shlokn/autogkb huggingface dataset:
Article: A Common β1-Adrenergic Receptor Polymorphism Predicts Favorable Response to Rate Control Therapy in Atrial Fibrillation
Gene: ADRB1
Variant/haplotype: rs1801252
Drug(s): atenolol, carvedilol, diltiazem, metoprolol, verapamil
Phenotype category: Efficacy
Significant: no
Association: Genotypes AG + GG are not associated with increased response to atenolol, carvedilol, diltiazem, metoprolol or verapamil in people with Atrial Fibrillation as compared to genotype AA.
Notes: Reported as 52% responders in carriers of minor allele group vs. 55% in Ser49Ser.  Ser corresponds to A on the + strand. [stat_test:chi square].
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): hydrochlorothiazide
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with response to hydrochlorothiazide in people with Hypertension as compared to allele A.
Article: Lumacaftor/Ivacaftor in Patients Aged 6–11 Years with Cystic Fibrosis and Homozygous for F508del-CFTR
Gene: CFTR
Variant/haplotype: rs113993960
Drug(s): ivacaftor, lumacaftor
Phenotype category: Efficacy
Significant: yes
Association: Genotype del/del is associated with response to ivacaftor and lumacaftor in children with Cystic Fibrosis.
Notes: F508del allele. Improvements seen in sweat chloride levels, BMI, CFQ-R score and LCI2.5 following 24 weeks of ivacaftor treatment.
Article: Low heritability in pharmacokinetics of talinolol: a pharmacogenetic twin study on the heritability of the pharmacokinetics of talinolol, a putative probe drug of MDR1 and other membrane transporters
Gene: ABCC2
Variant/haplotype: rs717620
Drug(s): talinolol
Phenotype category: Metabolism/PK
Significant: no
Association: Allele C is not associated with clearance of talinolol in healthy individuals as compared to allele T.
Notes: This was a twin study of monozygotic and dizygotic twins.
Article: Effect of UGT2B10, UGT2B17, FMO3, and OCT2 Genetic Variation on Nicotine and Cotinine Pharmacokinetics and Smoking in African Americans
Gene: UGT2B10
Variant/haplotype: rs61750900
Drug(s): cotinine
Phenotype category: Metabolism/PK
Significant: no
Association: Genotype GG is not associated with metabolism of cotinine in people with Tobacco Use Disorder as compared to genotype GT.
Notes: This SNP is not associated with the pharmacokinetic measures of cotinine.
Article: CYP2B6 Genotypes and Early Efavirenz-based HIV Treatment Outcomes in Botswana
Gene: CYP2B6
Variant/haplotype: rs28399499
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: not stated
Association: Genotypes CC + CT is associated with decreased clearance of efavirenz in people with HIV Infections as compared to genotype TT.
Notes: This is for CYP2B6 983T>C.
Article: Does CALU SNP rs1043550 Contribute Variability to Therapeutic Warfarin Dosing Requirements?
Gene: CALU
Variant/haplotype: rs1043550
Drug(s): warfarin
Phenotype category: Dosage
Significant: no
Association: Allele A is not associated with dose of warfarin as compared to allele G.
Notes: No significant differences in therapeutic warfarin dose (mg/wk) or error in predicted dose were seen between any of the genotypes (AA, AG, GG). Note that the study cohort differed from Hardy-Weinberg equilibrium.
Article: Pharmacogenetics of plasma dolutegravir exposure during 1-month rifapentine/isoniazid treatment of latent tuberculosis
Gene: AADAC
Variant/haplotype: rs1803155
Drug(s): dolutegravir
Phenotype category: Metabolism/PK
Significant: not stated
Association: Genotypes AG + GG is associated with increased dose-adjusted trough concentrations of dolutegravir in people with HIV infectious disease and Tuberculosis as compared to genotype AA.
Notes: "At day 0, there was no association between AADAC; rs1803155 and dolutegravir Ctrough. ... day 28, AADAC rs1803155 was associated with; dolutegravir Ctrough. Compared with rs1803155 AA poor; metabolizers, day 28 Ctrough was higher in AG intermediate metabolizers (GMR = 1.48; 90% CI: 1.14–1.90), and; in GG normal metabolizers (GMR = 1.79; 90% CI: 1.09–; 2.93). Relationships between AADAC rs1803155 genotype and dolutegravir Ctrough are shown in Fig. 1b"
Article: Concentration of Tacrolimus and Major Metabolites in Kidney Transplant Recipients as a Function of Diabetes Mellitus and Cytochrome P450 3A Gene Polymorphism
Gene: CYP3A5
Variant/haplotype: rs776746
Drug(s): tacrolimus
Phenotype category: Dosage, Metabolism/PK
Significant: yes
Association: Genotypes CT + TT are associated with increased metabolism of tacrolimus in people with Kidney Transplantation as compared to genotype CC.
Notes: Dose normalized trough and 2-hr post dose dose-adjusted tacrolimus blood levels were lower in CYP3A5 expresser (CYP3A5*1 carriers, n=15) than in non-expresser (CYP3A5*3/*3 homozygotes, n=33). Dose adjusted blood levels of metabolites 15-O-desmethyl tacrolimus, but not 13-O-desmethyl tacrolimus at 12hr post-dose, were also lower in CYP3A5 expressers than in CYP3A5 non-expressers.
Article: Genetic variants in combination with early partial improvement as a clinical utility predictor of treatment outcome in major depressive disorder: the result of two pooled RCTs
Gene: FGF2
Variant/haplotype: rs1449683
Drug(s): fluvoxamine
Phenotype category: Efficacy
Significant: yes
Association: Genotypes CC + CT are associated with decreased response to fluvoxamine in people with Depressive Disorder as compared to genotype TT.
Notes: depressive symptoms measured on Hamilton Rating Scale for Depression and outcome as change in symptoms, as measured 6 weeks after drug, following 10 days washout.
Article: Integration of population pharmacokinetics and pharmacogenetics: an aid to optimal nevirapine dose selection in HIV-infected individuals
Gene: CYP2B6
Variant/haplotype: rs28399499
Drug(s): nevirapine
Phenotype category: Toxicity, Metabolism/PK
Significant: not stated
Association: Genotype CT is associated with decreased clearance of nevirapine in people with HIV Infections as compared to genotype TT.
Notes: The 983TC genotype decreased clearance of Nevirapine by 40%.
Article: Combined approach with therapeutic drug monitoring and pharmacogenomics in renal transplant recipients
Gene: CYP3A5
Variant/haplotype: rs776746
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: not stated
Association: Genotype CC is associated with decreased metabolism of tacrolimus in Kidney Transplantation.
Notes: This is a case report of one woman in India. She had noted elevated maintenance tacrolimus levels despite low doses of the drug (2 mg/day). She was genotyped for CYP3A5 and ABCB1 alleles. She was mutant homozygous for CYP3A5*3(CC) alleles and MDR1-2677(TT) alleles, heterozygous for MDR1-1236(CT) alleles and wild-type homozygous for CYP3A5*6 (GG) and MDR1 3435C (CC) alleles. The author concluded this explained her elevated levels.
Article: Functional genetic variation in the Rev-Erbα pathway and lithium response in the treatment of bipolar disorder
Gene: PER3
Variant/haplotype: rs2859388
Drug(s): lithium
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with increased response to lithium in people with Bipolar Disorder as compared to allele A.
Article: The correlation between post-operative fentanyl requirements and μ-opioid receptor gene A118G polymorphism in patients undergoing radical gastrectomy
Gene: OPRM1
Variant/haplotype: rs1799971
Drug(s): fentanyl
Phenotype category: Dosage
Significant: no
Association: Allele G is not associated with dose of fentanyl in people with Pain, Postoperative as compared to allele A.
Article: Association and cis-mQTL analysis of variants in CHRNA3-A5, CHRNA7, CHRNB2, and CHRNB4 in relation to nicotine dependence in a Chinese Han population
Gene: CHRNA5
Variant/haplotype: rs667282
Drug(s): nicotine
Phenotype category: Other
Significant: no
Association: Allele C is not associated with exposure to nicotine in men as compared to allele T.
Notes: The C allele was initially associated with an increased likelihood of being a smoker but this lost significance following correction for multiple testing.
Article: Lack of Association between Opioid-Receptor Genotypes and Smoking Cessation Outcomes in a Randomized, Controlled Naltrexone Trial
Gene: OPRM1
Variant/haplotype: rs511435
Drug(s): naltrexone
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with response to naltrexone in people with Tobacco Use Disorder as compared to allele C.
Notes: No significant association between this variant and smoking quit rate when naltrexone was used as augmentation to nicotine patch therapy. This is a C/G/T SNP. Based on allele frequencies reported in dbSNP, it is assumed that the major allele in this study is C and the minor allele is T. Please note that alleles have been complemented to the positive strand.
Article: Novel CYP2A6 variants identified in African Americans are associated with slow nicotine metabolism in vitro and in vivo
Gene: CYP2A6
Variant/haplotype: CYP2A6*1, CYP2A6*41
Drug(s): nicotine
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2A6 *41 is associated with decreased metabolism of nicotine as compared to CYP2A6 *1.
Notes: Association with lower activity of the novel variant groups [CYP2A6*39 (V68M), CYP2A6*40 (I149M), CYP2A6*41 (R265Q; rs140471703), CYP2A6*42 (I268T), CYP2A6*43 (T303I), CYP2A6*44 (E390K; rs376817657), CYP2A6*44 (L462P)] was; tested using a one-way analysis of variance with Bonferroni tests used for post-hoc analysis, P<0.01. A comparison between CYP2A6*1/*1 and; the combined group was tested using an unpaired t-test, ***P<0.001
Article: CYP2C19 and STAT6 Variants Influence the Outcome of Proton Pump Inhibitor Therapy in Pediatric Eosinophilic Esophagitis
Gene: CYP2C19
Variant/haplotype: CYP2C19*1, CYP2C19*17
Drug(s): esomeprazole
Phenotype category: Efficacy
Significant: yes
Association: CYP2C19 *17 is associated with decreased response to esomeprazole in children with eosinophilic esophagitis as compared to CYP2C19 *1/*1.
Notes: children who were carriers of CYP2C19􏰀17 GOF had 8.2-fold better odds of receiving a PPI-nonresponsive EoE diagnosis than children who did not carry CYP2C19􏰀17 GOF (PPI-REE OR [95% CI] = 0.12 [0.02,0.67], P = 0.02; complete PPI-REE outcome OR [95% CI] = 0.15[0.03, 0.94], P = 0.04. GOF phenotype that characterizes EMs is defined as carriers of 1 or 2 copies of rs12248560 (diplotypes *1/*17 + *17/*17) without rs4244285 (*2). Most individuals within the pH probe cohort received a PPI dose within the range of 􏰃1.569 to <2.075 mg/kg/ day, which corresponds well with the IQR dose range of 􏰃1.54 to <2.05 mg/kg/day for the full cohort.
Article: CYP3A4 and CYP3A5 Polymorphisms and Blood Pressure Response to Amlodipine among African-American Men and Women with Early Hypertensive Renal Disease
Gene: CYP3A5
Variant/haplotype: rs776746
Drug(s): amlodipine
Phenotype category: Efficacy
Significant: no
Association: Genotype TT is not associated with response to amlodipine in women with Hypertension as compared to genotypes CC + CT.
Notes: No significant change in the likelihood of a woman reaching a target mean arterial pressure concentration of <= 92 mmHg or <= 107 mmHg was seen between genotypes. Please note alleles have been complemented to the plus chromosomal strand.
Article: Pharmacogenetic study of seven polymorphisms in three nicotinic acetylcholine receptor subunits in smoking-cessation therapies
Gene: CHRNA4
Variant/haplotype: rs2236196
Drug(s): bupropion, nicotine, varenicline
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with response to bupropion, nicotine and varenicline in people with Tobacco Use Disorder as compared to allele A.
Notes: Authors looked at the effect of variants on response to the smoking cessation therapies varenicline, bupropion and nicotine replacement therapy.; It is assumed that the authors tested the association between the G allele and nicotine dependence as compared to both the A and del alleles.; Please note that alleles have been complemented to the positive strand.
Article: Effect of CYP3A5 genotypes on pharmacokinetic of tacrolimus in colombian liver transplant patients
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 dose-adjusted trough concentrations of tacrolimus in people with Liver transplantation as compared to CYP3A5 *3/*3.
Notes: "Patients with CYP3A5 expressors displayed lower C0 and C0/dose ratio and higher doses than those no expressors, Table 1. We observed a lower C0/dose ratio in expresser recipients over 2 years of follow-up (Figure 1) (Table 2)." "This study reveals that expressing recipient patients presented significantly (p < 0.001) lower Co/dose, compared to non-expressing recipients, regardless of the genotype of the donor’s liver in the first weeks after transplantation. "
Article: A cis-eQTL in OPRM1 is Associated with Subjective Response to Alcohol and Alcohol Use
Gene: OPRM1
Variant/haplotype: rs3778150
Drug(s): ethanol
Phenotype category: Dosage
Significant: yes
Association: Genotypes CC + CT are associated with increased dose of ethanol as compared to genotype TT.
Notes: Subjects carrying the C allele had significantly higher drinking levels compared to individuals with the TT genotype.
Article: Smoking Cessation Pharmacogenetics: Analysis of Varenicline and Bupropion in Placebo-Controlled Clinical Trials
Gene: CYP2B6
Variant/haplotype: rs8109525
Drug(s): bupropion
Phenotype category: Efficacy
Significant: yes
Association: Genotype GG is associated with increased response to bupropion in people with Tobacco Use Disorder as compared to genotypes AA + AG.
Notes: Patients with the GG genotypes were more likely to have quit smoking in weeks 9-12 of varenicline treatment and at 52 weeks of follow-up.
Article: RRM1 and RRM2 pharmacogenetics: association with phenotypes in HapMap cell lines and acute myeloid leukemia patients
Gene: RRM2
Variant/haplotype: rs1130609
Drug(s): cladribine, cytarabine
Phenotype category: Efficacy
Significant: yes
Association: Genotypes GT + TT is associated with decreased response to cladribine and cytarabine in children with Leukemia, Myeloid, Acute as compared to genotype GG.
Notes: As measured by a poorer overall survival.
Article: Genome-wide study of methotrexate clearance replicates SLCO1B1
Gene: SLCO1B1
Variant/haplotype: rs11045872
Drug(s): methotrexate
Phenotype category: Efficacy, Toxicity, Metabolism/PK
Significant: no
Association: Allele G is associated with increased clearance of methotrexate in children with Precursor Cell Lymphoblastic Leukemia-Lymphoma.
Article: Genome-wide association study identifies ABCG2 (BCRP) as an allopurinol transporter and a determinant of drug response
Gene: ABCG2
Variant/haplotype: rs2231142
Drug(s): allopurinol
Phenotype category: Efficacy
Significant: yes
Association: Allele T is associated with decreased response to allopurinol in people with Gout as compared to allele G.
Notes: The authors designated "response to allopurinol" as  a reduction of serum uric acid levels to below 6 mg/dL. Mean age was 68 years, 75% were male. The elevated mean baseline SUA before treatment was 8.9 mg/dL. No other SNPs reached genome wide significance.
Article: Pharmacogenomic Next-Generation DNA Sequencing: Lessons from the Identification and Functional Characterization of Variants of Unknown Significance in CYP2C9 and CYP2C19
Gene: CYP2C19
Variant/haplotype: rs145119820
Drug(s): mephenytoin
Phenotype category: Metabolism/PK
Significant: yes
Association: Allele A is associated with decreased clearance of mephenytoin as compared to allele G.
Notes: In vitro analysis showed that intrinsic clearance of S-mephenytoin by CYP2C19 protein containing the A allele was 10.7% of that of the WT protein. Variant referred to as 337G>A in the paper.
Article: Role of TNFRSF1A and TNFRSF1B polymorphisms in susceptibility, severity, and therapeutic efficacy of etanercept in human leukocyte antigen-B27-positive Chinese Han patients with ankylosing spondylitis
Gene: TNFRSF1A
Variant/haplotype: rs2234649
Drug(s): etanercept
Phenotype category: Efficacy
Significant: no
Association: Genotype GT is not associated with response to etanercept in people with Spondylitis, Ankylosing as compared to genotypes GG + TT.
Notes: Response to etanercept was determined using the Assessment in Ankylosing Spondylitis 20 (ASAS20) and Assessment in Ankylosing Spondylitis 40 (ASAS40). No significant difference in response was seen between genotypes at either 3 months or 12 months after initiation of etanercept treatment. Please note that alleles have been complemented to the positive strand. Also note that there appears to be a typo in Figure 1 where rs2234649 is written as rs223464.
Article: Pharmacogenetic Predictors of Adverse Events and Response to Chemotherapy in Metastatic Colorectal Cancer: Results From North American Gastrointestinal Intergroup Trial N9741
Gene: CYP3A4
Variant/haplotype: CYP3A4*1, CYP3A4*3
Drug(s): fluorouracil, irinotecan, oxaliplatin
Phenotype category: Efficacy
Significant: no
Association: CYP3A4 *1 + *3 are not associated with response to fluorouracil, irinotecan or oxaliplatin in people with Colorectal Neoplasms.
Notes: Patients were taking either IFL (irinotecan + fluorouracil + leucovorin; n=114), FOLFOX (fluorouracil + oxaliplatin + leucovorin; n=299) or IROX (irinotecan + oxaliplatin; n=107). No significant associations were seen between these *1B (−329 A>G) and *3 (1334 T>C)  and confirmed response rate, overall survival or time to progression in any of the treatment groups OR all treatment groups considered together. Significance level was set at 0.01.
Article: Prediction of phenprocoumon maintenance dose and phenprocoumon plasma concentration by genetic and non-genetic parameters
Gene: CALU
Variant/haplotype: rs1043550
Drug(s): phenprocoumon
Phenotype category: Dosage, Metabolism/PK
Significant: no
Association: Genotype AA is not associated with increased dose of phenprocoumon as compared to genotypes AG + GG.
Notes: Daily dose of phenprocoumon is not significantly associated with this SNP. Daily dose is negatively correlated with age. This study published an algorithm for daily dose that includes height, although height was not significant in univariate analysis. This SNP is also not significantly associated with phenprocoumon concentration.
Article: The Role of Candidate Polymorphisms in Drug Transporter Genes on High‐Dose Methotrexate in the Consolidation Phase of the AIEOP‐BFM ALL 2009 Protocol
Gene: ABCC4
Variant/haplotype: rs7317112
Drug(s): methotrexate
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype GG is associated with increased clearance of methotrexate in children with Acute lymphoblastic leukemia as compared to genotypes AA + AG.
Notes: "MTX plasma levels at 24, 42, and 48 h were lower for young rs7317112 GG patients (group A) compared to rs7317112 non- GG teens (group D), with a clearly higher clearance of the drug (Figure 2)." "ABCC4 SNP (rs7317112): Carriers of the variant GG genotype showed accelerated MTX clearance"
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: NR1I2
Variant/haplotype: rs1054191
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: no
Association: Genotype GG is not associated with concentrations of efavirenz in people with HIV Infections as compared to genotypes AA + AG.
Article: Voriconazole plasma concentrations in immunocompromised pediatric patients vary by CYP2C19 diplotypes
Gene: CYP2C19
Variant/haplotype: CYP2C19*1, CYP2C19*17
Drug(s): voriconazole
Phenotype category: Dosage, Metabolism/PK
Significant: yes
Association: CYP2C19 *17/*17 (assigned as ultrarapid metabolizer phenotype) is associated with decreased dose-adjusted trough concentrations of voriconazole in children with Neoplasms as compared to CYP2C19 *1/*1 (assigned as normal metabolizer phenotype) .
Notes: Significantly lower trough concentrations (adjusted for daily dose) were observed in patients with the *17/*17 diplotype. All four patients with this diplotype had subtherapeutic levels - authors suggest that higher doses in these patients may overcome this. CYP2C19*17 was defined as rs12248560 c.-806C>T, *2A as rs4244285 c.681G>A, *2B as rs4244285 and rs17878459 c.276G>C, and *1 as none of these variants.
Article: Targeted pharmacogenetic analysis of antipsychotic response in the CATIE study
Gene: AGAP1
Variant/haplotype: rs1869295
Drug(s): risperidone
Phenotype category: Efficacy
Significant: yes
Association: Allele C is associated with response to risperidone in people with Schizophrenia.
Notes: as measured by changes in PANSS-T (positive and negative syndrome scale total score), using a mixed model repeated measures approach. Examined 6789 SNPs - p-value of p< or equal to 5x10-4 was considered significant. It was unclear whether the allele was associated with an increased or decreased response to drug.
Article: Effect of pharmacogenetics on plasma lumefantrine pharmacokinetics and malaria treatment outcome in pregnant women
Gene: ABCB1
Variant/haplotype: rs3842
Drug(s): lumefantrine
Phenotype category: Metabolism/PK
Significant: no
Association: Allele C is not associated with 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 were not significantly different and no more likely to have median concentrations of lumefantrine  >600 ng/ml between genotypes.
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: Metabolism/PK
Significant: no
Association: CYP2C19 *1/*2 + *2/*2 are not associated with concentrations of methadone in people with Opioid-Related Disorders as compared to CYP2C19 *1/*1.
Notes: No significant difference in concentrations of (R)-, (S)- or (R,S)-methadone concentrations between genotypes. No details about which specific variants/alleles were tested for.
Article: OPRM1, OPRK1 and COMT Genetic Polymorphisms Associated with Opioid Effects on Experimental Pain: A Randomized, Double-Blind, Placebo-Controlled Study
Gene: OPRM1
Variant/haplotype: rs1799971
Drug(s): morphine
Phenotype category: Efficacy
Significant: not stated
Association: Genotype AG is not associated with increased response to morphine in healthy individuals as compared to genotype AA.
Notes: Nominally significant difference in pressure pain at the masseter between genotype groups, but this association was not seen in other pain modalities. Study-wide significance was set to p<0.017.
Article: Prediction of tacrolimus metabolism and dosage requirements based on CYP3A4 phenotype and CYP3A5*3 genotype in Chinese renal transplant recipients
Gene: CYP3A5
Variant/haplotype: CYP3A5*1, CYP3A5*3
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP3A5 *3/*3 is associated with decreased dose of tacrolimus in people with Kidney Transplantation as compared to CYP3A5 *1/*1 + *1/*3.
Notes: The study also provided a regression equation to predict trough concentration and dose of tacrolimus based on CYP3A5 genotype, among other factors.