shlokn/autogkb huggingface dataset:
Article: Meta-Analysis on Pharmacogenetics of Platinum-Based Chemotherapy in Non Small Cell Lung Cancer (NSCLC) Patients
Gene: ERCC5
Variant/haplotype: rs1047768
Drug(s): Platinum compounds
Phenotype category: Efficacy
Significant: no
Association: Allele C is not associated with increased response to Platinum compounds in people with Carcinoma, Non-Small-Cell Lung as compared to allele T.
Notes: No significant relationship between genotype and drug response was detected.
Article: Genetic-based dosing in orthopedic patients beginning warfarin therapy
Gene: VKORC1
Variant/haplotype: rs9923231
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Allele A is associated with decreased dose of warfarin in people with total knee or hip arthroplasty as compared to allele G.
Notes: "Haplotype A" (defined by rs9923231A and elsewhere defined to = H1 and H2) was associated with 10.7%(95% CI 2.0 - 18.6%) reduction in therapeutic dose (defined as the dose that gave an INR in the target therapeutic range after 7 consecutive days) per copy as compared to "Haplotype B" (defined as H7,H8,H9 elsewhere).  There were 4 patients missing data for rs9923231, and for these cases haplotype was based on rs8050894 on the basis of high pairwise linkage disequilibrium.
Article: Efficacy of the pharmacologic chaperone migalastat in a subset of male patients with the classic phenotype of Fabry disease and migalastat-amenable variants: data from the phase 3 randomized, multicenter, double-blind clinical trial and extension study
Gene: GLA
Variant/haplotype: rs28935490
Drug(s): migalastat
Phenotype category: Efficacy
Significant: not stated
Association: Allele T is associated with increased response to migalastat in people with Fabry Disease.
Notes: Patients carrying the A allele showed improvements in renal function, cardiac geometry (specifically, reductions in left ventricular mass index) and gastrointestinal symptoms as well as reductions in GL-3 inclusions and plasma lyso-Gb3 and an increase in PBMC alpha-Gal A activity when treated with migalastat. Clinical benefit of migalastat was not substantially affected by disease severity. This variant was designated as an 'amenable variant' to migalastat treatment following an in vitro assay where migalastat increased the activity of alpha-Gal A by at least 3%. As all data were derived from post hoc analysis, statistical analyses were not carried out. Variant referred to as Asp313Tyr in the paper and was only found in combination with the Gly271Ser variant.
Article: Rooted in risk: genetic predisposition for low-density lipoprotein cholesterol level associates with diminished low-density lipoprotein cholesterol response to statin treatment
Gene: APOC1
Variant/haplotype: rs4420638
Drug(s): hmg coa reductase inhibitors
Phenotype category: Efficacy
Significant: yes
Association: Allele G is associated with decreased response to hmg coa reductase inhibitors in people with Cardiovascular Diseases or Hypercholesterolemia as compared to allele A.
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: Effect of the Most Relevant CYP3A4 and CYP3A5 Polymorphisms on the Pharmacokinetic Parameters of 10 CYP3A Substrates
Gene: CYP3A5
Variant/haplotype: CYP3A5*1, CYP3A5*3, CYP3A5*6, CYP3A5*7
Drug(s): amlodipine
Phenotype category: Metabolism/PK
Significant: not stated
Association: CYP3A5 *3 + *6 + *7 are associated with decreased clearance of amlodipine in healthy individuals as compared to CYP3A5 *1.
Notes: Clearance was decreased in the presence of CYP3A5 variants. Statistical analysis was not carried out due to the low number of subjects carrying CYP3A4 variants. *3 allele was identified using rs776746, *6 was identified using rs10264272 and *7 was identified using rs41303343.
Article: CYP2D6 function moderates the pharmacokinetics and pharmacodynamics of 3,4-methylene-dioxymethamphetamine in a controlled study in healthy individuals
Gene: CYP2D6
Variant/haplotype: CYP2D6*1, CYP2D6*2, CYP2D6*3, CYP2D6*4, CYP2D6*5, CYP2D6*6, CYP2D6*9, CYP2D6*10, CYP2D6*41
Drug(s): 3,4-methylenedioxymethamphetamine
Phenotype category: Efficacy
Significant: yes
Association: CYP2D6 *4/*4 + *3/*5 is associated with increased response to 3,4-methylenedioxymethamphetamine as compared to CYP2D6 *1/*4 + *1/*3 + *1/*6 + *2/*4 + *2/*5 + *9/*10 + *1/*41 + *1/*10 + *1/*9 + *2/*10 + *2/*41 + *1/*1 + *1/*2 + *2/*2.
Notes: Elevations in systolic blood pressure were greater in PMs compared with IMs (P = 0.02, *4/*10(6) *4/*41(4) *5/*10(2) *5/*41(1) *10/*41(4) *10/*10(1) *4/*9 (1)) and EMs (P = 0.01, *1/*3(2) *1/*6(2) *2/*4(15) *2/*5(1) *9/*10(2); *1/*41(4) *1/*10(2) *1/*9(3) *2/*10(3) *2/*41(5); *1/*1(22) *1/*2(23) *2/*2(16) *1/*4 (11)) at 0.6 h (F2,135 = 3.50, P = 0.03) and also tended to be greater at 1 h (F2,135 = 2.49, P = 0.09).
Article: Comprehensive Ara-C SNP score predicts leukemic cell intracellular ara-CTP levels in pediatric acute myeloid leukemia patients
Gene: SLC28A3
Variant/haplotype: rs17343066
Drug(s): ara-CTP
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype AA is associated with increased concentrations of ara-CTP in children with Leukemia, Myeloid, Acute as compared to genotypes AG + GG.
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: rs700518
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 A.
Notes: when taking letrozole alone or with lipid lowering agents (LLA), such as statins. 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 8.4).
Article: Genomic Association Analysis of Common Variants Influencing Antihypertensive Response to Hydrochlorothiazide
Variant/haplotype: rs221903
Drug(s): "diuretics", "hydrochlorothiazide", "Thiazides, plain"
Phenotype category: Efficacy
Significant: no
Association: Allele T is associated with decreased response to diuretics, hydrochlorothiazide or Thiazides, plain in people with Hypertension as compared to allele C.
Notes: There was a trend but significance was not attained. Observations: 1.77 mm Hg decreased reduction of diastolic blood pressure per T allele in PEAR + GERA, 0.08 mm Hg decreased reduction of diastolic blood pressure per T allele in NORDIL, and 1.15 mm Hg decreased reduction of diastolic blood pressure per T allele in PEAR + GERA + NORDIL.
Article: Pharmacogenetics-based area-under-curve model can predict efficacy and adverse events from axitinib in individual patients with advanced renal cell carcinoma
Gene: ABCB1
Variant/haplotype: rs1045642
Drug(s): axitinib
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele A is associated with concentrations of axitinib in people with Carcinoma, Renal Cell as compared to allele G.
Notes: The authors develop a prediction model and calculated area under the concentration curve (AUC) using 6 SNPs (rs17868323, rs3832043, rs2231142, rs2032582, rs1045642, rs35305980) was compared with actual AUC in 16 patients prospectively which significantly correlated with the objective response rate (P = 0.0002), hand-foot syndrome, P = 0.0055 and hypothyroidism, P = 0.0381, and correlated with actual AUC (P < 0.0001) - the validation study, calculated AUC prior to axitinib treatment precisely predicted actual AUC after axitinib treatment (P = 0.0066).
Article: Genome-Wide Association Study Identifies Pharmacogenomic Variants Associated With Metformin Glycemic Response in African American Patients With Type 2 Diabetes
Gene: ARFGEF3
Variant/haplotype: rs143276236
Drug(s): metformin
Phenotype category: Efficacy
Significant: yes
Association: Genotype AC is associated with decreased clinical benefit to metformin in people with Diabetes Mellitus, Type 2 as compared to genotype CC.
Notes: as measured by change in A1C. "Among individuals with; >425 mg/day average daily exposure to; metformin, individuals with the ARFGEF3; rs143276236 CC genotype had an average absolute HbA1c reduction of 0.59% whereas individuals with the AC genotype; had an average absolute HbA1c reduction; of 0.28%; these differences were statistically significant"
Article: Genetic variability in the glucocorticoid pathway and treatment outcomes in hospitalized patients with COVID-19: a pilot study
Gene: CYP3A4
Variant/haplotype: rs35599367
Drug(s): dexamethasone
Phenotype category: Efficacy
Significant: yes
Association: Genotype AG is associated with increased time to response to dexamethasone in people with COVID-19 as compared to genotype GG.
Notes: Alleles complemented. "The median duration of hospitalization in the carriers of CYP3A4 rs35599367TC genotype was 16 days longer when compared to the carriers of the CC genotype (p adj = 0.022) (Table 4)."
Article: CALCA and TRPV1 genes polymorphisms are related to a good outcome in female chronic migraine patients treated with OnabotulinumtoxinA
Gene: TRPV1
Variant/haplotype: rs222741
Drug(s): botulinum toxin type a
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with response to botulinum toxin type a in women with Migraine NOS as compared to allele A.
Notes: No significant difference in allele frequency between responders and non-responders. Please note that alleles have been complemented to the positive strand.
Article: Genome-Wide Association Study of Serum Creatinine Levels during Vancomycin Therapy
Gene: MIA3
Variant/haplotype: rs35397194
Drug(s): vancomycin
Phenotype category: Metabolism/PK
Significant: no
Association: Allele G is not associated with trough concentration of vancomycin as compared to allele A.
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: Impact of Single Nucleotide Polymorphisms on Plasma Concentrations of Efavirenz and Lopinavir/ritonavir in Chinese Children Infected with the Human Immunodeficiency Virus
Gene: SLCO1B1
Variant/haplotype: rs4149056
Drug(s): ritonavir
Phenotype category: Metabolism/PK
Significant: no
Association: Genotypes CC + CT are not associated with concentrations of ritonavir in children with HIV Infections as compared to genotype TT.
Article: Gene‐Wide Tagging Study of the Association Between KCNT1 Polymorphisms and the Susceptibility and Efficacy of Genetic Generalized Epilepsy in Chinese Population
Gene: KCNT1
Variant/haplotype: rs755722
Drug(s): antiepileptics
Phenotype category: Efficacy
Significant: no
Association: Allele C is not associated with response to antiepileptics in people with Epilepsy, Generalized as compared to allele T.
Notes: No significant differences in genotype frequencies were seen between patients who were responsive to antiepileptic drugs (n=279; those who had not experienced any type of seizure for a minimum of 1 year after receiving antiepileptic drugs) and patients who were resistant to antiepileptic drugs (n=204; those who had at least four seizures during the previous year while trying at least three antiepileptic medications at the maximal tolerated doses).
Article: Genetic Variants Associated With Uncontrolled Blood Pressure on Thiazide Diuretic/β‐Blocker Combination Therapy in the PEAR (Pharmacogenomic Evaluation of Antihypertensive Responses) and INVEST (International Verapamil‐SR Trandolapril Study) Trials
Gene: ALDH1A2
Variant/haplotype: rs261316
Drug(s): atenolol, hydrochlorothiazide
Phenotype category: Efficacy
Significant: yes
Association: Allele T is associated with decreased response to atenolol and hydrochlorothiazide in people with Hypertension as compared to allele C.
Notes: T allele associated with increased odds of uncontrolled blood pressure following thiazide diuretic/beta-blocker combination therapy. Variant only reached suggestive significance in discovery GWAS. Consistent direction of association found across discovery and replication cohorts and approached genome-wide significance in meta-analysis of all cohorts.
Article: PPAR-γ2 and PTPRD gene polymorphisms influence type 2 diabetes patients' response to pioglitazone in China
Gene: PTPRD
Variant/haplotype: rs17584499
Drug(s): pioglitazone
Phenotype category: Efficacy
Significant: yes
Association: Genotype CC is associated with increased response to pioglitazone in people with Diabetes Mellitus, Type 2 as compared to genotypes CT + TT.
Notes: Patients with the CC genotype showed significantly greater decreases in postprandial plasma glucose levels after 3 months of pioglitazone treatment. However, changes in other biochemical measures were not significant.
Article: Adiponectin Gene Polymorphism rs2241766 T/G Is Associated with Response to Pioglitazone Treatment in Type 2 Diabetic Patients from Southern China
Gene: ADIPOQ
Variant/haplotype: rs16861194
Drug(s): pioglitazone
Phenotype category: Efficacy
Significant: no
Association: Genotype AG are not associated with response to pioglitazone in people with Diabetes Mellitus as compared to genotype AA.
Notes: Response was defined as "any decrease greater than (or equal to) 15%" of glycated hemoglobin (HbA1C%).
Article: Genetic Variation of the Mu Opioid Receptor (OPRM1) and Dopamine D2 Receptor (DRD2) is Related to Smoking Differences in Patients with Schizophrenia but not Bipolar Disorder
Gene: DRD2
Variant/haplotype: rs1800497
Drug(s): nicotine
Phenotype category: Other
Significant: no
Association: Genotypes AA + AG are not associated with exposure to nicotine in people with Bipolar Disorder as compared to genotype GG.
Notes: Subgroup analysis of bipolar disorder patients only found no significant difference in number of cigarettes smoked per day between genotype groups.
Article: The effect of CYP2C9 and VKORC1 genetic polymorphisms on warfarin dose requirements in a pediatric population
Gene: CYP2C9
Variant/haplotype: CYP2C9*1, CYP2C9*2
Drug(s): warfarin
Phenotype category: Dosage
Significant: no
Association: CYP2C9 *2 is associated with decreased dose of warfarin in children as compared to CYP2C9 *1/*1.
Notes: The average daily warfarin dose required for maintenance therapy in patients with the CYP2C9*2 was 3.67±1.38, whereas it was 4.35±1.25 in those without this mutation.
Article: β1-adrenoceptor genetic varians and ethnicity independently affect response to β-blockade
Gene: ADRB1
Variant/haplotype: rs1801253
Drug(s): atenolol
Phenotype category: Efficacy
Significant: yes
Association: Allele C is associated with increased response to atenolol in healthy individuals as compared to allele G.
Notes: b1-AR Arg389 was independently associated with a greater reduction in heart rate area under the curve after exercise-induced tachycardia.
Article: Novel Polymorphisms Associated with Tacrolimus Trough Concentrations: Results from a Multicenter Kidney Transplant Consortium
Gene: CYP3A5
Variant/haplotype: rs776746
Drug(s): tacrolimus
Phenotype category: Efficacy, Metabolism/PK
Significant: yes
Association: Genotypes CT + TT are associated with increased dose of tacrolimus in people with Kidney Transplantation as compared to genotype CC.
Notes: T defines *1.
Article: PTPRD gene associated with blood pressure response to atenolol and resistant hypertension
Variant/haplotype: rs12346562
Drug(s): atenolol
Phenotype category: Efficacy
Significant: yes
Association: Genotypes AA + AC is associated with increased response to atenolol in people with Hypertension as compared to genotype CC.
Notes: The A allele of SNP rs12346562 was associated with better DBP response to atenolol, but with less pronounced response to hydrochlorothiazide. White participants with rs12346562 AA, AC, and CC genotypes had mean DBP responses of -15.0,-11.2, and -9.4 mmHg to atenolol (P=3.2x10-6, b=-2.4 mmHg; per A allele).
Article: Genetic polymorphisms are associated with individual susceptibility to dexmedetomidine
Gene: CYP2D6
Variant/haplotype: rs16947
Drug(s): dexmedetomidine
Phenotype category: Dosage
Significant: yes
Association: Genotype GG is associated with increased dose of dexmedetomidine in people with surgery as compared to genotypes AA + AG.
Notes: "In our study, homozygous carriers of the major allele (GG) took larger effective doses than those either heterozygous (GA) or homozygous for the minor allele (AA) (39.22 ± 11.76 vs. 34.84 ± 8.09, p = 0.02). The results revealed that carriers of the minor allele A) required less DXM to induce sedation."
Article: Genetic Factors Associated with Morphine Consumption in Women Undergoing Laparoscopic Cholecystectomy: A Prospective Cohort Study
Gene: METTL21A
Variant/haplotype: rs2952768
Drug(s): morphine
Phenotype category: Dosage
Significant: yes
Association: Genotype CC is associated with increased dose of morphine in women with Pain, Postoperative as compared to genotypes CT + TT.
Notes: All patients were Arab women undergoing laparoscopic cholecystectomy. "Both OPRM1 (rs1799971, A>G), and rs2952768 (T>C) showed statistically significant association with IO total morphine dose requirements.""patients homozygous for the rs2952768 (T>C) minor allele (CC) had a higher mean rank compared to the other genotypes"
Article: Evaluating metronidazole as a novel, safe CYP2A6 phenotyping probe in healthy adults
Gene: CYP2A6
Variant/haplotype: CYP2A6*1, CYP2A6*2, CYP2A6*9, CYP2A6*17
Drug(s): metronidazole
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2A6 *1/*2 + *1/*9 + *1/*17 (assigned as reduced metabolizers phenotype) are associated with decreased metabolism of metronidazole in healthy individuals as compared to CYP2A6 *1/*1 (assigned as normal metabolizer phenotype) .
Notes: Metabolite ratios for metronidazole were significantly reduced in reduced metabolizers compared to normal metabolizers. Subjects were genotyped for the *2, *4, *7, *9, *12, *17, *20, *23-*28, *31 and *35 alleles, although no details of rsIDs are given. No participants were found to have the *7 allele, so no testing for the *8 or *10 alleles was carried out.
Article: Functional characterization of novel rare CYP2A6 variants and potential implications for clinical outcomes
Gene: CYP2A6
Variant/haplotype: rs150247689
Drug(s): nicotine
Phenotype category: Metabolism/PK
Significant: not stated
Association: Allele T is not associated with metabolism of nicotine as compared to allele C.
Notes: Assigned as neutral function following in vitro assessments, in vivo associations and variant construct functional assignments.
Article: Association studies of dopamine synthesis and metabolism genes with multiple phenotypes of heroin dependence
Gene: DBH
Variant/haplotype: rs129882
Drug(s): heroin
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with response to heroin as compared to allele C.
Notes: No significant association between this variant and strength of euphoria on first heroin use.
Article: The Pharmacogenetics of Tacrolimus in Corticosteroid-Sparse Pediatric and Adult Kidney Transplant Recipients
Gene: CYP3A5
Variant/haplotype: CYP3A5*1, CYP3A5*3
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP3A5 *1/*1 + *1/*3 is associated with decreased trough concentration of tacrolimus in people with Kidney Transplantation as compared to CYP3A5 *3/*3.
Notes: For 1 year post-transplantation, CYP3A5*1 carriers had a 62% lower median tacrolimus Co/D compared with homozygote carriers of the CYP3A5*3 allele (1.34 vs 3.53 ng/ml/mg).
Article: Association of ABCB1 Polymorphisms with Efficacy and Adverse Drug Reactions of Valproic Acid in Children with Epilepsy
Gene: ABCB1
Variant/haplotype: rs1128503
Drug(s): valproic acid
Phenotype category: Efficacy
Significant: yes
Association: Genotype AA is associated with decreased clinical benefit to valproic acid in children with Epilepsy as compared to genotypes AG + GG.
Notes: Alleles complemented. "Moreover, recessive model analysis showed that the TT genotype had a higher frequency in the persistent seizure group compared with genotypes carrying at least one C allele (OR = 0.45, 95% CI = 0.24–0.85, p = 0.013),"
Article: A Common β1-Adrenergic Receptor Polymorphism Predicts Favorable Response to Rate Control Therapy in Atrial Fibrillation
Gene: ADRB1
Variant/haplotype: rs1801253
Drug(s): atenolol, carvedilol, diltiazem, metoprolol, verapamil
Phenotype category: Efficacy
Significant: yes
Association: Genotypes CG + GG are associated with increased response to atenolol, carvedilol, diltiazem, metoprolol or verapamil in people with Atrial Fibrillation as compared to genotype CC.
Notes: Reported as Gly389 carriers being more likely to respond favorably to ventricular rate control therapy and requiring the lowest doses of rate control medication compared to Arg389Arg (60 % vs 51 %). GC SNP; be careful.  Gly corresponds to G on the + strand. [stat_test: chi square].
Article: Clinical and genetic factors associated with warfarin maintenance dose in northern Chinese patients with mechanical heart valve replacement
Gene: CYP3A4
Variant/haplotype: rs28371759
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Genotype AA are associated with decreased dose of warfarin in people with heart valve replacement as compared to genotype AG.
Article: Polymorphism of the dopamine transporter type 1 gene modifies the treatment response in Parkinson’s disease
Gene: SLC6A3
Variant/haplotype: rs3836790
Drug(s): levodopa
Phenotype category: Efficacy
Significant: yes
Association: Genotype ACATACACACTCAGACACACATACCATGCA/ACATACACACTCAGACACACATACCATGCA is associated with increased response to levodopa in people with Parkinson Disease as compared to genotypes ACATACACACTCAGACACACATACCATGCA/del + del/del.
Notes: SLC6A3 rs3836790 genotype was significantly associated with the number of freezing of gait episodes, the number of steps and the completion time (with P-values of 0.004, 0.02 and 0.016, respectively). A multivariate analysis adjusted for age, gender, weight, disease duration and l-DOPA equivalent daily dose (or l-DOPA daily dose) revealed significant associations for the number of steps (P = 0.0005) the completion time (P = 0.001) and the number of freezing of gait episodes (P = 0.004).
Article: A randomized placebo-controlled trial of ataluren for the treatment of nonsense mutation cystic fibrosis
Gene: CFTR
Variant/haplotype: rs74597325
Drug(s): ataluren
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with response to ataluren in people with Cystic Fibrosis as compared to allele C.
Notes: Outcomes assessed for all nonsense mutations together (W1282X, G542X, R1162X, and R553X). Case-control study with placebo. Endpoint measured was change in Forced Expiratory Volume in 1 second. A difference was seen in the subset of patients on tobramycin.
Article: Association of carbamazepine major metabolism and transport pathway gene polymorphisms and pharmacokinetics in patients with epilepsy
Gene: ABCB1
Variant/haplotype: rs4148739
Drug(s): carbamazepine
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype TT is associated with decreased metabolism of carbamazepine in people with Epilepsy as compared to genotype CT.
Notes: as measured by a lower carbamazepine-10,11-transdihydrodiol:carbamazepine-10-11 epoxide metabolite ratio. This association was only significant in the African American patients and not in Caucasian patients.