shlokn/autogkb huggingface dataset:
Article: Replication of the pharmacogenetic effect of rs678849 on buprenorphine efficacy in African-Americans with opioid use disorder
Gene: OPRD1
Variant/haplotype: rs678849
Drug(s): buprenorphine
Phenotype category: Efficacy
Significant: yes
Association: Genotype CC is associated with decreased response to buprenorphine in people with Opioid-Related Disorders as compared to genotypes CT + TT.
Notes: Replication of the association first detailed in PMID 23612435. Efficacy was determined by the number of opioid-positive urine screens recorded during treatment.
Article: Pharmacogenetic associations of the type-3 metabotropic glutamate receptor (GRM3) gene with working memory and clinical symptom response to antipsychotics in first-episode schizophrenia
Gene: GRM3
Variant/haplotype: rs6465084
Drug(s): antipsychotics
Phenotype category: Toxicity
Significant: yes
Association: Genotype AA is associated with increased response to antipsychotics in people with Schizophrenia as compared to genotypes AG + GG.
Notes: Those with the AA genotype had reduced negative symptom severity (according to Brief Psychiatric Rating Scale (BPRS) negative symptoms subscale) as compared to those with the AG or GG genotype (who had minimal change or worsening in negative symptoms). Significant after correction for multiple comparisons.
Article: Evaluating Predictive Pharmacogenetic Signatures of Adverse Events in Colorectal Cancer Patients Treated with Fluoropyrimidines
Gene: DPYD
Variant/haplotype: rs3918290
Drug(s): capecitabine, fluorouracil
Phenotype category: Dosage
Significant: yes
Association: Genotype CT is associated with dose of capecitabine or fluorouracil in people with Colorectal Neoplasms as compared to genotype CC.
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. Note: the reported parameters for this SNP are really for a haplotype (the authors refer to it as a "signature") that includes any minor alleles for the following SNPs:  rs3918290 (T), rs67376798 (A), rs75017182(C), rs56038477 (T).
Article: ASSOCIATIONS OF ABCB1 3435C>T AND IL-10 -1082G>A POLYMORPHISMS WITH LONG-TERM SIROLIMUS DOSE REQUIREMENTS IN RENAL TRANSPLANT PATIENTS
Gene: CYP3A5
Variant/haplotype: CYP3A5*1, CYP3A5*6
Drug(s): sirolimus
Phenotype category: Metabolism/PK
Significant: no
Association: CYP3A5 *1/*1 is not associated with dose-adjusted trough concentrations of sirolimus in people with Kidney Transplantation as compared to CYP3A5 *1/*6 + *6/*6.
Notes: No significant difference in log-transformed dose-adjusted trough concentrations (C/D) was seen between the two genotype groups.
Article: Genetic Polymorphisms of Cytokines Might Affect Postoperative Sufentanil Dosage for Analgesia in Patients
Gene: NFKBIA
Variant/haplotype: rs8904
Drug(s): sufentanil
Phenotype category: Dosage
Significant: no
Association: Allele A is not associated with dose of sufentanil in people with Pain, Postoperative as compared to allele G.
Article: Variants in the CYP2B6 3′UTR alter in vitro and in vivo CYP2B6 activity: potential role of microRNAs
Gene: CYP2B6
Variant/haplotype: rs3181842
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotypes CC + CT are associated with increased metabolism of efavirenz in healthy individuals as compared to genotype TT.
Notes: "For rs3181842, an increase in CYP2B6 activity was observed between volunteers with T/T versus T/C (31.9% increase; p<0.05) and C/C genotypes (70.6% increase; p<0.0001)".
Article: Methadone dose in heroin-dependent patients: role of clinical factors, comedications, genetic polymorphisms and enzyme activity
Gene: ABCB1
Variant/haplotype: rs1045642
Drug(s): methadone
Phenotype category: Dosage
Significant: no
Association: Allele A is not associated with dose of methadone in people with Opioid-Related Disorders as compared to allele G.
Notes: Methadone maintenance dose was not associated with genotype of the SNP but it was correlated to the highest dose ever used. Multiple doses versus single dose, body weight, history of cocaine dependence and ethnicity (Asian>Caucasian>African) were independently associated with methadone dose in multiple regression analysis. Please note: alleles are complemented to the + chromosomal strand.
Article: Variants in Pharmacokinetic Transporters and Glycemic Response to Metformin: A Metgen Meta‐Analysis
Gene: SLC22A4
Variant/haplotype: rs272893
Drug(s): metformin
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with response to metformin in people with Diabetes Mellitus, Type 2 as compared to allele C.
Notes: This variant is not associated with metformin glycemic response assessed as HbA1c reduction in patients on metformin monotherapy.
Article: A GENOME-WIDE ASSOCIATION STUDY OF BRONCHODILATOR RESPONSE IN LATINOS IMPLICATES RARE VARIANTS
Variant/haplotype: rs77149876
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.
Article: Genetic Variation of the Mu Opioid Receptor (OPRM1) and Dopamine D2 Receptor (DRD2) is Related to Smoking Differences in Patients with Schizophrenia but not Bipolar Disorder
Gene: OPRM1
Variant/haplotype: rs1799971
Drug(s): nicotine
Phenotype category: Other
Significant: no
Association: Genotypes AG + GG are not associated with exposure to nicotine in people with Bipolar Disorder or Schizophrenia as compared to genotype AA.
Notes: Analysis of the total cohort found no significant difference in number of cigarettes smoked per day between genotype groups.
Article: Polymorphic Variants of SCN1A and EPHX1 Influence Plasma Carbamazepine Concentration, Metabolism and Pharmacoresistance in a Population of Kosovar Albanian Epileptic Patients
Gene: EPHX1
Variant/haplotype: rs2234922
Drug(s): carbamazepine
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype GG is associated with increased metabolism of carbamazepine in people with Epilepsy as compared to genotypes AA + AG.
Notes: The authors evaluated maintenance dose-adjusted concentrations of carbamazepine (CBZ), its active metabolite, CBZ-epoxide (CBZE), and its inactive metabolite CBZ-diol (CBZD) as well as CBZE:CBZ, CBZD:CBZ and CBZD:CBZE ratios. The GG genotype is associated with a lower mean dose adj. CBZD concentration (microgram/mL per mg/Kg) (0.13 for the GG genotype vs. 0.21-0.24 for the AG and GG genotypes, respectively). The GG genotype also had a lower mean CBZD:CBZ (0.13 for GG vs. 0.24-0.26 for the AG and AA genotypes, respectively). Finally, the GG genotype was associated with a lower mean CBZD:CBZE  (1.74 for GG vs. 3.95-3.08 for AG and AA, respectively).
Article: Effects of CYP2B6 and CYP1A2 Genetic Variation on Nevirapine Plasma Concentration and Pharmacodynamics as Measured by CD4 Cell Count in Zimbabwean HIV-Infected Patients
Gene: CYP2B6
Variant/haplotype: rs3745274
Drug(s): nevirapine
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype TT is associated with increased concentrations of nevirapine in people with HIV Infections as compared to genotypes GG + GT.
Notes: Nevirapine was given as part of HAART therapy.
Article: Replication study of polymorphisms associated with response to methotrexate in patients with rheumatoid arthritis
Gene: PTPRM
Variant/haplotype: rs6506569
Drug(s): methotrexate
Phenotype category: Efficacy
Significant: no
Association: Allele C is not associated with response to methotrexate in people with Arthritis, Rheumatoid as compared to allele T.
Article: An Expanded Analysis of Pharmacogenetics Determinants of Efavirenz Response that Includes 3′-UTR Single Nucleotide Polymorphisms among Black South African HIV/AIDS Patients
Gene: CYP2B6
Variant/haplotype: rs3745274
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele T is associated with increased concentrations of efavirenz in people with HIV Infections as compared to allele G.
Article: Genetic Variation in CYP3A43 Explains Racial Difference in Olanzapine Clearance
Gene: CYP3A43
Variant/haplotype: rs12535293
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: TOLLIP, MUC5B, and the Response to N-Acetylcysteine among Individuals with Idiopathic Pulmonary Fibrosis
Gene: TOLLIP
Variant/haplotype: rs5743890
Drug(s): acetylcysteine
Phenotype category: Efficacy
Significant: no
Association: Genotype TT is not associated with response to acetylcysteine in people with Pulmonary Fibrosis as compared to genotypes CC + CT.
Notes: Clinical endpoints included death, transplant, hospitalization, or FVC decline,  and risk was adjusted for age, sex, prednisone use, azathioprine use, FVC, diffusion capacity of the lung, and trial/center. Alleles given on reverse strand A and G.
Article: Assessing the Contribution of Opioid- and Dopamine-Related Genetic Polymorphisms to the Abuse Liability of Oxycodone
Variant/haplotype: rs6848893
Drug(s): oxycodone
Phenotype category: Efficacy
Significant: no
Association: Genotype CT is not associated with response to oxycodone as compared to genotype TT.
Notes: No association between this variant and analgesic response to oxycodone, as assessed by cold pressor test.
Article: OPRM1, OPRK1 and COMT Genetic Polymorphisms Associated with Opioid Effects on Experimental Pain: A Randomized, Double-Blind, Placebo-Controlled Study
Gene: OPRK1
Variant/haplotype: rs702764
Drug(s): morphine
Phenotype category: Efficacy
Significant: no
Association: Allele C is not associated with response to morphine in healthy individuals as compared to allele T.
Notes: Study-wide significance was set to p<0.017.
Article: Impact of polymorphisms of the GGCX gene on maintenance warfarin dose in Chinese populations: Systematic review and meta-analysis
Gene: GGCX
Variant/haplotype: rs12714145
Drug(s): warfarin
Phenotype category: Dosage
Significant: no
Association: Allele T is not associated with dose of warfarin as compared to genotype CC.
Notes: This meta-analysis in Chinese patients showed no difference in mean daily warfarin dose (MDWD) for various genotypes of GGCX  variant rs12714145.
Article: The influence of CYP3A, PPARA, and POR genetic variants on the pharmacokinetics of tacrolimus and cyclosporine in renal transplant recipients
Gene: CYP3A4
Variant/haplotype: rs35599367
Drug(s): cyclosporine
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele A is associated with decreased metabolism of cyclosporine in people with Kidney Transplantation as compared to allele G.
Notes: A single steady-state concentration of cyclosporine was collected for each patient 2-7 wks post-transplant and compared to dose of cyclosporine administered to patients at Oslo University Hospital. Reported concentrations are "steady-state dose-adjusted concentration" of cyclosporine. Steady-state is defined as at least 3 days after last dose adjustment for Tac and 4 days for cyclosporine.
Article: Limited predictive value of achieving beneficial plasma (Z)-endoxifen threshold level by CYP2D6 genotyping in tamoxifen-treated Polish women with breast cancer
Gene: CYP2D6
Variant/haplotype: CYP2D6*1, CYP2D6*2, CYP2D6*4, CYP2D6*5, CYP2D6*10, CYP2D6*17, CYP2D6*41
Drug(s): endoxifen
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2D6 *4/*41 + *4/*10 + *4/*17 + *5/*41 are associated with decreased concentrations of endoxifen in women with Breast Neoplasms as compared to CYP2D6 *1/*2 + *1/*1 + *2/*2.
Notes: Pre- and post menopausal patients received 20 mg/day tamoxifen for at least 1 month (median duration 21.5 month). DNA source was blood and CYP2D6 was genotyped with TaqMan allelic discrimination assays. PM (non-functional) alleles include: CYP2D6*3, *4, *5, *6, *7; IM (reduced function) alleles include: CYP2D6*9, *10, *17, *41; EM (wt; fully functional) alleles include CYP2D6*1 and *2; UM (increased function) alleles include: duplication of EM variants of the gene, such as CYP2D6*1XN and *2XN. Patients were assigned a CYP2D6 genotype depending on the combination of alleles they carry, as PM/PM, IM/PM, IM/IM, EM/PM, EM/IM, EM/EM or EM/UM.
Article: Pharmacogenomics of selective serotonin reuptake inhibitor treatment for major depressive disorder: genome-wide associations and functional genomics
Gene: RFK
Variant/haplotype: rs11144870
Drug(s): citalopram, escitalopram
Phenotype category: Efficacy
Significant: no
Association: Allele T is associated with decreased response to citalopram or escitalopram in people with Depressive Disorder, Major as compared to allele C.
Notes: No SNP reached the genome-wide level of significance (P<10-7), although this variant was shown in functional molecular experiments to influence transcription by a reporter gene assay and to alter nuclear protein binding using an electrophoretic mobility shift assay.
Article: The International SSRI Pharmacogenomics Consortium (ISPC): a genome-wide association study of antidepressant treatment response
Gene: MTMR12
Variant/haplotype: rs73069924
Drug(s): Selective serotonin reuptake inhibitors
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with response to Selective serotonin reuptake inhibitors in people with Depressive Disorder, Major as compared to allele A.
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: Tacrolimus pharmacokinetics are influenced by CYP3A5, age, and concomitant fluconazole in pediatric kidney transplant patients
Gene: CYP3A5
Variant/haplotype: CYP3A5 intermediate metabolizer and normal metabolizer
Drug(s): tacrolimus
Phenotype category: Dosage
Significant: yes
Association: CYP3A5 intermediate metabolizer and normal metabolizer is associated with increased dose of tacrolimus in children with Kidney Transplantation as compared to CYP3A5 poor metabolizer.
Notes: "For CYP3A5, *1 (the normal function allele), *3, *6, *7, and *8 alleles were detected. Patients were then classified into two phenotypic categories of CYP3A5 IM/NMs, or CYP3A5 PMs as defined in the CPIC guidelines"
Article: Impact of polymorphisms in CYP and UGT enzymes and ABC and SLCO1B1 transporters on the pharmacokinetics and safety of desvenlafaxine
Gene: UGT1A1
Variant/haplotype: UGT1A1 poor metabolizer
Drug(s): desvenlafaxine
Phenotype category: Metabolism/PK
Significant: no
Association: UGT1A1 poor metabolizer is associated with increased exposure to desvenlafaxine in healthy individuals as compared to UGT1A1 intermediate metabolizer and normal metabolizer.
Notes: as measured by increased Tmax. Authors state "UGT1A1 rs887829 (*80) was used as a surrogate biomarker for *28." but do not explicitly state how that is is used to define PM, IM or NM. "However, none of these associations; remained significant after Bonferroni correction for multiple; comparisons. "
Article: Induction of CYP3A4 by Vinblastine: Role of the Nuclear Receptor NR1I2
Gene: ABCB1
Variant/haplotype: rs1045642
Drug(s): midazolam
Phenotype category: Other, Metabolism/PK
Significant: no
Association: Allele A is not associated with increased clearance of midazolam in people with Carcinoma, Renal Cell as compared to allele G.
Notes: It's not clear exactly what genotype comparison was done. Subjects were treated with vinblastine/valspodar. [stat_test: nonparametric 2-sided Wilcoxon signed-rank]
Article: Effect of carboxylesterase 1 c.428G > A single nucleotide variation on the pharmacokinetics of quinapril and enalapril
Gene: CES1
Variant/haplotype: rs71647871
Drug(s): enalapril
Phenotype category: Metabolism/PK
Significant: no
Association: Genotype CT is not associated with clearance of enalapril in healthy individuals as compared to genotype CC.
Notes: This was a fixed-order crossover study with two phases: following overnight fasting participants took a 10 mg dose of quinapril and, after a washout period of at least 1 week, a 10 mg dose of enalapril with 150 ml water in the morning and EDTA-prepared blood samples were drawn before and up to 24 hr, and up to 48 h after ingestion for the determination of the concentrations of quinapril and its metabolite quinaprilat, as well as enalapril and its metabolite enalaprilat. Urine was collected up to 12 h after quinapril and enalapril. Only AUC (0-infinity) and amount excreted in urine of enalaprilat were significantly different between genotype groups. Other PK parameters that were tested and not significantly different were Cmax, Tmax, T(1/2), and renal clearance.
Article: Association of STAT-3 rs1053004 and VDR rs11574077 With FOLFIRI-Related Gastrointestinal Toxicity in Metastatic Colorectal Cancer Patients
Gene: RXRG
Variant/haplotype: rs3767344
Drug(s): irinotecan
Phenotype category: Metabolism/PK
Significant: no
Association: Allele G is not associated with metabolism of irinotecan in people with Colorectal Neoplasms as compared to allele C.
Article: ADH single nucleotide polymorphism associations with alcohol metabolism in vivo
Gene: ADH1B
Variant/haplotype: rs1229985
Drug(s): ethanol
Phenotype category: Toxicity, Metabolism/PK
Significant: yes
Association: Allele G is associated with metabolism of ethanol.
Notes: The authors did not report p-value correction for multiple hypotheses (103 snps tested).  Though they report multiple snps are significantly associated with alcohol metabolism (early or late) tested on blood or breath alcohol concentrations, this snp is NOT significant after Bonferroni correction (<0.00049).  Also, the authors did not state which alleles are associated with increased or decreased metabolism.  Instead, they simply report an association with the snp in general.  Note that this gene is on the minus strand.
Article: PDE4 Gene Family Variants Are Associated with Response to Apremilast Treatment in Psoriasis
Gene: TSPAN16
Variant/haplotype: rs322144
Drug(s): apremilast
Phenotype category: Efficacy
Significant: yes
Association: Allele C is associated with decreased clinical benefit to apremilast in people with Psoriasis as compared to allele G.
Notes: "Allele-based association tests detected 64 SNPs displaying nominal p values < 0.05 (Table 2) including 10 SNPs with p values ≤ 0.01. " Table 2 shows frequency of minor allele is responders and non-responders. Responder status maybe defined by PASI score improvement greater than 75% after 24–36 weeks of treatment.
Article: Impact of NFIB and CYP1A variants on clozapine serum concentration—A retrospective naturalistic cohort study on 526 patients with known smoking habits
Gene: NFIB
Variant/haplotype: rs28379954
Drug(s): clozapine
Phenotype category: Metabolism/PK
Significant: not stated
Association: Genotype CT is associated with decreased dose-adjusted trough concentrations of clozapine in people with Tobacco Use Disorder as compared to genotype TT.
Notes: significance is only given for combination of both CYP1A rs2472297 C>T and NFIB rs28379954 T>C genotypes
Article: TSPAN5, ERICH3 and selective serotonin reuptake inhibitors in major depressive disorder: pharmacometabolomics-informed pharmacogenomics
Gene: TSPAN5
Variant/haplotype: rs11947402
Drug(s): citalopram, escitalopram
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with response to citalopram and escitalopram in people with Depressive Disorder as compared to allele A.
Notes: This is one of SNP showed some association with plasma serotonin concentrations and was suspected to be associated with SSRI clinical response. When tested in the PGRN-AMPS GWAS and in two independent SSRI response GWAS (STAR*D and ISPC) it was not associated with response in any cohort.
Article: Association studies of dopamine synthesis and metabolism genes with multiple phenotypes of heroin dependence
Gene: DBH
Variant/haplotype: rs129915
Drug(s): heroin
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with response to heroin as compared to allele A.
Notes: No significant association between this variant and strength of euphoria on first heroin use.
Article: Genome-Wide Meta-Analysis of Cotinine Levels in Cigarette Smokers Identifies Locus at 4q13.2
Variant/haplotype: rs77107237
Drug(s): cotinine
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele G is associated with increased concentrations of cotinine in people with Tobacco Use Disorder as compared to allele A.
Notes: The authors conducted a GWAS meta-analysis to identify genetic variants associated with cotinine in current daily smokers (Caucasian). The following study cohorts were analyzed: ALSPAC, CARDIA, FinnTwin, Framingham, GenMets, MESA, NESDA, NTR, TwinsUK, YFS. The SNP was associated with a ~39 ng/ml increase in plasma/serum cotinine and accounted for 0.87% variance in cotinine levels.
Article: Correlation of pain perception and fentanyl consumption after major abdominal surgery with CGRP 4218T/C polymorphism: A prospective interventional study
Gene: CALCA
Variant/haplotype: rs145837941
Drug(s): fentanyl
Phenotype category: Dosage
Significant: yes
Association: Genotype GG is associated with increased dose of fentanyl in people with Pain, Postoperative as compared to genotypes AA + AG.
Notes: Mapped CGRP 4218T/C to rs145837941 in the CALCA gene using PMID:23237777. Alleles complemented. Was significant for all the timepoints (0-6, 6-12, 12-24 and total)."In the paired comparison of C/C versus T/C and C/C versus T/T, the C/C group had a significantly higher requirement of mean total postoperative fentanyl in the first 24 h than T/T (P < 0.001) and T/C (P < 0.001). "
Article: Individual and combined associations of genetic variants in CYP3A4, CYP3A5, and SLCO1B1 with simvastatin and simvastatin acid plasma concentrations
Gene: CYP3A4
Variant/haplotype: CYP3A4*1, CYP3A4*22
Drug(s): simvastatin
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP3A4 *1/*22 is associated with increased concentrations of simvastatin in people with Hypercholesterolemia as compared to CYP3A4 *1/*1.
Notes: Patients were followed for 6 weeks (40 mg simvastatin at bedtime) and seen at the clinic at 2 week intervals. Patients with the *1/*22 diplotype had 58% higher plasma simvastatin concentration at 12 hours, respectively, as compared to those with the *1/*1 diplotypes.; In a separate analysis, the authors combined patients into groups based on their expected simvastatin acid/ simvastatin ratios (SVA/SV). The groups were low, intermediate, or high. The low and medium SVA/SV group included patients with the *1/*22 diplotype. There was a significant difference in 12 hr plasma SVA/SV ratios between the low, intermediate, and high SVA/SV ratio genotype groups.
Article: Genetic variants in the KIF6 region and coronary event reduction from statin therapy
Gene: KIF6
Variant/haplotype: rs9471077
Drug(s): atorvastatin, pravastatin
Phenotype category: Efficacy
Significant: yes
Association: Genotypes AG + GG are associated with increased response to atorvastatin or pravastatin.
Article: Effect of UGT2B10, UGT2B17, FMO3, and OCT2 Genetic Variation on Nicotine and Cotinine Pharmacokinetics and Smoking in African Americans
Gene: UGT2B10
Variant/haplotype: rs2942857
Drug(s): cotinine
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype CC is associated with increased exposure to cotinine in people with Tobacco Use Disorder as compared to genotypes AA + AC.
Notes: This annotation was on rs116294140, but dbSNP has merged these two rs IDs.