shlokn/autogkb huggingface dataset:
Article: Pharmacogenetics of plasma dolutegravir exposure during 1-month rifapentine/isoniazid treatment of latent tuberculosis
Gene: UGT1A1
Variant/haplotype: rs887829
Drug(s): dolutegravir
Phenotype category: Metabolism/PK
Significant: not stated
Association: Genotypes CT + TT is associated with increased dose-adjusted trough concentrations of dolutegravir in people with HIV infectious disease and Tuberculosis as compared to genotype CC.
Notes: "At day 0 (before starting rifapentine/isoniazid), UGT1A1; rs887829 was associated with dolutegravir Ctrough.; Compared with rs887829 CC normal metabolizers, day; 0 Ctrough was higher in CT intermediate metabolizers; (GMR = 1.51; 90% CI: 1.10–2.07), and in TT poor metabolizers (GMR = 1.90; 90% CI: 1.09–3.28). At day 28 (with; rifapentine/isoniazid), UGT1A1 rs887829 was still associated with dolutegravir Ctrough, although the GMR values were somewhat less than at day 0. Compared with; rs887829 CC normal metabolizers, day 28 Ctrough was higher; in CT intermediate metabolizers (GMR = 1.38; 90% CI:; 1.02–1.86), and in TT poor metabolizers (GMR = 1.65;; 90% CI: 0.97–2.78). Relationships between UGT1A1 genotype and dolutegravir Ctrough are shown in Fig. 1a."
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: rs588765
Drug(s): nicotine
Phenotype category: Other
Significant: no
Association: Allele T is not associated with exposure to nicotine in men as compared to allele C.
Notes: The T allele was initially associated with an increased likelihood of being a smoker but this lost significance following correction for multiple testing.
Article: Pharmacokinetics of Metoprolol During Pregnancy and Lactation
Gene: CYP2D6
Variant/haplotype: CYP2D6 normal metabolizers
Drug(s): metoprolol
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2D6 normal metabolizer is associated with increased clearance of metoprolol in women with Pregnancy as compared to CYP2D6 intermediate metabolizer.
Notes: Mean apparent oral clearance was higher in CYP2D6 EM (one functional allele (*1, *35) in combination with another functional allele or one functional allele in combination with a reduced function allele (*9, *10, *17, *41) or two reduced function alleles) as compared to CYP2D6 IM (one non-functional allele (*3, *4, *5, *6) in combination with a functional allele or a non-functional allele in combination with a reduced function allele) at 22-26 weeks of pregnancy and between 34-38 weeks of pregnancy, but not in early pregnancy or > 3 months postpartum.
Article: Voriconazole plasma concentrations in immunocompromised pediatric patients vary by CYP2C19 diplotypes
Gene: CYP2C19
Variant/haplotype: CYP2C19*1, CYP2C19*2
Drug(s): voriconazole
Phenotype category: Dosage, Metabolism/PK
Significant: yes
Association: CYP2C19 *2/*2 (assigned as poor metabolizer phenotype) is associated with increased dose-adjusted trough concentrations of voriconazole in children with Neoplasms as compared to CYP2C19 *1/*1 (assigned as normal metabolizer phenotype) .
Notes: Diplotype was determined as *2A/*2A. Significantly higher trough concentrations (adjusted for daily dose) was observed in the one patient with the *2A/*2A  diplotype. 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: Association of ABCC2 −24C>T Polymorphism with High-Dose Methotrexate Plasma Concentrations and Toxicities in Childhood Acute Lymphoblastic Leukemia
Gene: ABCC4
Variant/haplotype: rs868853
Drug(s): methotrexate
Phenotype category: Metabolism/PK
Significant: no
Association: Allele C is not associated with clearance of methotrexate in children with Precursor Cell Lymphoblastic Leukemia-Lymphoma as compared to allele T.
Notes: All patients received four cycles of high dose MTX (5000mg per square meter of body surface area). 1/10th of the dose was administered over 30 minutes (rapid infusion) and the rest was administered continuously over 24hrs. Leucovorin rescue was administered every 6hrs starting 48 hrs after initiation of MTX infusion.
Article: Pharmacogenetics of tenofovir clearance among Southern Africans living with HIV
Gene: APOC1, APOE
Variant/haplotype: rs7412
Drug(s): tenofovir
Phenotype category: Metabolism/PK
Significant: no
Association: Allele T is not associated with clearance of tenofovir in people with HIV Infections as compared to allele C.
Notes: Significance threshold was set at 4.5E-3.
Article: Evaluation of CYP2C9- and VKORC1-based pharmacogenetic algorithm for warfarin dose in Gaza-Palestine
Gene: CYP2C9
Variant/haplotype: rs1799853
Drug(s): warfarin
Phenotype category: Dosage
Significant: no
Association: Allele T is associated with dose of warfarin in people with Cardiovascular Diseases as compared to allele C.
Notes: Although in the first analysis, the T allele was not found to be associated with warfarin dose in this population, the polymorphism was included in the International Warfarin Pharmacogenetic Consortium (IWPC), which was compared to a traditional clinical algorithm and the IWPC algorithm predicted dose better than the clinical algorithm.
Article: CYP3A5 and ABCB1 genotype influence tacrolimus and sirolimus pharmacokinetics in renal transplant recipients
Gene: CYP3A5
Variant/haplotype: CYP3A5*1, CYP3A5*3
Drug(s): sirolimus, tacrolimus
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP3A5 *3/*3 is associated with increased dose-adjusted trough concentrations of sirolimus or tacrolimus in people with Kidney Transplantation as compared to CYP3A5 *1/*1 + *1/*3.
Article: Targeted pharmacogenetic analysis of antipsychotic response in the CATIE study
Gene: NALCN
Variant/haplotype: rs9585618
Drug(s): ziprasidone
Phenotype category: Efficacy
Significant: yes
Association: Allele C is associated with response to ziprasidone 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: Testing genetic modifiers of behavior and response to atomoxetine in autism spectrum disorder with ADHD
Gene: CYP2D6
Variant/haplotype: CYP2D6 poor metabolizer and intermediate metabolizer genotypes
Drug(s): atomoxetine
Phenotype category: Efficacy
Significant: no
Association: CYP2D6 poor metabolizer and intermediate metabolizer genotypes are not associated with response to atomoxetine in people with Attention Deficit Disorder with Hyperactivity as compared to CYP2D6 normal metabolizer and ultra-metabolizer genotypes.
Notes: No significant association of CYP2D6 metabolizer phenotype with ADHD symptom response or compliance response. Metabolizer status was assigned based on CPIC guidelines and the presence of the *2, *3, *4, *6, *9 *10. *17 or *41 alleles or the variants rs5758550 or rs1080985.
Article: Multigene predictors of tacrolimus exposure in kidney transplant recipients
Gene: POR
Variant/haplotype: rs1057868
Drug(s): tacrolimus
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotypes CT + TT is associated with decreased trough concentration of tacrolimus in people with Kidney Transplantation as compared to genotype CC.
Notes: In a multivariable model adjusting for CYP3A5*1 status and clinical factors, one or two POR*28 alleles (rs1057868 CT + TT) were associated with a 4.63% reduction in trough concentrations. In a more detailed analysis, in a subset of CYP3A5 nonexpressors (*3/*3; n=997), patients with one or two POR*28 alleles had dose-adjusted trough concentrations reduced by 5.6% after adjustment for clinical factors (p=0.03). However, in a subset of CYP3A5 expressors (*1/*1 or *1/*3; n=432), with adjustment for clinical factors, the POR*28 alleles were NOT associated with trough concentrations (p=0.68). n=35,043 tacrolimus trough concentrations were available for analysis.
Article: No significant influence of OCT1 genotypes on the pharmacokinetics of morphine in adult surgical patients
Gene: SLC22A1
Variant/haplotype: rs72552763
Drug(s): morphine
Phenotype category: Metabolism/PK
Significant: no
Association: Allele del is not associated with exposure to morphine in people with Pain, Postoperative as compared to allele GAT.
Notes: Analyzed as part of haplotypes with rs12208357, rs34059508 and rs34130495. There was a non-significant trend for patients carrying reduced function alleles to have increased exposure to morphine, but the change in exposure is not large enough to be of clinical importance.
Article: A single tumour necrosis factor haplotype influences the response to adalimumab in rheumatoid arthritis
Gene: TNF
Variant/haplotype: rs361525
Drug(s): adalimumab
Phenotype category: Efficacy
Significant: yes
Association: Genotype GG is associated with decreased response to adalimumab in people with Arthritis, Rheumatoid.
Notes: When in a haplotype with rs1800629 and rs1799724.  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: Pharmacogenomics of insulin-like growth factor-I generation during GH treatment in children with GH deficiency or Turner syndrome
Gene: CDK4
Variant/haplotype: rs2069502
Drug(s): somatropin recombinant
Phenotype category: Efficacy
Significant: yes
Association: Genotype CC is associated with decreased response to somatropin recombinant in children with Turner Syndrome as compared to genotypes CT + TT.
Notes: Response to growth hormone treatment assessed by 1-month insulin-like growth factor-I (IGF-I) generation. Multiple test correction was done for 1182 SNPs. Corrected p values was given.
Article: ADH single nucleotide polymorphism associations with alcohol metabolism in vivo
Gene: ADH7
Variant/haplotype: rs1154461
Drug(s): ethanol
Phenotype category: Toxicity, Metabolism/PK
Significant: yes
Association: Allele C is associated with metabolism of ethanol.
Notes: The authors did not report p-value correction for multiple hypotheses (103 snps tested).  Though they report multiple snps are significantly associated with alcohol metabolism (early or late) tested on blood or breath alcohol concentrations, this is the only snp that survived Bonferroni correction for multiple hypotheses (<0.00049).  It was only significant for blood early metabolism, and the authors did not state which alleles are associated with increased or decreased metabolism.  Instead, they simply report an association with the snp in general.  Note that this gene is on the minus strand.
Article: The Association of Transporter Genes Polymorphisms and Lung Cancer Chemotherapy Response
Gene: POU2F2
Variant/haplotype: rs1883306
Drug(s): platinum
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to platinum in people with Lung Neoplasms as compared to allele C.
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: Association of corticotropin releasing hormone receptor 2 (CRHR2) genetic variants with acute bronchodilator response in asthma
Gene: CRHR2
Variant/haplotype: rs7793837
Drug(s): salbutamol, selective beta-2-adrenoreceptor agonists
Phenotype category: Efficacy
Significant: yes
Association: Allele T is associated with decreased response to salbutamol and selective beta-2-adrenoreceptor agonists in people with Asthma as compared to allele A.
Article: Effects of UGT1A1 Genotype on the Pharmacokinetics, Pharmacodynamics, and Toxicities of Belinostat Administered by 48-Hour Continuous Infusion in Patients With Cancer
Gene: UGT1A1
Variant/haplotype: UGT1A1*1, UGT1A1*60
Drug(s): belinostat
Phenotype category: Metabolism/PK
Significant: yes
Association: UGT1A1 *1/*60 + *60/*60 is associated with increased concentrations of Belinostat in people with Neoplasms.
Notes: The dose-normalized area under the plasma concentration-time curve (AUC) was increased in carriers of the *60 alleles (*1/*60 n=7; *60/*60 n=4) in those who received a belinostat dose greater than 400 mg/m2/24h. Significant results were also seen when considering *28 and *60 alleles combined. Patients received belinostat in combination with cisplatin and etoposide. p < 0.01 was considered statistically significant.
Article: Functional genetic variation in the Rev-Erbα pathway and lithium response in the treatment of bipolar disorder
Gene: PER2
Variant/haplotype: rs2304672
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 C.
Article: Effect of AGTR1 and BDKRB2 gene polymorphisms on atorvastatin metabolism in a Mexican population
Gene: BDKRB2
Variant/haplotype: rs1799722
Drug(s): atorvastatin
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype CT is associated with increased exposure to atorvastatin in healthy individuals as compared to genotypes CC + TT.
Notes: AUC (0-time t) and AUC (0-infinity) values were significantly higher in the CT genotype (180.66±78.48 and 194.17±77.38 ng/ml/h, respectively) vs the TT + CC genotypes combined (145.22±91.08 and 159.54±92.80 ng/ml/h, respectively) (P<0.05). Clearance was significantly lower in the CT genotype (469.55±168.36 l/h) vs TT+CC (643.68±304.85 l/h) (P<0.05 & adjusted R2=0.093, P=0.01). Genotype was not associated with half-life, Cmax, or elimination rate constant of atorvastatin.
Article: Association between CXCL10 and DPP4 Gene Polymorphisms and a Complementary Role for Unfavorable IL28B Genotype in Prediction of Treatment Response in Thai Patients with Chronic Hepatitis C Virus Infection
Gene: DPP4
Variant/haplotype: rs13015258
Drug(s): peginterferon alfa-2a, peginterferon alfa-2b
Phenotype category: Efficacy
Significant: no
Association: Genotype GG is not associated with response to peginterferon alfa-2a or peginterferon alfa-2b in people with Hepatitis C, Chronic as compared to genotypes GT + TT.
Notes: PEG-interferon alfa (2a and b) was co-adminstered with ribavirin. Response was assessed by sustained virological response (SVR) percent by genotype. Please note, alleles have been complemented to the + chromosomal strand.
Article: Effect of ABCB1 (MDR1) haplotypes derived from G2677T/C3435T on the pharmacokinetics of amlodipine in healthy subjects
Gene: ABCB1
Variant/haplotype: rs1045642
Drug(s): amlodipine
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype GG is associated with decreased clearance of amlodipine in healthy individuals as compared to genotypes AA + AG.
Notes: When analyzed in combination with genotypes from rs2032582. The haplotypes were: 2677CC/3435GG, 2677AC/3435AG, 2677AA/3435AA, where rs2032582 = position 2677 and rs1045642 = position 3435.; Individuals with the 2677CC/3435GG haplotype had increased area under the time-concentration curve from 0 to 144 hours (AUC0-144) and from 0 to infinity (AUC0-infinity) and decreased oral clearance (CL/F) as compared to haplotypes 2677AA/3435AA + 2677AC/3435AG, and increased peak plasma concentration (Cmax) as compared to haplotype 2677AA/3435AA ONLY. Please note alleles have been complemented to the plus chromosomal strand.
Article: Evaluation of genetic association of neurodevelopment and neuroimmunological genes with antipsychotic treatment response in schizophrenia in Indian populations
Gene: NRG1
Variant/haplotype: rs13250975
Drug(s): antipsychotics
Phenotype category: Efficacy
Significant: yes
Association: Allele G is associated with increased response to antipsychotics in people with Schizophrenia as compared to allele A.
Notes: In high severity schizophrenia patient subgroup
Article: The role of organic anion-transporting polypeptides and their common genetic variants in mycophenolic acid pharmacokinetics
Gene: SLCO1B3
Variant/haplotype: rs4149117
Drug(s): mycophenolate mofetil
Phenotype category: Metabolism/PK
Significant: no
Association: Allele G is not associated with clearance of mycophenolate mofetil in people with Kidney Transplantation as compared to allele T.
Notes: This finding is for patients also treated with cyclosporine.
Article: Pharmacogenetic association of the APOA1/C3/A4/A5 gene cluster and lipid responses to fenofibrate: the Genetics of Lipid-Lowering Drugs and Diet Network study
Gene: APOA1
Variant/haplotype: rs2727784
Drug(s): fenofibrate
Phenotype category: Efficacy
Significant: no
Association: Genotypes CC + CT are not associated with response to fenofibrate in people with Hypertriglyceridemia as compared to genotype TT.
Notes: No significant difference in the change in plasma triglyceride (TG) or high-density lipoprotein (HDL) levels between genotypes was seen, after three weeks of treatment with fenofibrate. Please note alleles have been complemented to the plus chromosomal strand.
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
Variant/haplotype: rs6942227
Drug(s): lithium
Phenotype category: Efficacy
Significant: yes
Association: Allele A is associated with decreased response to lithium in people with Bipolar Disorder as compared to allele G.
Article: Replication study of polymorphisms associated with response to methotrexate in patients with rheumatoid arthritis
Gene: ATIC
Variant/haplotype: rs16853834
Drug(s): methotrexate
Phenotype category: Efficacy
Significant: no
Association: Allele C is not associated with response to methotrexate in people with Arthritis, Rheumatoid as compared to allele T.
Article: A genetic variant in NRP1 is associated with worse response to ranibizumab treatment in neovascular age-related macular degeneration
Gene: NRP1
Variant/haplotype: rs2804495
Drug(s): ranibizumab
Phenotype category: Efficacy
Significant: no
Association: Allele G is not associated with response to ranibizumab in people with Macular Degeneration as compared to allele T.
Notes: Response was measured as change in visual acuity after 3 months of treatment in patients who received three monthly ranibizumab injections.
Article: Pharmacogenetics Meets Metabolomics: Discovery of Tryptophan as a New Endogenous OCT2 Substrate Related to Metformin Disposition
Gene: SLC22A2
Variant/haplotype: rs316019
Drug(s): l-tryptophan
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype CC is associated with increased clearance of l-tryptophan as compared to genotypes AA + AC.
Notes: A gene dose effect was observed in that clearance of tryptophan decreased in the following manner: CC>AC>AA.
Article: Association of serotonin transporter (SLC6A4) & receptor (5HTR1A, 5HTR2A) polymorphisms with response to treatment with escitalopram in patients with major depressive disorder: A preliminary study
Gene: HTR2A
Variant/haplotype: rs6311
Drug(s): escitalopram
Phenotype category: Efficacy
Significant: no
Association: Allele T is not associated with response to escitalopram Depressive Disorder, Major as compared to allele C.
Article: Polymorphisms in STAT4, PTPN2, PSORS1C1 and TRAF3IP2 Genes Are Associated with the Response to TNF Inhibitors in Patients with Rheumatoid Arthritis
Gene: PSORS1C1
Variant/haplotype: rs2233945
Drug(s): etanercept
Phenotype category: Efficacy
Significant: yes
Association: Allele C is associated with decreased response to etanercept in people with Arthritis, Rheumatoid as compared to allele A.
Notes: The degree of response was determined by EULAR score.; A significant association between rs2233945 and response to etanercept was seen at six months after beginning treatment. No significant association was seen at two years after beginning treatment.; No significant associations were seen at either time point when response was measured as number of patients in remission or with low disease activity.
Article: Genetic Polymorphisms of Cytokines Might Affect Postoperative Sufentanil Dosage for Analgesia in Patients
Gene: TNF
Variant/haplotype: rs1800629
Drug(s): sufentanil
Phenotype category: Dosage
Significant: no
Association: Allele A is not associated with dose of sufentanil in people with Pain, Postoperative as compared to allele G.
Article: Sex‐Dependent Effects of CYP2D6 on the Pharmacokinetics of Berberine in Humans
Gene: CYP2D6
Variant/haplotype: CYP2D6 poor metabolizer
Drug(s): berberine
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2D6 poor metabolizer is associated with decreased metabolism of berberine in women as compared to CYP2D6 normal metabolizer.
Notes: "The effects of CYP2D6 on berberine pharmacokinetics were only observed in females and not in males (Figure 5c). Females who were poor CYP2D6 metabolizers showed 79% lower M1-to-berberine ratios compared with females with reference genotype (P = 2.3 × 10 −4 , Welch’s t-test on log 2 values). In contrast, no genotype-dependent difference was observed in males." "Poor CYP2D6 metabolizers were defined as homozygous or compound heterozygous carriers of CYP2D6 alleles *3, *4, *5 or *6. In the reference group, we included carriers of two fully active alleles of OCT1 (OCT1*1) and CYP2D6(CYP2D6*1, *2, and *35) without duplication"
Article: Impact of CYP2C9, VKORC1 and CYP4F2 genetic polymorphisms on maintenance warfarin dosage in Han-Chinese patients: A systematic review and meta-analysis
Gene: CYP4F2
Variant/haplotype: rs2108622
Drug(s): warfarin
Phenotype category: Dosage
Significant: no
Association: Allele T is associated with increased dose of warfarin as compared to allele C.
Article: Estimating the In Vivo Function of CYP2D6 Alleles through Population Pharmacokinetic Modeling of Brexpiprazole
Gene: CYP2D6
Variant/haplotype: CYP2D6*1, CYP2D6*2
Drug(s): brexpiprazole
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2D6 *2 is associated with decreased metabolism of brexpiprazole as compared to CYP2D6 *1.
Notes: in patients and healthy individuals from clinical studies.  "CYP2D6*2 allele (n = 183); was associated with only 10% enzyme activity relative to the wild-type allele (CYP2D6*1)"
Article: Pharmacokinetics and pharmacodynamics following maintenance doses of prasugrel and clopidogrel in Chinese carriers of CYP2C19 variants
Gene: CYP2C19
Variant/haplotype: CYP2C19*1, CYP2C19*2, CYP2C19*3
Drug(s): prasugrel
Phenotype category: Efficacy
Significant: no
Association: CYP2C19 *2/*2 + *2/*3 are not associated with response to prasugrel in healthy individuals as compared to CYP2C19 *1/*1.
Notes: Response to prasugrel treatment was unaffected by CYP2C19 genetic variation based on IPA to 20 mM ADP as measured by LTA, the VN P2Y12 assay and VASP phosphorylation.