and neutropenia. She was found to have markedly prolonged elimination half-life of fluorouracil (159 min), decreased clearance (70 ml/min/m2) and no evidence of fluorouracil catabolites were seen in plasma or cerebrospinal fluid. She was found to have complete deficiency of DPYD enzyme activity in peripheral blood mononuclear cells. Her father and children had partial deficiency.
Article: Association of single nucleotide polymorphisms in MTHFR and ABCG2 with the different efficacy of first-line chemotherapy in metastatic colorectal cancer
Gene: MTHFR
Variant/haplotype: rs1801131
Drug(s): antineoplastic agents
Phenotype category: Efficacy
Significant: no
Association: Genotype TT is not associated with response to antineoplastic agents in people with Colorectal Neoplasms as compared to genotypes GG + GT.
Notes: No significant difference in response rate or progression-free survival time was seen between the genotypes. Patients were either receiving FOLFOX/XELOX or FOLFIRI regimens (respectively: fluorouracil, leucovorin, oxaliplatin; capecitabine, oxaliplatin; fluorouracil, leucovorin, irinotecan). Please note alleles have been complemented to the plus chromosomal strand.
Article: Pharmacogenetic Influence on Stereoselective Steady-State Disposition of Bupropion
Gene: CYP2B6
Variant/haplotype: CYP2B6*6
Drug(s): bupropion
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2B6 *6 is associated with increased exposure to bupropion in people with Depressive Disorder, Major.
Notes: "Hydroxylation was 25-50% lower in CYP2B6*6 carriers and one-third to one-half less in 516T; carriers." "CYP2B6*6 carriers had lower; bupropion hydroxylation compared with CYP2B6*1 participants, and CYP2B6*6 homozygotes; had lower S-bupropion apparent oral clearance (Table 1). CYP2B6 genotype had no influence; on bupropion renal clearance (Table 2)"
Article: Gemcitabine Metabolic and Transporter Gene Polymorphisms Are Associated with Drug Toxicity and Efficacy in Patients with Locally Advanced Pancreatic Cancer
Gene: SLC28A3
Variant/haplotype: rs7867504
Drug(s): gemcitabine
Phenotype category: Efficacy, Toxicity
Significant: no
Association: Genotype CC is not associated with increased response to gemcitabine in people with Pancreatic Neoplasms as compared to genotypes CT + TT.
Notes: Tumor response to therapy, progression free survival, and risk of neutropenia development did not significantly differ between genotype groups.
Article: A cis-eQTL in OPRM1 is Associated with Subjective Response to Alcohol and Alcohol Use
Gene: OPRM1
Variant/haplotype: rs3778150
Drug(s): ethanol
Significant: yes
Association: Genotypes CC + CT are associated with decreased response to ethanol as compared to genotype TT.
Notes: Individuals carrying the C allele showed decreased reported sensitivity to alcohol overall, during the last three-month period of drinking and at the period of heaviest drinking in their lives compared to individuals with the TT genotype. C allele carriers also showed lower reported sensitivity to the sedating effects of alcohol and experimental alcohol stimulation compared to TT subjects. However, there was no significant association between this variant and reported alcohol sensitivity during the participants' first five drinking episodes, reported sensitivity to the stimulating effects of alcohol, experimental alcohol-related sedation or subjective intoxication.
Article: Pharmacogenetic Predictors of Methylphenidate Dose-Response in Attention-Deficit/Hyperactivity Disorder
Gene: COMT
Variant/haplotype: rs4680
Drug(s): methylphenidate
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with response to methylphenidate in children with Attention Deficit Disorder with Hyperactivity as compared to allele A.
Notes: Vanderbilt ADHD Parent Rating Scales and Vanderbilt ADHD Teacher Rating Scales - hyperactive-impulsive domain score was derived by totaling scores from the nine hyperactive-impulsive symptoms.
Article: Association studies of dopamine synthesis and metabolism genes with multiple phenotypes of heroin dependence
Gene: TH
Variant/haplotype: rs10770140
Drug(s): heroin
Phenotype category: Dosage
Significant: no
Association: Allele T is not associated with dose of heroin in people with Heroin Dependence as compared to allele C.
Article: Integration of genetic, clinical, and INR data to refine warfarin dosing
Gene: VKORC1
Variant/haplotype: rs9923231
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Allele T is associated with decreased dose of warfarin as compared to allele C.
Notes: Each T allele resulted in a 20% (17-23%) decrease in therapeutic dose on Day 4 or 5 of therapy.
Article: Polymorphisms in Dopamine Transporter (SLC6A3) are Associated with Stimulant Effects of d-Amphetamine: An Exploratory Pharmacogenetic Study Using Healthy Volunteers
Gene: SLC6A3
Variant/haplotype: rs460000
Drug(s): amphetamine
Phenotype category: Dosage, Efficacy
Significant: no
Association: Genotype GG is associated with increased response to amphetamine in healthy individuals as compared to genotypes GT + TT.
Notes: This association was not significant after correction for multiple testing.  Association was with changes on the stimulation scale and on the euphoria scale.