shlokn/autogkb huggingface dataset:
Article: The correlation between CYP2D6 isoenzyme activity and haloperidol efficacy and safety profile in patients with alcohol addiction during the exacerbation of the addiction
Gene: CYP2D6
Variant/haplotype: rs3892097
Drug(s): haloperidol
Phenotype category: Efficacy
Significant: yes
Association: Genotype CC is associated with decreased response to haloperidol in men with Alcohol-Related Disorders, Alcoholic psychosis NOS and Alcoholism as compared to genotype CT.
Notes: as measured by a smaller difference in score between day 0 and day 5 on SoPA, Scale of Pathological Addiction; HARS, Hamilton Anxiety Rating Scale; BAI, Beck Anxiety Inventory; CARS, Covi Anxiety Scale; ZARS, Zung Self-Rating Anxiety Scale; SARS, Sheehan Clinical Anxiety Rating Scale; HDRS, Hamilton Rating Scale for Depression.
Article: Integrative genomic analysis of methylphenidate response in attention-deficit/hyperactivity disorder
Gene: GGH
Variant/haplotype: rs17279558
Drug(s): methylphenidate
Phenotype category: Efficacy
Significant: no
Association: Allele C 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: OPRM1, OPRK1 and COMT Genetic Polymorphisms Associated with Opioid Effects on Experimental Pain: A Randomized, Double-Blind, Placebo-Controlled Study
Gene: COMT
Variant/haplotype: rs4680
Drug(s): butorphanol
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to butorphanol in healthy individuals as compared to allele G.
Notes: Study-wide significance was set to p<0.017.
Article: Cytochrome P450 (CYP2C9*2,*3) & vitamin-K epoxide reductase complex (VKORC1 -1639G<A) gene polymorphisms & their effect on acenocoumarol dose in patients with mechanical heart valve replacement
Gene: CYP2C9
Variant/haplotype: CYP2C9*1, CYP2C9*2
Drug(s): acenocoumarol
Phenotype category: Dosage
Significant: yes
Association: CYP2C9 *2 is associated with decreased dose of acenocoumarol as compared to CYP2C9 *1.
Notes: The CYP2C9*2, *3 and VKORC1 rs9923231 are analyzed together. Patients carrying any of the variant alleles was 34% among those receiving a low dose of =20 mg/wk while it was 13.8 per cent in those receiving >20 mg/wk (P=0.014).
Article: Atazanavir pharmacokinetics in genetically determined CYP3A5 expressors versus non-expressors
Gene: ABCB1
Variant/haplotype: rs1045642
Drug(s): ritonavir
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype AA is associated with increased clearance of ritonavir in healthy individuals as compared to genotypes AG + GG.
Notes: For the haplotype "1236C/2677G/3435C" "overall ritonavir CL/F was ∼1.9-fold faster in subjects with zero versus two CGC haplotype""and was 1.47-fold faster in subjects with zero versus one CGC copy". In this two-phase study, healthy participants were given atazanavir only for 7 days and then were co-administered ritonavir as a booster for days 8-14. The results here are for day 8-14 (atazanavir plus ritonavir).
Article: PXR and CAR single nucleotide polymorphisms influence plasma efavirenz levels in South African HIV/AIDS patients
Gene: NR1I2
Variant/haplotype: rs3732356
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: no
Association: Genotype GG is not associated with metabolism of efavirenz in people with HIV Infections as compared to genotype TT.
Notes: Plasma levels of efavirenz were not statistically significantly different between TT, GT, GG genotypes of this SNP.
Article: Pharmacogenetic association of the APOA1/C3/A4/A5 gene cluster and lipid responses to fenofibrate: the Genetics of Lipid-Lowering Drugs and Diet Network study
Gene: APOC3
Variant/haplotype: rs2542051
Drug(s): fenofibrate
Phenotype category: Efficacy
Significant: no
Association: Genotypes AC + CC are not associated with response to fenofibrate in people with Hypertriglyceridemia as compared to genotype AA.
Notes: No significant difference in the change in plasma triglyceride (TG) or high-density lipoprotein (HDL) levels between genotypes was seen, after three weeks of treatment with fenofibrate.
Article: A GENOME-WIDE ASSOCIATION STUDY OF BRONCHODILATOR RESPONSE IN LATINOS IMPLICATES RARE VARIANTS
Gene: CRHR2
Variant/haplotype: rs73294475
Drug(s): salbutamol
Phenotype category: Efficacy
Significant: yes
Association: Genotype CT is associated with increased response to salbutamol in children with Asthma as compared to genotype TT.
Notes: The allele associated with increased response and low frequency is not explicitly stated.  Response is increased for carriers of the rare, minor allele.  GALAII genotyping was done using the Affymetrix LAT1 Array, which was designed to capture Latino population variation.  This was assessed as a replication attempt for a previously reported association of a different CRHR2 SNP with response to bronchodilators.  Bonferroni correction was performed according to the number of SNPs included that are within 50 kb up and downstream of CRHR2.
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): risperidone
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotypes CG + GG is associated with increased concentrations of risperidone in men with Schizophrenia as compared to genotype CC.
Notes: At 6 weeks, "statistically significant difference in plasma concentration between genotypes at the rs6295 locus (t = 2.113, P = 0.048) (Table 4)."
Article: Influence of Cytochrome P450 2C19 Genotype on Helicobacter pylori Proton Pump Inhibitor-Amoxicillin-Clarithromycin Eradication Therapy: A Meta-Analysis
Gene: CYP2C19
Variant/haplotype: CYP2C19 normal metabolizer genotype
Drug(s): amoxicillin, clarithromycin, omeprazole
Phenotype category: Efficacy
Significant: yes
Association: CYP2C19 normal metabolizer is associated with decreased clinical benefit to amoxicillin, clarithromycin and omeprazole in people with Helicobacter Infections as compared to CYP2C19 poor metabolizer.
Notes: "RR of failed eradication in CYP2C19 EMs compared with PMs was 1.66 (95% CI: 1.12–2.46, p = 0.01)."
Article: Effect of zinc supplementation on insulin secretion: interaction between zinc and SLC30A8 genotype in Old Order Amish
Gene: SLC30A8
Variant/haplotype: rs13266634
Drug(s): insulin recombinant, zinc acetate
Phenotype category: Efficacy
Significant: yes
Association: Genotypes CT + TT is associated with increased response to insulin recombinant and zinc acetate in healthy individuals as compared to genotype CC.
Notes: The aim of the study was to determine whether zinc supplements improved insulin response in people with the CT+TT genotypes as compared to people with the CC genotypes. After being administered insulin without zinc, fasting characteristics were similar across genotypes except for C-peptide:insulin ratio, insulin AUC at 5 and 10 minutes, which were significantly lower in the CC genotype group. The proinsulin:insulin ratio at 5 and 10 minutes after insulin and glucose as well as the C-peptide:insulin ratio at 5 and 10 minutes after insulin and glucose were also lower in the CC genotype group compared to the CT+TT genotype group.   People with the CT+TT genotypes had significantly improved responses to insulin when it was supplemented with zinc acetate as compared to CC genotypes.
Article: Genetic Variation in CYP3A43 Explains Racial Difference in Olanzapine Clearance
Variant/haplotype: rs2527894
Drug(s): olanzapine
Phenotype category: Metabolism/PK
Significant: no
Association: Allele A is not associated with clearance of olanzapine in people with Schizophrenia as compared to allele G.
Article: Optimizing the initial tacrolimus dosage in Chinese children with lung transplantation within normal hematocrit levels
Gene: CYP3A5
Variant/haplotype: CYP3A5*1
Drug(s): tacrolimus
Phenotype category: Dosage
Significant: not stated
Association: CYP3A5 *1 is associated with increased dose of tacrolimus in children with lung transplantation.
Notes: "For children with lung transplantation who do not carry the CYP3A5*1 gene and have coadministration with voriconazole, tacrolimus dosages of 0.01 and 0.02 mg/kg/day split into two doses are recommended for children weighing 10-17 and 17-40 kg, respectively. For children with lung transplantation who carry the CYP3A5*1 gene and have coadministration with voriconazole, a tacrolimus dosage of 0.02 mg/kg/day split into two doses is recommended for children weighing 10-40 kg."
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: rs1165016
Drug(s): antiepileptics
Phenotype category: Efficacy
Significant: no
Association: Allele C is not associated with response to antiepileptics in people with Epilepsy, Generalized as compared to allele T.
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: ABCC3 and OCT1 genotypes influence pharmacokinetics of morphine in children
Gene: ABCB1
Variant/haplotype: rs1045642
Drug(s): morphine
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype AA is associated with increased metabolism of morphine in children as compared to genotypes AG + GG.
Notes: Children with the AA genotype had higher levels of morphine-3-glucuronide metabolite formation - no difference between genotypes of this SNP were seen for morphine-6-glucuronide formation or morphine clearance. Alleles have been complemented to the plus chromosomal strand.
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: rs2230808
Drug(s): fenofibrate
Phenotype category: Efficacy
Significant: yes
Association: Genotype CC is associated with increased response to fenofibrate in people with Hypertriglyceridemia as compared to genotype TT.
Notes: Patients with the CC genotype had a greater small high-density lipoprotein (HDL) particle concentration (units = umol/L) and a greater total HDL particle concentration after fenofibrate treatment for 3 weeks, as compared to patients with the TT genotype.
Article: Genetic Variation in BDNF is Associated with Antipsychotic Treatment Resistance in Patients with Schizophrenia
Gene: BDNF-AS
Variant/haplotype: rs10501087
Drug(s): antipsychotics
Phenotype category: Efficacy
Significant: yes
Association: Genotypes CC + CT is associated with increased resistance to antipsychotics in people with Schizophrenia as compared to genotype TT.
Notes: The C 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.
Article: Association between opioid receptor mu 1 (OPRM1) gene polymorphisms and tobacco and alcohol consumption in a Spanish population
Gene: OPRM1
Variant/haplotype: rs1799971
Drug(s): ethanol
Phenotype category: Dosage
Significant: yes
Association: Genotypes AG + GG are associated with decreased dose of ethanol in women as compared to genotype AA.
Notes: Women who carried the G allele were significantly less likely to be alcohol consumers than other groups.
Article: The International SSRI Pharmacogenomics Consortium (ISPC): a genome-wide association study of antidepressant treatment response
Variant/haplotype: rs13015447
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 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 polymorphisms in P2Y12 receptor signaling pathway on antiplatelet response to clopidogrel in coronary heart disease
Gene: PIK3CA
Variant/haplotype: rs77576241
Drug(s): clopidogrel
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with increased resistance to clopidogrel in people with Coronary Disease as compared to allele C.
Article: Genetic Variation in CYP3A43 Explains Racial Difference in Olanzapine Clearance
Variant/haplotype: rs2527887
Drug(s): olanzapine
Phenotype category: Metabolism/PK
Significant: no
Association: Allele A is not associated with clearance of olanzapine in people with Schizophrenia as compared to allele T.
Article: The Relation Between CYP2C19 Genotype and Phenotype in Stented Patients on Maintenance Dual Antiplatelet Therapy
Gene: CYP2C19
Variant/haplotype: rs12248560
Drug(s): aspirin, clopidogrel
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with increased response to aspirin and clopidogrel in people with Coronary Artery Disease.
Notes: These patients had coronary arterial stenting. Comparison was T carriers (TT + CT) vs non-carriers (CC) but the template doesn't accommodate this choice.  *17 SNP.  ADP-induced ex vivo platelet aggregation was measured.  [stat_test: chi-square]
Article: Pharmacogenetics predictors of methylphenidate efficacy in childhood ADHD
Gene: ADGRL3
Variant/haplotype: rs6551665
Drug(s): methylphenidate
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to methylphenidate in children with Attention Deficit Disorder with Hyperactivity as compared to allele G.
Article: ABC Transporter Polymorphisms are Associated with Irinotecan Pharmacokinetics and Neutropenia
Gene: ABCC1
Variant/haplotype: rs215095
Drug(s): SN-38
Phenotype category: Metabolism/PK
Significant: no
Association: Genotypes AG + GG are not associated with exposure to SN-38 in people with Colorectal Neoplasms as compared to genotype AA.
Notes: AUC of SN-38 was adjusted for irinotecan dose.
Article: Sodium channel mutation SCN1A T875M, D188V and associated dysfunction with drug resistant epilepsy
Gene: SCN1A
Variant/haplotype: rs121918623
Drug(s): antiepileptics
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with increased resistance to antiepileptics in people with Epilepsy as compared to allele G.
Notes: Alleles complemented. "Whereas, on comparing the distribution of SCN1A rs121918623 C/T* genotypic variants, no significant difference was observed across both the study groups, with a P value of 1.00 (Table 2)."
Article: CALCA and TRPV1 genes polymorphisms are related to a good outcome in female chronic migraine patients treated with OnabotulinumtoxinA
Gene: MEF2D
Variant/haplotype: rs1050316
Drug(s): botulinum toxin type a
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with response to botulinum toxin type a in women with Migraine NOS as compared to allele G.
Notes: No significant difference in allele frequency between responders and non-responders.
Article: Genetic markers in CYP2C19 and CYP2B6 for prediction of cyclophosphamide's 4‐hydroxylation, efficacy and side effects in Chinese patients with systemic lupus erythematosus
Gene: CYP2B6
Variant/haplotype: rs3745274
Drug(s): cyclophosphamide
Phenotype category: Metabolism/PK
Significant: no
Association: Allele G is not associated with metabolism of cyclophosphamide in people with as compared to allele T.
Article: Association of corticotropin releasing hormone receptor 2 (CRHR2) genetic variants with acute bronchodilator response in asthma
Gene: CRHR2
Variant/haplotype: rs255100
Drug(s): salbutamol
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with decreased response to salbutamol in people with Asthma as compared to allele T.
Notes: in replication cohort with adult patients.
Article: Genetic variation in OPRD1 and the response to treatment for opioid dependence with buprenorphine in European American females
Gene: OPRD1
Variant/haplotype: rs581111
Drug(s): buprenorphine, methadone
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to buprenorphine or methadone in men with Opioid-Related Disorders as compared to allele G.
Notes: Opioid dependence. This genetic variant did not have a significant effect on the percentage of opioid-positive urine drug screens or missing urine drug screens in males. Note that significant results were seen for females. Patients were treated with buprenorphine or methadone for 24 weeks.
Article: Meta-Analysis on Pharmacogenetics of Platinum-Based Chemotherapy in Non Small Cell Lung Cancer (NSCLC) Patients
Gene: ERCC2
Variant/haplotype: rs1799793
Drug(s): Platinum compounds
Phenotype category: Efficacy
Significant: no
Association: Allele C is not associated with increased response to Platinum compounds in people with Carcinoma, Non-Small-Cell Lung as compared to allele T.
Notes: No significant relationship between genotype and drug response was detected.
Article: IL-3 and CTLA4 gene polymorphisms may influence the tacrolimus dose requirement in Chinese kidney transplant recipients
Gene: CTLA4
Variant/haplotype: rs4553808
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype AA is associated with increased exposure to tacrolimus in people with Kidney Transplantation as compared to genotypes AG + GG.
Notes: This association was significant in CYP3A5 expressors but the opposite association was seen in CYP3A5 expressers. The time of measurement was 30 days after transplantation. Day 7 and day 90 after transplantation did not show a significant association.
Article: Identification of Candidate Single-Nucleotide Polymorphisms in NRXN1 Related to Antipsychotic Treatment Response in Patients with Schizophrenia
Gene: NRXN1
Variant/haplotype: rs10490162
Drug(s): antipsychotics
Phenotype category: Efficacy
Significant: yes
Association: Genotype TT is associated with increased response to antipsychotics in people with Schizophrenia as compared to genotypes CC + CT.
Notes: Patients homozygous for the T allele had significant improvement in positive symptoms (p=0.0045), general psychopathology (p=0.0146), thought disturbance (p=0.0029), activation (p=0.008), anergia (p=0.0266) and negative symptoms (p=0.0047), while patients carrying the C allele showed no overall response. No significant results were seen for paranoid belligerence (p=0.1598) or depression (p=0.1869). Additionally, no significant results were seen when the associations for positive and negative symptoms and general psychopathology were tested for replication in a different cohort (CATIE study). Please note that alleles have been complemented to the plus chromosomal strand.
Article: Genome-Wide Association Study of Serum Creatinine Levels during Vancomycin Therapy
Gene: MIA3
Variant/haplotype: rs17163303
Drug(s): vancomycin
Phenotype category: Metabolism/PK
Significant: no
Association: Allele T 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 CYP3A5*3, CYP3A4*18 & CYP2B6*6 polymorphisms with imatinib treatment outcome in Azerbaijani chronic myeloid leukaemia patients
Gene: CYP3A4
Variant/haplotype: rs28371759
Drug(s): imatinib
Phenotype category: Efficacy
Significant: yes
Association: Genotype AG is associated with increased response to imatinib in people with Leukemia, Myelogenous, Chronic, BCR-ABL Positive as compared to genotype AA.
Notes: Alleles complemented to plus chromosomal strand. No GG homozygotes were observed. Authors describe effect as ""In contrast, the frequency of the; CYP3A4*18 allele was significantly elevated in; the poor responders (100%) compared to the good; responders (97.1%; P=0.036; Table II)." but the table lists *18 as present (Heterozygous (TC)) in the IM good responders and not the IM resistant.
Article: Pharmacogenetic Variants and Plasma Concentrations of Antiseizure Drugs: A Systematic Review and Meta-Analysis
Gene: UGT1A6
Variant/haplotype: UGT1A6*1a, UGT1A6*2a
Drug(s): valproic acid
Phenotype category: Metabolism/PK
Significant: yes
Association: UGT1A6 *2a is associated with decreased concentrations of valproic acid as compared to UGT1A6 *1a/*1a.
Notes: "Compared with homozygous carriers of the major UGT1A6 allele, heterozygous carriers of the UGT1A6*2 allele exhibited a 9% (95% CI, 3%-15%) reduction in valproate plasma concentrations, while the reduction in homozygous UGT1A6*2 carriers did not reach statistical significance (Table 3)." "UGT1A6*2: rs6759892, rs2070959, or rs1105879"
Article: A Longitudinal HbA1c Model Elucidates Genes Linked to Disease Progression on Metformin
Gene: CSMD1
Variant/haplotype: rs2954625
Drug(s): metformin
Phenotype category: Efficacy
Significant: yes
Association: Genotypes CT + TT are associated with decreased response to metformin in people with Diabetes Mellitus as compared to genotype CC.
Notes: using computational model-based approaches and genetic, demographic, and long-term HbA1c data from 1,056 patients.
Article: Functional characterization of novel rare CYP2A6 variants and potential implications for clinical outcomes
Gene: CYP2A6
Variant/haplotype: rs199515342
Drug(s): nicotine
Phenotype category: Metabolism/PK
Significant: not stated
Association: Allele A is associated with decreased metabolism of nicotine as compared to allele G.
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: Monitoring of peripheral blood cluster of differentiation 4+ adenosine triphosphate activity and CYP3A5 genotype to determine the pharmacokinetics, clinical effects and complications of tacrolimus in patients with autoimmune diseases
Gene: CYP3A5
Variant/haplotype: CYP3A5*1, CYP3A5*3
Drug(s): tacrolimus
Phenotype category: Efficacy
Significant: no
Association: CYP3A5 *1/*1 + *1/*3 is not associated with response to tacrolimus in people with Kidney Transplantation as compared to CYP3A5 *3/*3.
Notes: No significant difference in the occurrence rate of inadequate response to treatment was seen between the genotypes.
Article: Genetic polymorphisms of patients on stable warfarin maintenance therapy in a Ghanaian population
Gene: VKORC1
Variant/haplotype: rs9934438
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Genotype AG is associated with increased dose of warfarin in people with Atrial Fibrillation, Cardiomyopathies, heart valve replacement, Peripheral Vascular Diseases, Pulmonary Embolism and Venous Thrombosis as compared to genotype GG.