shlokn/autogkb huggingface dataset:
Article: Influence of IL-18 and IL-10 Polymorphisms on Tacrolimus Elimination in Chinese Lung Transplant Patients
Gene: IL10
Variant/haplotype: rs1800871
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: no
Association: Genotypes AG + GG is not associated with dose-adjusted trough concentrations of tacrolimus in people with lung transplantation as compared to genotype AA.
Notes: No significant difference in dose-adjusted trough concentration was seen between patients with the AG + GG genotypes and those with the AA genotype at weeks 1, 2, 3 or 4 post-transplant. This rsID is referred to as "rs3021097" in the paper. Please note that alleles have been complemented to the plus chromosomal strand.
Article: Targeted pharmacogenetic analysis of antipsychotic response in the CATIE study
Gene: CNTN4
Variant/haplotype: rs17194378
Drug(s): ziprasidone
Phenotype category: Efficacy
Significant: yes
Association: Allele A is associated with response to ziprasidone in people with Schizophrenia.
Notes: as measured by changes in PANSS-T (positive and negative syndrome scale total score), using a mixed model repeated measures approach. Examined 6789 SNPs - p-value of p< or equal to 5x10-4 was considered significant. It was unclear whether the allele was associated with an increased or decreased response to drug.
Article: Genomic Association Analysis of Common Variants Influencing Antihypertensive Response to Hydrochlorothiazide
Gene: HS3ST4
Variant/haplotype: rs9933692
Drug(s): "diuretics", "hydrochlorothiazide", "Thiazides, plain"
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to diuretics, hydrochlorothiazide or Thiazides, plain in people with Hypertension as compared to allele G.
Notes: There was a trend but significance was not attained. Observations: 2.09 mm Hg increased reduction of diastolic blood pressure per A allele in PEAR + GERA, 0.05 mm Hg decreased reduction of diastolic blood pressure per A allele in NORDIL (small, opposite direction effect), and 1.36 mm Hg increased reduction of diastolic blood pressure per A allele in PEAR + GERA + NORDIL.
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: ABCB1
Variant/haplotype: rs1128503
Drug(s): methadone
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to methadone in people with Heroin Dependence as compared to allele G.
Notes: This SNP was not significantly associated with compliance with methadone maintenance therapy or 'negative rate of morphine urine test'.; Please note that alleles have been complemented to the positive strand.
Article: Genetic variation in the Catechol-O-Methyltransferase (COMT) gene and morphine requirements in cancer patients with pain
Gene: COMT, TXNRD2
Variant/haplotype: rs7287550
Drug(s): morphine
Phenotype category: Dosage, Efficacy
Significant: yes
Association: Allele C is associated with decreased dose of morphine in people with Neoplasms as compared to allele T.
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 rs2075507,rs737866, 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: Impact of CYP2C19 Polymorphisms on Serum Concentration of Voriconazole in Iranian Hematological Patients
Gene: CYP2C19
Variant/haplotype: CYP2C19*1, CYP2C19*2, CYP2C19*17
Drug(s): voriconazole
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2C19 *1/*2 is associated with increased concentrations of voriconazole in people with Mycoses as compared to CYP2C19 *1/*1 + *1/*17.
Notes: Patients who were classified as intermediate metabolizers (IMs; n=9; *1/*2) had higher serum concentrations of voriconazole at day 4 of treatment as compared to those classified as extensive metabolizers (EMs; n=18; *1/*1) or ultrarapid metabolizers (UMs; n=8; *1/*17). Significant differences were observed when comparing IMs vs UMs (p<0.0001), IMs vs EMs (p<0.001) and EMs vs UMs (p<0.001). Patients had hematologic malignancies and were treated with voriconazole for invasive aspergillosis.
Article: Dopamine D2 receptor genetic variation and clinical response to antipsychotic drug treatment: A meta-analysis
Gene: ANKK1
Variant/haplotype: rs1800497
Drug(s): antipsychotics
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to antipsychotics in people with Schizophrenia as compared to allele G.
Notes: in a meta-analysis.
Article: Attempted validation of 44 reported SNPs associated with tacrolimus troughs in a cohort of kidney allograft recipients
Gene: ABCB1
Variant/haplotype: rs9282564
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 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.
Article: Genome-Wide Association Study of Serum Creatinine Levels during Vancomycin Therapy
Gene: MIA3
Variant/haplotype: rs904323
Drug(s): vancomycin
Phenotype category: Metabolism/PK
Significant: no
Association: Allele A is not associated with trough concentration of vancomycin as compared to allele G.
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: Association of Pharmacogenetic Markers with Premature Discontinuation of First-line Anti-HIV Therapy: An Observational Cohort Study
Gene: ABCC4
Variant/haplotype: rs899494
Drug(s): tenofovir
Phenotype category: Toxicity
Significant: no
Association: Genotypes AA + AG is not associated with increased discontinuation of tenofovir in people with HIV Infections as compared to genotype GG.
Article: Pharmacogenetics of tenofovir clearance among Southern Africans living with HIV
Gene: GIMAP6
Variant/haplotype: rs34940374
Drug(s): tenofovir
Phenotype category: Metabolism/PK
Significant: no
Association: Allele A is not associated with clearance of tenofovir in people with HIV Infections as compared to allele G.
Notes: Significance threshold was set at 6.0E-7.
Article: Genomic Association Analysis of Common Variants Influencing Antihypertensive Response to Hydrochlorothiazide
Variant/haplotype: rs2776546
Drug(s): "diuretics", "hydrochlorothiazide", "Thiazides, plain"
Phenotype category: Efficacy
Significant: yes
Association: Allele A is associated with increased response to diuretics, hydrochlorothiazide or Thiazides, plain in people with Hypertension as compared to allele C.
Notes: The association was with diastolic blood pressure response.  Observations: 3.24 mm Hg greater reduction of diastolic blood pressure per A allele in PEAR + GERA, 0.88mm Hg greater reduction in diastolic blood pressure per A allele in NORDIL
Article: An Intronic Variant in OPRD1 Predicts Treatment Outcome for Opioid Dependence in African-Americans
Variant/haplotype: rs10753331
Drug(s): methadone
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to methadone in people with Opioid-Related Disorders as compared to allele G.
Notes: Efficacy was determined based on the number of opioid-positive drug screens that each patient had during treatment.
Article: Genetic Variants in CPA6 and PRPF31 Are Associated With Variation in Response to Metformin in Individuals With Type 2 Diabetes
Gene: PRPF31
Variant/haplotype: rs254271
Drug(s): metformin
Phenotype category: Efficacy
Significant: yes
Association: Allele C is associated with decreased response to metformin in people with Diabetes Mellitus, Type 2 as compared to allele G.
Notes: This SNP is associated with changes in HbA1C when all races are combined.
Article: Genetic polymorphisms are associated with individual susceptibility to dexmedetomidine
Gene: WBP2NL
Variant/haplotype: rs5758550
Drug(s): dexmedetomidine
Phenotype category: Toxicity
Significant: yes
Association: Genotypes AG + GG is associated with increased response to dexmedetomidine in people with surgery as compared to genotype AA.
Notes: as measured by decreased in mean arterial pressure. "homozygosity for the major allele significantly changed less in MAP during DXM sedation period than either heterozygosity or homozygosity for the minor allele (−8.19 ± 9.96 vs. −12.85 ± 6.68, p = 0.025). Thus, heterozygosity or homozygosity for the gene’s minor allele G) may cause a higher susceptibility to the cardiovascular impact of DXM."
Article: Evaluating Predictive Pharmacogenetic Signatures of Adverse Events in Colorectal Cancer Patients Treated with Fluoropyrimidines
Gene: TYMP
Variant/haplotype: rs11479
Drug(s): capecitabine, fluorouracil
Phenotype category: Dosage
Significant: yes
Association: Genotypes AA + AG is associated with dose of capecitabine or fluorouracil in people with Colorectal Neoplasms as compared to genotype GG.
Notes: Clinical data about adverse events were collected from patient records and laboratory charts for 12 weeks after the initiation of therapy. Delays or reductions in the administration of 5'FU or capecitabine due to adverse events were recorded as primary outcomes, and grade 3,4,5 adverse events were analyzed as secondary outcomes. "Dose" here refers to dose modification.
Article: Combination therapy with cystic fibrosis transmembrane conductance regulator modulators augment the airway functional microanatomy
Gene: CFTR
Variant/haplotype: rs113993960
Drug(s): ivacaftor
Phenotype category: Efficacy
Significant: yes
Association: Allele del is associated with increased response to ivacaftor in people with Cystic Fibrosis.
Notes: Cell based assays looking at monolayers to report that F508del cells exhibit increased mucociliary transport and decreased mucus effective viscosity when ivacaftor is added to the full regimen with C18. Result not seen with ivacaftor alone or with c18 alone.
Article: Attempted validation of 44 reported SNPs associated with tacrolimus troughs in a cohort of kidney allograft recipients
Gene: CYP2C19
Variant/haplotype: rs4986893
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: no
Association: Allele A 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. This corresponds to CYP2C19*3 and was very rare - zero people in the EA cohort had the variant and frequency in AA cohort was 0.001.
Article: Attempted validation of 44 reported SNPs associated with tacrolimus troughs in a cohort of kidney allograft recipients
Gene: CYP3A4
Variant/haplotype: rs2242480
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 was one of the variants that passed validation in both populations. Direction of effect was not stated.
Article: ST13 polymorphisms and their effect on exacerbations in steroid-treated asthmatic children and young adults
Gene: ST13
Variant/haplotype: rs138337
Drug(s): corticosteroids
Phenotype category: Efficacy
Significant: yes
Association: Allele G is associated with decreased response to corticosteroids in children with Asthma as compared to allele A.
Notes: Outcome measured was hospital visits for airway exacerbation. Effect is additive, measured per G allele.
Article: Individualized treatment based on CYP3A5 single-nucleotide polymorphisms with tacrolimus in ulcerative colitis
Gene: CYP3A5
Variant/haplotype: CYP3A5*1, CYP3A5*3
Drug(s): tacrolimus
Phenotype category: Dosage
Significant: yes
Association: CYP3A5 *1/*1 + *1/*3 is associated with increased dose of tacrolimus in people with Arthritis, Rheumatoid or Colitis, Ulcerative as compared to CYP3A5 *3/*3.
Notes: Patients with the *1/*1 or *1/*3 genotype required significantly higher doses of tacrolimus in order to maintain a stable blood trough level of 10 ng/mL. The required dosages were 0.27 (*1/*1), 0.17 (*1/*3) and 0.09 ng/mL (*3/*3). The authors used these required doses in order to test whether genotype-guided tacrolimus dosing helped achieve target levels more quickly.
Article: Candidate‐Gene Study of Functional Polymorphisms in SLCO1B1 and CYP3A4/5 and the Cholesterol‐Lowering Response to Simvastatin
Gene: SLCO1B1
Variant/haplotype: rs4149056
Drug(s): simvastatin
Phenotype category: Efficacy
Significant: yes
Association: Allele C is associated with decreased response to simvastatin as compared to genotype TT.
Notes: in Whites.
Article: Prolonged Half-life of Voriconazole in a CYP2C19 Homozygous Poor Metabolizer Receiving Vincristine Chemotherapy: Avoiding a Serious Adverse Drug Interaction
Gene: CYP2C19
Variant/haplotype: CYP2C19*2
Drug(s): voriconazole
Phenotype category: Metabolism/PK
Significant: not stated
Association: CYP2C19 *2/*2 (assigned as poor metabolizer phenotype) is associated with increased concentrations of voriconazole.
Notes: Case report: Patient taking normal doses of voriconazole and trough concentration elevated (6.1-6.7 mcg/ml) resulting in discontinuation of drug.
Article: Attempted validation of 44 reported SNPs associated with tacrolimus troughs in a cohort of kidney allograft recipients
Gene: NR1I2
Variant/haplotype: rs6785049
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: no
Association: Allele G is not associated with trough concentration of tacrolimus in people with Kidney Transplantation and Transplantation as compared to allele A.
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: CYP3A5, ABCB1 and SLCO1B1 Polymorphisms and Pharmacokinetics and Virologic Outcome of Lopinavir/Ritonavir in HIV-infected Children
Gene: SLCO1B1
Variant/haplotype: rs2306283
Drug(s): lopinavir, ritonavir
Phenotype category: Metabolism/PK
Significant: no
Association: Allele G is not associated with clearance of lopinavir or ritonavir in children with HIV Infections as compared to allele A.
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 A388G.
Article: Pharmacogenomic Next-Generation DNA Sequencing: Lessons from the Identification and Functional Characterization of Variants of Unknown Significance in CYP2C9 and CYP2C19
Gene: CYP2C19
Variant/haplotype: rs144928727
Drug(s): mephenytoin
Phenotype category: Metabolism/PK
Significant: no
Association: Allele G is associated with decreased clearance of mephenytoin as compared to allele A.
Notes: In vitro analysis showed that intrinsic clearance of S-mephenytoin by CYP2C19 protein containing the G allele was 36.2% of that of the WT protein. However, this difference was not found to be statistically significant. Variant referred to as 65A>G in the paper.
Article: Population pharmacokinetics of primaquine and its metabolites in African males
Gene: G6PD
Variant/haplotype: G6PD deficiency
Drug(s): carboxyprimaquine, primaquine, primaquine n-carbamoyl glucuronide
Phenotype category: Metabolism/PK
Significant: no
Association: G6PD deficiency is not associated with increased concentrations of carboxyprimaquine, primaquine or primaquine n-carbamoyl glucuronide in men as compared to G6PD non-deficient.
Notes: "In summary, the population pharmacokinetic properties of PQ, CPQ, and PQCG have been characterized and reported here. No statistically significant relationships were seen between the pharmacokinetic parameters and the change in haemoglobin levels in G6PD-deficient patients after a single low dose of primaquine. A single low dose (0.50 mg/kg) of PQ was haematologically safe in this population of G6PD-deficient African males without malaria."
Article: Genomic Association Analysis of Common Variants Influencing Antihypertensive Response to Hydrochlorothiazide
Gene: HS3ST4
Variant/haplotype: rs4074471
Drug(s): "diuretics", "hydrochlorothiazide", "Thiazides, plain"
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with response to diuretics, hydrochlorothiazide or Thiazides, plain in people with Hypertension as compared to allele G.
Notes: There was a trend but significance was not attained. Observations: 2.09 mm Hg decreased reduction of diastolic blood pressure per T allele in PEAR + GERA, 0.05 mm Hg increased reduction of diastolic blood pressure per T allele in NORDIL (opposite, though small effect), and 1.36 mm Hg decreased reduction of diastolic blood pressure per T allele in PEAR + GERA + NORDIL.
Article: Prediction of Warfarin Dose Reductions in Puerto Rican Patients, Based on Combinatorial CYP2C9 and VKORC1 Genotypes
Gene: CYP2C9
Variant/haplotype: CYP2C9*1, CYP2C9*2, CYP2C9*3, CYP2C9*5
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: CYP2C9 *1/*2 + *1/*3 + *2/*3 + *2/*2 + *1/*5 + *2/*5 is associated with decreased dose of warfarin as compared to CYP2C9 *1/*1.
Notes: This variant is analyzed along with VKORC1 variants.
Article: Association of STAT-3 rs1053004 and VDR rs11574077 With FOLFIRI-Related Gastrointestinal Toxicity in Metastatic Colorectal Cancer Patients
Gene: VDR
Variant/haplotype: rs11574077
Drug(s): irinotecan
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype TT is associated with increased metabolism of irinotecan in people with Colorectal Neoplasms as compared to genotype CT.
Notes: The pharmacokinetic analysis focused on markers that, even if not presenting a significant effect in the replication cohort (p > 0.05), presented a concordant effect on the toxicity risk in both cohorts (same size effect according to the same genetic model). The association of these polymorphisms with the pharmacokinetic parameters was investigated in a subset of 71 patients from the discovery cohort, and the most relevant results (p < 0.1; concordant genetic model) .
Article: Impact of the CYP2C8 *3 polymorphism on the drug–drug interaction between gemfibrozil and pioglitazone
Gene: CYP2C8
Variant/haplotype: CYP2C8*1, CYP2C8*3
Drug(s): pioglitazone
Phenotype category: Metabolism/PK
Significant: no
Association: CYP2C8 *1/*1 is not associated with concentrations of pioglitazone in healthy individuals as compared to CYP2C8 *1/*3 + *3/*3.
Notes: Cmax
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: rs398123226
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 Asp226Glu in the paper.
Article: Influence of CYP2D6 and CYP3A5 Polymorphisms on the Pharmacokinetics and Pharmacodynamics of Bisoprolol in Hypertensive Chinese Patients
Gene: CYP3A5
Variant/haplotype: CYP3A5*1, CYP3A5*3
Drug(s): bisoprolol
Phenotype category: Efficacy
Significant: no
Association: CYP3A5 *3 is not associated with response to bisoprolol in people with Hypertension as compared to CYP3A5 *1.
Notes: There was no significant change in bisoprolol concentrations nor various blood pressure measurements due to CYP3A5 genotype categories.
Article: Pharmacogenetics of tenofovir clearance among Southern Africans living with HIV
Gene: FARP1, STK24
Variant/haplotype: rs58896682
Drug(s): tenofovir
Phenotype category: Metabolism/PK
Significant: no
Association: Allele ATTTATTTT is not associated with clearance of tenofovir in people with HIV Infections as compared to allele ATTTT.
Notes: Significance threshold was set at 6.0E-7. Listed as rs144511092 in the paper, which has been merged into rs58896682.
Article: Pharmacogenetics of tenofovir clearance among Southern Africans living with HIV
Gene: IFNL3, IFNL4
Variant/haplotype: rs8099917
Drug(s): tenofovir
Phenotype category: Metabolism/PK
Significant: no
Association: Allele G is not associated with clearance of tenofovir in people with HIV Infections as compared to allele T.
Notes: Significance threshold was set at 4.5E-3.
Article: Effects of the CYP3A4*1B Genetic Polymorphism on the Pharmacokinetics of Tacrolimus in Adult Renal Transplant Recipients: A Meta-Analysis
Gene: CYP3A4
Variant/haplotype: rs2740574
Drug(s): tacrolimus
Phenotype category: Dosage
Significant: yes
Association: Allele C is associated with increased dose of tacrolimus in people with Kidney Transplantation as compared to allele T.
Notes: The C allele (CYP3A4 *1B) was associated with a higher dose of tacrolimus at 7 days ((weight mean difference) WMD (-0.048); 95% CI: (-0.083_ -0.014), 6 months (WMD -0.058); 95% CI (-0.081_ -0.036), and 1 year (WMD -0.096_-0.027) post-transplantation.
Article: CYP2D6 Haplotype Determination Using Long Range Allele-Specific Amplification: Resolution of a Complex Genotype and a Discordant Genotype Involving the CYP2D6*59 Allele
Gene: CYP2D6
Variant/haplotype: CYP2D6*2, CYP2D6*59
Drug(s): dextromethorphan
Phenotype category: Metabolism/PK
Significant: not stated
Association: CYP2D6 *2/*59 (assigned as normal metabolizer phenotype) is not associated with decreased metabolism of dextromethorphan.
Notes: A subject with the *2/*59 diplotype had a dextromethorphan/dextrorphan urinary metabolic ratio of 0.024 with was consistent with extensive metabolizer phenotype.
Article: Pharmacogenetics of Asthma Controller Treatment
Gene: CHRM2
Variant/haplotype: rs6962027
Drug(s): fluticasone/salmeterol
Phenotype category: Efficacy
Significant: yes
Association: Allele A is associated with response to fluticasone/salmeterol in people with Asthma as compared to allele T.
Notes: The "major" allele is associated with increased response.  It is not clear whether that is A or T on the positive chromosomal strand.