shlokn/autogkb huggingface dataset:
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: rs496503
Drug(s): antiepileptics
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to antiepileptics in people with Epilepsy, Generalized as compared to allele G.
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: Genome-wide study of resistant hypertension identified from electronic health records
Gene: CLNK
Variant/haplotype: rs13144136
Drug(s): Antihypertensives
Phenotype category: Efficacy
Significant: yes
Association: Allele G is associated with increased response to Antihypertensives in people with Hypertension as compared to allele T.
Article: Influence of ABCB1 polymorphisms on aripiprazole and dehydroaripiprazole plasma concentrations
Gene: ABCB1
Variant/haplotype: rs2032582
Drug(s): aripiprazole, dehydroaripiprazole
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype CC is associated with increased concentrations of aripiprazole and dehydroaripiprazole as compared to genotype AA.
Notes: Alleles complemented. "Regarding ARI/DHA ratio, significant differences between the different variants were observed in the three SNPs analyzed. Specifically, for C3434T it was obtained an ARI/DHA ratio 37.4% higher for CC (2.35) compared to the TT variant (1.71), for G2677T 93% higher for GG (3.27) vs TT (1.69) and for C1236T 64.2% higher for CC (2.93) vs TT (1.78) (Fig. 1A). Comparing Non-T carriers vs. T carriers variants as a whole, yielded 22.3%, 70.07% and 47.43% more respectively, maintaining statistical significance (Fig. 1B)." "For ABCB1, the following variants were analyzed: C3435T (rs1045642), C2677 T/A (rs2032582) and C1236T (rs1128503)."
Article: SNPs in PRKG1 and SPATA13-AS1 are associated with bronchodilator response: A pilot study during acute asthma exacerbations in African American children
Variant/haplotype: rs7081864
Drug(s): salbutamol
Phenotype category: Efficacy
Significant: yes
Association: Allele A is associated with decreased response to salbutamol in children with Asthma as compared to allele G.
Notes: rs7903366 was significantly negatively associated with having a high bronchodilator response category in an adjusted analysis. Risk allele not explicit stated in text only in table 1 summarizing prior studies.
Article: Polymorphism of Drug Transporters, Rather Than Metabolizing Enzymes, Conditions the Pharmacokinetics of Rasagiline
Gene: ABCB1
Variant/haplotype: rs1045642
Drug(s): rasagiline
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotypes AA + AG is associated with decreased clearance of rasagiline in healthy individuals as compared to genotype GG.
Notes: lower Vd/F and Cl/F and higher AUC0-∞/DW were significant and Vd/F remained significant after Bonferroni.
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: FCGR3A
Variant/haplotype: rs396991
Drug(s): cetuximab, panitumumab
Phenotype category: Efficacy
Significant: no
Association: Allele C 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: CYP4F2 rs2108622: a minor significant genetic factor of warfarin dose in Han Chinese patients with mechanical heart valve replacement
Gene: VKORC1
Variant/haplotype: rs7294
Drug(s): warfarin
Phenotype category: Dosage, Efficacy
Significant: yes
Association: Genotypes CT + TT are associated with increased dose of warfarin in people with mechanical heart valve replacement as compared to genotype CC.
Article: Combined study of genetic and epigenetic biomarker risperidone treatment efficacy in Chinese Han schizophrenia patients
Gene: COMT
Variant/haplotype: rs9606186
Drug(s): risperidone
Phenotype category: Efficacy
Significant: no
Association: Allele C is not associated with response to risperidone in people with Schizophrenia as compared to allele G.
Notes: Please note that alleles have been complemented to the positive strand.
Article: Variation in the Gene Encoding the Serotonin 2A Receptor Is Associated with Outcome of Antidepressant Treatment
Gene: HTR2A
Variant/haplotype: rs6313
Drug(s): citalopram
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to citalopram in people with Depressive Disorder, Major as compared to allele G.
Notes: Remitters achieved a QIDS-C score of <= 5 at the last treatment visit; probable remitters achieved a score of 6 or 7. Non- remitters had a QIDS-C16 score of >= 10 at the last visit. Those with a final QIDS-C16 score in the borderline range of 8 and 9 were excluded from analysis. Responders achieved at least a 50% reduction in base- line QIDS-C16 at the last treatment visit; probable respond- ers achieved a 45%–50% reduction. Nonresponders did not achieve even a 40% reduction in baseline QIDS-C score at the last treatment visit. Those with a reduction in QIDS-C16 in the borderline range of 40%–45% were excluded from analysis.
Article: Genetic Variants Influencing Plasma Renin Activity in Hypertensive Patients from the Pharmacogenomic Evaluation of Antihypertensive Responses (PEAR) Study
Variant/haplotype: rs16872401
Drug(s): hydrochlorothiazide
Phenotype category: Efficacy
Significant: yes
Association: Allele C is associated with increased response to hydrochlorothiazide in people with Hypertension as compared to allele T.
Notes: The C allele was associated with an increased systolic blood pressure response to hydrochlorothiazide.
Article: Genetic variants related to successful migraine prophylaxis with verapamil
Gene: PCDHB8
Variant/haplotype: rs3733694
Drug(s): verapamil
Phenotype category: Efficacy
Significant: yes
Association: Allele G is associated with decreased clinical benefit to verapamil in people with Migraine NOS as compared to allele A.
Notes: "There are 3 highly significant SNPs (p‐value < 0.008) in both the arithmetic and percentage change models: rs2230433 within the Integrin Subunit Alpha L gene (ITGAL) [OMIM#153370], rs17844444 in Protocadherin Beta 6 gene (PCDHB6) [OMIM#606332] and rs3733694 in Protocadherin Beta 7 gene (PCDHB7) [OMIM#606333]." "rs17844444 (PCDHB6) and rs3733694 (PCDHB7), the minor alleles predicted non‐response to verapamil."
Article: Association of variants in NEDD4L with blood pressure response and adverse cardiovascular outcomes in hypertensive patients treated with thiazide diuretics
Gene: NEDD4L
Variant/haplotype: rs4149601
Drug(s): atenolol
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with response to atenolol in people with Hypertension as compared to allele A.
Article: Effect of CYP2B6 Gene Polymorphisms on Efavirenz Plasma Concentrations in Chinese Patients with HIV Infection
Gene: CYP2B6
Variant/haplotype: rs3745274
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotypes GT + TT are associated with increased concentrations of efavirenz in people with HIV Infections as compared to genotype GG.
Article: TOLLIP, MUC5B, and the Response to N-Acetylcysteine among Individuals with Idiopathic Pulmonary Fibrosis
Gene: TOLLIP
Variant/haplotype: rs5743854
Drug(s): acetylcysteine
Phenotype category: Efficacy
Significant: no
Association: Genotype CC is not associated with response to acetylcysteine in people with Pulmonary Fibrosis as compared to genotypes CG + GG.
Notes: Clinical endpoints included death, transplant, hospitalization, or FVC decline,  and risk was adjusted for age, sex, prednisone use, azathioprine use, FVC, diffusion capacity of the lung, and trial/center. Alleles given on reverse strand A and G.
Article: The International SSRI Pharmacogenomics Consortium (ISPC): a genome-wide association study of antidepressant treatment response
Variant/haplotype: rs6889896
Drug(s): Selective serotonin reuptake inhibitors
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with response to Selective serotonin reuptake inhibitors in people with Depressive Disorder, Major as compared to allele G.
Notes: The allele did not reach genome wide significance in the discovery or replication cohorts. GWA analyses were performed for two phenotypes: ‘% change in HRSD-17 score’ (% HRSD defined as the change in HRSD-17 score divided by the baseline score) and ‘response’ (defined as greater than or equal to 50% reduction in HRSD-17 score from baseline to 4-week visit).
Article: Association of the PPP3CA c.249G>A variant with clinical outcomes of tacrolimus-based therapy in kidney transplant recipients
Gene: PPP3CA
Variant/haplotype: rs3730251
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: no
Association: Genotypes CT + TT is not associated with exposure to tacrolimus in people with Kidney Transplantation as compared to genotype CC.
Notes: No association was found between this variant and dose, concentration or dose-adjusted concentration of tacrolimus. The authors do not show the data underlying these results in the paper. Please note that alleles have been complemented to the plus chromosomal strand.
Article: Impact of CYP3A4*1G Allele on Clinical Pharmacokinetics and Pharmacodynamics of Clopidogrel
Gene: CYP3A4
Variant/haplotype: rs2242480
Drug(s): clopidogrel
Phenotype category: Efficacy
Significant: no
Association: Genotype C/T is not associated with metabolism of clopidogrel in people with Coronary Artery Disease as compared to genotype C/C.
Notes: No significant difference in concentrations of clopidogrel or its metabolites between genotype groups. The publication reports the finding for CYP3A4*1G. PharmVar re-assigned CYP3A4*1G to CYP3A4*36. Previously, this annotation used CYP3A4*36 which has been retired by PharmVar. All references to *36 have been replaced by rs2242480 alleles.
Article: The International SSRI Pharmacogenomics Consortium (ISPC): a genome-wide association study of antidepressant treatment response
Variant/haplotype: rs16871297
Drug(s): Selective serotonin reuptake inhibitors
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with response to Selective serotonin reuptake inhibitors in people with Depressive Disorder, Major as compared to allele A.
Notes: The allele did not reach genome wide significance in the discovery or replication cohorts. GWA analyses were performed for two phenotypes: ‘% change in HRSD-17 score’ (% HRSD defined as the change in HRSD-17 score divided by the baseline score) and ‘response’ (defined as greater than or equal to 50% reduction in HRSD-17 score from baseline to 4-week visit).
Article: Naltrexone Modification of Drinking Effects in a Sub-Acute Treatment and Bar-Lab Paradigm: Influence of OPRM1 and Dopamine Transporter (SCL6A3) Genes
Gene: OPRM1
Variant/haplotype: rs1799971
Drug(s): naltrexone
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to naltrexone in people with Alcoholism as compared to allele G.
Notes: It should be noted that no overall effect of naltrexone treatment on alcohol consumption was observed. The authors suggest that this may be due to differences in the study cohort, bias or a type II error.
Article: Diplotype analysis of NUDT15 variants and 6-mercaptopurine sensitivity in pediatric lymphoid neoplasms
Gene: NUDT15
Variant/haplotype: NUDT15*1, NUDT15*2, NUDT15*3, NUDT15*5, NUDT15*6
Drug(s): mercaptopurine
Phenotype category: Dosage, Toxicity
Significant: no
Association: NUDT15 *1/*3 is associated with decreased dose of mercaptopurine in children with Precursor Cell Lymphoblastic Leukemia-Lymphoma as compared to NUDT15 *1/*1 + *1/*5 + *1/*6 + *1/*2.
Notes: Doses were adjusted to give maintain a leukocyte count of 1500–3000 /µl. Mean dose for *1/*1, *1/*2, *1/*5 or *1/*6 was approximately 40mg/m2, and for *1/*3 was approx 20mg/m2 and for *3/*3 and *3/*5 was approx 5mg/m2.
Article: Single nucleotide polymorphisms in the apolipoprotein B and low density lipoprotein receptor genes affect response to antihypertensive treatment
Gene: APOB
Variant/haplotype: rs1367117
Drug(s): irbesartan
Phenotype category: Efficacy
Significant: yes
Association: Genotype GG is associated with response to irbesartan in people with Hypertension.
Notes: reduction in systolic blood pressure.  Treatment was with 150 mg/day for 12 weeks.  The dose was doubled; after six weeks if the diastolic blood pressure was >= 90; mmHg.; Avg reduction in G carriers was 14 mm Hg.
Article: A single tumour necrosis factor haplotype influences the response to adalimumab in rheumatoid arthritis
Gene: TNF
Variant/haplotype: rs1799724
Drug(s): adalimumab
Phenotype category: Efficacy
Significant: yes
Association: Genotype CC is associated with decreased response to adalimumab in people with Arthritis, Rheumatoid.
Notes: When in a haplotype with rs1800629 and rs361525.  Response defined as a 50% percent response to adalimumab therapy according to the American College of Rheumatology criteria (ACR50 responders) at week 12 after treatment initiation. Those homozygous for the GGC (rs361525-rs1800629-rs1799724) haplotype had a significantly lower ACR50 response rate as compared to subjects with any other diplotype (see paper for diplotypes present in population). This effect was more important in a subgroup of patients receiving concomitant methotrexate.
Article: Genome-Wide Meta-Analysis of Cotinine Levels in Cigarette Smokers Identifies Locus at 4q13.2
Gene: CHRNA5
Variant/haplotype: rs16969968
Drug(s): cotinine
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele A is associated with increased concentrations of cotinine in people with Tobacco Use Disorder as compared to allele G.
Notes: The authors conducted a GWAS meta-analysis to identify genetic variants associated with cotinine in current daily smokers (Caucasian). The following study cohorts were analyzed: ALSPAC, CARDIA, FinnTwin, Framingham, GenMets, MESA, NESDA, NTR, TwinsUK, YFS. This SNP was re-analyzed because of previous evidence demonstrating association with smoking quantity. It was also significantly associated with cotinine levels in the meta-analysis.
Article: Pharmacogenetic association with early response to intravitreal ranibizumab for age-related macular degeneration in a Korean population
Gene: VEGFA
Variant/haplotype: rs833069
Drug(s): ranibizumab
Phenotype category: Efficacy
Significant: yes
Association: Genotypes CC + CT are associated with increased response to ranibizumab in people with Macular Degeneration as compared to genotype TT.
Notes: Age-related macular degeneration. Patients with the CC or CT genotype had greater decreases in central subfield macular thickness (CSMT) between baseline and 3 or 6 months of treatment, as compared to those with the TT genotype. This indicates a better visual outcome. Please note alleles have been complemented to the plus chromosomal strand.
Article: Functional genetic variation in the Rev-Erbα pathway and lithium response in the treatment of bipolar disorder
Gene: CLOCK
Variant/haplotype: rs3736544
Drug(s): lithium
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with increased response to lithium in people with Bipolar Disorder as compared to allele G.
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: GABRA1
Variant/haplotype: rs2290732
Drug(s): carbamazepine
Phenotype category: Efficacy
Significant: yes
Association: Genotypes AA + AG are associated with increased response to carbamazepine in people with Epilepsy as compared to genotype GG.
Notes: Patients with the AA and AG genotypes have increased tolerability to carbamazepine. Tolerability was assessed by retention rates, or the proportion of patients that continued to take carbamazepine for seizures over the previous 3 months. Patients were assessed every 3 months for 24 months. The retention rates for the AA + AG genotypes were significantly greater than the retention rate for the GG genotype during months 9 - 24 of treatment.
Article: Effects of genetic polymorphisms on methotrexate levels and toxicity in Chinese patients with acute lymphoblastic leukemia
Gene: SLC19A1
Variant/haplotype: rs3788200
Drug(s): methotrexate
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotypes AG + GG is associated with increased concentrations of methotrexate in people with Precursor Cell Lymphoblastic Leukemia-Lymphoma as compared to genotype AA.
Notes: at 24 hours.
Article: Genetic variant in folate homeostasis is associated with lower warfarin dose in African Americans
Gene: FPGS
Variant/haplotype: rs7856096
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Allele G is associated with decreased dose of warfarin as compared to allele A.
Notes: In the discovery cohort the uncorrected p-value was 1.82E-8. P-values were adjusted using Bonferroni correction, with a significance cutoff of 3.22E-7 based on the 155,186 SNPs tested in the discovery cohort.
Article: Pharmacokinetics and Safety of Voriconazole Intravenous-to-Oral Switch Regimens in Immunocompromised Japanese Pediatric Patients
Gene: CYP2C19
Variant/haplotype: CYP2C19*1, CYP2C19*2, CYP2C19*3, CYP2C19*17
Drug(s): voriconazole
Phenotype category: Metabolism/PK
Significant: not stated
Association: CYP2C19 *1/*2 + *1/*3 + *2/*2 + *2/*3 + *3/*3 is associated with increased concentrations of voriconazole in children as compared to CYP2C19 *1/*1 + *1/*17 (assigned as normal metabolizer phenotype) .
Notes: Patients were being switched from intravenous (IV) to oral voriconazole. 20 patients were present for the IV portion, and 18 for the oral portion. In both the IV and oral treatment groups, those who were CYP2C19 poor metabolizers (PM; n=2; *2/*2, *2/*3 or *3/*3 genotype) had the highest area under the curve over dosing interval at steady state (AUC0-12,ss), peak plasma concentration at steady state (Cmax, ss) and trough plasma concentration at steady state (Cmin, ss), followed by heterozygous extensive metabolizers (HEM; n=10; *1/*2 or *1/*3) and then extensive metabolizers (EM; n=8 for IV and n=6 for oral; *1/*1 or *1/*17). That is, PM > HEM > EM for AUC0-12, Cmax and Cmin. Concordant results were also found when considering the N-oxide metabolite/voriconazole ratio of AUC0-12,ss, with PMs having the lowest ratio, followed by HEMs and then EMs. However: 1) no statistical analyses were done on these differences, 2) the authors do not state whether each of these genotypes were actually present in the population, and 3) the authors state that there was substantial overlap in voriconazole concentrations between the EM and HEM groups.
Article: Polymorphisms in the VKORC1 gene are strongly associated with warfarin dosage requirements in patients receiving anticoagulation
Gene: VKORC1
Variant/haplotype: rs2359612
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Allele G is associated with increased dose of warfarin as compared to allele A.
Article: Population Pharmacokinetics of Oral Topotecan in Infants and Very Young Children with Brain Tumors Demonstrates a Role of ABCG2 rs4148157 on the Absorption Rate Constant
Gene: ABCG2
Variant/haplotype: rs4148157
Drug(s): topotecan
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotypes AA + AG is associated with increased concentrations of topotecan in children with Brain Neoplasms as compared to genotype GG.
Notes: Absorption rate constant and circulating concentrations. Patients homozygous or heterozygous for G>A demonstrated Ka 2-fold higher than patients with GG genotype, and also a 2-fold higher maximal concentration. Patients stratified into one of three risk arms base on stage of metastasis, diagnosis, extent of resection, histologic subtype, and age at diagnosis (into low, intermediate, high). Each treatment arm had induction, consolidation, maintenance. During maintenance, patients got oral topotecan (0.8 mg/m2) for ten days and oral cyclophosphamide (30 mg/m2) for 21 days on a 28-day cycle for three cycles.
Article: Attempted validation of 44 reported SNPs associated with tacrolimus troughs in a cohort of kidney allograft recipients
Gene: CYP3A7
Variant/haplotype: rs2257401
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele C is associated with trough concentration of tacrolimus in people with Kidney Transplantation and Transplantation as compared to allele G.
Notes: This study was attempting to validate reported variants and tacrolimus trough concentration in a large population of African American and European American kidney transplant patients, this passed validation in the EA cohort. Direction of effect was not stated.
Article: CYP4F2 rs2108622: a minor significant genetic factor of warfarin dose in Han Chinese patients with mechanical heart valve replacement
Gene: VKORC1
Variant/haplotype: rs9923231
Drug(s): warfarin
Phenotype category: Dosage, Efficacy
Significant: yes
Association: Genotype TT is associated with decreased dose of warfarin in people with mechanical heart valve replacement as compared to genotypes CC + CT.
Notes: 2.6 mg/day vs 4.0 mg/day.
Article: CBR1 and CBR3 pharmacogenetics and their influence on doxorubicin disposition in Asian breast cancer patients
Gene: CBR1
Variant/haplotype: rs20572
Drug(s): doxorubicin
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype CC is associated with decreased concentrations of doxorubicin in people with Breast Neoplasms as compared to genotype CT.
Article: CYP2C9*1B Promoter Polymorphisms, in Linkage with CYP2C19*2, Affect Phenytoin Autoinduction of Clearance and Maintenance Dose
Gene: CYP2C9
Variant/haplotype: rs12782374
Drug(s): phenytoin
Phenotype category: Dosage, Metabolism/PK
Significant: yes
Association: Genotypes AA + AG are associated with decreased dose of phenytoin in people with Epilepsy as compared to genotype GG.
Notes: Statistics given for haplotype *1B measured by rs71486745delTG and rs12782374G>A.
Article: A multi-factorial analysis of response to warfarin in a UK prospective cohort
Gene: CYP4F2
Variant/haplotype: rs2108622
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Allele T is associated with dose of warfarin as compared to allele C.
Notes: The CYP4F2 variant only plays a small effect on warfarin mean weekly dose (MWD). It explained only a further 0.5 % of the MWD variance.