Population-scale tissue transcriptomics maps long non-coding RNAs to complex disease | Zendy

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Population-scale tissue transcriptomics maps long non-coding RNAs to complex disease

Author(s) -

Olivia M. de Goede,

Daniel Nachun,

Nicole M. Ferraro,

Michael J. Gloudemans,

Abhiram Rao,

Craig Smail,

Tiffany Eulalio,

François Aguet,

Bernard Ng,

Jishu Xu,

Alvaro Barbeira,

Stephane E. Castel,

Sarah Kim-Hellmuth,

YoSon Park,

Alexandra J. Scott,

Benjamin J. Strober,

Christopher D. Brown,

Xiaoquan Wen,

Ira M. Hall,

Alexis Battle,

Tuuli Lappalainen,

Hae Kyung Im,

Kristin Ardlie,

Sara Mostafavi,

Thomas Quertermous,

Karla Kirkegaard,

Stephen B. Montgomery,

Shankara Anand,

Stacey Gabriel,

Gad Getz,

Aaron Graubert,

Kane Hadley,

Robert E. Handsaker,

Katherine Huang,

Xiao Li,

Daniel G. MacArthur,

Samuel R. Meier,

Jared L. Nedzel,

Duyen T. Nguyen,

Ayellet V. Segrè,

Ellen Todres,

Brunilda Balliu,

Rodrigo Bonazzola,

Andrew Brown,

Donald F. Conrad,

Daniel J. Cotter,

Nancy J. Cox,

Sayantan Das,

Emmanouil T. Dermitzakis,

Jonah Einson,

Barbara E. Engelhardt,

Eleazar Eskin,

Elise D. Flynn,

Laure Frésard,

Eric R. Gamazon,

Diego Garrido-Martín,

Nicole R. Gay,

Roderic Guigó,

Andrew R. Hamel,

Yuan He,

Paul Hoffman,

Farhad Hormozdiari,

Lei Hou,

Brian Jo,

Silva Kasela,

Seva Kashin,

Manolis Kellis,

Alan Kwong,

Xin Li,

Yanyu Liang,

Serghei Mangul,

Pejman Mohammadi,

Manuel Muñoz-Aguirre,

Andrew B. Nobel,

Meritxell Oliva,

YongJin Park,

Princy Parsana,

Ferrán Reverter,

John M. Rouhana,

Chiara Sabatti,

Ashis Saha,

Matthew Stephens,

Barbara E. Stranger,

Nicole A. Teran,

Ana Viñuela,

Gao Wang,

Fred A. Wright,

Valentin Wucher,

Yuxin Zou,

Pedro G. Ferreira,

Gen Li,

Marta Melé,

Esti YegerLotem,

Debra Bradbury,

Tanya Krubit,

Jeffrey A. McLean,

Liqun Qi,

Karna Robinson,

Nancy Roche,

Anna M. Smith,

David E. Tabor,

Anita H. Undale,

Jason Bridge,

Lori E. Brigham,

Barbara A. Foster,

Bryan M. Gillard,

Richard Hasz,

Marcus Hunter,

Christopher Johns,

Mark R. Johnson,

Ellen Karasik,

Gene Kopen,

William F. Leinweber,

Alisa McDonald,

Michael T. Moser,

Kevin Myer,

Kimberley D. Ramsey,

Brian Roe,

Saboor Shad,

Jeffrey A. Thomas,

Gary Walters,

Michael Washington,

J. Gary Wheeler,

Scott D. Jewell,

Daniel C. Rohrer,

Dana R. Valley,

David A. Davis,

Deborah C. Mash,

Mary E. Barcus,

Philip A. Branton,

Leslie H. Sobin,

Laura K. Barker,

Heather M. Gardiner,

Maghboeba Mosavel,

Laura A. Siminoff,

Paul Flicek,

Maximilian Haeussler,

Thomas Juettemann,

W. James Kent,

Christopher M. Lee,

Conner C. Powell,

Kate R. Rosenbloom,

Magali Ruffier,

Dan Sheppard,

Kieron Taylor,

Stephen J. Trevanion,

Daniel R. Zerbino,

Nathan S. Abell,

Joshua M. Akey,

Lin Chen,

Kathryn Demanelis,

Jennifer A. Doherty,

Andrew P. Feinberg,

Kasper D. Hansen,

Peter F. Hickey,

Farzana Jasmine,

Lihua Jiang,

Rajinder Kaul,

Muhammad G. Kibriya,

Jin Billy Li,

Qin Li,

Shin Lin,

Sandra E. Linder,

Brandon L. Pierce,

Lindsay F. Rizzardi,

Andrew D. Skol,

Kevin S. Smith,

M Snyder,

J Stamatoyannopoulos,

Hua Tang,

Meng Wang,

Latarsha J. Carithers,

Ping Guan,

Susan E. Koester,

A. Roger Little,

Helen M. Moore,

Concepcion R. Nierras,

Abhi K. Rao,

Jimmie B. Vaught,

Simona Volpi

Publication year - 2021

Publication title -

cell

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 26.304

H-Index - 776

eISSN - 1097-4172

pISSN - 0092-8674

DOI - 10.1016/j.cell.2021.03.050

Subject(s) - biology , gene , trait , quantitative trait locus , genetics , transcriptome , expression quantitative trait loci , genome wide association study , computational biology , disease , population , gene expression , genetic association , long non coding rna , rna , genotype , single nucleotide polymorphism , medicine , sociology , computer science , programming language , demography , pathology

Long non-coding RNA (lncRNA) genes have well-established and important impacts on molecular and cellular functions. However, among the thousands of lncRNA genes, it is still a major challenge to identify the subset with disease or trait relevance. To systematically characterize these lncRNA genes, we used Genotype Tissue Expression (GTEx) project v8 genetic and multi-tissue transcriptomic data to profile the expression, genetic regulation, cellular contexts, and trait associations of 14,100 lncRNA genes across 49 tissues for 101 distinct complex genetic traits. Using these approaches, we identified 1,432 lncRNA gene-trait associations, 800 of which were not explained by stronger effects of neighboring protein-coding genes. This included associations between lncRNA quantitative trait loci and inflammatory bowel disease, type 1 and type 2 diabetes, and coronary artery disease, as well as rare variant associations to body mass index.

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