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Uncovering the role of admixture in disease and drug response: Association of hepatocyte gene expression and DNA methylation with African Ancestry in African Americans

https://doi.org/10.1101/491225
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Association of Genetic Variants With Warfarin-Associated Bleeding Among Patients of African Descent
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Incidence of testicular germ cell tumors among US men by census region
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Quantitative RT-PCR Measurement of Human Cytochrome P-450s: Application to Drug Induction Studies
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Primary Hepatocytes in Sandwich Culture
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Cytochrome allelic variants and clopidogrel metabolism in cardiovascular diseases therapy
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Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples
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DNA hypermethylation markers of poor outcome in laryngeal cancer
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Racial disparity with on-treatment platelet reactivity in patients undergoing percutaneous coronary intervention
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Contribution of Four Comorbid Conditions to Racial/Ethnic Disparities in Mortality Risk
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Gene Body Methylation Can Alter Gene Expression and Is a Therapeutic Target in Cancer
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Identifying Recent Adaptations in Large-Scale Genomic Data
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Genetic Ancestry and Natural Selection Drive Population Differences in Immune Responses to Pathogens
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Impact of CYP2C19 gene polymorphism on warfarin maintenance doses in patients with non-valvular atrial fibrillation
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Association between P2RY12 gene polymorphisms and adverse clinical events in coronary artery disease patients treated with clopidogrel: A systematic review and meta-analysis
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Innate lymphoid cells type 2 – emerging immune regulators of obesity and atherosclerosis
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The Uncertain Significance of Low Vitamin D Levels in African Descent Populations: A Review of the Bone and Cardiometabolic Literature
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Vitamin D Receptor Signaling in Renal and Cardiovascular Protection
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APOL1 Nephropathy: A Population Genetics and Evolutionary Medicine Detective Story
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High density DNA methylation array with single CpG site resolution
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The Role of the t-PA I/D and PAI-1 4G/5G Polymorphisms in African-American Adults With a Diagnosis of Myocardial Infarction or Venous Thromboembolism
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Genetic variants associated with warfarin dose in African-American individuals: a genome-wide association study
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Venous thrombosis in relation to fibrinogen and factor VII genes among African-Americans
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Pharmacogenomics Knowledge for Personalized Medicine
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Single-cell spatial reconstruction reveals global division of labour in the mammalian liver
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Genetic effects on gene expression across human tissues
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The Genotype-Tissue Expression (GTEx) project
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Estimating the causal tissues for complex traits and diseases
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Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts
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Natural selection has driven population differentiation in modern humans
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Data quality control in genetic case-control association studies
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Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses
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Interleukin-33 in health and disease
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Vitamin D Metabolism-Related Gene Haplotypes and Their Association with Metabolic Disturbances Among African-American Urban Adults
inferredcites →https://doi.org/10.1038/srep20642openalex-snapshot
RNF135, RING finger protein, promotes the proliferation of human glioblastoma cells in vivo and in vitro via the ERK pathway
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Genetic Determinants of Response to Clopidogrel and Cardiovascular Events
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Genetic Ancestry in Lung-Function Predictions
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Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma
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A Fast and Flexible Statistical Model for Large-Scale Population Genotype Data: Applications to Inferring Missing Genotypes and Haplotypic Phase
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Quantification of Multiple Human Cytochrome P450 mRNA Molecules Using Competitive Reverse Transcriptase-PCR
inferredcites →https://doi.org/10.1093/bioinformatics/bts034openalex-snapshot
The sva package for removing batch effects and other unwanted variation in high-throughput experiments
inferredcites →https://doi.org/10.1093/bioinformatics/bts680openalex-snapshot
A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data
inferredcites →https://doi.org/10.1093/bioinformatics/btt311openalex-snapshot
Gene-set analysis is severely biased when applied to genome-wide methylation data
inferredcites →https://doi.org/10.1093/bioinformatics/btt684openalex-snapshot
ChAMP: 450k Chip Analysis Methylation Pipeline
inferredcites →https://doi.org/10.1093/bioinformatics/btu049openalex-snapshot
Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays
inferredcites →https://doi.org/10.1093/bioinformatics/btu316openalex-snapshot
A systems-level integrative framework for genome-wide DNA methylation and gene expression data identifies differential gene expression modules under epigenetic control
inferredcites →https://doi.org/10.1093/bioinformatics/btu638openalex-snapshot
HTSeq—a Python framework to work with high-throughput sequencing data
inferredcites →https://doi.org/10.1093/biostatistics/kxj037openalex-snapshot
Adjusting batch effects in microarray expression data using empirical Bayes methods
inferredcites →https://doi.org/10.1093/epirev/mxx005openalex-snapshot
Vitamin D and Cancer Risk and Mortality: State of the Science, Gaps, and Challenges
inferredcites →https://doi.org/10.1093/nar/gkv007openalex-snapshot
limma powers differential expression analyses for RNA-sequencing and microarray studies
inferredcites →https://doi.org/10.1093/nar/gkw1133openalex-snapshot
The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog)
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g:Profiler—a web server for functional interpretation of gene lists (2016 update)
inferredcites →https://doi.org/10.1096/fj.201600344ropenalex-snapshot
The ENTPD1 promoter polymorphism −860 A > G (rs3814159) is associated with increased gene transcription, protein expression, CD39/NTPDase1 enzymatic activity, and thromboembolism risk
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Inflammation and thrombosis in cardiovascular disease
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Mutation screening of the ubiquitin ligase gene RNF135 in French patients with autism
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The population pharmacokinetics of R‐ and S‐warfarin: effect of genetic and clinical factors
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P2RY1 and P2RY12 polymorphisms and on‐aspirin platelet reactivity in patients with coronary artery disease
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Epigenetics, chromatin and genome organization: recent advances from the ENCODE project
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Cardiovascular Pharmacogenomics: Does It Matter If You're Black or White?
inferredcites →https://doi.org/10.1146/annurev.genom.9.081307.164258openalex-snapshot
African Genetic Diversity: Implications for Human Demographic History, Modern Human Origins, and Complex Disease Mapping
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Polymorphisms of Human Aldehyde Dehydrogenases
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Chronic Kidney Disease: Novel Insights from Genome-Wide Association Studies
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P2 receptors, platelet function and pharmacological implications
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Dimorphism in the P2Y1 ADP Receptor Gene Is Associated With Increased Platelet Activation Response to ADP
inferredcites →https://doi.org/10.1161/01.atv.17.4.755openalex-snapshot
Gene Polymorphisms Predicting High Plasma Levels of Coagulation and Fibrinolysis Proteins
inferredcites →https://doi.org/10.1161/atvbaha.113.302088openalex-snapshot
Genome-Wide Association Study for Circulating Tissue Plasminogen Activator Levels and Functional Follow-Up Implicates Endothelial STXBP5 and STX2
inferredcites →https://doi.org/10.1161/circgenetics.113.000303openalex-snapshot
Cytochrome P450 Gene Variants, Race, and Mortality Among Clopidogrel-Treated Patients After Acute Myocardial Infarction
inferredcites →https://doi.org/10.1161/circulationaha.105.547836openalex-snapshot
Comprehensive Survey of Common Genetic Variation at the Plasminogen Activator Inhibitor-1 Locus and Relations to Circulating Plasminogen Activator Inhibitor-1 Levels
inferredcites →https://doi.org/10.1182/blood-2015-09-668525openalex-snapshot
Novel genetic predictors of venous thromboembolism risk in African Americans
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A genome-wide integrative study of microRNAs in human liver
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De novo identification of differentially methylated regions in the human genome
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A scaling normalization method for differential expression analysis of RNA-seq data
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Genome-wide signatures of differential DNA methylation in pediatric acute lymphoblastic leukemia
inferredcites →https://doi.org/10.1186/s13059-014-0550-8openalex-snapshot
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
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Gateways to the FANTOM5 promoter level mammalian expression atlas
inferredcites →https://doi.org/10.1186/s13072-018-0191-3openalex-snapshot
Age-related DNA methylation changes are tissue-specific with ELOVL2 promoter methylation as exception
inferredcites →https://doi.org/10.13110/humanbiology.87.4.0295openalex-snapshot
Interaction of Alu Polymorphisms and Novel Measures of Discrimination in Association with Blood Pressure in African Americans Living in Tallahassee, Florida
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Mapping the Genetic Architecture of Gene Expression in Human Liver
inferredcites →https://doi.org/10.1371/journal.pgen.1002078openalex-snapshot
Identification, Replication, and Functional Fine-Mapping of Expression Quantitative Trait Loci in Primary Human Liver Tissue
inferredcites →https://doi.org/10.1371/journal.pgen.1002264openalex-snapshot
Genetic Association for Renal Traits among Participants of African Ancestry Reveals New Loci for Renal Function
inferredcites →https://doi.org/10.1371/journal.pgen.1006059openalex-snapshot
The Great Migration and African-American Genomic Diversity
inferredcites →https://doi.org/10.1371/journal.pone.0008274openalex-snapshot
An Epigenetic Signature in Peripheral Blood Predicts Active Ovarian Cancer
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Vitamin D Receptor Gene Polymorphisms and Prognosis of Breast Cancer among African-American and Hispanic Women
inferredcites →https://doi.org/10.1371/journal.pone.0165870openalex-snapshot
Evidence of Recent Intricate Adaptation in Human Populations
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fastSTRUCTURE: Variational Inference of Population Structure in Large SNP Data Sets
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Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments
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Vegfa Protects the Glomerular Microvasculature in Diabetes
inferredcites →https://doi.org/10.2459/jcm.0b013e328364bb04openalex-snapshot
Genetic and nongenetic factors influencing the response to clopidogrel
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Population-Specific Associations of Deleterious Rare Variants in Coding Region of P2RY1–P2RY12 Purinergic Receptor Genes in Large-Vessel Ischemic Stroke Patients
inferredcites →https://doi.org/10.3791/50615openalex-snapshot
Isolation of Human Hepatocytes by a Two-step Collagenase Perfusion Procedure
inferredcites →https://doi.org/10.3945/jn.116.244962openalex-snapshot
Vitamin D Receptor and Megalin Gene Polymorphisms Are Associated with Longitudinal Cognitive Change among African-American Urban Adults
inferredcites →https://doi.org/10.4049/jimmunol.1601983openalex-snapshot
TGF-β1 Suppresses IL-33–Induced Mast Cell Function
inferredcites →https://doi.org/10.7554/elife.20532openalex-snapshot
Differential methylation between ethnic sub-groups reflects the effect of genetic ancestry and environmental exposures

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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The Advantages and Challenges of Diversity in Pharmacogenomics: Can Minority Populations Bring Us Closer to Implementation?
inferred← citeshttps://doi.org/10.1101/2020.06.09.143271openalex-snapshot
Differential expression of COVID-19-related genes in European Americans and African Americans
inferred← citeshttps://doi.org/10.1101/2025.01.23.634506openalex-snapshot
MeQTL Mapping in African American Hepatocytes Reveals Shared Genetic Regulators of DNA Methylation and Gene Expression
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