Genetics and Genomics of Coronary Artery Disease

Disentangling the Effects of Colocalizing Genomic Annotations to Functionally Prioritize Non-coding Variants within Complex-Trait Loci

(2015) Gosia Trynka et al.   AMERICAN JOURNAL OF HUMAN GENETICS

From Locus Association to Mechanism of Gene Causality: Figure.

(2015) Clint L. Miller et al.   ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY

Myocardial Infarction-Associated SNP at 6p24 Interferes With MEF2 Binding and Associates With PHACTR1 Expression Levels in Human Coronary Arteries

(2015) M. Beaudoin et al.   ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY

Assessing allele-specific expression across multiple tissues from RNA-seq read data

(2015) Matti Pirinen et al.   BIOINFORMATICS

Adapt-Mix: learning local genetic correlation structure improves summary statistics-based analyses

(2015) Danny S. Park et al.   BIOINFORMATICS

Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions

(2015) Alicia N. Schep et al.   GENOME RESEARCH

RNA-Seq identifies novel myocardial gene expression signatures of heart failure

(2015) Yichuan Liu et al.   GENOMICS

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis

(2015) Matthew C. Canver et al.   NATURE

A comprehensive 1000 Genomes–based genome-wide association meta-analysis of coronary artery disease

(2015) Majid Nikpay et al.   NATURE GENETICS

Sensitive detection of chromatin-altering polymorphisms reveals autoimmune disease mechanisms

(2015) Ricardo Cruz-Herrera del Rosario et al.   NATURE METHODS

WASP: allele-specific software for robust molecular quantitative trait locus discovery

(2015) Bryce van de Geijn et al.   NATURE METHODS

Coronary Artery Disease Associated Transcription Factor TCF21 Regulates Smooth Muscle Precursor Cells That Contribute to the Fibrous Cap

(2015) Sylvia T. Nurnberg et al.   PLoS Genetics

Lipid-Induced Epigenomic Changes in Human Macrophages Identify a Coronary Artery Disease-Associated Variant that Regulates PPAP2B Expression through Altered C/EBP-Beta Binding

(2015) Michael E. Reschen et al.   PLoS Genetics

Characterization of TCF21 Downstream Target Regions Identifies a Transcriptional Network Linking Multiple Independent Coronary Artery Disease Loci

(2015) Olga Sazonova et al.   PLoS Genetics

Modulators of Hepatic Lipoprotein Metabolism Identified in a Search for Small-Molecule Inducers of Tribbles Pseudokinase 1 Expression

(2015) Marek M. Nagiec et al.   PLoS One

Integrative DNA, RNA, and Protein Evidence Connects TREML4 to Coronary Artery Calcification

(2014) Shurjo K. Sen et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Identification and Initial Functional Characterization of a Human Vascular Cell–Enriched Long Noncoding RNA

(2014) Robert D. Bell et al.   ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY

Developmental Heterogeneity of Cardiac Fibroblasts Does Not Predict Pathological Proliferation and Activation

(2014) Shah R. Ali et al.   CIRCULATION RESEARCH

Permanent Alteration of PCSK9 With In Vivo CRISPR-Cas9 Genome Editing

(2014) Qiurong Ding et al.   CIRCULATION RESEARCH

Dissecting the Causal Genetic Mechanisms of Coronary Heart Disease

(2014) Clint L. Miller et al.   Current Atherosclerosis Reports

CDH13 promoter SNPs with pleiotropic effect on cardiometabolic parameters represent methylation QTLs

(2014) Margus Putku et al.   HUMAN GENETICS

Expanding the genetic editing tool kit: ZFNs, TALENs, and CRISPR-Cas9

(2014) Rajat M. Gupta et al.   JOURNAL OF CLINICAL INVESTIGATION

Cyclin-dependent kinase inhibitor 2B regulates efferocytosis and atherosclerosis

(2014) Yoko Kojima et al.   JOURNAL OF CLINICAL INVESTIGATION

DNA methylation and body-mass index: a genome-wide analysis

(2014) Katherine J Dick et al.   LANCET

Obesity-associated variants within FTO form long-range functional connections with IRX3

(2014) Scott Smemo et al.   NATURE

Genetic and epigenetic fine mapping of causal autoimmune disease variants

(2014) Kyle Kai-How Farh et al.   NATURE

The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance

(2014) Charles Wang et al.   NATURE BIOTECHNOLOGY

Comparison of RNA-Seq and Microarray in Transcriptome Profiling of Activated T Cells

(2014) Shanrong Zhao et al.   PLoS One

A Bayesian Method to Incorporate Hundreds of Functional Characteristics with Association Evidence to Improve Variant Prioritization

(2014) Sarah A. Gagliano et al.   PLoS One

A Novel Role of CDX1 in Embryonic Epicardial Development

(2014) Min Chu et al.   PLoS One

Functional annotation of colon cancer risk SNPs

(2014) Lijing Yao et al.   Nature Communications

Comprehensive Functional Annotation of 77 Prostate Cancer Risk Loci

(2014) Dennis J. Hazelett et al.   PLoS Genetics

Methylation QTLs Are Associated with Coordinated Changes in Transcription Factor Binding, Histone Modifications, and Gene Expression Levels

(2014) Nicholas E. Banovich et al.   PLoS Genetics

Integrating Functional Data to Prioritize Causal Variants in Statistical Fine-Mapping Studies

(2014) Gleb Kichaev et al.   PLoS Genetics

Coronary Heart Disease-Associated Variation in TCF21 Disrupts a miR-224 Binding Site and miRNA-Mediated Regulation

(2014) Clint L. Miller et al.   PLoS Genetics

Integrative Genomics Reveals Novel Molecular Pathways and Gene Networks for Coronary Artery Disease

(2014) Ville-Petteri Mäkinen et al.   PLoS Genetics

A Systems Biology Framework Identifies Molecular Underpinnings of Coronary Heart Disease

(2013) Tianxiao Huan et al.   ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY

DNase-seq predicts regions of rotational nucleosome stability across diverse human cell types

(2013) D. R. Winter et al.   GENOME RESEARCH

Cas9 as a versatile tool for engineering biology

(2013) Prashant Mali et al.   NATURE METHODS

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Detection of histone modifications at specific gene loci in single cells in histological sections

(2013) Delphine Gomez et al.   NATURE METHODS

An Erythroid Enhancer of BCL11A Subject to Genetic Variation Determines Fetal Hemoglobin Level

(2013) D. E. Bauer et al.   SCIENCE

Disease-Related Growth Factor and Embryonic Signaling Pathways Modulate an Enhancer of TCF21 Expression at the 6q23.2 Coronary Heart Disease Locus

(2013) Clint L. Miller et al.   PLoS Genetics

DNA methylation age of human tissues and cell types

(2013) Steve Horvath   GENOME BIOLOGY

Animal Models of Atherosclerosis

(2012) Godfrey S. Getz et al.   ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY

Loss of CDKN2B Promotes p53-Dependent Smooth Muscle Cell Apoptosis and Aneurysm Formation

(2012) Nicholas J. Leeper et al.   ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY

Effect of 9p21.3 Coronary Artery Disease Locus Neighboring Genes on Atherosclerosis in Mice

(2012) Juyong Brian Kim et al.   CIRCULATION

The bHLH transcription factor Tcf21 is required for lineage-specific EMT of cardiac fibroblast progenitors

(2012) A. Acharya et al.   DEVELOPMENT

Pod1/Tcf21 is regulated by retinoic acid signaling and inhibits differentiation of epicardium-derived cells into smooth muscle in the developing heart

(2012) Caitlin M. Braitsch et al.   DEVELOPMENTAL BIOLOGY

Annotation of functional variation in personal genomes using RegulomeDB

(2012) A. P. Boyle et al.   GENOME RESEARCH

Functional analyses of coronary artery disease associated variation on chromosome 9p21 in vascular smooth muscle cells

(2012) A. Motterle et al.   HUMAN MOLECULAR GENETICS

Hi–C: A comprehensive technique to capture the conformation of genomes

(2012) Jon-Matthew Belton et al.   METHODS

Systems analysis of eleven rodent disease models reveals an inflammatome signature and key drivers

(2012) I.-M. Wang et al.   Molecular Systems Biology

DNase I sensitivity QTLs are a major determinant of human expression variation

(2012) Jacob F. Degner et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Interpreting noncoding genetic variation in complex traits and human disease

(2012) Lucas D Ward et al.   NATURE BIOTECHNOLOGY

Bone Marrow p16INK4a-Deficiency Does Not Modulate Obesity, Glucose Homeostasis or Atherosclerosis Development

(2012) Kristiaan Wouters et al.   PLoS One

The Chromosome 9p21.3 Coronary Heart Disease Risk Allele Is Associated with Altered Gene Expression in Normal Heart and Vascular Tissues

(2012) Anna P. Pilbrow et al.   PLoS One

The mystery of missing heritability: Genetic interactions create phantom heritability

(2012) O. Zuk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cdkn2a Is an Atherosclerosis Modifier Locus That Regulates Monocyte/Macrophage Proliferation

(2011) Chao-Ling Kuo et al.   ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY

Increased gene dosage of the Ink4/Arf locus does not attenuate atherosclerosis development in hypercholesterolaemic mice

(2011) José J. Fuster et al.   ATHEROSCLEROSIS

Genetic variants at the 9p21 locus contribute to atherosclerosis through modulation of ANRIL and CDKN2A/B

(2011) Ada Congrains et al.   ATHEROSCLEROSIS

Genetic Mechanisms Mediating Atherosclerosis Susceptibility at the Chromosome 9p21 Locus

(2011) Michael S. Cunnington et al.   Current Atherosclerosis Reports

Efficient inducible Cre-mediated recombination in Tcf21cell lineages in the heart and kidney

(2011) Asha Acharya et al.   GENESIS

Long-range DNA looping and gene expression analyses identify DEXI as an autoimmune disease candidate gene

(2011) Lucy J. Davison et al.   HUMAN MOLECULAR GENETICS

9p21 DNA variants associated with coronary artery disease impair interferon-γ signalling response

(2011) Olivier Harismendy et al.   NATURE

Large-scale association analysis identifies 13 new susceptibility loci for coronary artery disease

(2011) Heribert Schunkert et al.   NATURE GENETICS

Determinants and dynamics of genome accessibility

(2011) Oliver Bell et al.   NATURE REVIEWS GENETICS

deFuse: An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data

(2011) Andrew McPherson et al.   PLoS Computational Biology

Expression of Chr9p21 genes CDKN2B (p15INK4b), CDKN2A (p16INK4a, p14ARF) and MTAP in human atherosclerotic plaque

(2010) Lesca Miriam Holdt et al.   ATHEROSCLEROSIS

p19ARFDeficiency Reduces Macrophage and Vascular Smooth Muscle Cell Apoptosis and Aggravates Atherosclerosis

(2010) Herminia González-Navarro et al.   JOURNAL OF THE AMERICAN COLLEGE OF CARDIOLOGY

Targeted deletion of the 9p21 non-coding coronary artery disease risk interval in mice

(2010) Axel Visel et al.   NATURE

Epigenomics reveals a functional genome anatomy and a new approach to common disease

(2010) Andrew P Feinberg   NATURE BIOTECHNOLOGY

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

DNA Methylation as a Biomarker for Cardiovascular Disease Risk

(2010) Myungjin Kim et al.   PLoS One

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chromosome 9p21 SNPs Associated with Multiple Disease Phenotypes Correlate with ANRIL Expression

(2010) Michael S. Cunnington et al.   PLoS Genetics

Functional Analysis of the Chromosome 9p21.3 Coronary Artery Disease Risk Locus

(2009) Olga Jarinova et al.   ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY

Finding the missing heritability of complex diseases

(2009) Teri A. Manolio et al.   NATURE

An oestrogen-receptor-α-bound human chromatin interactome

(2009) Melissa J. Fullwood et al.   NATURE

Detecting gene–gene interactions that underlie human diseases

(2009) Heather J Cordell   NATURE REVIEWS GENETICS

INK4/ARF Transcript Expression Is Associated with Chromosome 9p21 Variants Linked to Atherosclerosis

(2009) Yan Liu et al.   PLoS One

Relationship between CAD Risk Genotype in the Chromosome 9p21 Locus and Gene Expression. Identification of Eight New ANRIL Splice Variants

(2009) Lasse Folkersen et al.   PLoS One

Dynamic Regulation of Nucleosome Positioning in the Human Genome

(2008) Dustin E. Schones et al.   CELL

Detection of Altered Global DNA Methylation in Coronary Artery Disease Patients

(2008) Priyanka Sharma et al.   DNA AND CELL BIOLOGY

The same sequence variant on 9p21 associates with myocardial infarction, abdominal aortic aneurysm and intracranial aneurysm

(2008) Anna Helgadottir et al.   NATURE GENETICS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS