shlokn/autogkb huggingface dataset:
Article: Correlation of aldo-ketoreductase (AKR) 1C3 genetic variant with doxorubicin pharmacodynamics in Asian breast cancer patients
Gene: AKR1C3
Variant/haplotype: rs1937840
Drug(s): docetaxel, doxorubicin
Phenotype category: Efficacy
Significant: yes
Association: Genotype GG is associated with increased response to docetaxel and doxorubicin in women with Breast Neoplasms as compared to genotypes CC + CG.
Notes: GG genotype was associated with increases in both overall survival and progression-free survival. IMPORTANT NOTE: Multiple correction was NOT conducted in this study (Many different time points, many different measurement/calculations and 7 different SNPs were analyzed)
Article: Influences of an NR1I2 polymorphism on heterogeneous antiplatelet reactivity responses to clopidogrel and clinical outcomes in acute ischemic stroke patients
Gene: CYP2C19
Variant/haplotype: rs4244285
Drug(s): clopidogrel
Phenotype category: Efficacy
Significant: yes
Association: Genotypes AA + AG is associated with decreased response to clopidogrel in people with Coronary Artery Disease as compared to genotype GG.
Notes: This variant is associated with decreased H4 concentration, and decreased antiplatelet effects of clopidogrel with a higher PRU.
Article: Impact of the Superoxide Dismutase 2 Val16Ala Polymorphism on the Relationship between Valproic Acid Exposure and Elevation of γ-Glutamyltransferase in Patients with Epilepsy: A Population Pharmacokinetic-Pharmacodynamic Analysis
Gene: CYP2C19
Variant/haplotype: CYP2C19*1, CYP2C19*2, CYP2C19*3
Drug(s): valproic acid
Phenotype category: Metabolism/PK
Significant: no
Association: CYP2C19 *2 + *3 are not associated with clearance of valproic acid in people with Epilepsy as compared to CYP2C19 *1.
Notes: Clearance here refers to apparent oral clearance as assayed by serum concentration of valproic acid (VPA) (micrograms/ml). The authors used NONEM to assess serum concentration of VPA.
Article: Genome-Wide Association Study of Serum Creatinine Levels during Vancomycin Therapy
Variant/haplotype: rs3008607
Drug(s): vancomycin
Phenotype category: Metabolism/PK
Significant: no
Association: Allele A is not associated with trough concentration of vancomycin as compared to allele G.
Notes: The SNP was not associated with trough levels of vancomycin (first vancomycin trough documented in EMR after at least 3 doses vancomycin). Elimination constants were also calculated.
Article: Association of complement factor H and LOC387715 genotypes with response of exudative age-related macular degeneration to photodynamic therapy
Gene: ARMS2
Variant/haplotype: rs10490924
Drug(s): Photodynamic therapy
Phenotype category: Efficacy
Significant: no
Association: Genotypes GG + GT are not associated with response to photodynamic therapy in people with Macular Degeneration as compared to genotype TT.
Notes: While there was no significant association between genotype and response to PDT, there was a trend between visual acuity post treatment and genotype.  Visual acuity post-PDT declined 1.0 line for the TT genotype, 2.1 lines for the GT genotype and 4.1 lines for the GG genotype.  This is interesting because, while it is not statistically significant (P=0.08), the allele that puts patients at higher risk of developing age-related macular degeneration (allele T) seems to also confer a better treatment outcome.
Article: Genetic Polymorphisms of Cytokines Might Affect Postoperative Sufentanil Dosage for Analgesia in Patients
Gene: IL10
Variant/haplotype: rs1800896
Drug(s): sufentanil
Phenotype category: Dosage
Significant: no
Association: Allele C is not associated with dose of sufentanil in people with Pain, Postoperative as compared to allele T.
Article: Contribution of Cytochrome P450 and ABCB1 Genetic Variability on Methadone Pharmacokinetics, Dose Requirements, and Response
Gene: CYP2B6
Variant/haplotype: CYP2B6*1, CYP2B6*4, CYP2B6*6
Drug(s): methadone
Phenotype category: Efficacy
Significant: no
Association: CYP2B6 *1/*4 + *1/*6 + *4/*6 + *6/*6 are not associated with response to methadone in people with Opioid-Related Disorders as compared to CYP2B6 *1/*1.
Notes: No significant difference in genotype or phenotype frequencies between responders and non-responders, as defined by drug misuse during methadone maintenance therapy. No details about which specific variants/alleles were tested for, however the authors state that genotyping of *1/*6 individuals did not exclude the possibility of them actually being *4/*9.
Article: Variation in CYP2A6 and nicotine metabolism among two American Indian tribal groups differing in smoking patterns and risk for tobacco-related cancer
Gene: CYP2A6
Variant/haplotype: CYP2A6*1, CYP2A6*46
Drug(s): nicotine
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2A6 *46/*46 is associated with increased metabolism of nicotine in healthy individuals as compared to CYP2A6 *1/*1.
Notes: Study was among smokers. Please note that the *46 allele is described as the *1B1 allele in the paper and has subsequently been reassigned by PharmVar.
Article: Influence of pharmacogenetic polymorphisms and demographic variables on metformin pharmacokinetics in an admixed Brazilian cohort
Gene: SLC22A1
Variant/haplotype: rs12208357
Drug(s): metformin
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele T is associated with increased exposure to metformin in healthy individuals as compared to allele C.
Article: Effect of Multidrug-Resistant 1 (MDR1) and CYP3A4*1B Polymorphisms on Cyclosporine-Based Immunosuppressive Therapy in Renal Transplant Patients
Gene: CYP3A4
Variant/haplotype: rs2740574
Drug(s): cyclosporine
Phenotype category: Dosage
Significant: no
Association: Genotype TT is associated with decreased dose of cyclosporine in people with Kidney Transplantation as compared to genotype CT.
Notes: Patients with the *1/*1 genotype had lower mean cyclosporine A doses than patients with the *1/*1B genotype. Mapped *1B to rs2740574 C and *1A to rs2740574 T based on PharmVAR consolidation of core alleles. However, this was not a significant association.
Article: An Acenocoumarol Dosing Algorithm Using Clinical and Pharmacogenetic Data in Spanish Patients with Thromboembolic Disease
Gene: VKORC1
Variant/haplotype: rs9923231
Drug(s): acenocoumarol
Phenotype category: Dosage
Significant: yes
Association: Allele T is associated with dose of acenocoumarol.
Notes: This variant was significantly associated with acenocoumarol dose, and explained 22% of the variability in dose. Clinical variables (Age, BMI, Enzyme inducers status and Amiodarone status) explained 22% of the variability in dose. This study developed an algorithm for acenocoumarol dosing using clinical and pharmacogenetic data.
Article: Genome-wide association study identifies a potent locus associated with human opioid sensitivity
Variant/haplotype: rs2952768
Drug(s): opioids
Phenotype category: Efficacy
Significant: yes
Association: Genotype CC is associated with decreased response to opioids in people with Pain, Postoperative as compared to genotypes CT + TT.
Notes: The C/C genotype of this SNP was also significantly associated with the elevated expression of a neighboring gene, CREB1.
Article: Pharmacogenetics of unboosted atazanavir in HIV-infected individuals in resource-limited settings: a sub-study of the AIDS Clinical Trials Group (ACTG) PEARLS study (NWCS 342)
Gene: NR1I2
Variant/haplotype: rs1523130
Drug(s): atazanavir
Phenotype category: Metabolism/PK
Significant: no
Association: Genotype CC (assigned as deficiency phenotype) is not associated with concentrations of atazanavir in people with HIV Infections as compared to genotypes CT + TT.
Notes: Looked at CL/F, concentration at 24 hours, and ratios of metabolites M1 and M2 to atazanavir.
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 and intermediate metabolizers
Drug(s): efavirenz, maraviroc
Phenotype category: Efficacy
Significant: no
Association: CYP3A5 intermediate metabolizer and poor metabolizer are not associated with response to efavirenz or maraviroc in people with HIV Infections as compared to CYP3A5 normal metabolizer.
Notes: There was no statistical significant difference in the number of subjects with HIV-1 RNA <50 and <400 copies/mL at weeks 48 and 96 of maraviroc and efavirenz treatment between CYP3A5 metabolizer phenotypes.
Article: CYP3A4 and CYP3A5 Polymorphisms and Blood Pressure Response to Amlodipine among African-American Men and Women with Early Hypertensive Renal Disease
Gene: CYP3A4
Variant/haplotype: rs2246709
Drug(s): amlodipine
Phenotype category: Efficacy
Significant: no
Association: Genotypes AG + GG are not associated with response to amlodipine in people with Hypertension as compared to genotype AA.
Notes: No significant change in the likelihood of a patient reaching a target mean arterial pressure concentration of <= 107 mmHg was seen between genotypes. Please note alleles have been complemented to the plus chromosomal strand.
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: yes
Association: CYP3A5 poor metabolizer is associated with decreased concentrations of maraviroc in people with HIV Infections as compared to CYP3A5 normal metabolizer.
Notes: In study A4001026, CYP3A5 poor metabolizers had a significant decrease in average maraviroc plasma concentrations compared to extensive metabolizers, contrary to what would be expected. The authors suggest that that this result may have been influenced by a number of variables, including HIV infection, in the study. This significance was lost when the 'black' and 'white' cohorts were analyzed separately. The authors determined this difference in maraviroc concentrations to not be clinically significant.
Article: Genetic markers associated with abstinence length in alcohol-dependent subjects treated with acamprosate
Gene: GRIN2B
Variant/haplotype: rs2160733
Drug(s): acamprosate
Phenotype category: Efficacy
Significant: no
Association: Allele C is not associated with response to acamprosate in people with Alcoholism as compared to allele A.
Notes: Tag SNPs (518 total) were selected within genes associated with alcoholism as well as genes encoding enzymes involved in glycine metabolism, glycine transporters, subunits of glycine receptors, NMDA receptors, genes involved in glutamate reuptake, synthesis or degradation and genes with reported associations with acamprosate treatment outcomes in human or animal studies. The length of time to first alcohol use “survival analysis method” was used to examine associations between clinical variables and genetic markers with efficacy of acomprasate (its ability to length  the duration of abstinence from alcohol).  The analyses were replicated in a subset of 110 participants from PREDICT, a double-blind randomized controlled trial that compared treatment outcomes including length of abstinence among alcohol- dependent subjects of German descent recruited from inpatient facilities and treated with acamprosate, naltrexone or placebo for 3 months.
Article: Replication study of polymorphisms associated with response to methotrexate in patients with rheumatoid arthritis
Gene: MTRR
Variant/haplotype: rs1801394
Drug(s): methotrexate
Phenotype category: Efficacy
Significant: yes
Association: Allele A is associated with decreased response to methotrexate in people with Arthritis, Rheumatoid as compared to allele G.
Notes: The A allele was independently associated with worse response using two distinct measures of response 1) the difference in Disease Activity Score 28 between baseline and 6 months later (deltaDAS28) and 2) the European League Against Rheumatism (EULAR) criteria. For DAS28, each A allele corresponded to 0.14 deltaDAS28 units in an additive model vs the G allele (indicating worse response assoc. with A allele). Using EULAR criteria the A allele also had an increased OR=1.39 for non-response (95% CI 1.11–1.75).
Article: Patients carrying CYP2C8*3 have shorter systemic paclitaxel exposure
Gene: CYP2C8
Variant/haplotype: CYP2C8*3
Drug(s): paclitaxel
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2C8 *3 is associated with decreased exposure to paclitaxel in women with Breast Neoplasms.
Notes: as measured by time above threshold concentration. CYP2C8*1/*3 or CYP2C8*3/*3 mean = 8.92 h, CYP2C8*1/*1 mean = 11.03 h
Article: Association studies of dopamine synthesis and metabolism genes with multiple phenotypes of heroin dependence
Gene: TH
Variant/haplotype: rs3842727
Drug(s): heroin
Phenotype category: Dosage
Significant: no
Association: Allele T is not associated with dose of heroin in people with Heroin Dependence as compared to allele G.
Article: Combined study of genetic and epigenetic biomarker risperidone treatment efficacy in Chinese Han schizophrenia patients
Gene: HTR1A
Variant/haplotype: rs6295
Drug(s): risperidone
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with response to risperidone in people with Schizophrenia as compared to allele C.
Article: CYP3A4 and CYP3A5 Polymorphisms and Blood Pressure Response to Amlodipine among African-American Men and Women with Early Hypertensive Renal Disease
Gene: CYP3A4
Variant/haplotype: rs2740574
Drug(s): amlodipine
Phenotype category: Efficacy
Significant: yes
Association: Genotypes CT + TT are associated with increased response to amlodipine in women with Hypertension as compared to genotype CC.
Notes: Women who were carriers for the T allele were more likely to reach the target mean arterial pressure of <= 107 mm Hg when treated with amlodipine. Please note alleles have been complemented to the plus chromosomal strand.
Article: Association of genetic variation in pharmacodynamic factors with methadone dose required for effective treatment of opioid addiction
Gene: DRD2
Variant/haplotype: rs2283265
Drug(s): methadone
Phenotype category: Dosage
Significant: no
Association: Genotypes AA + AC are associated with decreased dose of methadone in people with Heroin Dependence as compared to genotype CC.
Notes: This association was not statistically significant after permutation analysis based on 40,000 replicates, and not statistically significant after adjusting for testing for multiple SNPs (Bonferroni correction). Note; this association may be linked to the association with rs7118900 in the ANKK1 gene. Alleles were reported as T/G, here they are complemented for the positive chromosomal strand with A representing T and C representing G.
Article: Genetic determinants of apixaban plasma levels and their relationship to bleeding and thromboembolic events
Gene: ABCG2
Variant/haplotype: rs2231142
Drug(s): apixaban
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele G is associated with decreased concentrations of apixaban in people with Atrial Fibrillation as compared to allele T.
Notes: was significant for 3 measures of PK : AUCss, Cmax,ss, and Cmin,ss.
Article: Pharmacokinetics and pharmacogenetics of the MEK1/2 inhibitor, selumetinib, in Asian and Western healthy subjects: a pooled analysis
Gene: CYP2C19
Variant/haplotype: rs4986893
Drug(s): selumetinib
Phenotype category: Metabolism/PK
Significant: no
Association: Allele G is not associated with dose of selumetinib in healthy individuals as compared to allele A.
Notes: Not associated with normalized dose when allele was assessed within ethnic groups (Asian, White, Black) and when all ethnic groups were pooled together.
Article: Genotypic variation in the SV2C gene impacts response to atypical antipsychotics the CATIE Study
Gene: SV2C
Variant/haplotype: rs10214163
Drug(s): quetiapine
Phenotype category: Efficacy
Significant: no
Association: Genotype TT is not associated with response to quetiapine in people with Schizophrenia as compared to genotypes CC + CT.
Notes: Not significant after correction for multiple testing using the False Discovery Rate. Response was assessed by change in the total Positive and Negative Syndrome Scale (PANSS) score.
Article: Association of BDNF, HTR2A, TPH1, SLC6A4, and COMT polymorphisms with tDCS and escitalopram efficacy: ancillary analysis of a double-blind, placebo-controlled trial
Gene: TPH1
Variant/haplotype: rs1800532
Drug(s): escitalopram
Phenotype category: Efficacy
Significant: yes
Association: Genotypes GT + TT are associated with decreased response to escitalopram in people with Depression as compared to genotype GG.
Article: Association of IL28B gene variations with mathematical modeling of viral kinetics in chronic hepatitis C patients with IFN plus ribavirin therapy
Gene: IFNL3
Variant/haplotype: rs8099917
Drug(s): peginterferon alfa-2a, ribavirin
Phenotype category: Efficacy
Significant: yes
Association: Genotype TT is associated with increased response to peginterferon alfa-2a and ribavirin in people with Hepatitis C, Chronic as compared to genotype GT.
Notes: no GG patients were seen. SVR (at 24 weeks) was seen in 87% TT vs. 50% GT.
Article: Effects of various factors on steady-state plasma concentrations of risperidone and 9-hydroxyrisperidone: lack of impact of MDR-1 genotypes
Gene: ABCB1
Variant/haplotype: rs1045642
Drug(s): risperidone
Phenotype category: Metabolism/PK
Significant: no
Association: Allele G is not associated with increased metabolism of risperidone in people with Schizophrenia as compared to allele A.
Notes: No association was seen between this SNP and metabolism of risperidone.
Article: New genetic variant that might improve warfarin dose prediction in African Americans
Gene: PRSS53, VKORC1
Variant/haplotype: rs17886199
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Allele A is associated with decreased dose of warfarin as compared to allele G.
Notes: independent of the VKORC1 1173C>T and CYP2C9*2 and *3 variants in African Americans.
Article: Genetic Polymorphism of Cytochrome P450 4F2, Vitamin E Level and Histological Response in Adults and Children with Nonalcoholic Fatty Liver Disease Who Participated in PIVENS and TONIC Clinical Trials
Gene: CYP4F2
Variant/haplotype: rs3093105
Drug(s): vitamin e
Phenotype category: Efficacy
Significant: no
Association: Allele C is not associated with response to vitamin e in people with Fatty liver disease as compared to allele A.
Notes: The C allele is not significantly associated with improved liver histology in pediatric or adult patients receiving vitamin E (alpha-tocopherol) supplements.
Article: Exonuclease 1 genetic variant is associated with clinical outcomes of pemetrexed chemotherapy in lung adenocarcinoma
Gene: CAMKK2
Variant/haplotype: rs1653586
Drug(s): pemetrexed
Phenotype category: Efficacy
Significant: yes
Association: Genotype GT is associated with decreased clinical benefit to pemetrexed in people with Lung Neoplasms as compared to genotype GG.
Notes: Figure 1 has "GG vs GT+TT" but table 4 shows that no TT individuals were reported.
Article: Association of serum cotinine level with a cluster of three nicotinic acetylcholine receptor genes (CHRNA3/CHRNA5/CHRNB4) on chromosome 15
Gene: CHRNA3
Variant/haplotype: rs1051730
Drug(s): nicotine
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele A is associated with increased dose of nicotine as compared to allele G.
Notes: Serum Cotinine levels were measured to test for association between nicotine intake and this SNP. AA>AG>GG for serum cotinine levels in daily smokers.  Authors noted that the variance was very high (R-squared = 4.3%).  Effect size of this SNP was 0.30 . Cigarettes per day was also associated but not significantly so after correction for multiple testing.
Article: Association between UGT2B7 gene polymorphisms and fentanyl sensitivity in patients undergoing painful orthognathic surgery
Gene: UGT2B7
Variant/haplotype: rs10028494
Drug(s): fentanyl
Phenotype category: Efficacy
Significant: yes
Association: Genotype CC is associated with decreased response to fentanyl in people with Pain, Postoperative as compared to genotypes AA + AC.
Notes: There was a significant difference in PPLpost-PPLpre between the genotype groups.
Article: Dual specificity phosphatase-1 as a pharmacogenetic modifier of inhaled steroid response among asthma patients
Gene: DUSP1
Variant/haplotype: rs881152
Drug(s): salbutamol
Phenotype category: Efficacy
Significant: not stated
Association: Allele G is associated with increased response to salbutamol in people with Asthma as compared to allele A.
Notes: Subjects were taking inhaled corticosteroids.
Article: ABC Transporter Polymorphisms are Associated with Irinotecan Pharmacokinetics and Neutropenia
Gene: ABCC1
Variant/haplotype: rs8187843
Drug(s): SN-38
Phenotype category: Metabolism/PK
Significant: no
Association: Genotypes AA + AG are not associated with exposure to SN-38 in people with Colorectal Neoplasms as compared to genotype GG.
Notes: AUC of SN-38 was adjusted for irinotecan dose.
Article: Integrative genomic analysis of methylphenidate response in attention-deficit/hyperactivity disorder
Gene: SENP3
Variant/haplotype: rs9901673
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: CYP3A4 and CYP3A5 Polymorphisms and Blood Pressure Response to Amlodipine among African-American Men and Women with Early Hypertensive Renal Disease
Gene: CYP3A4
Variant/haplotype: rs2740574
Drug(s): amlodipine
Phenotype category: Efficacy
Significant: no
Association: Genotypes CT + TT are not associated with response to amlodipine in women with Hypertension as compared to genotype CC.
Notes: No significant change in the likelihood of a woman reaching a target mean arterial pressure concentration of <= 92 mmHg was seen between genotypes. Please note alleles have been complemented to the plus chromosomal strand.
Article: Association studies of dopamine synthesis and metabolism genes with multiple phenotypes of heroin dependence
Gene: SLC6A3
Variant/haplotype: rs1042098
Drug(s): heroin
Phenotype category: Dosage
Significant: no
Association: Allele G is not associated with dose of heroin in people with Heroin Dependence as compared to allele A.
Article: Sub‐ and supratherapeutic efavirenz plasma concentrations with risk for HIV therapy failure are mainly genetically explained in Ugandan children: The prospective GENEFA cohort study
Gene: CYP2B6
Variant/haplotype: CYP2B6 intermediate metabolizer
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2B6 intermediate metabolizer and poor metabolizer is associated with increased concentrations of efavirenz in children with HIV infectious disease as compared to CYP2B6 normal metabolizer.
Notes: "extensive metabolizer (EM), 516GGj983TT, intermediate metabolizer (IM), 516GGj983TC or 516GTj983TT, slow metabolizer (SM) 516GTj983TC or 516TTj983TT. " " Both IM and SM phenotype were significantly associated with higher loge EFV plasma concentra-tion compared to EM (P = .03 and .00, respectively)."