shlokn/autogkb huggingface dataset:
Article: Association of carbamazepine major metabolism and transport pathway gene polymorphisms and pharmacokinetics in patients with epilepsy
Gene: NR1I2
Variant/haplotype: rs2461817
Drug(s): carbamazepine
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele C is associated with increased metabolism of carbamazepine in people with Epilepsy as compared to allele A.
Notes: This association was significant in the whole cohort. As measured by a higher carbamazepine-10-11 epoxide: carbamazepine ratio. However, Allele C was associated with decreased clearance in African American patients (p=0.03, n=30).
Article: Pharmacogenomics and Placebo Response in a Randomized Clinical Trial in Asthma
Variant/haplotype: rs2392165
Drug(s): nedocromil
Phenotype category: Efficacy
Significant: no
Association: Genotypes AG + GG are not associated with response to nedocromil in children with Asthma as compared to genotype AA.
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: rs4818
Drug(s): morphine
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with response to morphine in healthy individuals as compared to allele C.
Notes: Study-wide significance was set to p<0.017.
Article: Germline Variation in Colorectal Risk Loci Does Not Influence Treatment Effect or Survival in Metastatic Colorectal Cancer
Variant/haplotype: rs7014346
Drug(s): fluorouracil, irinotecan, oxaliplatin
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to fluorouracil, irinotecan and oxaliplatin in people with Colorectal Neoplasms and Neoplasm Metastasis as compared to allele G.
Notes: SNPs were investigated for their effects on response rate, time to progression and overall survival. After accounting for multiple testing there was no association with any SNPs and outcomes of patients with metastatic colorectal cancer.
Article: Functional genetic variation in the Rev-Erbα pathway and lithium response in the treatment of bipolar disorder
Gene: PER3
Variant/haplotype: rs228697
Drug(s): lithium
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with increased response to lithium in people with Bipolar Disorder as compared to allele C.
Article: Integrative genomic analysis of methylphenidate response in attention-deficit/hyperactivity disorder
Gene: FXR2
Variant/haplotype: rs9901675
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: Lack of Association between Opioid-Receptor Genotypes and Smoking Cessation Outcomes in a Randomized, Controlled Naltrexone Trial
Gene: OPRK1
Variant/haplotype: rs6473797
Drug(s): naltrexone
Phenotype category: Efficacy
Significant: no
Association: Allele C is not associated with response to naltrexone in people with Tobacco Use Disorder as compared to allele T.
Notes: No significant association between this variant and smoking quit rate when naltrexone was used as augmentation to nicotine patch therapy. Please note that alleles have been complemented to the positive strand.
Article: Pharmacogenetic analysis of opioid dependence treatment dose and dropout rate
Gene: CYP2D6
Variant/haplotype: CYP2D6 poor metabolizers and intermediate metabolizers
Drug(s): buprenorphine, methadone
Phenotype category: Efficacy
Significant: no
Association: CYP2D6 poor metabolizers and intermediate metabolizers is not associated with response to buprenorphine or methadone in people with Opioid-Related Disorders as compared to CYP2D6 normal metabolizer and ultra-metabolizer.
Notes: Response defined by changes in the rate of dropout from treatment between metabolizer phenotypes. Study genotyped for the CYP2D6 *1, *2,; *2A, *3, *4, *5, *6, *7, *8, *9, *10, *11, *12, *14, *15, *17 and; *41 alleles as well as gene duplication and then assigned metabolizer phenotypes.
Article: Association between imatinib transporters and metabolizing enzymes genotype and response in newly diagnosed chronic myeloid leukemia patients receiving imatinib therapy
Gene: SLC22A1
Variant/haplotype: rs2282143
Drug(s): imatinib
Phenotype category: Efficacy
Significant: no
Association: Genotype CC is not associated with response to imatinib in people with Leukemia, Myelogenous, Chronic, BCR-ABL Positive as compared to genotypes CT + TT.
Notes: This genotype was not significantly with associated with likelihood of achieving a major cytogenetic response (MCgR) within 12 months. MCgR was defined as achieving either a complete or partial cytogenetic response (CCgR; PCgR). Cytogenetic response was based on bone marrow assessment, where CCgR was 0% Ph+ cells, and PCgR was >0 to 35% Ph+ cells.
Article: Replication study of polymorphisms associated with response to methotrexate in patients with rheumatoid arthritis
Gene: ATIC
Variant/haplotype: rs4673990
Drug(s): methotrexate
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to methotrexate in people with Arthritis, Rheumatoid as compared to allele G.
Article: IL-4 receptor polymorphisms predict reduction in asthma exacerbations during response to an anti–IL-4 receptor α antagonist
Gene: IL4R
Variant/haplotype: rs1805010
Drug(s): pitrakinra
Phenotype category: Efficacy
Significant: yes
Association: Genotype AA is associated with increased response to pitrakinra in people with Asthma as compared to genotypes AG + GG.
Notes: Subjects with the AA genotype have a reduced frequency of asthma exacerbations compared to those with the AG + GG genotypes.
Article: Prediction of phenprocoumon maintenance dose and phenprocoumon plasma concentration by genetic and non-genetic parameters
Gene: CYP2C9
Variant/haplotype: CYP2C9*1, CYP2C9*2, CYP2C9*3
Drug(s): phenprocoumon
Phenotype category: Dosage
Significant: no
Association: CYP2C9 *1/*2 + *2/*2 + *2/*3 + *1/*3 + *3/*3 are not associated with decreased dose of phenprocoumon as compared to CYP2C9 *1/*1.
Notes: CYP2C9 affected the phenprocoumon concentration, but not the dose requirements.
Article: Discordant Associations between SLCO1B1 521T→C and Plasma Levels of Ritonavir-boosted Protease Inhibitors in AIDS Clinical Trials Group Study A5146
Gene: CYP3A5
Variant/haplotype: rs776746
Drug(s): lopinavir
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele C is associated with increased trough concentration of lopinavir in people with HIV Infections as compared to allele T.
Notes: Association was significant in white patients only. Please note that alleles have been complemented to the positive strand.
Article: Genotypic and Phenotypic Factors Influencing Drug Response in Mexican Patients With Type 2 Diabetes Mellitus
Gene: KCNJ11
Variant/haplotype: rs5219
Drug(s): sulfonamides, urea derivatives
Phenotype category: Efficacy
Significant: yes
Association: Genotype CT is associated with increased response to sulfonamides, urea derivatives in people with Diabetes Mellitus as compared to genotypes CC + TT.
Notes: The CT genotype was associated with increased response to sulfonylureas (a greater than or equal to 7% decrease in Hb1Ac levels at least 3 months after beginning treatment).
Article: Genetic variants of ABCB1 and CES1 genes on dabigatran metabolism in the Kazakh population
Gene: CES1
Variant/haplotype: rs2244613
Drug(s): dabigatran
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotypes GG + GT is associated with decreased concentrations of dabigatran in people with Atrial Fibrillation as compared to genotype TT.
Notes: "Patients with the rs2244613 GG genotype had a lower concentration (55.27 ± 34.22 ng/ml) compared to those with the TT genotype (63.33 ± 52.25 ng/ml) (additive model, P = 0.000).  "
Article: Genetic Variation at the LDL Receptor and HMG CoA Reductase Gene Loci, Lipid Levels, Statin Response, and Cardiovascular Disease Incidence in PROSPER
Gene: HMGCR
Variant/haplotype: rs17238540
Drug(s): pravastatin
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with response to pravastatin in people with Vascular Diseases as compared to allele T.
Notes: PROSPER study. Baseline Lipid Values,  LDL-C lowering response,trial CHD and CVD outcomes were measured.  40 mg/day pravastatin.  There was also no association with baseline lipid level or baseline CVD.
Article: The Pharmacogenetics of Tacrolimus in Corticosteroid-Sparse Pediatric and Adult Kidney Transplant Recipients
Gene: POR
Variant/haplotype: rs1057868
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: no
Association: Genotypes CT + TT is not associated with trough concentration of tacrolimus in people with Kidney Transplantation as compared to genotype CC.
Notes: reported for *28 (rs1057868 T).
Article: Association of the SLC30A8 missense polymorphism R325W with proinsulin levels at baseline and after lifestyle, metformin or troglitazone intervention in the Diabetes Prevention Program
Gene: SLC30A8
Variant/haplotype: rs13266634
Drug(s): metformin
Phenotype category: Efficacy
Significant: no
Association: Allele C is not associated with response to metformin in people with high risk of developing diabetes as compared to allele T.
Notes: This was measured at 1 year.
Article: Pharmacogenetics of tenofovir clearance among Southern Africans living with HIV
Gene: ABCC2
Variant/haplotype: rs3740066
Drug(s): tenofovir
Phenotype category: Metabolism/PK
Significant: no
Association: Allele T is not associated with clearance of tenofovir in people with HIV Infections as compared to allele C.
Notes: Based on available allele frequency data, it is assumed that the paper compares the C and T alleles.
Article: Genetic factors influencing warfarin dose in Black-African patients: a systematic review and meta-analysis
Gene: VKORC1
Variant/haplotype: rs2884737
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Genotypes AC + CC are associated with decreased dose of warfarin as compared to genotype AA.
Notes: In this meta-analysis of warfarin Dose in Black-African Patients, this variant is associated with 19.6mg/week less warfarin dose requirement compared to wild-type homozygotes.
Article: Correlation of MDR1 gene polymorphism with propofol combined with remifentanil anesthesia in pediatric tonsillectomy
Gene: ABCB1
Variant/haplotype: rs1128503
Drug(s): propofol, remifentanil
Phenotype category: Efficacy
Significant: yes
Association: Genotype GG is associated with increased response to propofol and remifentanil in children as compared to genotypes AA + AG.
Notes: Referred to as 1236 C>T in the paper. Please note that alleles have been complemented to the positive strand.; Patients with the GG genotype were determined to have an increased response to propofol/remifentanil anesthesia compared to patients with the AA or AG genotypes as patients with the GG genotype had a decreased time of induction, respiration recovery, eye-opening and extubation in addition to reduced blood pressure and heart rate values, increased postsurgery analgesia (as determined by VAS score) and decreased postsurgery sedation (as determined by Ramsey score). However, GG patients also had increased FLACC score, indicating increased pain following extubation.
Article: Possible association of norepinephrine transporter -3081(A/T) polymorphism with methylphenidate response in attention deficit hyperactivity disorder
Gene: SLC6A2
Variant/haplotype: rs28386840
Drug(s): methylphenidate
Phenotype category: Efficacy
Significant: not stated
Association: Genotypes AT + TT are associated with increased response to methylphenidate in children with Attention Deficit Disorder with Hyperactivity as compared to genotype AA.
Notes: ADHD Rating Scale-IV (ARS) and Clinical Global Impression (CGI) were used to assess response. Of the subjects who had the T allele as one of the alleles (A/T or T/T genotypes) at the -3081(A/T) polymorphism, 61.4% (51 of 83) showed a good response (CGI-I = 1 or 2) to MPH treatment. However, only 37.9% (11 of 29) of the subjects with the A/A genotype showed a good response to MPH treatment  (p = 0.03) = trend of significance.
Article: Gemcitabine Metabolic and Transporter Gene Polymorphisms Are Associated with Drug Toxicity and Efficacy in Patients with Locally Advanced Pancreatic Cancer
Gene: RRM1
Variant/haplotype: rs1042858
Drug(s): gemcitabine
Phenotype category: Efficacy, Toxicity
Significant: no
Association: Genotype AA is not associated with increased response to gemcitabine in people with Pancreatic Neoplasms as compared to genotypes AG + GG.
Notes: Tumor response to therapy, progression free survival, and risk of neutropenia development did not significantly differ between genotype groups.
Article: CBR1 and CBR3 pharmacogenetics and their influence on doxorubicin disposition in Asian breast cancer patients
Gene: CBR1
Variant/haplotype: rs9024
Drug(s): doxorubicin
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype GG is associated with decreased exposure to doxorubicin in people with Breast Neoplasms as compared to genotype AG.
Article: An Intronic Variant in OPRD1 Predicts Treatment Outcome for Opioid Dependence in African-Americans
Gene: OPRD1
Variant/haplotype: rs1042114
Drug(s): methadone
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with response to methadone in people with Opioid-Related Disorders as compared to allele T.
Notes: Efficacy was determined based on the number of opioid-positive drug screens that each patient had during treatment.
Article: α-ADDUCIN POLYMORPHISM ASSOCIATED WITH INCREASED RISK OF ADVERSE CARDIOVASCULAR OUTCOMES: RESULTS FROM INVEST-GENES
Gene: ADD1
Variant/haplotype: rs4961
Drug(s): atenolol, verapamil
Phenotype category: Efficacy
Significant: no
Association: Genotype GG is not associated with increased response to atenolol or verapamil in people with Hypertension as compared to genotypes GT + TT.
Notes: The effect of diuretic use on risk of cardiovascular outcomes did not vary by rs4961 genotype.
Article: Population pharmacokinetic and pharmacogenetic analysis of tacrolimus in paediatric liver transplant patients
Gene: CYP3A5
Variant/haplotype: rs776746
Drug(s): tacrolimus
Phenotype category: Dosage, Metabolism/PK
Significant: yes
Association: Genotypes CT + TT is associated with increased dose of tacrolimus in children with liver transplantation as compared to genotype CC.
Notes: Median value for C/D over one year post-transplantation was lower for CYP3A5*1 carriers compared to CYP3A5*3 homozygotes.
Article: The Influence of 5-HTTLPR Genotype on the Association between the Plasma Concentration and Therapeutic Effect of Paroxetine in Patients with Major Depressive Disorder
Gene: SLC6A4
Variant/haplotype: SLC6A4 HTTLPR long form (L allele), SLC6A4 HTTLPR short form (S allele)
Drug(s): paroxetine
Phenotype category: Efficacy
Significant: no
Association: SLC6A4 HTTLPR long form (L allele) is not associated with response to paroxetine in people with Depressive Disorder, Major as compared to SLC6A4 HTTLPR short form (S allele).
Notes: The 5-HTTLPR was not associated with significant differences in response (non-/responder, MADRS improvement (%) per time) in patients receiving paroxetine.
Article: SLCO1B1 Genetic Variation Influence on Atorvastatin Systemic Exposure in Pediatric Hypercholesterolemia
Gene: SLCO1B1
Variant/haplotype: rs4149056
Drug(s): atorvastatin
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele C is associated with increased dose-adjusted trough concentrations of atorvastatin in children with Hypercholesterolemia as compared to allele T.
Notes: "The mean AVA AUC0–24 was 2.8-fold higher in the c.521C/C group and 1.7-fold higher in the c.521T/C group relative to the participants with the reference genotype (Figure 3B, Table 2)."
Article: Identification of two novel genes SLC15A2 and SLCO1B3 associated with maintenance dose variability of warfarin in a Chinese population
Gene: SLCO1B3
Variant/haplotype: rs4149117
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Genotype GG is associated with decreased dose of warfarin as compared to genotypes GT + TT.
Article: A Genome-Wide Association Study of Citalopram Response in Major Depressive Disorder
Variant/haplotype: rs6966038
Drug(s): citalopram
Phenotype category: Efficacy
Significant: no
Association: Allele G is associated with increased response to citalopram in people with Depressive Disorder, Major as compared to allele A.
Notes: It was also associated with remission.  Neither association was significant after correction (430,198 SNPs tested).  Frequencies listed below are for responders vs. nonresponders.  Authors point out the lack of placebo control.
Article: Impact of Pharmacogenetic Markers of CYP2B6, Clinical Factors, and Drug-Drug Interaction on Efavirenz Concentrations in HIV/Tuberculosis-Coinfected Patients
Gene: CYP2B6
Variant/haplotype: CYP2B6*6
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2B6 *6/*6 is associated with decreased clearance of efavirenz in people with HIV.
Notes: *6/*6 is associated with high plasma efavirenz concentrations (units = mg/L), as shown through multivariate analysis. Fasting plasma efavirenz concentrations were measured 12 hours after the last dose, and after 12 weeks of treatment.
Article: Genetic Variation in CYP3A43 Explains Racial Difference in Olanzapine Clearance
Variant/haplotype: rs4729562
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: Comprehensive Ara-C SNP score predicts leukemic cell intracellular ara-CTP levels in pediatric acute myeloid leukemia patients
Gene: CDA
Variant/haplotype: rs12404655
Drug(s): ara-CTP
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotypes AG + GG is associated with increased concentrations of ara-CTP in children with Leukemia, Myeloid, Acute as compared to genotype AA.
Article: The largest prospective warfarin-treated cohort supports genetic forecasting
Gene: CYP2C9
Variant/haplotype: CYP2C9*3
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: CYP2C9 *3 is associated with decreased dose of warfarin.
Notes: CYP2C9*2 and *3 explained 12% (P = 6.63 x 10(-34)) of the variation in warfarin dose.
Article: Attempted validation of 44 reported SNPs associated with tacrolimus troughs in a cohort of kidney allograft recipients
Gene: IL3
Variant/haplotype: rs657075
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. Authors described association as suggestive in the EA population but it did not survive multiple testing correction. Direction of effect not stated. This is a proxy SNP for rs181781.
Article: Functional characterization of novel rare CYP2A6 variants and potential implications for clinical outcomes
Gene: CYP2A6
Variant/haplotype: rs137904044
Drug(s): nicotine
Phenotype category: Metabolism/PK
Significant: not stated
Association: Allele A is associated with decreased metabolism of nicotine as compared to allele C.
Notes: Assigned as decreased function following in vitro assessments, in vivo associations and variant construct functional assignments.
Article: Integrative genomic analysis of methylphenidate response in attention-deficit/hyperactivity disorder
Gene: ZDHHC7
Variant/haplotype: rs3210967
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: Association between the rs7583431 single nucleotide polymorphism close to the activating transcription factor 2 gene and the analgesic effect of fentanyl in the cold pain test
Gene: ATF2
Variant/haplotype: rs1153702
Drug(s): fentanyl
Phenotype category: Efficacy
Significant: no
Association: Allele C is not associated with response to fentanyl in people with Pain, Postoperative as compared to allele T.
Article: A single tumour necrosis factor haplotype influences the response to adalimumab in rheumatoid arthritis
Gene: TNF
Variant/haplotype: rs361525
Drug(s): adalimumab
Phenotype category: Efficacy
Significant: no
Association: Genotype GG is not associated with response to adalimumab in people with Arthritis, Rheumatoid as compared to genotypes AA + AG.
Notes: No significant difference in genotype frequencies was seen between those who were responders to treatment and those who were non-responders. Response defined as a 50% percent response to adalimumab therapy according to the American College of Rheumatology criteria (ACR50 responders) at week 12 after treatment initiation.
Article: Genome-wide association study of patient and clinician rated global impression severity during antipsychotic treatment
Gene: TNFRSF11A
Variant/haplotype: rs2980976
Drug(s): risperidone
Phenotype category: Efficacy
Significant: yes
Association: Allele A is associated with decreased response to risperidone in people with Schizophrenia as compared to allele G.
Notes: The number of A alleles present in a patient was positively associated with CGI-S score.
Article: Rooted in risk: genetic predisposition for low-density lipoprotein cholesterol level associates with diminished low-density lipoprotein cholesterol response to statin treatment
Gene: SORT1
Variant/haplotype: rs629301
Drug(s): hmg coa reductase inhibitors
Phenotype category: Efficacy
Significant: yes
Association: Allele T is associated with decreased response to hmg coa reductase inhibitors in people with Cardiovascular Diseases and Hypercholesterolemia as compared to allele G.
Notes: as measured by lesser reductions in LDL-C. These individuals were also more likely to start out with higher LDL-C before treatment.
Article: Precision Dosing for Tacrolimus Using Genotypes and Clinical Factors in Kidney Transplant Recipients of European Ancestry
Gene: CYP3A5
Variant/haplotype: rs776746
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotypes CT + TT are associated with increased clearance of tacrolimus in people with Kidney Transplantation as compared to genotype CC.
Notes: The C allele is equivalent to the CYP3A5*3 allele.