shlokn/autogkb huggingface dataset:
Article: Association between opioid receptor mu 1 (OPRM1) gene polymorphisms and tobacco and alcohol consumption in a Spanish population
Gene: OPRM1
Variant/haplotype: rs10485057
Drug(s): ethanol
Phenotype category: Dosage
Significant: yes
Association: Genotype AA is associated with increased dose of ethanol as compared to genotype AG.
Notes: Subjects with the AA genotype has a significantly increased pure alcohol intake and were significantly more likely to be alcohol consumers compared to subjects with the AG genotype.
Article: Hypertension Susceptibility Loci and Blood Pressure Response to Antihypertensives – Results from the Pharmacogenomic Evaluation of Antihypertensive Responses (PEAR) Study
Gene: MOV10
Variant/haplotype: rs2932538
Drug(s): atenolol
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to atenolol in people with Hypertension as compared to allele G.
Notes: Not significant when using Bonferroni-corrected alpha of 0.0014. Response was assessed by change in systolic blood pressure (SBP) and diastolic blood pressure (DBP) after 9 weeks of treatment. Please note alleles have been complemented to the plus chromosomal strand.
Article: A genome-wide association study of plasma concentrations of warfarin enantiomers and metabolites in sub-Saharan black-African patients
Gene: GRID2
Variant/haplotype: rs558364281
Drug(s): 6-hydroxy r-warfarin, 6-hydroxy s-warfarin
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele G is associated with increased concentrations of 6-hydroxy r-warfarin and 6-hydroxy s-warfarin in people with Atrial Fibrillation, venous thromboembolism or Heart Valve Diseases as compared to allele A.
Notes: measured as increased RS-6OH-warfarin and using a genome wide significance threshold of < 3.846 × 10−9.
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: UGT1A1
Variant/haplotype: rs887829
Drug(s): 2-hydroxyatorvastatin lactone, 4-hydroxyatorvastatin lactone, atorvastatin lactone
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype CC is associated with decreased concentrations of 2-hydroxyatorvastatin lactone, 4-hydroxyatorvastatin lactone and atorvastatin lactone in people with Coronary Disease as compared to genotypes CT + TT.
Notes: Comparison was for "UGT1A1 CC and UGT1A3 no *2 allele" vs "UGT1A1 CT or TT and/or UGT1A3 one or two *2 alleles" and sum of lactones in plasma or muscle. (Supplementary 2-Table 2. )
Article: The effects of CYP2D6 and CYP3A activities on the pharmacokinetics of immediate release oxycodone
Gene: CYP2D6
Variant/haplotype: CYP2D6 ultrarapid metabolizer genotype
Drug(s): noroxycodone
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2D6 ultrarapid metabolizer is associated with decreased exposure to noroxycodone in healthy individuals as compared to CYP2D6 normal metabolizer.
Notes: AUC for noroxycodone was significantly lower in poor metabolizers than in extensive metabolizers. However, differences in Cmax between the two metabolizer genotypes failed to reach significance.
Article: Pharmacogenetic association with early response to intravitreal ranibizumab for age-related macular degeneration in a Korean population
Gene: KDR
Variant/haplotype: rs2071559
Drug(s): ranibizumab
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to ranibizumab in people with Macular Degeneration as compared to allele G.
Notes: Age-related macular degeneration. No significant differences in best-corrected visual acuity (BCVA) changes or central subfield macular thickness (CSMT) changes were seen between baseline and 3 or 6 months of treatment between any of the genotypes.
Article: Potential of a Pharmacogenetic-Guided Algorithm to Predict Optimal Warfarin Dosing in a High-Risk Hispanic Patient: Role of a Novel NQO1*2 Polymorphism
Gene: NQO1
Variant/haplotype: rs1800566
Drug(s): warfarin
Phenotype category: Efficacy
Significant: not stated
Association: Allele A is associated with decreased response to warfarin in women with Thrombosis as compared to allele G.
Notes: Case study of one woman who developed deep abdominal vein thrombosis secondary to the use of contraceptives.
Article: The effect of CYP2C9 and VKORC1 genetic polymorphisms on warfarin dose requirements in a pediatric population
Gene: VKORC1
Variant/haplotype: rs9923231
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Allele T is associated with decreased dose of warfarin in children as compared to allele C.
Notes: The average daily warfarin dose required for maintenance therapy in patients with T allele was 4.26±1.24, whereas it was 4.80±1.55in those without this mutation.
Article: Underlying genetic structure impacts the association between CYP2B6 polymorphisms and response to efavirenz and nevirapine
Gene: CYP2B6
Variant/haplotype: rs34097093
Drug(s): efavirenz, non-nucleoside reverse transcriptase inhibitors
Phenotype category: Efficacy
Significant: no
Association: Allele C is not associated with response to efavirenz or non-nucleoside reverse transcriptase inhibitors in women with HIV Infections as compared to genotype TT.
Article: No Clinical Impact of CYP3A5 Gene Polymorphisms on the Pharmacokinetics and/or Efficacy of Maraviroc in Healthy Volunteers and HIV‐1–Infected Subjects
Gene: CYP3A5
Variant/haplotype: CYP3A5 poor metabolizers
Drug(s): maraviroc
Phenotype category: Metabolism/PK
Significant: no
Association: CYP3A5 poor metabolizer is not associated with concentrations of maraviroc in people with HIV Infections as compared to CYP3A5 intermediate metabolizer.
Notes: There was no significant difference in average maraviroc plasma concentrations between CYP3A5 intermediate and poor metabolizers.
Article: Pharmacokinetic profiles of significant adverse events with crizotinib in Japanese patients with ABCB1 polymorphism
Gene: ABCB1
Variant/haplotype: rs1045642
Drug(s): crizotinib
Phenotype category: Metabolism/PK
Significant: no
Association: Genotype AA is associated with increased exposure to crizotinib in people with.
Notes: There was only one individual who was AA at all three locations that define *2 (rs1128503, rs2032582 and rs1045642). Individuals who were AA at one location (n=3) also had slightly increased exposure compared to "wild type or heterozygotes" (n=4). Increased exposure was significantly associated with toxicity. (alleles complemented to plus chromosomal strand)
Article: Functional characterization of novel rare CYP2A6 variants and potential implications for clinical outcomes
Gene: CYP2A6
Variant/haplotype: rs61605570
Drug(s): nicotine
Phenotype category: Metabolism/PK
Significant: not stated
Association: Allele T is associated with decreased metabolism of nicotine as compared to allele A.
Notes: Assigned as loss-of-function following in vitro assessments, in vivo associations and variant construct functional assignments. Please note that alleles have been complemented to the positive strand.
Article: Pharmacogenetic analysis of opioid dependence treatment dose and dropout rate
Gene: OPRM1
Variant/haplotype: rs1799971
Drug(s): buprenorphine, methadone
Phenotype category: Efficacy
Significant: no
Association: Genotypes AA + AG is not associated with response to buprenorphine or methadone in people with Opioid-Related Disorders as compared to genotype AA.
Notes: Response defined by changes in the rate of dropout from treatment between genotypes.
Article: Comparison of the effect of enalapril and losartan in conjunction with surgical coronary revascularisation versus revascularisation alone on systemic endothelial function
Gene: ACE
Variant/haplotype: rs1799752
Drug(s): enalapril, losartan
Phenotype category: Efficacy
Significant: yes
Association: Genotype ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC is associated with increased response to enalapril and losartan in men with Coronary Disease as compared to genotypes ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC/del + del/del.
Notes: Patients with the ATA.../ATA... genotype had greater percent improvement in brachial artery flow mediated dilation (FMD; a way to analyze endothelial function) after enalapril or losartan treatment for 5 months, as compared to those with the remaining genotypes. Please note that patients underwent coronary artery bypass graft surgery 2 months into treatment with these drugs.
Article: Integrative genomic analysis of methylphenidate response in attention-deficit/hyperactivity disorder
Gene: CORO7
Variant/haplotype: rs3810818
Drug(s): methylphenidate
Phenotype category: Efficacy
Significant: no
Association: Allele A is associated with increased response to methylphenidate in people with Attention Deficit Disorder with Hyperactivity.
Notes: The authors carried out a GWAS in a Spanish cohort of pediatric patients, than performed a meta-analysis using data from the Spanish cohort and data from a Brazilian adult patient cohort.; This variant was not significant in the meta-analysis after Bonferroni correction had been applied, and was nominally significant (i.e did not reach genome-wide significance) in the initial GWAS in the Spanish cohort.; Response was measured on the Clinical Global Impression-Improvement scale (CGI-I). A CGI-I score of two points or less after eight weeks of treatment was considered a good response.
Article: Polymorphic Variants of SCN1A and EPHX1 Influence Plasma Carbamazepine Concentration, Metabolism and Pharmacoresistance in a Population of Kosovar Albanian Epileptic Patients
Gene: SCN1A
Variant/haplotype: rs3812718
Drug(s): carbamazepine
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype TT is associated with increased dose of carbamazepine in people with Epilepsy as compared to genotypes CC + CT.
Notes: The authors evaluated daily dose and maintenance dose and calculated the means for each genotype. The TT genotype is associated with a higher mean daily dose and higher mean maintenance dose of carbamazepine (CBZ). Mean CBZ daily dose (mg/day) for the TT genotype was 694 vs. 509-531 for the CT and CC genotypes, respectively. Mean CBZ maintenance dose for the TT genotype was 10.48 versus 7.79-7.96 for the CC and CT genotypes, respectively. Please note: alleles have been complemented to the + chromosomal strand.
Article: Effects of SCN1A and GABA Receptor Genetic Polymorphisms on Carbamazepine Tolerability and Efficacy in Chinese Patients with Partial Seizures: 2‐Year Longitudinal Clinical Follow‐Up
Gene: SCN1A
Variant/haplotype: rs2298771
Drug(s): carbamazepine
Phenotype category: Efficacy
Significant: yes
Association: Genotype TT is associated with increased response to carbamazepine in people with Epilepsy as compared to genotypes CC + CT.
Notes: Patients with the TT genotype were more likely to have a "good" response to carbamazepine. A "good" response was classified as seizure free over 24 months of treatment. A "bad" response was classified as anything other than seizure free. This significant result was only seen for months 3-15 of treatment. No significant result was seen for months 15-24 months of treatment. Please note alleles have been complemented to the plus chromosomal strand.
Article: The effect of genetic variation in PCSK9 on the LDL-cholesterol response to statin therapy
Gene: PCSK9
Variant/haplotype: rs11591147
Drug(s): hmg coa reductase inhibitors
Phenotype category: Efficacy
Significant: yes
Association: Allele T is associated with increased response to hmg coa reductase inhibitors in people with Hypercholesterolemia as compared to genotype GG.
Notes: There was a 55.6% greater reduction in low-density lipoprotein cholesterol (LDL-C) in carriers of the T alleles as compared to those with the GG genotype. Note that carriers of the T allele were also associated with significantly decreased LDL-C levels at baseline (p=0.00022), though the result for response to statins was adjusted for this association. A p-value <0.0045 was considered statistically significant. The authors do not specify the composition of T allele carriers (i.e. heterozygotes, homozygotes, or both).
Article: Influence of ABCB1 and ABCG2 polymorphisms on doxorubicin disposition in Asian breast cancer patients
Gene: ABCB1
Variant/haplotype: rs1045642
Drug(s): doxorubicin
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype AA is associated with decreased metabolism of doxorubicin in people with Breast Neoplasms as compared to genotype GG.
Notes: Significance given for the haplotype of ABCB1 c.1236C>T, c.2677G>A/T, and c.3435C>T (rs1128503, rs2032582 and rs1045642) which was associated with increased drug exposure and reduced clearance. Patients harboring the CC-GG-CC genotypes had significantly lower peak plasma concentrations of doxorubicinol compared to patients who had TT-TT-TT genotypes (P = 0.03).
Article: Brain/blood ratios of methadone and ABCB1 polymorphisms in methadone-related deaths
Gene: ABCB1
Variant/haplotype: rs2032582
Drug(s): methadone
Phenotype category: Metabolism/PK
Significant: no
Association: Allele A is not associated with concentrations of methadone as compared to allele C.
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: Effect of Genetic Variants on Rosuvastatin Pharmacokinetics in Healthy Volunteers: Involvement of ABCG2, SLCO1B1 and NAT2
Gene: ABCG2
Variant/haplotype: ABCG2 poor metabolizer
Drug(s): rosuvastatin
Phenotype category: Metabolism/PK
Significant: yes
Association: ABCG2 poor metabolizer and reduced metabolizers is associated with increased dose-adjusted trough concentrations of rosuvastatin in healthy individuals as compared to ABCG2 normal metabolizer.
Notes: "A significant increase was observed in AUC∞/DW(803.58±256.17h*ng*kg/mL*mg, p<0.001; pmv<0.001,β=0.467,R2=0.264),AUC72h/DW(766.54±289.52h*ng*kg/mL*mg, p<0.001;pmv<0.001,β=0.449,R2=0.302)andCmax/DW(76.98±31.87ng*kg/mL*mg, p<0.001; pmv<0.001,β=0.480,R2=0.292) in decreased function(DF)+poor function(PF) volunteers forABCG2 transporter in comparison to normal function(NF) volunteers(Table3)." Authors reference CPIc and Dutch guidelines but do not specify which variants were measured in ABCG2.
Article: Oxidative Stress-Related Genetic Polymorphisms Are Associated with the Prognosis of Metastatic Gastric Cancer Patients Treated with Epirubicin, Oxaliplatin and 5-Fluorouracil Combination Chemotherapy
Gene: NQO1
Variant/haplotype: rs10517
Drug(s): epirubicin, fluorouracil, oxaliplatin
Phenotype category: Efficacy
Significant: not stated
Association: Allele G is not associated with response to epirubicin, fluorouracil and oxaliplatin in people with Neoplasm Metastasis and Stomach Neoplasms.
Notes: Please note: alleles have been complemented to the + chromosomal strand.
Article: Pharmacogenetics of tenofovir clearance among Southern Africans living with HIV
Variant/haplotype: rs9305223
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 C.
Notes: Significance threshold was set at 5E-9. This variant was in strong linkage disequilibrium with rs4816969 and rs2226443.
Article: Association studies of dopamine synthesis and metabolism genes with multiple phenotypes of heroin dependence
Gene: DBH
Variant/haplotype: rs5320
Drug(s): methadone
Phenotype category: Dosage
Significant: no
Association: Allele A is not associated with dose of methadone in people with Heroin Dependence as compared to allele G.
Article: Genetic variants in combination with early partial improvement as a clinical utility predictor of treatment outcome in major depressive disorder: the result of two pooled RCTs
Gene: SLC6A4
Variant/haplotype: SLC6A4 L allele-rs25531C, SLC6A4 L allele-rs25531T
Drug(s): milnacipran
Phenotype category: Efficacy
Significant: no
Association: SLC6A4 L allele-rs25531T is not associated with response to milnacipran in people with Depressive Disorder, Major as compared to SLC6A4 L allele-rs25531C/L allele-rs25531C.
Notes: The 5-HTTLPR + rs25531 was not associated with significant differences in HAMD score change at week 6 in patients receiving milnacipran. LA allele vs S/S (S=LG)
Article: CYP2C19 and CYP2J2 genotypes predict praziquantel plasma exposure among Ethiopian school-aged children
Gene: CYP2J2
Variant/haplotype: rs890293
Drug(s): trans 4-hydroxypraziquantel
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotypes AA + AC is associated with increased concentrations of trans 4-hydroxypraziquantel in children with Schistosomiasis as compared to genotype CC.
Notes: Alleles complemented. "Our study also found a borderline association between CYP2J2 genotype (p = 0.05) and PZQ plasma concentration, where higher PZQ plasma concentrations were observed among CYP2J2 *1/*1 genotypes compared to CYP2J2 *7 carriers. CYP2J2 genotype was significantly associated with both trans-4-OH-PZQ/PZQ and cis 4-OH-PZQ/PZQ) the metabolic ratios, being higher among CYP2J2 *7 carriers than the wild type (CYP2J2 *1/*1). The CYP2J2 *7 variant allele is reported to be associated with increased enzyme activity, which is in line with our findings." *7 mapped to  rs890293A.
Article: DRD2, DRD3, and HTR2A Single-Nucleotide Polymorphisms Involvement in High Treatment Resistance to Atypical Antipsychotic Drugs
Gene: DRD3
Variant/haplotype: rs6280
Drug(s): antipsychotics
Phenotype category: Efficacy
Significant: yes
Association: Genotypes CT + TT is associated with increased resistance to antipsychotics in people with Mood Disorders or Schizophrenia as compared to genotype CC.
Notes: "The DRD3 rs6280 C|T vs. C|C genotype (OR = 22.195; B = 3.1; p = 0.002) and the T|T vs C|C genotype (OR = 18.47; B = 2.916; p = 0.003) significantly predicted the HTR group membership. In addition, the DRD3 rs6280 C|C vs. T|T genotype inversely predicted the HTR group membership (OR = 0.054; B = −2.916; p = 0.003)." " high treatment resistance (HTR) group (current treatment with two SGAs, or clozapine, or classic neuroleptics for a failure of previous SGAs trials"
Article: Genetic Variation in CYP3A43 Explains Racial Difference in Olanzapine Clearance
Variant/haplotype: rs1492899
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 T.
Article: Tell-Tale SNPs: The Role of CYP2B6 in Methadone Fatalities
Gene: CYP2B6
Variant/haplotype: rs4803419
Drug(s): methadone
Phenotype category: Metabolism/PK
Significant: no
Association: Allele T is not associated with concentrations of methadone as compared to allele C.
Article: Relationship of CYP3A5 genotype and ABCB1 diplotype to tacrolimus disposition in Brazilian kidney transplant patients
Gene: CYP3A5
Variant/haplotype: CYP3A5*1, CYP3A5*3
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP3A5 *3/*3 is associated with decreased metabolism of tacrolimus in people with Kidney Transplantation as compared to CYP3A5 *1/*1 + *1/*3.
Notes: 3 - 12 months post-transplant. Patients with the *3/*3 genotype had statistically significantly increased trough concentrations (using chi-squared analysis) and dose-adjusted trough concentrations (using multivariate linear regression) of tacrolimus as compared to patients with the *1/*1 or *1/*3 genotype.
Article: Genetic Variation in BDNF is Associated with Antipsychotic Treatment Resistance in Patients with Schizophrenia
Gene: BDNF
Variant/haplotype: rs11030104
Drug(s): antipsychotics
Phenotype category: Efficacy
Significant: yes
Association: Genotypes AG + GG is associated with increased resistance to antipsychotics in people with Schizophrenia as compared to genotype AA.
Notes: The G allele is associated with increased odds of resistance to antipsychotic treatment. Resistance was assessed by whether patients were taking clozapine, since clozapine is indicated for patients poorly responsive or resistant to first-line treatments. Please note alleles have been complemented to the plus chromosomal strand.
Article: Pharmacogenetics of tenofovir clearance among Southern Africans living with HIV
Gene: C1QTNF7
Variant/haplotype: rs10032941
Drug(s): tenofovir
Phenotype category: Metabolism/PK
Significant: no
Association: Allele C is not associated with clearance of tenofovir in people with HIV Infections as compared to allele T.
Notes: Significance threshold was set at 6E-7.
Article: Childhood asthma exacerbations and the Arg-16 beta2 receptor polymorphism: a meta-analysis stratified by treatment
Gene: ADRB2
Variant/haplotype: rs1042713
Drug(s): corticosteroids, Leukotriene receptor antagonists
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to corticosteroids and Leukotriene receptor antagonists in children with Asthma as compared to genotype GG.
Article: Haplotypes of P2RX7 gene polymorphisms are associated with both cold pain sensitivity and analgesic effect of fentanyl
Gene: P2RX7
Variant/haplotype: rs1718125
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. Please note that alleles have been complemented to the positive strand.
Article: Therapeutic efficacy of generic artemether–lumefantrine in the treatment of uncomplicated malaria in Ghana: assessing anti-malarial efficacy amidst pharmacogenetic variations
Gene: CYP2B6
Variant/haplotype: CYP2B6*1, CYP2B6*6, CYP2B6*18
Drug(s): desbutyl lumefantrine, lumefantrine
Phenotype category: Metabolism/PK
Significant: no
Association: CYP2B6 *1/*18 + *1/*6 + *6/*6 + *18/*18 is not associated with decreased concentrations of desbutyl lumefantrine or lumefantrine in people with Malaria, Falciparum as compared to CYP2B6 *1/*1.
Notes: "Plasma lumefantrine and DBL in relation to CYP2B6 is shown in Fig. 4. No significant difference was observed between normal expressor (*1/*1) and reduced expressors. However, it was observed that the median plasma concentration for normal expressor *1/*1 was relatively higher for day 7 plasma lumefantrine and desbutyl lumefantrine in comparison to reduced expressors."
Article: No major role of norepinephrine transporter gene variations in the cardiostimulant effects of MDMA
Gene: SLC6A2
Variant/haplotype: rs168924
Drug(s): 3,4-methylenedioxymethamphetamine
Phenotype category: Other
Significant: no
Association: Allele G is not associated with response to 3,4-methylenedioxymethamphetamine as compared to allele A.
Article: A pharmacogenetic study of docetaxel and thalidomide in patients with castration-resistant prostate cancer using the DMET genotyping platform
Gene: PPARD
Variant/haplotype: rs1883322
Drug(s): docetaxel, thalidomide
Phenotype category: Efficacy
Significant: yes
Association: Allele C is associated with increased response to docetaxel and thalidomide in people with Prostatic Neoplasms as compared to allele T.
Notes: (allele inferred by frequency comparison with dbSNP, actual base not listed in paper, dbSNP changed designation of this allele from G/A to C/T at build 132)
Article: DPYD Variants as Predictors of 5-fluorouracil Toxicity in Adjuvant Colon Cancer Treatment (NCCTG N0147)
Gene: DPYD
Variant/haplotype: rs3918290
Drug(s): fluorouracil
Phenotype category: Efficacy
Significant: no
Association: Genotype CT is not associated with response to fluorouracil in people with Colonic Neoplasms as compared to genotype CC.
Notes: The T allele was not associated with disease-free survival time. Allele referred to in the paper as the DPYD*2A allele.