shlokn/autogkb huggingface dataset:
Article: Association between imatinib transporters and metabolizing enzymes genotype and response in newly diagnosed chronic myeloid leukemia patients receiving imatinib therapy
Gene: SLC22A4
Variant/haplotype: rs1050152
Drug(s): imatinib
Phenotype category: Efficacy
Significant: no
Association: Genotype TT is not associated with response to imatinib in people with Leukemia, Myelogenous, Chronic, BCR-ABL Positive as compared to genotypes CC + CT.
Notes: This genotype was not significantly with associated with likelihood of achieving complete molecular response (CMR) within 12 months. CMR was classified based on BCR-ABL to control gene transcript ratios, expressed on the International Scale; CMR was a ratio <= 0.0032%.
Article: Exploration of CYP450 and drug transporter genotypes and correlations with nevirapine exposure in Malawians
Gene: NR1I2
Variant/haplotype: rs3842689
Drug(s): nevirapine
Phenotype category: Dosage, Metabolism/PK
Significant: yes
Association: Genotypes GAGAAG/del + del/del are associated with increased clearance of nevirapine in people with HIV Infections as compared to genotype GAGAAG/GAGAAG.
Notes: as measured by decreased area under the concentration time curve and increased apparent oral clearance of the drug. This was not statistically significant after multiple comparison correction. [stat_test: linear regression]
Article: Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) Potentiator VX-770 (Ivacaftor) Opens the Defective Channel Gate of Mutant CFTR in a Phosphorylation-dependent but ATP-independent Manner
Gene: CFTR
Variant/haplotype: rs75527207
Drug(s): ivacaftor
Phenotype category: Efficacy
Significant: not stated
Association: Allele A is associated with increased response to ivacaftor.
Notes: In vitro studies using proteoliposomes containing CFTR, or CFTR with the G551D mutation (rs75527207 allele A), or CFTR with the F508del mutation (rs113993960 allele del). Ivacaftor in the presence of ATP potentiated channel activity of CFTR-G551D.
Article: Pharmacogenetic Interactions of Rifapentine plus Isoniazid with Efavirenz or Nevirapine
Gene: NAT2
Variant/haplotype: NAT2 slow acetylator
Drug(s): nevirapine
Phenotype category: Metabolism/PK
Significant: not stated
Association: NAT2 slow acetylator is associated with increased concentrations of nevirapine in people with HIV Infections.
Notes: NAT2 slow acetylators also had greater plasma efavirenz and nevirapine concentration increases from baseline to week 4, and greater decreases from baseline in clearance.
Article: CYP2B6 Variants and Plasma Efavirenz Concentrations during Antiretroviral Therapy in Port-au-Prince, Haiti
Gene: CYP2B6
Variant/haplotype: rs3745274
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele T (assigned as poor metabolizer phenotype) is associated with decreased metabolism of efavirenz in people with HIV Infections as compared to allele G (assigned as normal metabolizer phenotype) .
Notes: As determined by significantly higher efavirenz plasma levels. Composite analysis with rs3745274: extensive metabolizers were defined as having no variant alleles at positions 516 (allele G) or (983 allele T), intermediate metabolizers had a single variant at one of the positions but not both, slow metabolizers (described as "poor" here) had 2 variant alleles (either genotype 516TT, 983CC, or 516 GT with 983 TC). Significant after Bonferroni correction for multiple comparisons.
Article: Genetic polymorphisms in the long noncoding RNA MIR2052HG offer a pharmacogenomic basis for the response of breast cancer patients to aromatase inhibitor therapy
Variant/haplotype: rs4476990
Drug(s): anastrozole, exemestane
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with increased response to anastrozole and exemestane in women with Breast Neoplasms as compared to allele C.
Notes: Patients included postmenopausal women with resected stage I–III breast cancer that was ERa and/or PgR positive and randomized to five years of anastrozole or exemestane. Did not reach statistical significance for GWAS (P<5 x 10^-8).
Article: A Pharmacogenetics-Based Warfarin Maintenance Dosing Algorithm from Northern Chinese Patients
Gene: F11
Variant/haplotype: rs3756009
Drug(s): warfarin
Phenotype category: Dosage
Significant: no
Association: Allele G is not associated with dose of warfarin in people with heart valve replacement as compared to allele A.
Notes: Samples, genotypes and INRs from a cohort of 551 patients were used to derive an algorithm which was used to predict daily warfarin maintenance dose in a second cohort of 236 patients. Note: the authors state that "SNPs were tested for deviations from HWE using the chi-squared test, and for their association with the warfarin dose by Spearman correlation analysis using a *co-dominant* model."
Article: Association between Polymorphisms in Vascular Endothelial Growth Factor Gene and Response to Chemotherapies in Colorectal Cancer: A Meta-Analysis
Gene: VEGFA
Variant/haplotype: rs699947
Drug(s): bevacizumab, capecitabine, fluorouracil, irinotecan, leucovorin, oxaliplatin
Phenotype category: Efficacy
Significant: yes
Association: Genotype CC is associated with increased response to bevacizumab, capecitabine, fluorouracil, irinotecan, leucovorin and oxaliplatin in people with Colorectal Neoplasms as compared to genotype AC.
Notes: Response to treatment was determined by RECIST criteria.
Article: Ethnic and genetic factors in methadone pharmacokinetics: A population pharmacokinetic study
Gene: CYP2B6
Variant/haplotype: rs3745274
Drug(s): methadone
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele T is associated with decreased clearance of methadone in people with Opioid-Related Disorders as compared to allele G.
Article: Pharmacogenetic Analysis of Pediatric Patients with Acute Lymphoblastic Leukemia: A Possible Association between Survival Rate and ITPA Polymorphism
Gene: TPMT
Variant/haplotype: TPMT*1, TPMT*3A
Drug(s): mercaptopurine, methotrexate
Phenotype category: Dosage
Significant: no
Association: TPMT *1/*1 is associated with increased dose of mercaptopurine and methotrexate in children with Precursor Cell Lymphoblastic Leukemia-Lymphoma as compared to TPMT *1/*3A.
Notes: The median dose percent of 6-MP and MTX for the TPMT wild type was higher than variant types. There was no significant difference in the dose percents by TPMT genotypes, although there was only six *1/*3A and *1/*3C patients and one *2*2 patient.
Article: Impact of the CYP2C8 *3 polymorphism on the drug–drug interaction between gemfibrozil and pioglitazone
Gene: CYP2C8
Variant/haplotype: CYP2C8*1, CYP2C8*3
Drug(s): pioglitazone
Phenotype category: Metabolism/PK
Significant: no
Association: CYP2C8 *1/*1 is not associated with metabolism of pioglitazone in healthy individuals as compared to CYP2C8 *1/*3 + *3/*3.
Notes: When co-administered with gemfibrozil. Patients taking pioglitazone and gemfibrozil. No significant results when considering Cmax (p=0.51), AUC0-inf (p=0.99), AUC0-48h (p=0.39), CL/F (p=0.712) or t1/2 (p=0.3).
Article: Influences of UGT2B7 rs7439366 and rs12233719 Polymorphisms on Fentanyl Sensitivity in Chinese Gynecologic Patients
Gene: UGT2B7
Variant/haplotype: rs7439366
Drug(s): fentanyl
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with response to fentanyl in women with Pain, Postoperative as compared to allele C.
Notes: No significant differences in postoperative fentanyl consumption or VAS scores at 24 hours post-surgery between genotypes.
Article: TRAF1/C5 but Not PTPRC Variants Are Potential Predictors of Rheumatoid Arthritis Response to Anti-Tumor Necrosis Factor Therapy
Gene: PTPRC
Variant/haplotype: rs10919563
Drug(s): Tumor necrosis factor alpha (TNF-alpha) inhibitors
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with decreased response to Tumor necrosis factor alpha (TNF-alpha) inhibitors in people with Arthritis, Rheumatoid as compared to allele G.
Notes: using either the absolute change in DAS28 or the proportion of good responders and non-responders as outcomes.
Article: Impact of CYP2C19 polymorphism on the pharmacokinetics of nelfinavir in patients with pancreatic cancer
Gene: CYP2C19
Variant/haplotype: CYP2C19*1, CYP2C19*2
Drug(s): nelfinavir
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2C19 *1/*2 is associated with decreased metabolism of nelfinavir in people with as compared to CYP2C19 *1/*1.
Notes: All patients were genotyped for CYP2C19 by RFLP analysis. Female and male patients were initially administered 750 or 900 mg/m2 gemcitabine IV over 30 min, 50 mg/m2 leucovorin IV over 30 min, and 2700 mg/m2 5-FU IV over 24 hours on day 1 weekly for 2 of 3 weeks for three cycles (day 1-63). Oral nelfinavir was given at 625 mg or 1250 mg twice daily for 3 weeks starting 2 weeks prior to initiation of radiation (days 56-75). 625 mg is better tolerated and preferred by patients. 1250 mg is the standard dose of nelfinavir when used to treat HIV patients. Metabolic ratio, as determined by AUC0–12 h of M8 over AUC0–12 h of nelfinavir, was significantly lower in CYP2C19 *1/*2 as compared to CYP2C19 *1/*1 (0.24 vs. 0.30) in the 1250 mg group.
Article: Pharmacogenetic Predictors of Adverse Events and Response to Chemotherapy in Metastatic Colorectal Cancer: Results From North American Gastrointestinal Intergroup Trial N9741
Gene: XRCC1
Variant/haplotype: rs25487
Drug(s): fluorouracil, irinotecan, oxaliplatin
Phenotype category: Efficacy
Significant: no
Association: Genotype CC is not associated with response to fluorouracil, irinotecan or oxaliplatin in people with Colorectal Neoplasms as compared to genotypes CT + TT.
Notes: Patients were taking either IFL (irinotecan + fluorouracil + leucovorin; n=114), FOLFOX (fluorouracil + oxaliplatin + leucovorin; n=299) or IROX (irinotecan + oxaliplatin; n=107). No significant association was seen between this variant and confirmed response rate, overall survival or time to progression in any of the treatment groups OR all treatment groups considered together. Significance level was set at 0.01.
Article: Variation in Maturity-Onset Diabetes of the Young Genes Influence Response to Interventions for Diabetes Prevention
Gene: HNF4A
Variant/haplotype: rs11086926
Drug(s): metformin
Phenotype category: Efficacy
Significant: no
Association: Genotype GG is not associated with response to metformin as compared to genotypes GT + TT.
Notes: Subjects were at high risk of diabetes and were recruited from Diabetes Prevention Program (DPP) and were followed for a year. The authors measured changes in response to insulin at baseline and one year after treatment. Although the GG genotype was not associated with response to metformin, it was associated with changes in lifestyle as subjects with that genotype were less likely to develop diabetes compared with persons with the same genotype in the placebo (P=0.02) and metformin (P=0.02) groups.
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): amprenavir, saquinavir
Phenotype category: Metabolism/PK
Significant: no
Association: Allele C is not associated with trough concentration of amprenavir or saquinavir in people with HIV Infections as compared to allele T.
Notes: Please note that alleles have been complemented to the positive strand.
Article: Pharmacogenetic analysis of opioid dependence treatment dose and dropout rate
Gene: CYP2C9
Variant/haplotype: CYP2C9 poor metabolizer
Drug(s): buprenorphine, methadone
Phenotype category: Efficacy
Significant: no
Association: CYP2C9 poor metabolizer is not associated with response to buprenorphine or methadone in people with Opioid-Related Disorders as compared to CYP2C9 intermediate metabolizer and normal metabolizer.
Notes: Response defined by changes in the rate of dropout from treatment between metabolizer phenotypes. Study genotyped for the CYP2C9 *1, *2, *3, *4, *5 and *6 alleles and then assigned metabolizer phenotypes.
Article: Association of Variants in Candidate Genes with Lipid Profiles in Women with Early Breast Cancer on Adjuvant Aromatase Inhibitor Therapy
Gene: CYP19A1
Variant/haplotype: rs3759811
Drug(s): triglycerides
Phenotype category: Other
Significant: yes
Association: Allele C is associated with decreased concentrations of triglycerides in women with Breast Neoplasms and Menopause as compared to allele T.
Notes: when taking letrozole. Data are from a sub-analysis of the Exemestane and Letrozole Pharmacogenomics (ELPh) study, where post-menopausal women with early stage breast cancer were randomized to receive exemestane or letrozole. Of the 303 eligible women, 160 were randomized to the letrozole group, 52 of whom were also taking LLA. This SNP was associated with decreases in triglycerides of 32.3 mg/dL (SE 9.0).
Article: Effects of SCN1A and GABA Receptor Genetic Polymorphisms on Carbamazepine Tolerability and Efficacy in Chinese Patients with Partial Seizures: 2‐Year Longitudinal Clinical Follow‐Up
Gene: SCN1A
Variant/haplotype: rs3812718
Drug(s): carbamazepine
Phenotype category: Dosage
Significant: yes
Association: Genotype TT is associated with increased dose of carbamazepine in people with Epilepsy as compared to genotype CC.
Notes: Patients with the TT genotype have increased maintenance dose and serum levels of carbamazepine between 3 and 12 months of treatment. No significant difference between genotypes was seen between 15 and 24 months of treatment. Please note alleles have been complemented to the plus chromosomal strand.
Article: β-2 Adrenergic receptor gene polymorphism and response to propranolol in cirrhosis
Gene: ADRB2
Variant/haplotype: rs1042713
Drug(s): propranolol
Phenotype category: Efficacy
Significant: yes
Association: Genotype GG is associated with increased response to propranolol in people with Liver Cirrhosis as compared to genotype AA.
Notes: all patients had decrease in heart rate and variceal pressure in response to propranolol but decrease was greater in Gly16-GluGln27 group (rs1042713G)(rs1042714) compared to Arg16-Gln27, with compound heterozygotes as intermediate responders.
Article: Whole-Genome Sequencing of Pharmacogenetic Drug Response in Racially Diverse Children with Asthma
Variant/haplotype: rs17834628
Drug(s): salbutamol
Phenotype category: Efficacy
Significant: yes
Association: Allele A is associated with increased response to salbutamol in children with as compared to allele G.
Notes: Direction of the response not explicit stated in the article.
Article: Association of genetic variation in pharmacodynamic factors with methadone dose required for effective treatment of opioid addiction
Gene: BDNF
Variant/haplotype: rs1491850
Drug(s): methadone
Phenotype category: Dosage
Significant: no
Association: Genotype CC is associated with decreased dose of methadone in people with Heroin Dependence as compared to genotypes CT + TT.
Notes: This association was statistically significant after permutation analysis based on 40,000 replicates, but not statistically significant after adjusting for testing for multiple SNPs (Bonferroni correction).
Article: Thymidylate Synthase Genotype-Directed Chemotherapy for Patients with Gastric and Gastroesophageal Junction Cancers
Gene: TYMS
Variant/haplotype: rs11280056
Drug(s): fluorouracil, leucovorin, oxaliplatin
Phenotype category: Efficacy
Significant: no
Association: Allele del is not associated with response to fluorouracil, leucovorin and oxaliplatin in people with Esophageal Neoplasms and Stomach Neoplasms.
Notes: This association was originally mapped to rs34489327 and subsequently migrated to the analogous SNP rs151264360. rs151264360 has now been merged into rs11280056. This annotation replaces VA 1184886864.
Article: Influence of (ATP)-Binding Cassette Transporter Subfamily B Member 1 (ABCB1) Gene Polymorphism on the Efficacy of Remifentanil
Gene: ABCB1
Variant/haplotype: rs1045642
Drug(s): remifentanil
Phenotype category: Efficacy
Significant: no
Association: Genotype AG is not associated with response to remifentanil as compared to genotypes AA + GG.
Notes: No significant different in analepsia time, autonomous respiratory recovery time or orientation recovery time between patients with the AG or AA genotypes, or between patients with the AG or GG genotypes.
Article: A functional variant in the serotonin receptor 7 gene (HTR7), rs7905446, is associated with good response to SSRIs in bipolar and unipolar depression
Gene: HTR7
Variant/haplotype: rs7905446
Drug(s): fluoxetine, paroxetine
Phenotype category: Efficacy
Significant: yes
Association: Genotype TT is associated with decreased response to fluoxetine or paroxetine in people with Bipolar Disorder as compared to genotypes GG + GT.
Notes: A 'good' response was determined as a 50% reduction in symptoms or episode frequency during the course of the illness.; This analysis was carried out on patients who were treated with fluoxetine or paroxetine. This association remained statistically significant in the paroxetine group, but significance was lost in the fluoxetine group.
Article: Pharmacogenetics of warfarin in a paediatric population: Time in therapeutic range, initial and stable dosing, and adverse effects
Gene: CYP2C9
Variant/haplotype: CYP2C9*1, CYP2C9*2
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: CYP2C9 *2 is associated with decreased dose of warfarin in children as compared to CYP2C9 *1.
Notes: with an approximate decrease of daily dose of 0.82mg.
Article: Genetic Analysis of Mu and Kappa Opioid Receptor and COMT Enzyme in Cancer Pain Tunisian Patients Under Opioid Treatment
Gene: COMT
Variant/haplotype: rs4680
Drug(s): morphine
Phenotype category: Dosage, Efficacy
Significant: no
Association: Allele G is not associated with dose of morphine in people with Pain as compared to allele A.
Notes: No association was observed between this variant and a patient's initial dose requirement or their need to escalate their dose of morphine.
Article: Ethnic Stratification of the Association of RGS4 Variants with Antipsychotic Treatment Response in Schizophrenia
Gene: RGS4
Variant/haplotype: rs951439
Drug(s): quetiapine, ziprasidone
Phenotype category: Efficacy
Significant: not stated
Association: Genotype TT is associated with increased response to quetiapine and ziprasidone in people with Schizophrenia as compared to genotype CC.
Article: Influence of Vitamin D-Related Gene Polymorphisms (CYP27B and VDR) on the Response to Interferon/Ribavirin Therapy in Chronic Hepatitis C
Gene: IFNL3, IFNL4
Variant/haplotype: rs12979860
Drug(s): peginterferon alfa-2b, ribavirin
Phenotype category: Efficacy
Significant: yes
Association: Allele T is associated with decreased response to peginterferon alfa-2b and ribavirin in people with Hepatitis C, Chronic as compared to allele C.
Notes: This genotype is associated with sustained virological response (SVR).
Article: Association studies of dopamine synthesis and metabolism genes with multiple phenotypes of heroin dependence
Gene: SLC6A3
Variant/haplotype: rs10064525
Drug(s): heroin
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with response to heroin as compared to allele T.
Notes: No significant association between this variant and strength of euphoria on first heroin use.
Article: An Intronic Variant in OPRD1 Predicts Treatment Outcome for Opioid Dependence in African-Americans
Gene: OPRD1
Variant/haplotype: rs678849
Drug(s): methadone
Phenotype category: Efficacy
Significant: yes
Association: Genotype CC is associated with increased response to methadone in people with Opioid-Related Disorders as compared to genotypes CT + TT.
Notes: Efficacy was determined based on the number of opioid-positive drug screens that each patient had during treatment. Patients with the CC genotype had significantly fewer positive drug screens during 24 weeks of treatment than the combined group of patients with the CT or TT genotypes.
Article: Attempted validation of 44 reported SNPs associated with tacrolimus troughs in a cohort of kidney allograft recipients
Gene: ABCB1
Variant/haplotype: rs117937072
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: no
Association: Allele G is not associated with trough concentration of tacrolimus in people with Kidney Transplantation and Transplantation as compared to allele A.
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. This is a proxy for rs2229109 (1199G/A).
Article: Impact of CYP3A4*1G Polymorphism on Fentanyl Analgesia Assessed by Analgesia Nociception Index in Chinese Patients Undergoing Hysteroscopy
Gene: CYP3A4
Variant/haplotype: rs2242480
Drug(s): fentanyl
Phenotype category: Efficacy
Significant: yes
Association: Genotype TT is associated with increased response to fentanyl in women with Pain, Postoperative as compared to genotypes CC + CT.
Notes: The A allele is also referred to in the paper as the CYP3A4*1G allele. PharmVar reassigned *1G to *36.
Article: Impact of CYP2C19 Gene Variants on Long-Term Treatment with Atorvastatin in Patients with Acute Coronary Syndromes
Gene: CYP2C19
Variant/haplotype: CYP2C19*1, CYP2C19*2, CYP2C19*4, CYP2C19*8, CYP2C19*11
Drug(s): atorvastatin
Phenotype category: Efficacy
Significant: yes
Association: CYP2C19 *2 + *4 + *8 (assigned as poor metabolizer phenotype) is associated with decreased clinical benefit to atorvastatin in people with Cardiovascular Diseases as compared to CYP2C19 *1 + *11.
Notes: "Carriers of the CYP2C19*2, CYP2C19*4, and CYP2C19*8 alleles were considered poor metabolizers, while all other patients were considered normal metabolizers." "The multivariable logistic regression model showed (Table 5) that poor CYP2C19 metabolizing phenotype, patient age, and smoking increased the odds of undertreatment in patients (∆LDL-C (mmol/L) < 1) who received standard atorvastatin cholesterol-lowering therapy."
Article: Association between UGT2B7 gene polymorphisms and fentanyl sensitivity in patients undergoing painful orthognathic surgery
Gene: UGT2B7
Variant/haplotype: rs12645107
Drug(s): fentanyl
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to fentanyl in people with Pain, Postoperative as compared to allele G.
Notes: There was no significant difference in PPLpost-PPLpre between the genotype groups.
Article: Effect of GSTA1 Variants on Busulfan-Based Conditioning Regimen Prior to Allogenic Hematopoietic Stem-Cell Transplantation in Pediatric Asians
Gene: GSTA1
Variant/haplotype: rs3957357
Drug(s): busulfan
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele A is associated with decreased clearance of busulfan in children with hematopoietic stem cell transplantation as compared to allele G.
Notes: Alleles complemented. "The carriers of the variant allele GSTA1*B had a lower CL, which in turn reduced the elimination of busulfan; this was associated with increased AUC." There are two variants C-69T (rs3957357) and G-52A (rs3957356) which combine to form *A and *B alleles where -69C, -52G, designated as GSTA1*A; -69T, -52A, designated as GSTA1*B.
Article: Interleukin-6 (IL-6) haplotypes and the response to therapy of chronic hepatitis C virus infection
Gene: IL6
Variant/haplotype: rs1800796
Drug(s): peginterferon alfa-2a
Phenotype category: Efficacy
Significant: yes
Association: Allele G is associated with decreased response to peginterferon alfa-2a in people with Hepatitis C, Chronic as compared to allele C.
Notes: This association is as part of a haplotype which also includes rs1800797G and rs1800795G.  This is a GC SNP so the listed associated allele may be incorrect.