Multi-ancestry genetic analysis of gene regulation in coronary arteries prioritizes disease risk loci
暂无分享,去创建一个
P. Peyser | S. W. van der Laan | S. Onengut-Gumuscu | C. Hodonsky | N. Leeper | A. Turner | D. Wong | Mohammad Daud Khan | Jose Verdezoto Mosquera | W. Ma | Gaelle Auguste | N. Lopez | Nelson B. Barrientos | Ruben Methorst | Lijiang Ma | M. Kavousi | Emily Farber | Clint L. Miller | Jason C. Kovacic | Johan L.M. Björkegren | Jason C Kovacic | J. L. Björkegren | R. Methorst
[1] Clint L. Miller,et al. Multi-ancestry genome-wide study identifies effector genes and druggable pathways for coronary artery calcification , 2023, Nature Genetics.
[2] J. Witte,et al. Principles and methods for transferring polygenic risk scores across global populations , 2023, Nature reviews. Genetics.
[3] Clint L. Miller,et al. Integrative single-cell meta-analysis reveals disease-relevant vascular cell states and markers in human atherosclerosis , 2023, bioRxiv.
[4] Wei Zhou. Global Biobank Meta-analysis Initiative: Powering genetic discovery across human disease , 2022, Cell genomics.
[5] B. Browning,et al. Fast, accurate local ancestry inference with FLARE , 2022, bioRxiv.
[6] Yan V. Sun,et al. Large-scale genome-wide association study of coronary artery disease in genetically diverse populations , 2022, Nature Medicine.
[7] William T. Harvey,et al. A draft human pangenome reference , 2022, bioRxiv.
[8] Pilar Martín,et al. The impact of type 2 immunity and allergic diseases in atherosclerosis , 2022, Allergy.
[9] Byoungjin Park,et al. Dyslipidaemia—Genotype Interactions with Nutrient Intake and Cerebro-Cardiovascular Disease , 2022, Biomedicines.
[10] Alexander E. Lopez,et al. High heritability of ascending aortic diameter and trans-ancestry prediction of thoracic aortic disease , 2022, Nature Genetics.
[11] S. Chanock,et al. The case for increasing diversity in tissue-based functional genomics datasets to understand human disease susceptibility , 2022, Nature Communications.
[12] Clint L. Miller,et al. Single-nucleus chromatin accessibility profiling highlights regulatory mechanisms of coronary artery disease risk , 2022, Nature Genetics.
[13] Hagen U. Tilgner,et al. Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue , 2022, Nature Biotechnology.
[14] M. Kaikkonen,et al. The Power of Single-Cell RNA Sequencing in eQTL Discovery , 2022, Genes.
[15] G. Davey Smith,et al. Characterising metabolomic signatures of lipid-modifying therapies through drug target mendelian randomisation , 2022, PLoS biology.
[16] E. Schadt,et al. A mechanistic framework for cardiometabolic and coronary artery diseases , 2022, Nature Cardiovascular Research.
[17] M. Nóbrega,et al. Common Genetic Variants Contribute to Risk of Transposition of the Great Arteries , 2021, Circulation research.
[18] Christopher D. Brown,et al. The power of genetic diversity in genome-wide association studies of lipids , 2021, Nature.
[19] H. Snieder,et al. Twenty-Five Novel Loci for Carotid Intima-Media Thickness: A Genome-Wide Association Study in >45 000 Individuals and Meta-Analysis of >100 000 Individuals , 2021, Arteriosclerosis, thrombosis, and vascular biology.
[20] Clint L. Miller,et al. Intersecting single-cell transcriptomics and genome-wide association studies identifies crucial cell populations and candidate genes for atherosclerosis , 2021, medRxiv.
[21] Michael E. Hall,et al. Whole Genome Sequence Analysis of the Plasma Proteome in Black Adults Provides Novel Insights Into Cardiovascular Disease , 2021, Circulation.
[22] Alicia R. Martin,et al. Responsible use of polygenic risk scores in the clinic: potential benefits, risks and gaps , 2021, Nature Medicine.
[23] Yonghong Zhang,et al. LncRNA TARID induces cell proliferation through cell cycle pathway associated with coronary artery disease , 2021, Molecular Biology Reports.
[24] Kuender D Yang,et al. Perspective of Immunopathogenesis and Immunotherapies for Kawasaki Disease , 2021, Frontiers in Pediatrics.
[25] Jill A. Madden,et al. A homozygous stop-gain variant in ARHGAP42 is associated with childhood interstitial lung disease, systemic hypertension, and immunological findings , 2021, PLoS genetics.
[26] Meixiang Xiang,et al. TBX20 Contributes to Balancing the Differentiation of Perivascular Adipose-Derived Stem Cells to Vascular Lineages and Neointimal Hyperplasia , 2021, Frontiers in Cell and Developmental Biology.
[27] T. Lönnberg,et al. Single-Cell Epigenomics and Functional Fine-Mapping of Atherosclerosis GWAS Loci , 2021, Circulation research.
[28] E. Riboli,et al. GWAS of allometric body-shape indices in UK Biobank identifies loci suggesting associations with morphogenesis, organogenesis, adrenal cell renewal and cancer , 2021, Scientific Reports.
[29] A. von Eckardstein,et al. The Endothelium Is Both a Target and a Barrier of HDL’s Protective Functions , 2021, Cells.
[30] Ryan L. Collins,et al. Genome-wide enhancer maps link risk variants to disease genes , 2021, Nature.
[31] Xiumeng Hua,et al. Single-Cell Transcriptomic Atlas of Different Human Cardiac Arteries Identifies Cell Types Associated With Vascular Physiology , 2021, Arteriosclerosis, thrombosis, and vascular biology.
[32] C. Wallace. A more accurate method for colocalisation analysis allowing for multiple causal variants , 2021, bioRxiv.
[33] Yan V. Sun,et al. Genome-wide analysis identifies novel susceptibility loci for myocardial infarction. , 2021, European heart journal.
[34] Wei Sun,et al. Promoting roles of long non-coding RNA FAM83H-AS1 in bladder cancer growth, metastasis, and angiogenesis through the c-Myc-mediated ULK3 upregulation , 2020, Cell cycle.
[35] Trevor Hastie,et al. Genetics of 35 blood and urine biomarkers in the UK Biobank , 2020, Nature Genetics.
[36] H. Aburatani,et al. Population-specific and trans-ancestry genome-wide analyses identify distinct and shared genetic risk loci for coronary artery disease , 2020, Nature Genetics.
[37] Sri V. V. Deevi,et al. Spontaneous Coronary Artery Dissection , 2020, Circulation. Genomic and precision medicine.
[38] Mingyao Li,et al. Single-Cell Genomics Reveals a Novel Cell State During Smooth Muscle Cell Phenotypic Switching and Potential Therapeutic Targets for Atherosclerosis in Mouse and Human , 2020, Circulation.
[39] Shuhong Zhao,et al. rMVP: A Memory-efficient, Visualization-enhanced, and Parallel-accelerated Tool for Genome-wide Association Study , 2020, bioRxiv.
[40] R. Guigó,et al. Identification and analysis of splicing quantitative trait loci across multiple tissues in the human genome , 2020, Nature Communications.
[41] M. Whalen,et al. Systems Genetics in Human Endothelial Cells Identifies Non-coding Variants Modifying Enhancers, Expression, and Complex Disease Traits. , 2020, American journal of human genetics.
[42] K. Ardlie,et al. A scalable unified framework of total and allele-specific counts for cis-QTL, fine-mapping, and prediction , 2020, Nature Communications.
[43] S. Anders,et al. DEqMS: A Method for Accurate Variance Estimation in Differential Protein Expression Analysis* , 2020, Molecular & Cellular Proteomics.
[44] A. Torkamani,et al. Decoding the transcriptome of atherosclerotic plaque at single-cell resolution , 2020, bioRxiv.
[45] S. Mirarab,et al. Sequence Analysis , 2020, Encyclopedia of Bioinformatics and Computational Biology.
[46] L. Liang,et al. Shared Genetic and Experimental Links between Obesity-Related Traits and Asthma Subtypes in UK Biobank. , 2020, The Journal of allergy and clinical immunology.
[47] T. Quertermous,et al. Coronary Disease-Associated Gene TCF21 Inhibits Smooth Muscle Cell Differentiation by Blocking the Myocardin-Serum Response Factor Pathway , 2019, Circulation research.
[48] W. Desmet,et al. Eosinophil-platelet interactions promote atherosclerosis and stabilize thrombosis by eosinophil extracellular traps. , 2019, Blood.
[49] Christopher D. Brown,et al. Impact of admixture and ancestry on eQTL analysis and GWAS colocalization in GTEx , 2019, Genome Biology.
[50] G. Engström,et al. Associations of Interleukin-5 With Plaque Development and Cardiovascular Events , 2019, JACC. Basic to translational science.
[51] Stephane E. Castel,et al. Cell type–specific genetic regulation of gene expression across human tissues , 2019, Science.
[52] Christopher D. Brown,et al. The GTEx Consortium atlas of genetic regulatory effects across human tissues , 2019, Science.
[53] B. Chichkov,et al. Heparanase-2 protects from LPS-mediated endothelial injury by inhibiting TLR4 signalling , 2019, Scientific Reports.
[54] B. Wang,et al. Phosphorylation of Ci/Gli by Fused Family Kinases Promotes Hedgehog Signaling. , 2019, Developmental cell.
[55] Stephanie A. Bien,et al. The Future of Genomic Studies Must Be Globally Representative: Perspectives from PAGE. , 2019, Annual review of genomics and human genetics.
[56] Y. Kamatani,et al. Transethnic meta-analysis of genome-wide association studies identifies three new loci and characterizes population-specific differences for coronary artery disease , 2019, bioRxiv.
[57] Anshul Kundaje,et al. The ENCODE Blacklist: Identification of Problematic Regions of the Genome , 2019, Scientific Reports.
[58] Clint L. Miller,et al. Atheroprotective roles of smooth muscle cell phenotypic modulation and the TCF21 disease gene as revealed by single-cell analysis , 2019, Nature Medicine.
[59] Stephanie A. Bien,et al. Genetic analyses of diverse populations improves discovery for complex traits , 2019, Nature.
[60] Clint L. Miller,et al. Genetic Insights Into Smooth Muscle Cell Contributions to Coronary Artery Disease. , 2019, Arteriosclerosis, thrombosis, and vascular biology.
[61] Yizhen Zhong,et al. On Using Local Ancestry to Characterize the Genetic Architecture of Human Traits: Genetic Regulation of Gene Expression in Multiethnic or Admixed Populations. , 2019, American journal of human genetics.
[62] J. Vilo,et al. g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update) , 2019, Nucleic Acids Res..
[63] Ash A. Alizadeh,et al. Determining cell-type abundance and expression from bulk tissues with digital cytometry , 2019, Nature Biotechnology.
[64] Malene B. Rasmussen,et al. Haploinsufficiency of ARHGAP42 is associated with hypertension , 2019, European Journal of Human Genetics.
[65] P. Eriksson,et al. Copy number variation analysis in bicuspid aortic valve-related aortopathy identifies TBX20 as a contributing gene , 2019, European Journal of Human Genetics.
[66] David G. Knowles,et al. Predicting Splicing from Primary Sequence with Deep Learning , 2019, Cell.
[67] Matthew Stephens,et al. A simple new approach to variable selection in regression, with application to genetic fine-mapping , 2018, bioRxiv.
[68] Andrew D. Johnson,et al. GWAS and colocalization analyses implicate carotid intima-media thickness and carotid plaque loci in cardiovascular outcomes , 2018, Nature Communications.
[69] Manuel Mayr,et al. In Aptamers They Trust: Caveats of the SOMAscan Biomarker Discovery Platform From SomaLogic , 2018, Circulation.
[70] Alkes L. Price,et al. Annotations capturing cell-type-specific TF binding explain a large fraction of disease heritability , 2018, bioRxiv.
[71] Mark Gerstein,et al. GENCODE reference annotation for the human and mouse genomes , 2018, Nucleic Acids Res..
[72] Ahmed Mahfouz,et al. Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells , 2018, Nature Biotechnology.
[73] Christopher D. Brown,et al. Genetic and Epigenetic Fine Mapping of Complex Trait Associated Loci in the Human Liver , 2018, bioRxiv.
[74] Andrew D. Johnson,et al. Genetic analysis of over 1 million people identifies 535 new loci associated with blood pressure traits , 2018, Nature Genetics.
[75] J. Cooke,et al. TBX20 Regulates Angiogenesis Through the Prokineticin 2–Prokineticin Receptor 1 Pathway , 2018, Circulation.
[76] B. Browning,et al. A one penny imputed genome from next generation reference panels , 2018, bioRxiv.
[77] Michael J. Gloudemans,et al. Genetic regulatory mechanisms of smooth muscle cells map to coronary artery disease risk loci , 2018, bioRxiv.
[78] N. Samani,et al. Network analysis of coronary artery disease risk genes elucidates disease mechanisms and druggable targets , 2018, Scientific Reports.
[79] Pim van der Harst,et al. Identification of 64 Novel Genetic Loci Provides an Expanded View on the Genetic Architecture of Coronary Artery Disease , 2017, Circulation research.
[80] Kathryn S. Burch,et al. Leveraging polygenic functional enrichment to improve GWAS power , 2017, bioRxiv.
[81] David A. Knowles,et al. Annotation-free quantification of RNA splicing using LeafCutter , 2017, Nature Genetics.
[82] O. Smithies,et al. GRAF3 serves as a blood volume-sensitive rheostat to control smooth muscle contractility and blood pressure , 2017, Small GTPases.
[83] Nicola J. Rinaldi,et al. Genetic effects on gene expression across human tissues , 2017, Nature.
[84] G. Dotto,et al. The ULK3 Kinase Is Critical for Convergent Control of Cancer-Associated Fibroblast Activation by CSL and GLI. , 2017, Cell reports.
[85] J. Danesh,et al. Association analyses based on false discovery rate implicate new loci for coronary artery disease , 2017, Nature Genetics.
[86] Peter J. Park,et al. NGSCheckMate: software for validating sample identity in next-generation sequencing studies within and across data types , 2017, Nucleic acids research.
[87] A. Khera,et al. Genetics of coronary artery disease: discovery, biology and clinical translation , 2017, Nature Reviews Genetics.
[88] He Zhang,et al. Systematic Evaluation of Pleiotropy Identifies 6 Further Loci Associated With Coronary Artery Disease , 2017, Journal of the American College of Cardiology.
[89] A. Viera,et al. Blood pressure–associated polymorphism controls ARHGAP42 expression via serum response factor DNA binding , 2017, The Journal of clinical investigation.
[90] R. Pfundt,et al. Loss-of-Function Mutations in YY1AP1 Lead to Grange Syndrome and a Fibromuscular Dysplasia-Like Vascular Disease. , 2017, American journal of human genetics.
[91] N. Risch,et al. Genome-wide association analyses using electronic health records identify new loci influencing blood pressure variation , 2016, Nature Genetics.
[92] Stephane E. Castel,et al. Quantifying the regulatory effect size of cis-acting genetic variation using allelic fold change , 2016, bioRxiv.
[93] Roland Eils,et al. Complex heatmaps reveal patterns and correlations in multidimensional genomic data , 2016, Bioinform..
[94] Christopher R. Gignoux,et al. Human demographic history impacts genetic risk prediction across diverse populations , 2016, bioRxiv.
[95] Tom Michoel,et al. Cardiometabolic risk loci share downstream cis- and trans-gene regulation across tissues and diseases , 2016, Science.
[96] Olivier Delaneau,et al. A complete tool set for molecular QTL discovery and analysis , 2016, Nature Communications.
[97] D. MacArthur,et al. TOR1AIP1 as a cause of cardiac failure and recessive limb-girdle muscular dystrophy , 2016, Neuromuscular Disorders.
[98] Clint L. Miller,et al. Integrative functional genomics identifies regulatory mechanisms at coronary artery disease loci , 2016, Nature Communications.
[99] Stephane E. Castel,et al. Rare variant phasing and haplotypic expression from RNA sequencing with phASER , 2016, Nature Communications.
[100] Eleazar Eskin,et al. Improved methods for multi-trait fine mapping of pleiotropic risk loci , 2016, bioRxiv.
[101] David A. Knowles,et al. RNA splicing is a primary link between genetic variation and disease , 2016, Science.
[102] P. Visscher,et al. Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets , 2016, Nature Genetics.
[103] E. F. da Cruz e Silva,et al. Genetic mutations strengthen functional association of LAP1 with DYT1 dystonia and muscular dystrophy. , 2015, Mutation research. Reviews in mutation research.
[104] Gabor T. Marth,et al. A global reference for human genetic variation , 2015, Nature.
[105] Jonathan K. Pritchard,et al. WASP: allele-specific software for robust molecular quantitative trait locus discovery , 2015, Nature Methods.
[106] Sebastian M. Armasu,et al. A comprehensive 1000 Genomes-based genome-wide association meta-analysis of coronary artery disease , 2015, Nature Genetics.
[107] T. Littlewood,et al. Akt isoforms in vascular disease , 2015, Vascular pharmacology.
[108] Jeremy G. Carlton,et al. ULK3 regulates cytokinetic abscission by phosphorylating ESCRT-III proteins , 2015, eLife.
[109] Jun S. Liu,et al. The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans , 2015, Science.
[110] Daniel J. Gaffney,et al. Fine-mapping cellular QTLs with RASQUAL and ATAC-seq , 2015, Nature Genetics.
[111] B. Frey,et al. The human splicing code reveals new insights into the genetic determinants of disease , 2015, Science.
[112] W. Huber,et al. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.
[113] Carson C Chow,et al. Second-generation PLINK: rising to the challenge of larger and richer datasets , 2014, GigaScience.
[114] Roland Eils,et al. circlize implements and enhances circular visualization in R , 2014, Bioinform..
[115] C. Plass,et al. Long noncoding RNA TARID directs demethylation and activation of the tumor suppressor TCF21 via GADD45A. , 2014, Molecular cell.
[116] Clint L. Miller,et al. Coronary Heart Disease-Associated Variation in TCF21 Disrupts a miR-224 Binding Site and miRNA-Mediated Regulation , 2014, PLoS genetics.
[117] Jingwen,et al. A meta-analysis of genome-wide association studies for adiponectin levels in East Asians identifies a novel locus near WDR11-FGFR2. , 2014, Human molecular genetics.
[118] M. Rojas,et al. The smooth muscle-selective RhoGAP GRAF3 is a critical regulator of vascular tone and hypertension , 2013, Nature Communications.
[119] Jean-François Zagury,et al. Haplotype estimation using sequencing reads. , 2013, American journal of human genetics.
[120] P. Schulze,et al. Lamina-associated polypeptide-1 interacts with the muscular dystrophy protein emerin and is essential for skeletal muscle maintenance. , 2013, Developmental cell.
[121] Pedro G. Ferreira,et al. Transcriptome and genome sequencing uncovers functional variation in humans , 2013, Nature.
[122] C. Bustamante,et al. RFMix: a discriminative modeling approach for rapid and robust local-ancestry inference. , 2013, American journal of human genetics.
[123] Karen Cheng,et al. Disease-Related Growth Factor and Embryonic Signaling Pathways Modulate an Enhancer of TCF21 Expression at the 6q23.2 Coronary Heart Disease Locus , 2013, PLoS genetics.
[124] B. Stranger,et al. Chromatin marks identify critical cell types for fine mapping complex trait variants , 2012, Nature Genetics.
[125] David Levine,et al. A high-performance computing toolset for relatedness and principal component analysis of SNP data , 2012, Bioinform..
[126] G. Abecasis,et al. Detecting and estimating contamination of human DNA samples in sequencing and array-based genotype data. , 2012, American journal of human genetics.
[127] Raymond K. Auerbach,et al. An Integrated Encyclopedia of DNA Elements in the Human Genome , 2012, Nature.
[128] Pablo Cingolani,et al. © 2012 Landes Bioscience. Do not distribute. , 2022 .
[129] R. Durbin,et al. Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses , 2012, Nature Protocols.
[130] P. Deloukas,et al. Integrating Genome-Wide Genetic Variations and Monocyte Expression Data Reveals Trans-Regulated Gene Modules in Humans , 2011, PLoS genetics.
[131] Colin N. Dewey,et al. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome , 2011, BMC Bioinformatics.
[132] Andrey A. Shabalin,et al. Matrix eQTL: ultra fast eQTL analysis via large matrix operations , 2011, Bioinform..
[133] Thomas W. Mühleisen,et al. Large-scale association analysis identifies 13 new susceptibility loci for coronary artery disease , 2011, Nature Genetics.
[134] H. Hakonarson,et al. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data , 2010, Nucleic acids research.
[135] P. Kogerman,et al. Identification of a novel serine/threonine kinase ULK3 as a positive regulator of Hedgehog pathway. , 2010, Experimental cell research.
[136] Gonçalo R. Abecasis,et al. The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..
[137] Andrew D. Johnson,et al. Genome-wide association study of blood pressure and hypertension , 2009, Nature Genetics.
[138] Claude-Alain H. Roten,et al. Fast and accurate short read alignment with Burrows–Wheeler transform , 2009, Bioinform..
[139] E. Olson. Gene Regulatory Networks in the Evolution and Development of the Heart , 2006, Science.
[140] Martin Farrall,et al. Genetic susceptibility to coronary artery disease: from promise to progress , 2006, Nature Reviews Genetics.
[141] R. Collins,et al. Age-specific relevance of usual blood pressure to vascular mortality: a meta-analysis of individual data for one million adults in 61 prospective studies , 2002, The Lancet.
[142] J. Kinet,et al. Direct effects of interleukin-13 on signaling pathways for physiological responses in cultured human airway smooth muscle cells. , 2001, American journal of respiratory and critical care medicine.
[143] C. De-Fraja,et al. Upregulation and activation of Stat6 precede vascular smooth muscle cell proliferation in carotid artery injury model. , 2000, Arteriosclerosis, thrombosis, and vascular biology.
[144] J. Slack,et al. Identification of 40 genes on a 1-Mb contig around the IL-4 cytokine family gene cluster on mouse chromosome 11. , 2000, Genomics.
[145] Kelsy C. Cotto,et al. RegTools: Integrated analysis of genomic and transcriptomic data for the discovery of splicing variants in cancer , 2020 .
[146] H. Nader,et al. The Good and Bad Sides of Heparanase-1 and Heparanase-2. , 2020, Advances in experimental medicine and biology.
[147] Thomas R. Gingeras,et al. STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..
[148] Aaron R. Quinlan,et al. BIOINFORMATICS APPLICATIONS NOTE , 2022 .