shlokn/autogkb huggingface dataset:
Article: Race influences warfarin dose changes associated with genetic factors
Gene: CYP2C9
Variant/haplotype: CYP2C9*1, CYP2C9*5, CYP2C9*6, CYP2C9*11
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: CYP2C9 *5 + *6 + *11 are associated with decreased dose of warfarin as compared to CYP2C9 *1/*1.
Notes: in African Americans.
Article: Potentially Functional SNPs (pfSNPs) as Novel Genomic Predictors of 5-FU Response in Metastatic Colorectal Cancer Patients
Gene: PTEN
Variant/haplotype: rs17431184
Drug(s): capecitabine, fluorouracil
Phenotype category: Efficacy
Significant: not stated
Association: Allele C is associated with increased response to capecitabine and fluorouracil in people with Neoplasm Metastasis as compared to allele T.
Notes: pfSNP identified 2800 SNPS associated with key-words: 5-FU, capecitabine and oxilaplatin and colorectal cancer. Various criteria were used to determine 1536 SNPs to genotype. These SNPs were genotyped in a discovery cohort (N=62) and tested in a validation cohort (N=27). Both cohorts consisted of patients with colorectal cancer metastasis in liver. Five SNPs (rs2289310 G>T; rs1047840 G>A;  rs17431184 T>C; rs17160359 G>T; rs2236722 A>G)  were identified as distinguishing the "non-responder" phenotype from the "responder" phenotype when using a logistic regression multivariate model. The AUC for the receiver operating characteristic curve of the 5 SNPs is 0.875. This logistic-based multivariate model is said to be able to identify 39.1% of non-responders.
Article: Genome-Wide Association Study of Serum Creatinine Levels during Vancomycin Therapy
Variant/haplotype: rs3002143
Drug(s): vancomycin
Phenotype category: Metabolism/PK
Significant: no
Association: Allele C is not associated with trough concentration of vancomycin as compared to allele T.
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: Developmental pharmacogenetics of CYP2C19 in neonates and young infants: omeprazole as a probe drug
Gene: ABCB1
Variant/haplotype: rs1045642
Drug(s): omeprazole
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotypes AA + AG are associated with increased concentrations of omeprazole in infants with Gastroesophageal Reflux as compared to genotype GG.
Notes: The authors referred to the "ABCB1 C3435T genotype" as the most important  covariate  influencing  the absorption rate constant (Ka) and that their "Model-predicted  Ka  is  6.93  times  higher  in  ABCB1  homozygous  mutant patients,  1.86  times  higher  in  ABCB1  heterozygous  patients  than  that  in  ABCB1 homozygous wild-type patients." This is taken to mean that the higher Ka is for the TT and CT genotypes as compared to the CC genotypes. Complementing alleles back to the complement on the + strand means that the higher Ka is for the AA and AG genotypes as compared to the GG genotypes.
Article: The largest prospective warfarin-treated cohort supports genetic forecasting
Gene: VKORC1
Variant/haplotype: rs9923231
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Allele T is associated with decreased dose of warfarin.
Notes: This SNP explained 29% (P = 1.03 x 10(-97)) of the variation in warfarin dose.
Article: Correlation of CYP2C19 genotype with plasma voriconazole exposure in South-western Chinese Han patients with invasive fungal infections
Gene: CYP2C19
Variant/haplotype: CYP2C19*1, CYP2C19*2, CYP2C19*3
Drug(s): voriconazole
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2C19 *2/*2 + *2/*3 is associated with decreased metabolism of voriconazole in people with as compared to CYP2C19 *1/*1.
Notes: Patients who were poor metabolizers (*2/*2 or *2/*3) had increased trough concentrations (C0) and dose-adjusted trough concentrations (C0/D) as compared to those who were normal metabolizers (*1/*1). Significant results were also seen for C0/D when *2/*2 individually was compared against *1/*1; no significant results were seen for C0.
Article: Effect of Fenofibrate Therapy and ABCA1 Polymorphisms on High Density Lipoprotein Subclasses in the Genetics of Lipid Lowering Drugs and Diet Network
Gene: ABCA1
Variant/haplotype: rs2230806
Drug(s): fenofibrate
Phenotype category: Efficacy
Significant: yes
Association: Genotype CT is associated with increased response to fenofibrate in people with Hypertriglyceridemia as compared to genotype CC.
Notes: Patients with the CT genotype had a greater small high-density lipoprotein (HDL) particle concentration (units = umol/L) after fenofibrate treatment for 3 weeks, as compared to patients with the CC genotype.
Article: The N680S variant in the follicle-stimulating hormone receptor gene identifies hyperresponders to controlled ovarian stimulation
Gene: FSHR
Variant/haplotype: rs6166
Drug(s): follitropin beta, urofollitropin
Phenotype category: Toxicity
Significant: not stated
Association: Allele T is associated with increased response to follitropin beta or urofollitropin as compared to allele C.
Notes: The ovarian hyperstimulation syndrome incidence was 6% (36 cases): 13 with the AA and 23 with the AG and no cases with the GG genotype. The N680S polymorphism was associated with ovarian hyperstimulation syndrome (Ptrend = 0.004 and Pallele = 0.038), with carriers of asparagine having an odds ratio for ovarian hyperstimulation syndrome of 1.7, 95% confidence interval: 1.0–2.8, P = 0.04, in comparison with carriers of serine.
Article: Two Novel Loci of RELN Associated With Antipsychotics Response in Chinese Han Population
Gene: RELN
Variant/haplotype: rs7341475
Drug(s): aripiprazole, olanzapine, perphenazine, quetiapine, risperidone
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to aripiprazole, olanzapine, perphenazine, quetiapine or risperidone in people with Schizophrenia as compared to allele G.
Notes: Response was assessed by changes in PANSS score. A reduction of 50% or more in PANSS score was classified as a good response.
Article: Population pharmacokinetics of Daunorubicin in adult patients with acute myeloid leukemia
Gene: CBR1
Variant/haplotype: rs25678
Drug(s): daunorubicin
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype CC is associated with decreased exposure to daunorubicin in people with Leukemia, Myeloid, Acute as compared to genotypes CG + GG.
Notes: as measured by lower AUC of daunorubicin. Patients who achieved complete remission (CR) had significantly lower plasma Daunorubicin AUC, but relationship of variant and clinical outcome was not tested.
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: yes
Association: Genotype CT is associated with decreased metabolism 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: Race, Gender, and Genetic Polymorphism Contribute to Variability in Acetaminophen Pharmacokinetics, Metabolism, and Protein-Adduct Concentrations in Healthy African-American and European-American Volunteers
Gene: CYP3A5
Variant/haplotype: rs776746
Drug(s): acetaminophen
Phenotype category: Metabolism/PK
Significant: no
Association: Allele C is not associated with metabolism of acetaminophen in healthy individuals as compared to allele T.
Article: Analysis of Genetic and Clinical Factors Associated with Buprenorphine Response
Variant/haplotype: rs7205113
Drug(s): buprenorphine
Phenotype category: Efficacy
Significant: yes
Association: Allele T is associated with increased response to buprenorphine in people with Opioid-Related Disorders as compared to allele C.
Notes: Authors note that this association is nominally significant.
Article: Pharmacogenetics of tenofovir clearance among Southern Africans living with HIV
Variant/haplotype: rs7282679
Drug(s): tenofovir
Phenotype category: Metabolism/PK
Significant: no
Association: Allele A is not associated with clearance of tenofovir in people with HIV Infections as compared to allele T.
Notes: Significance threshold was set at 5E-9. This variant was in linkage disequilibrium with rs2829679.
Article: Replication study of polymorphisms associated with response to methotrexate in patients with rheumatoid arthritis
Gene: TYMS
Variant/haplotype: rs2847153
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: Positive effects of methylphenidate on hyperactivity are moderated by monoaminergic gene variants in children with autism spectrum disorders
Gene: DRD1
Variant/haplotype: rs5326
Drug(s): methylphenidate
Phenotype category: Efficacy
Significant: yes
Association: Genotypes CT + TT are associated with increased response to methylphenidate in children with Autism Spectrum Disorder as compared to genotype CC.
Notes: Positive response defined as Clinical Global Impression-Improvement (CGI-I) rating of 'much improved' or 'very much improved', and decrease in Aberrant Behavior Checklist-Hyperactivity subscale of >25% from baseline. This result was not significant when considering correction for multiple testing (p<0.002). Please note that alleles have been complemented to the plus chromosomal strand.
Article: Variation in KCNQ1 is associated with therapeutic response to sulphonylureas
Gene: KCNQ1
Variant/haplotype: rs163184
Drug(s): gliclazide, glimepiride, glipizide, glyburide
Phenotype category: Efficacy
Significant: yes
Association: Genotypes GT + TT is associated with increased clinical benefit to gliclazide, glimepiride, glipizide or glyburide in people with Diabetes Mellitus, Type 2 as compared to genotype GG.
Notes: "After sulphonylurea therapy, patients in the TT+TG group achieved significantly lower FPG levels in comparison with patients with the GG genotype (6.95±0.13 vs. 7.50±0.21 mmol/L, p=0.033). Consequently, ΔFPG was significantly higher in the TT+TG group compared to the GG group (1.58±0.13 vs. 1.04±0.18 mmol/L, p=0.016) (Table 3)."
Article: Effect of CYP3A4 and PPARA polymorphism on concentration-to-dose ratio and adverse effects of tacrolimus in Pakistani liver transplant recipients
Gene: CYP3A4
Variant/haplotype: rs35599367
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotypes AA + AG is associated with increased concentrations of tacrolimus in people with liver transplantation as compared to genotype GG.
Notes: Alleles complemented to plus chromosomal strand. Difference was seen at week 1 and 2 but not 3 and 4.
Article: Population pharmacokinetic approach to evaluate the effect of CYP2D6, CYP3A, ABCB1, POR and NR1I2 genotypes on donepezil clearance
Gene: ABCB1
Variant/haplotype: rs2032582
Drug(s): donepezil
Phenotype category: Metabolism/PK
Significant: no
Association: Genotype CC is not associated with clearance of donepezil in people with Alzheimer Disease as compared to genotype AA.
Notes: Genotypes of AA, AC and CC did not influence donepezil clearance in a covariate model. Alleles have been complemented to the plus chromosomal strand.
Article: Possible Genetic Determinants of Response to Phenytoin in a Group of Colombian Patients With Epilepsy
Gene: SCN1A
Variant/haplotype: rs3812718
Drug(s): phenytoin
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with resistance to phenytoin in people with Epilepsy as compared to allele C.
Notes: No significant association between the variant and the number of patients with drug-resistant epilepsy. Please note that alleles have been complemented to the positive strand.
Article: Genetic variants in CYP2A6 and UGT1A9 genes associated with urinary nicotine metabolites in young Mexican smokers
Gene: CYP2A6
Variant/haplotype: CYP2A6*1, CYP2A6*12
Drug(s): 3-hydroxycotinine
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2A6 *1/*12 is associated with decreased concentrations of 3-hydroxycotinine as compared to CYP2A6 *1/*1.
Article: The role of IL10 and IL17 gene polymorphisms in treatment response in children and adolescents with severe asthma
Gene: IL10
Variant/haplotype: rs3024498
Drug(s): budesonide, fluticasone/salmeterol, formoterol, omalizumab
Phenotype category: Efficacy
Significant: yes
Association: Genotypes CC + CT is associated with decreased clinical benefit to budesonide, fluticasone/salmeterol, formoterol or omalizumab in children with Asthma as compared to genotype TT.
Notes: "As can be seen in Table 3, patients with at least one rs3024498 C allele in the IL10 gene were found to be at a greater risk of having uncontrolled asthma despite regular treatment. " "Some patients were using dry-powder inhalers that delivered a combination of budesonide and formoterol, whereas others were using pressurized metered-dose inhalers that delivered a combination of fluticasone and salmeterol or omalizumab only"
Article: Effects of Genetic Polymorphisms of Drug Metabolizing Enzymes and co-Medications on Tamoxifen Metabolism in Black South African Women with Breast Cancer
Gene: CYP2D6
Variant/haplotype: CYP2D6*1, CYP2D6*2, CYP2D6*17, CYP2D6*29
Drug(s): endoxifen
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2D6 *17/*29 + *17/*17 (assigned as poor metabolizer phenotype) is associated with decreased concentrations of endoxifen in women with Breast Neoplasms as compared to CYP2D6 *1/*1 + *1/*2 + *2/*2 (assigned as normal metabolizer phenotype) .
Notes: in patients treated with tamoxifen.
Article: Novel Associations of VKORC1 Variants with Higher Acenocoumarol Requirements
Gene: VKORC1
Variant/haplotype: rs61742245
Drug(s): acenocoumarol
Phenotype category: Dosage
Significant: yes
Association: Genotypes AA + AC is associated with increased dose of acenocoumarol as compared to genotype CC.
Notes: 22 mg/week carriers vs 14 mg/week non-carriers.
Article: Genome-wide association study of antidepressant response: involvement of the inorganic cation transmembrane transporter activity pathway
Gene: NBEA
Variant/haplotype: rs9315310
Drug(s): antidepressants
Phenotype category: Efficacy
Significant: yes
Association: Allele T is associated with increased response to antidepressants in people with Depressive Disorder, Major as compared to allele C.
Notes: Identity of minor allele not specified, so minor allele of dbSNP used here. Remission considered to be score < or equal to 7 at discharge of the Hamilton Rating Scale for Depression (HRSD17). Patients measured at admission and discharge, 4-6 weeks later. Specific antidepressants not listed.
Article: G PROTEIN RECEPTOR KINASE 4 (GRK4) POLYMORPHISMS: BETA-BLOCKER PHARMACOGENETICS AND TREATMENT RELATED OUTCOMES IN HYPERTENSION
Gene: GRK4
Variant/haplotype: rs2960306
Drug(s): atenolol
Phenotype category: Efficacy
Significant: yes
Association: Allele T is associated with decreased response to atenolol in people with Hypertension as compared to allele G.
Notes: This decrease in response was only significant*  when considered as part of a haplotype with rs1024323.  The finding was that  increasing copies of rs2960306T-rs1024323T haplotype were associated with significantly reduced atenolol-induced diastolic blood pressure lowering (-9.1±6.8 versus -6.8±7.1 versus -5.3±6.4 mm Hg in participants with 0, 1, and 2 copies respectively).  Analysis of the SNP alone showed a trend towards decreased response with the T allele.  The association of the haplotype was only observed in rs1801253 CC genotypes in Whites.; *= authors state that the data are statistically significant when Bonferroni-corrected for the number of SNPs tested in the analysis but that they do not meet chip-wide Bonferroni-corrected significance.
Article: Opioid response in paediatric cancer patients and the Val158Met polymorphism of the human catechol-O-methyltransferase (COMT) gene: an Italian study on 87 cancer children and a systematic review
Gene: COMT
Variant/haplotype: rs4680
Drug(s): opioids
Phenotype category: Dosage
Significant: yes
Association: Genotype AG is associated with decreased dose of opioids in children as compared to genotype GG.
Notes: Patients with the AG genotype had reduced consumption of opioids compared to those with the GG genotype.
Article: A pharmacogenetic study of docetaxel and thalidomide in patients with castration-resistant prostate cancer using the DMET genotyping platform
Gene: PPARD
Variant/haplotype: rs7769719
Drug(s): docetaxel, thalidomide
Phenotype category: Efficacy
Significant: yes
Association: Allele G is associated with increased response to docetaxel and thalidomide in people with Prostatic Neoplasms as compared to allele A.
Notes: (allele inferred by frequency comparison with dbSNP, actual base not listed in paper)
Article: Functional characterization of novel rare CYP2A6 variants and potential implications for clinical outcomes
Gene: CYP2A6
Variant/haplotype: rs5031016
Drug(s): nicotine
Phenotype category: Metabolism/PK
Significant: not stated
Association: Allele G is associated with decreased metabolism of nicotine as compared to allele A.
Notes: Assigned as loss-of-function following in vitro assessments, in vivo associations and variant construct functional assignments. This variant is referred to in the paper as being equivalent to *7 however, this variant is found in multiple CYP2A6 alleles.
Article: The Association of Transporter Genes Polymorphisms and Lung Cancer Chemotherapy Response
Variant/haplotype: rs2077737
Drug(s): platinum
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with response to platinum in people with Lung Neoplasms as compared to allele C.
Notes: 26 SNPs were selected which satisfied the following criteria: 1) SNPs were from HapMap Project Phase II of the Han Chinese population 2) were haplotype tagger SNPs 3) SNP minor allele frequency was higher than 5% in Han Chinese 4) the pairwise linkage disequilibrium correlation coefficient (r-squared) was greater than 0.8. After Bonferroni corrections no SNPs remained significantly associated with platinum drug efficacy.
Article: Cytochrome P450 Genetic Variation Associated with Tamoxifen Biotransformation in American Indian and Alaska Native People
Gene: CYP3A4
Variant/haplotype: CYP3A4 poor metabolizer and intermediate metabolizer genotypes
Drug(s): N-desmethyltamoxifen
Phenotype category: Metabolism/PK
Significant: no
Association: CYP3A4 poor metabolizer and intermediate metabolizer genotypes are not associated with concentrations of n-desmethyltamoxifen in women with Breast Neoplasms.
Article: Genetic polymorphisms are associated with individual susceptibility to dexmedetomidine
Gene: KCNMA1
Variant/haplotype: rs16934182
Drug(s): dexmedetomidine
Phenotype category: Dosage
Significant: yes
Association: Genotypes AA + AG is associated with decreased dose of dexmedetomidine in people with surgery as compared to genotype GG.
Notes: "In our study, carriers of the minor allele (GA/AA) required less DXM to reach the ideal sedation status than homozygosity for the major allele (GG) (29.16 ± 1.38 vs. 38.23 ± 11.02, p = 0.034). Heterozygosity or homozygosity for the minor allele A) of KCNMA1 rs16934182 was a factor in more sensitizing to DXM sedation."
Article: Genetic Variations in Attention Deficit Hyperactivity Disorder Subtypes and Treatment Resistant Cases
Gene: COMT
Variant/haplotype: rs4680
Drug(s): methylphenidate
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with response to methylphenidate in children with Attention Deficit Disorder with Hyperactivity as compared to allele A.
Notes: Patients underwent the same naturalistic assessment procedure to evaluate the treatment response, which included the reapplication of the CPRS, CTRS, CGI-S, GAS, CPT and TMT A and B. Treatment responders were defined as follows: patients registering 2 points or greater improvement on the CGI-S and a total GAS score of 60 points or greater (out of 108 subjects 66.6% responded to the treatment, while 33.3% did not). No association for distribution of genotypes according to treatment response.
Article: The Polymorphic Nuclear Factor NFIB Regulates Hepatic CYP2D6 Expression and Influences Risperidone Metabolism in Psychiatric Patients
Gene: NFIB
Variant/haplotype: rs28379954
Drug(s): paliperidone, risperidone
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype CT is associated with increased concentrations of paliperidone and risperidone as compared to genotype TT.
Notes: among CYP2D6 normal metabolizers measuring metabolite-to-parent ratio (MPR) of risperidone and 9-hydroxyrisperidone (paliperidone). No CC were reported.
Article: Secondary metabolism pathway polymorphisms and plasma efavirenz concentrations in HIV-infected adults with CYP2B6 slow metabolizer genotypes
Gene: CYP2A6
Variant/haplotype: rs28399433
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele C is associated with decreased metabolism of efavirenz in people with HIV Infections as compared to allele A.
Notes: As measured by increased plasma concentrations in patients with the AC genotype compared to the CC genotype. One White subject had the C on one allele and a CYP2A6 deletion of the other allele. When this subject was removed from univariate analysis the association with this SNP remained (p=9.4x10-4).  *Note: All participants were CYP2B6 slow metabolizers (defined by the following genotypes of two SNPs: rs3745274 TT, or  rs3745274 T/rs28399499 C or rs28399499 CC).* Alleles have been complemented to the plus chromosomal strand.
Article: Germline Polymorphisms as Biomarkers of Tumor Response in Colorectal Cancer Patients Treated with Anti-EGFR Monoclonal Antibodies: A Systematic Review and Meta-Analysis
Gene: FCGR2A
Variant/haplotype: rs1801274
Drug(s): cetuximab, panitumumab
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with response to cetuximab or panitumumab in people with Colorectal Neoplasms as compared to allele A.
Notes: Meta-analysis with 15 studies. The authors did not provide the exact number of patients but stated that "the median number of patients per analysis was 110 (range 50 - 740)". Most definitions of response were variations of the RECIST criteria. Please note that alleles have been complemented to the plus chromosomal strand.
Article: Personalized CFTR Modulator Therapy for G85E and N1303K Homozygous Patients with Cystic Fibrosis
Gene: CFTR
Variant/haplotype: rs75961395
Drug(s): elexacaftor / tezacaftor / ivacaftor
Phenotype category: Efficacy
Significant: not stated
Association: Genotype AA is associated with increased clinical benefit to elexacaftor / tezacaftor / ivacaftor in people with Cystic Fibrosis.
Notes: "Elexacaftor/tezacaftor/ivacaftor (ETI) therapy improves clinical outcomes in the G85E/G85E patient."