shlokn/autogkb huggingface dataset:
Article: Integrative genomic analysis of methylphenidate response in attention-deficit/hyperactivity disorder
Gene: ETFDH
Variant/haplotype: rs11559290
Drug(s): methylphenidate
Phenotype category: Efficacy
Significant: no
Association: Allele C is associated with increased response to methylphenidate in people with Attention Deficit Disorder with Hyperactivity.
Notes: The authors carried out a GWAS in a Spanish cohort of pediatric patients, than performed a meta-analysis using data from the Spanish cohort and data from a Brazilian adult patient cohort.; This variant was not significant in the meta-analysis after Bonferroni correction had been applied, and was nominally significant (i.e did not reach genome-wide significance) in the initial GWAS in the Spanish cohort.; Response was measured on the Clinical Global Impression-Improvement scale (CGI-I). A CGI-I score of two points or less after eight weeks of treatment was considered a good response.
Article: An Expanded Analysis of Pharmacogenetics Determinants of Efavirenz Response that Includes 3′-UTR Single Nucleotide Polymorphisms among Black South African HIV/AIDS Patients
Gene: CYP2B6
Variant/haplotype: rs4803419
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: no
Association: Genotype CC is not associated with concentrations of efavirenz in people with HIV Infections as compared to genotypes CT + TT.
Article: A two-stage genome-wide association study identifies novel germline genetic variations in CACNA2D3 associated with radiotherapy response in nasopharyngeal carcinoma
Gene: CACNA2D3
Variant/haplotype: rs11130424
Drug(s): radiotherapy
Phenotype category: Efficacy
Significant: yes
Association: Genotypes AG + GG is associated with increased resistance to radiotherapy in people with Nasopharyngeal Neoplasms as compared to genotype AA.
Notes: "The G allele carriers were more resistant to radiotherapy" "The efficacy was better in minor allele carriers of rs11130424 than major allele"
Article: Variation in the Gene Encoding the Serotonin 2A Receptor Is Associated with Outcome of Antidepressant Treatment
Gene: HTR2A
Variant/haplotype: rs6311
Drug(s): citalopram
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with response to citalopram in people with Depressive Disorder, Major as compared to allele C.
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: Does i-T744C P2Y12 Polymorphism Modulate Clopidogrel Response among Moroccan Acute Coronary Syndromes Patients?
Gene: P2RY12
Variant/haplotype: rs2046934
Drug(s): clopidogrel
Phenotype category: Efficacy
Significant: no
Association: Allele G is associated with resistance to clopidogrel in people with Acute coronary syndrome as compared to allele A.
Notes: The G allele frequency was higher among resistant than nonresistant patients (30% versus 20.8%, resp.).
Article: A cis-eQTL in OPRM1 is Associated with Subjective Response to Alcohol and Alcohol Use
Gene: OPRM1
Variant/haplotype: rs1799971
Drug(s): ethanol
Phenotype category: Dosage
Significant: no
Association: Genotypes AG + GG are not associated with dose of ethanol as compared to genotype AA.
Notes: No significant association between this variant and drinking levels.
Article: CYP2D6 Phenotyping Using Urine, Plasma, and Saliva Metabolic Ratios to Assess the Impact of CYP2D6∗10 on Interindividual Variation in a Chinese Population
Gene: CYP2D6
Variant/haplotype: CYP2D6*1, CYP2D6*10
Drug(s): dextromethorphan
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2D6 *10/*10 is associated with decreased metabolism of dextromethorphan in healthy individuals as compared to CYP2D6 *1/*10.
Notes: Single dose study with 15mg dextromethorphan DM. Urine, Plasma, and Saliva Metabolic Ratios were accessed. Subjects were  genotyped by DNA sequencing analysis for CYP2D6*1, *2, *3, *4, *6, *7, *10, *14, *18, *21, *28, *33, *34, *35, *36, *39, *41, *43, *49, *51, *52, *54, *60, *63, *65, *69, *71, and *75 and CNV were determined. *1/*10 n= 93; *10/*10 n=85. The urinary, plasma, or salivary MRs increased successively in subjects with CYP*1/*1, *1/*10, *10/*10, and *5/*10 with statistical significance (all P-values < 0.001).
Article: The International SSRI Pharmacogenomics Consortium (ISPC): a genome-wide association study of antidepressant treatment response
Variant/haplotype: rs35806662
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: Association of BDNF, HTR2A, TPH1, SLC6A4, and COMT polymorphisms with tDCS and escitalopram efficacy: ancillary analysis of a double-blind, placebo-controlled trial
Gene: HTR2A
Variant/haplotype: rs6313
Drug(s): escitalopram
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to escitalopram in people with Depression as compared to allele G.
Article: The involvement of Kras gene 3′-UTR polymorphisms in risk of cancer and influence on patient response to anti-EGFR therapy in metastatic colorectal cancer: a meta-analysis
Gene: KRAS
Variant/haplotype: rs61764370
Drug(s): cetuximab, panitumumab
Phenotype category: Efficacy
Significant: no
Association: Genotypes AC + CC is not associated with response to cetuximab or panitumumab in people with Colorectal Neoplasms as compared to genotype AA.
Notes: In the results section the uncorrected p value listed looks good but when looking at Table 3 can see the corrected p value is not significant and authors state result is not significant.
Article: The Relationship Between Single Nucleotide Polymorphisms in 5-HT2A Signal Transduction-Related Genes and the Response Efficacy to Selective Serotonin Reuptake Inhibitor Treatments in Chinese Patients with Major Depressive Disorder
Gene: ADCY9
Variant/haplotype: rs2230739
Drug(s): antidepressants
Phenotype category: Efficacy
Significant: yes
Association: Genotype CC is associated with increased response to antidepressants in people with Depressive Disorder, Major as compared to genotypes CT + TT.
Notes: long term response measured using HAMD
Article: TET2 and CSMD1genes affect SBP response to hydrochlorothiazide in never-treated essential hypertensives
Variant/haplotype: rs9285669
Drug(s): hydrochlorothiazide
Phenotype category: Efficacy
Significant: no
Association: Allele A is associated with decreased response to hydrochlorothiazide in people with Essential hypertension as compared to allele T.
Notes: The SNP was discovered in two independent cohorts, although no SNPs reached genome wide significance. The authors then considered P<1 x10^-5 as a threshold for significance (based on the results from a Q-Q plot distribution reference line). Using this revised threshold the authors reported that this SNP was associated with a lower decrease in systolic blood pressure after hydrochlorothiazide treatment.
Article: Association of Polygenic Score for Schizophrenia and HLA Antigen and Inflammation Genes With Response to Lithium in Bipolar Affective Disorder: A Genome-Wide Association Study
Gene: ZNF804A
Variant/haplotype: rs62200793
Drug(s): lithium
Phenotype category: Efficacy
Significant: yes
Association: Allele T is associated with increased response to lithium in people with Bipolar Disorder as compared to allele C.
Article: The impact of non-genetic and genetic factors on a stable warfarin dose in Thai patients
Gene: CYP2C9
Variant/haplotype: rs1057910
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Genotypes AC + CC are associated with decreased dose of warfarin in people with Atrial Fibrillation, heart valve replacement, Hypertension, Pulmonary, Pulmonary Embolism and Venous Thrombosis as compared to genotype AA.
Article: Comprehensive Ara-C SNP score predicts leukemic cell intracellular ara-CTP levels in pediatric acute myeloid leukemia patients
Gene: RRM1
Variant/haplotype: rs11030918
Drug(s): ara-CTP
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotypes CT + TT is associated with decreased concentrations of ara-CTP in children with Leukemia, Myeloid, Acute as compared to genotype CC.
Article: An increase in urinary primaquine and a reduction in urinary primaquine-5,6-orthoquinone in the Thai population with CYP2D6 reduced enzyme function
Gene: CYP2D6
Variant/haplotype: CYP2D6 intermediate metabolizer
Drug(s): primaquine
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2D6 intermediate metabolizer is associated with decreased metabolism of primaquine in healthy individuals as compared to CYP2D6 normal metabolizer.
Notes: "For urine data, CYP2D6 IM showed a significant increase in normalized total CAE of primaquine compared to CYP2D6 NM (2444 (1697–3594) vs. 1757 (1092–2185) μg/mg/kg, respectively, p = 0.039, Table 3, Fig. 2, Fig. 3A), but not for CLr. The normalized total CAE of POQ was significantly lower in CYP2D6 IM than in CYP2D6 NM (115 (46–297) vs. 318 (92–498) μg/mg/kg, respectively, p = 0.047, Table 3, Fig. 2, Fig. 3B). "
Article: Pharmacokinetic Evaluation of Tacrolimus in Chinese Adult Patients during the Early Stages Post-Lung Transplantation
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 increased clearance of tacrolimus in people with lung transplantation as compared to CYP3A5 *3/*3.
Notes: Cohort was predominantly male (n=12). There was one *1/*1, 8 *1/*3 and 5 *3/*3. CYP3A5*3 (rs776746) and CYP3A4*1G (rs2242480) were genotyped. Patients received voriconazole.
Article: Genetic Variation in CYP3A43 Explains Racial Difference in Olanzapine Clearance
Gene: CYP1A2
Variant/haplotype: rs2069522
Drug(s): olanzapine
Phenotype category: Metabolism/PK
Significant: no
Association: Allele C is not associated with clearance of olanzapine in people with Schizophrenia as compared to allele T.
Article: Influence of Genetic Polymorphisms Involved in the Hypothalamic–Pituitary–Adrenal Axis and their Interactions with Environmental Factors on Antidepressant Response
Gene: CRHR1
Variant/haplotype: rs28364032
Drug(s): antidepressants
Phenotype category: Efficacy
Significant: yes
Association: Genotypes AA + AG is associated with increased response to antidepressants in people with Depressive Disorder, Major as compared to genotype GG.
Notes: Those who were classified as "remitters" had a higher frequency of the AA+AG genotype as compared to "non-remitters". Remission was defined as total HAMD-17 score of <= 7 after 8 weeks of treatment. Corrected p-values using permutation testing. Note that significant results were also seen when considering only SSRIs (allelic association p=0.024) or SNRIs (allelic association p=0.010), but these results did not withstand permutation testing.
Article: Association of genetic variation in pharmacodynamic factors with methadone dose required for effective treatment of opioid addiction
Gene: ANKK1
Variant/haplotype: rs7118900
Drug(s): methadone
Phenotype category: Dosage
Significant: no
Association: Genotypes AA + AG are associated with decreased dose of methadone in people with Heroin Dependence as compared to genotype GG.
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). Note; this association may be linked to the association with rs2283265 in the DRD2 gene.
Article: The effect of genetic variants in the transcription factor TSPYL family on the CYP3A4 mediated cyclosporine metabolism in kidney transplant patients
Gene: TSPYL1
Variant/haplotype: rs3828743
Drug(s): cyclosporine
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotypes AG + GG is associated with increased clearance of cyclosporine in men with Kidney Transplantation as compared to genotype AA.
Notes: This was significant in whole group but not in women only group. "Rs3828743 homozygous carriers showed a decreased cyclosporine CL/F compared to the combined heterozygous carriers and wildtypes (28.72 vs. 35.03, p = 0.018; Figure 2 and Table 3). Furthermore, after adjusting for CYP3A4*22 genotype, steroid usage, and body weight, the effect size of rs3828743 on cyclosporine clearance increased compared to the univariate analysis. In the multivariate model, cyclosporine clearance was 18% lower when comparing homozygous carriers to heterozygous and wildtype patients." "Interestingly, the effect of rs3828743 was only observed in men. In men, homozygous variant carriers had an ~21% decreased clearance compared to heterozygous carriers and wildtypes (28.57 vs. 35.97, p = 0.0052; Figure S2 and Table 4). By contrast, no effect of rs3828743 genotypes was observed in women with the exception of a significantly increased clearance (p = 0.026) in the heterozygous carriers compared to the wildtype women (Figure S3)."
Article: Effect of pharmacogenetics on plasma lumefantrine pharmacokinetics and malaria treatment outcome in pregnant women
Gene: CYP3A5
Variant/haplotype: rs776746
Drug(s): lumefantrine
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele C is associated with increased concentrations of lumefantrine in women with Malaria and Pregnancy as compared to allele T.
Notes: Median concentrations of lumefantrine 7 days after beginning treatment with artemether-lumefantrine was significantly higher in carriers of the C allele as compared to non-carriers.
Article: Ivacaftor: Five‐year outcomes in the West of Scotland cystic fibrosis population
Gene: CFTR
Variant/haplotype: rs75527207
Drug(s): ivacaftor
Phenotype category: Efficacy
Significant: yes
Association: Allele A is associated with increased clinical benefit to ivacaftor in children with Cystic Fibrosis.
Notes: as measured by FEV improvement after 1 and 2 years of treatment compared to baseline FEV. Patients had "at least one G551D mutation" (which is a class III) and most (75-86%) had a second mutation of class II/severe.
Article: The Cyp2b6 Gene Polymorphism and Phenotypic Correlation of Efavirenz-Based Combination Therapy Among the Niger Delta Ethnic Population: Implications in Modern Pharmacogenomics
Gene: CYP2B6
Variant/haplotype: CYP2B6*6
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: not stated
Association: CYP2B6 *6 is associated with increased concentrations of efavirenz in people with HIV Infections.
Notes: p value given for concordance of genotype with observed phenotype (UM, EM, IM, PM) where PM = 4.0–6.0ml/L plasma efavirenz (600 mg of efavirenz for at least 3 weeks) and concordant with *6/*6 and IM = 1.0–3.9mg/L plasma efavirenz and concordant with *1/*6.
Article: Induction of CYP3A4 by Vinblastine: Role of the Nuclear Receptor NR1I2
Gene: CYP3A5
Variant/haplotype: rs776746
Drug(s): midazolam
Phenotype category: Other, Metabolism/PK
Significant: no
Association: Allele T is not associated with increased clearance of midazolam in people with Carcinoma, Renal Cell as compared to allele C.
Notes: It's not clear exactly what genotype comparison was done or what the genotypes were, but there was approximately one CT subject and 5 CC subjects, and frequency entered below was based upon that. Subjects were treated with vinblastine/valspodar.   [stat_test: nonparametric 2-sided Wilcoxon signed-rank].
Article: A Novel Admixture-Based Pharmacogenetic Approach to Refine Warfarin Dosing in Caribbean Hispanics
Gene: VKORC1
Variant/haplotype: rs9923231
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Genotypes CT + TT are associated with decreased dose of warfarin as compared to genotype CC.
Notes: The authors aimed to develop an admixture-adjusted (genetic ancestry) PGx dosing algorithm for warfarin in Caribbean Hispanics from Puerto Rico. [Algorithm R sq.=0.70, MAE = 0.72 mg/day]. When externally validated with 55 individuals from an independent cohort the novel algorithm predicted 58% of the warfarin dose variance [MAE = 0.89 mg/day, 24% mean bias]. Please note: the derivation cohort was 99% male.
Article: HLA-G 3’UTR Polymorphisms Impact the Prognosis of Stage II-III CRC Patients in Fluoropyrimidine-Based Treatment
Gene: HLA-G
Variant/haplotype: rs371194629
Drug(s): capecitabine, fluorouracil
Phenotype category: Efficacy
Significant: yes
Association: Genotypes ATTTGTTCATGCCT/ATTTGTTCATGCCT + ATTTGTTCATGCCT/del is associated with increased response to capecitabine or fluorouracil in people with Colorectal Neoplasms as compared to genotype del/del.
Notes: The authors examined disease free survival (DFS) as well as overall survival (OS). The ins/del + ins/ins genotypes were associated with improved DFS, but not OS.
Article: NUDT15 c.415C>T increases risk of 6-mercaptopurine induced myelosuppression during maintenance therapy in children with acute lymphoblastic leukemia
Gene: ITPA
Variant/haplotype: rs1127354
Drug(s): mercaptopurine
Phenotype category: Dosage
Significant: no
Association: Genotype CC is not associated with dose of mercaptopurine in children with Precursor Cell Lymphoblastic Leukemia-Lymphoma as compared to genotypes AA + AC.
Notes: No significant difference in median cumulative dose was seen between the genotypes at 2 months (p=0.55), 4 months (p=0.81) or 6 months (p=0.78) of the mercaptopurine maintenance phase.
Article: Association of Polygenic Score for Schizophrenia and HLA Antigen and Inflammation Genes With Response to Lithium in Bipolar Affective Disorder: A Genome-Wide Association Study
Gene: EPHX2
Variant/haplotype: rs59724122
Drug(s): lithium
Phenotype category: Efficacy
Significant: yes
Association: Allele T is associated with increased response to lithium in people with Bipolar Disorder as compared to allele C.
Article: Lack of Association between Opioid-Receptor Genotypes and Smoking Cessation Outcomes in a Randomized, Controlled Naltrexone Trial
Gene: OPRM1
Variant/haplotype: rs2075572
Drug(s): naltrexone
Phenotype category: Efficacy
Significant: no
Association: Allele C is not associated with response to naltrexone in people with Tobacco Use Disorder as compared to allele G.
Notes: No significant association between this variant and smoking quit rate when naltrexone was used as augmentation to nicotine patch therapy.
Article: Exudative Age-Related Macular Degeneration: Association between Treatment Efficacy and Single-Nucleotide Variants in RAD51B, TRIB1, COL8A1, COL10A1, IL-9, IL-10, and VEGFA Genes
Gene: TRIB1
Variant/haplotype: rs4351379
Drug(s): VEGF/VEGFR (Vascular Endothelial Growth Factor) inhibitors
Phenotype category: Efficacy
Significant: no
Association: Genotypes CC + CG is associated with decreased response to VEGF/VEGFR (Vascular Endothelial Growth Factor) inhibitors in people with Macular Degeneration as compared to genotype GG.
Notes: "Also, we revealed that CMT decreased more for rs4351379 heterozygous and homozygous minor allele carriers than for wild-type genotype carriers after 6 months of treatment (p = 0.030), but these results did not survive the strict Bonferroni correction for multiple comparison."
Article: Pharmacokinetic profiles of significant adverse events with crizotinib in Japanese patients with ABCB1 polymorphism
Gene: ABCB1
Variant/haplotype: rs2032582
Drug(s): crizotinib
Phenotype category: Metabolism/PK
Significant: no
Association: Genotype AA is associated with increased exposure to crizotinib in people with.
Notes: There was only one individual who was AA at all three locations that define *2 (rs1128503, rs2032582 and rs1045642). Individuals who were AA at one location (n=3) also had slightly increased exposure compared to "wild type or heterozygotes" (n=4). Increased exposure was significantly associated with toxicity. (alleles complemented to plus chromosomal strand)
Article: Impact of the CYP2C19*17 Allele on the Pharmacokinetics of Omeprazole and Pantoprazole in Children: Evidence for a Differential Effect
Gene: CYP2C19
Variant/haplotype: CYP2C19*1, CYP2C19*2, CYP2C19*17
Drug(s): pantoprazole
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2C19 *1/*1 + *1/*17 is associated with increased metabolism of pantoprazole in children as compared to CYP2C19 *1/*2 + *2/*17.
Notes: There was not a statistically significant difference for PK parameters between *1/*1 and *1/*17, but there was a statistically significant difference between groups with 2 functional alleles vs. 1 functional allele (*1/*17+*2/*17) for AUC.
Article: Association of genetic variation in pharmacodynamic factors with methadone dose required for effective treatment of opioid addiction
Gene: NGF
Variant/haplotype: rs2239622
Drug(s): methadone
Phenotype category: Dosage
Significant: no
Association: Genotype AA is not associated with decreased dose of methadone in people with Heroin Dependence as compared to genotypes AG + GG.
Notes: This association was not statistically significant. Alleles were reported as T/C, here they are complemented with A representing T and G representing C for the positive chromosomal strand.
Article: Antipsychotic pharmacogenomics in first episode psychosis: a role for glutamate genes
Gene: GRID2
Variant/haplotype: rs1875705
Drug(s): risperidone
Phenotype category: Efficacy
Significant: yes
Association: Genotype GG is associated with increased response to risperidone in people with as compared to genotypes AA + AG.
Notes: Psychotic-naive or minimal antipsychotic exposure. Improvement measured with Brief Psychiatric Rating Scale.
Article: Genotypic and Phenotypic Factors Influencing Drug Response in Mexican Patients With Type 2 Diabetes Mellitus
Gene: SLC22A1
Variant/haplotype: rs12208357
Drug(s): sulfonamides, urea derivatives
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with response to sulfonamides, urea derivatives in people with Diabetes Mellitus as compared to allele C.
Article: Ethnic Stratification of the Association of RGS4 Variants with Antipsychotic Treatment Response in Schizophrenia
Gene: RGS4
Variant/haplotype: rs2842030
Drug(s): risperidone
Phenotype category: Efficacy
Significant: not stated
Association: Genotype GG is associated with increased response to risperidone in people with Schizophrenia as compared to genotypes GT + TT.
Notes: compared to perphenazine, quetiapine, and ziprasidone treatment
Article: Pharmacokinetics and safety of mavacamten in healthy Chinese participants with different CYP2C19 phenotypes
Gene: CYP2C19
Variant/haplotype: CYP2C19*1, CYP2C19*2, CYP2C19*3, CYP2C19*17
Drug(s): mavacamten
Phenotype category: Metabolism/PK
Significant: not stated
Association: CYP2C19 *1/*2 + *1/*3 + *2/*3 + *2/*2 (assigned as intermediate metabolizer and poor metabolizer phenotype) is associated with increased exposure to mavacamten in healthy individuals as compared to CYP2C19 *1/*1 + *1/*17 (assigned as normal metabolizer and rapid metabolizer phenotype) .
Notes: "The total exposures for CYP2C19 IM and CYP2C19 PM were increased approximately 1.8‐ to 4‐fold when compared to CYP2C19 UM/RM/NM." There were no UM (*17/*17) or *3/*3.