shlokn/autogkb huggingface dataset:
Article: Combined study of genetic and epigenetic biomarker risperidone treatment efficacy in Chinese Han schizophrenia patients
Gene: COMT
Variant/haplotype: rs4818
Drug(s): risperidone
Phenotype category: Efficacy
Significant: no
Association: Allele G is associated with increased response to risperidone in people with Schizophrenia as compared to allele C.
Notes: The G allele was initially significantly more frequent in patients designated as responders to risperidone (i.e. >50% reduction in PANSS score compared to the cohort average). However, significance was lost following correction for multiple testing.
Article: Assessing the Contribution of Opioid- and Dopamine-Related Genetic Polymorphisms to the Abuse Liability of Oxycodone
Gene: OPRM1
Variant/haplotype: rs1799971
Drug(s): oxycodone
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with response to oxycodone as compared to allele A.
Notes: No association between this variant and analgesic response to oxycodone, as assessed by cold pressor test, subjective effects of oxycodone.
Article: Effects of genetic variants of organic cation transporters on metformin response in newly diagnosed patients with type 2 diabetes
Gene: SLC47A2
Variant/haplotype: rs34399035
Drug(s): metformin
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with decreased clinical benefit to metformin in people with Diabetes Mellitus, Type 2 as compared to allele C.
Notes: "Other SNPs (rs4621031, rs34399035, rs1800058, and rs11212617) had no significant impact on metformin response. "
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: rs2082940
Drug(s): pioglitazone
Phenotype category: Efficacy
Significant: no
Association: Genotype CC are not associated with response to pioglitazone in people with Diabetes Mellitus as compared to genotypes CT + TT.
Notes: Response was defined as "any decrease greater than (or equal to) 15%" of glycated hemoglobin (HbA1C%).
Article: A Pharmacogenetics-Based Warfarin Maintenance Dosing Algorithm from Northern Chinese Patients
Gene: F5
Variant/haplotype: rs7542281
Drug(s): warfarin
Phenotype category: Dosage
Significant: no
Association: Allele C is not associated with dose of warfarin in people with heart valve replacement as compared to allele T.
Notes: Samples, genotypes and INRs from a cohort of 551 patients were used to derive an algorithm which was used to predict daily warfarin maintenance dose in a second cohort of 236 patients. Note: the authors state that "SNPs were tested for deviations from HWE using the chi-squared test, and for their association with the warfarin dose by Spearman correlation analysis using a *co-dominant* model."
Article: The Association of Transporter Genes Polymorphisms and Lung Cancer Chemotherapy Response
Gene: POU2F2
Variant/haplotype: rs195862
Drug(s): platinum
Phenotype category: Efficacy
Significant: no
Association: Allele C is not associated with response to platinum in people with Lung Neoplasms as compared to allele A.
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: Comprehensive Pharmacogenomic Study Reveals an Important Role of UGT1A3 in Montelukast Pharmacokinetics
Gene: ABCC9
Variant/haplotype: rs704212
Drug(s): montelukast
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele T is associated with decreased concentrations of montelukast in healthy individuals as compared to allele C.
Notes: This variant is associated with reduced area under the plasma concentration-time curve (AUC) of montelukast (13.7% reduction per copy of each minor allele, P=2.19 × 10-4).
Article: Pharmacogenomic Next-Generation DNA Sequencing: Lessons from the Identification and Functional Characterization of Variants of Unknown Significance in CYP2C9 and CYP2C19
Gene: CYP2C9
Variant/haplotype: rs149158426
Drug(s): tolbutamide
Phenotype category: Metabolism/PK
Significant: no
Association: Allele T is not associated with clearance of tolbutamide as compared to allele C.
Notes: In vitro analysis showed that intrinsic clearance of tolbutamide by CYP2C9 protein containing the C allele was 98.1% of that of the WT protein. Variant referred to as 801C>T in the paper.
Article: A Pharmacogenetics-Based Warfarin Maintenance Dosing Algorithm from Northern Chinese Patients
Gene: CYP4F2
Variant/haplotype: rs3093158
Drug(s): warfarin
Phenotype category: Dosage
Significant: no
Association: Allele T is not associated with dose of warfarin in people with heart valve replacement as compared to allele C.
Notes: Samples, genotypes and INRs from a cohort of 551 patients were used to derive an algorithm which was used to predict daily warfarin maintenance dose in a second cohort of 236 patients. Note: the authors state that "SNPs were tested for deviations from HWE using the chi-squared test, and for their association with the warfarin dose by Spearman correlation analysis using a *co-dominant* model."
Article: The pharmacokinetic and pharmacodynamic interaction of clopidogrel and cilostazol in relation to CYP2C19 and CYP3A5 genotypes
Gene: CYP2C19
Variant/haplotype: CYP2C19*1, CYP2C19*2, CYP2C19*3
Drug(s): cilostazol
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2C19 *2 + *3 are associated with increased concentrations of cilostazol in healthy individuals as compared to CYP2C19 *1.
Notes: The authors observed significant differences in AUC (ng*hr/ml) of cilostazol and cilostazol metabolites (3,4-dehydro cilostozal and 4" turns-hydroxyl cilostazol) when comparing between CYP2C19 metabolizer groups  [extensive (CYP2C19 *1/*1), intermediate (CYP2C19 *1/*2, *1/*3), and poor (CYP2C19 *2/*2, *2/*3, *3/*3). Significant differences were not generally observed in AUC of cilostazole, or cilostozol metabolites when comparing within metabolizer groups, or between metabolizer groups when clopidogrel was co-adminsitered with cilostazol.
Article: The efficacies of clozapine and haloperidol in refractory schizophrenia are related to DTNBP1 variation
Gene: DTNBP1
Variant/haplotype: rs742105
Drug(s): clozapine
Phenotype category: Efficacy
Significant: yes
Association: Genotypes CT + TT are associated with increased response to clozapine in people with Schizophrenia as compared to genotype CC.
Notes: Significance for genotype shown for african americans, significance not shown for the genotype for european american but was significant for diplotype with rs909706.
Article: Relationship between Genotypes Sult1a2 and Cyp2d6 and Tamoxifen Metabolism in Breast Cancer Patients
Gene: CYP2D6
Variant/haplotype: CYP2D6*1, CYP2D6*3, CYP2D6*4, CYP2D6*5, CYP2D6*6, CYP2D6*9, CYP2D6*10, CYP2D6*17, CYP2D6*41
Drug(s): endoxifen
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2D6 *3/*9 + *4/*4 + *4/*5 + *4/*10 + *4/*41 + *5/*17 + *5/*41 + *41/*41 are associated with decreased concentrations of endoxifen in women with Breast Neoplasms as compared to CYP2D6 *1/*1 + *1/*3 + *1/*4 + *1/*5 + *1/*6 + *1/*9 + *1/*17 + *1/*41.
Notes: Please note: article provides diplotypes as wt/wt or wt/*3 etc. CYP2D6 wt includes *1, *2, *35 but the individual diplotypes concerning wt alleles are not included so  compared to diplotypes are examples with *1 could be *2 or *35. Pre and postmenopausal woman with estrogen receptor-positive breast cancer undergoing tam treatment after surgery and chemotherapy/radiation. Patients were excluded if tamoxifen therapy was started with either chemotherapy or radiation, SSRI treatment was allowed. Roche-AmpliChip® CYP450 Test was used. Genotypes were classified into the three groups: wt/wt, patients with 2 or more copies of any functional allele; wt/v, patients carrying one functional allele and one variant -intermediate or null- allele; v/v, patients featuring intermediate or null alleles. [pre-menopausal][post-menopausal] [adjuvant] [DNA source: blood] [HWE: yes]
Article: OPRM1 c.118A>G Polymorphism and Duration of Morphine Treatment Associated with Morphine Doses and Quality-of-Life in Palliative Cancer Pain Settings
Gene: COMT
Variant/haplotype: rs4680
Drug(s): morphine
Phenotype category: Dosage
Significant: no
Association: Allele G is not associated with dose of morphine in people with Neoplasms as compared to allele A.
Notes: The setting was for palliative care of cancer patients.
Article: Serotonin transporter 5-HTTLPR polymorphism and escitalopram treatment response in patients with major depressive disorder
Gene: HTR2A
Variant/haplotype: rs9316233
Drug(s): escitalopram
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with decreased response to escitalopram in people with Major Depressive Disorder as compared to allele C (assigned as normal metabolizer phenotype) .
Notes: "No significant relationship between HTR2A rs9316233 and BDNF rs962369 variants with response to escitalopram treatment was observed." Table 3 lists G as minor allele and C as common allele.
Article: Impact of Single Nucleotide Polymorphisms on Plasma Concentrations of Efavirenz and Lopinavir/ritonavir in Chinese Children Infected with the Human Immunodeficiency Virus
Gene: ABCB1
Variant/haplotype: rs1045642
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: no
Association: Genotypes AA + AG are not associated with concentrations of efavirenz in children with HIV Infections as compared to genotype GG.
Notes: "An association between ABCB1 3435C>T and EFV concentrations was suggested (p=0.0827) without statistical significance".
Article: The influence of folate pathway polymorphisms on high-dose methotrexate-related toxicity and survival in children with non-Hodgkin malignant lymphoma
Gene: MTHFR
Variant/haplotype: rs1801133
Drug(s): methotrexate
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotypes AA + AG are associated with increased concentrations of methotrexate in children with Lymphoma, Non-Hodgkin as compared to genotype GG.
Notes: Please note that alleles have been complemented to the positive strand.
Article: A randomized placebo-controlled trial of ataluren for the treatment of nonsense mutation cystic fibrosis
Gene: CFTR
Variant/haplotype: rs74767530
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 single nucleotide polymorphisms in MTHFR and ABCG2 with the different efficacy of first-line chemotherapy in metastatic colorectal cancer
Gene: ABCG2
Variant/haplotype: rs2231137
Drug(s): antineoplastic agents
Phenotype category: Efficacy
Significant: no
Association: Genotype CC is not associated with response to antineoplastic agents in people with Colorectal Neoplasms as compared to genotypes CT + TT.
Notes: No significant difference in response rate or progression-free survival time was seen between the genotypes. Patients were either receiving FOLFOX/XELOX or FOLFIRI regimens (respectively: fluorouracil, leucovorin, oxaliplatin; capecitabine, oxaliplatin; fluorouracil, leucovorin, irinotecan). Please note alleles have been complemented to the plus chromosomal strand.
Article: Associations of the SLCO1B1 Polymorphisms With Hepatic Function, Baseline Lipid Levels, and Lipid-lowering Response to Simvastatin in Patients With Hyperlipidemia
Gene: SLCO1B1
Variant/haplotype: rs4149056
Drug(s): simvastatin
Phenotype category: Efficacy
Significant: yes
Association: Genotype TT is associated with increased response to simvastatin in people with Hypercholesterolemia as compared to genotypes CC + CT.
Notes: Patients carrying 521TT genotype had greater TC and LDL-C reduction in response to simvastatin after 4 weeks of treatment.
Article: Effects of cytochrome P450 2B6 and constitutive androstane receptor genetic variation on Efavirenz plasma concentrations among HIV patients in Kenya
Gene: CYP2B6
Variant/haplotype: rs3745274
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele T is associated with increased concentrations of efavirenz in people with HIV Infections as compared to allele G.
Notes: Described as 516G>T.
Article: Impact of Single Nucleotide Polymorphisms (SNPs) on Immunosuppressive Therapy in Lung Transplantation
Gene: ABCC2
Variant/haplotype: rs2273697
Drug(s): mycophenolic acid
Phenotype category: Metabolism/PK
Significant: no
Association: Genotype AG is associated with increased concentrations of mycophenolic acid in people with lung transplantation as compared to genotype GG.
Notes: Concentrations measured as trough blood drug concentrations. Differences in concentrations were seen in the later time points after transplantation -- 90 and 180 days after transplant.
Article: The effect of alpha-2A adrenergic receptor (ADRA2A) genetic polymorphisms on the depth of sedation of dexmedetomidine: a genetic observational pilot study
Gene: ADRA2A
Variant/haplotype: rs553668
Drug(s): dexmedetomidine
Phenotype category: Dosage
Significant: no
Association: Allele G is not associated with dose of dexmedetomidine in men as compared to allele A.
Article: Effects of Opioid Receptor Gene Variation on Targeted Nalmefene Treatment in Heavy Drinkers
Gene: OPRM1
Variant/haplotype: rs648893
Drug(s): nalmefene
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with response to nalmefene in people with Alcoholism as compared to allele A.
Article: Influence of the CYP3A5 and MDR1 genetic polymorphisms on the pharmacokinetics of tacrolimus in healthy Korean subjects
Gene: CYP3A5
Variant/haplotype: rs776746
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotypes CT + TT is associated with increased clearance of tacrolimus in healthy individuals as compared to genotype CC.
Notes: Healthy subjects with the CYP3A5*1/*1 (TT) or *1/*3 (CT) genotype had significantly lower AUC and Cmax values when compared with subjects with the CYP3A5*3/*3 (CC) genotype.
Article: Pharmacogenetics of methylphenidate in childhood attention-deficit/hyperactivity disorder: long-term effects
Gene: GRM7
Variant/haplotype: rs3792452
Drug(s): methylphenidate
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with response to methylphenidate in children with Attention Deficit Disorder with Hyperactivity as compared to allele C.
Notes: Clinical Global Impression-Severity (CGI-S) scale and the Children’s Global Assessment Scale (CGAS).
Article: Association studies of dopamine synthesis and metabolism genes with multiple phenotypes of heroin dependence
Gene: DDC
Variant/haplotype: rs12666409
Drug(s): heroin
Phenotype category: Dosage
Significant: no
Association: Allele A is not associated with dose of heroin in people with Heroin Dependence as compared to allele T.
Article: IL-4 receptor polymorphisms predict reduction in asthma exacerbations during response to an anti–IL-4 receptor α antagonist
Gene: IL4R
Variant/haplotype: rs1110470
Drug(s): pitrakinra
Phenotype category: Efficacy
Significant: yes
Association: Genotype AA is associated with increased response to pitrakinra in people with Asthma as compared to genotypes AG + GG.
Notes: Subjects with the AA genotype have a reduced frequency of asthma exacerbations compared to those with the AG + GG genotypes.
Article: Predictive Value of UGT1A1*28 Polymorphism In Irinotecan-based Chemotherapy
Gene: UGT1A1
Variant/haplotype: rs4148323
Drug(s): irinotecan
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to irinotecan in people with Lung Neoplasms as compared to allele G.
Notes: Meta-analysis of studies of Asian subjects with lung cancer (small-cell and non-small cell) from China, Korea, and Japan treated with irinotecan-based chemotherapy.
Article: No Clinical Impact of CYP3A5 Gene Polymorphisms on the Pharmacokinetics and/or Efficacy of Maraviroc in Healthy Volunteers and HIV‐1–Infected Subjects
Gene: CYP3A5
Variant/haplotype: CYP3A5 intermediate metabolizers
Drug(s): maraviroc
Phenotype category: Metabolism/PK
Significant: no
Association: CYP3A5 intermediate metabolizer is not associated with concentrations of maraviroc in people with HIV Infections as compared to CYP3A5 normal metabolizer.
Notes: There was no significant difference in average maraviroc plasma concentrations between CYP3A5 intermediate and extensive metabolizers.
Article: An Investigational Study on the Role of CYP2D6, CYP3A4 and UGTs Genetic Variation on Fesoterodine Pharmacokinetics in Young Healthy Volunteers
Gene: CYP2D6
Variant/haplotype: CYP2D6 intermediate metabolizer
Drug(s): fesoterodine
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2D6 intermediate metabolizer and poor metabolizer is associated with decreased clearance of fesoterodine in healthy individuals as compared to CYP2D6 normal metabolizer.
Notes: "Lastly, Cl/F was significantly higher in the CYP2D6 UMs compared to the NMs and IMs/PMs (puv = 0.008 and puv < 0.001, respectively; β = −0.131, R2 =0.409, pmv = 0.001) and lower in the CYP2D6 IMs/PMs compared to the NMs (puv = 0.005) (Table 3)." The 21 SNPs for CYP2D6 measured are listed in table 5 and methods states that "deletion (*5), duplication, and the presence of hybrid structures were analyzed".
Article: Hypertension Susceptibility Loci and Blood Pressure Response to Antihypertensives – Results from the Pharmacogenomic Evaluation of Antihypertensive Responses (PEAR) Study
Gene: CAPZA1
Variant/haplotype: rs12076902
Drug(s): atenolol
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to atenolol in people with Hypertension as compared to allele G.
Notes: Not significant when using Bonferroni-corrected alpha of 0.0014. Response was assessed by change in diastolic blood pressure (DBP) after 9 weeks of treatment.
Article: Genetic variability in the glucocorticoid pathway and treatment outcomes in hospitalized patients with COVID-19: a pilot study
Gene: NR3C1
Variant/haplotype: rs33388
Drug(s): dexamethasone
Phenotype category: Efficacy
Significant: yes
Association: Genotype AA is associated with increased time to response to dexamethasone in people with COVID-19 as compared to genotypes AT + TT.
Notes: "the median duration of hospitalization was longer in homozygotes for NR3C1 rs33388 reference allele (12 days) when compared to carriers of one or two polymorphic alleles (both 9 days) (Pdom adj = 0.006)." Caution this is an A/T snp in a gene on the minus strand and it is unclear about which allele is major allele or risk allele.
Article: Interaction between ABCG2 421C>A polymorphism and valproate in their effects on steady‐state disposition of lamotrigine in adults with epilepsy
Gene: ABCB1
Variant/haplotype: rs1128503
Drug(s): lamotrigine
Phenotype category: Metabolism/PK
Significant: no
Association: Allele A is not associated with concentrations of lamotrigine in people with Epilepsy as compared to allele G.
Article: The largest prospective warfarin-treated cohort supports genetic forecasting
Gene: CYP2C9
Variant/haplotype: rs4917639
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Allele A is associated with dose of warfarin.
Notes: This SNP explained 12% (P = 4.61 x 10(-30)) of the variation in warfarin dose.  The direction of the allele:dose relationship is not given.
Article: Genetic factors influencing warfarin dose in Black-African patients: a systematic review and meta-analysis
Gene: VKORC1
Variant/haplotype: rs7294
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Genotypes CT + TT are associated with increased dose of warfarin as compared to genotype CC.
Notes: In this meta-analysis of warfarin Dose in Black-African Patients, this variant is associated with 6.9mg/week more warfarin dose requirement compared to wild-type homozygotes.
Article: Genome-wide association analysis of common genetic variants of resistant hypertension
Variant/haplotype: rs11749255
Drug(s): Antihypertensives
Phenotype category: Efficacy
Significant: no
Association: Allele A is associated with decreased response to Antihypertensives in people with Hypertension as compared to allele G.
Notes: The A allele was associated with increased odds of a patient developing resistant-hypertension. Participants were classified as having resistant hypertension if their SBP was ≥140 or DBP ≥ 90 using three or more medications, or if they were using four or greater antihypertensive medications regardless of BP. This SNP was suggestive in the INVEST and SPS3 cohorts but reached genome-wide significance when the two cohorts were combined.  Additionally, this association could not be validated in an eMERGE dataset.
Article: Contribution of Cytochrome P450 and ABCB1 Genetic Variability on Methadone Pharmacokinetics, Dose Requirements, and Response
Gene: CYP2C19
Variant/haplotype: CYP2C19*1, CYP2C19*2
Drug(s): methadone
Phenotype category: Dosage
Significant: no
Association: CYP2C19 *1/*2 + *2/*2 are not associated with dose of methadone in people with Opioid-Related Disorders as compared to CYP2C19 *1/*1.
Notes: No significant difference in methadone dose between genotypes. No details about which specific variants/alleles were tested for.
Article: Candidate‐Gene Study of Functional Polymorphisms in SLCO1B1 and CYP3A4/5 and the Cholesterol‐Lowering Response to Simvastatin
Gene: CYP3A4
Variant/haplotype: CYP3A4*1, CYP3A4*22
Drug(s): simvastatin
Phenotype category: Efficacy
Significant: no
Association: CYP3A4 *22 is not associated with response to simvastatin as compared to CYP3A4 *1.
Notes: 609 self-reported white and 335 self-reported African American men and women with baseline total serum cholesterol level between 160 and 400 mg/dL received 40 mg simvastatin daily for 6 weeks. Clinic visits occurred at 2-week intervals during the 6-week study.
Article: Pharmacogenetic Influence on Stereoselective Steady-State Disposition of Bupropion
Gene: CYP2B6
Variant/haplotype: rs3745274
Drug(s): bupropion
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele T is associated with increased exposure to bupropion in people with Depressive Disorder, Major as compared to allele G.
Notes: "516T carriers generally had; greater bupropion and lesser hydroxybupropion plasma exposure, compared with non-carriers."
Article: A novel polymorphism in ABCB1 gene, CYP2B6*6 and sex predict single-dose efavirenz population pharmacokinetics in Ugandans
Gene: ABCB1
Variant/haplotype: rs3842
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype CC is associated with increased exposure to efavirenz in healthy individuals as compared to genotype TT.
Notes: "Efavirenz relative bioavailability was 26% higher in subjects homozygous for ABCB1 (rs3842)."
Article: Integration of population pharmacokinetics and pharmacogenetics: an aid to optimal nevirapine dose selection in HIV-infected individuals
Gene: CYP2B6
Variant/haplotype: rs3745274
Drug(s): nevirapine
Phenotype category: Toxicity, Metabolism/PK
Significant: not stated
Association: Genotypes GT + TT is associated with decreased clearance of nevirapine in people with HIV Infections as compared to genotype GG.
Notes: " The impact of 516G > T was tested including heterozygous and homozygous subjects, showing that both genotypes influenced CL/F to a significant extent (ΔOFV = −27.8). Particularly significant was the effect of the 516TT genotype, which decreased CL/F by 37%. Importantly, there was a gene–dose effect with 516GT decreasing CL/F by 15% compared with the 516GG genotype. "