A vast resource of allelic expression data spanning human tissues
Stephane E. Castel, François Aguet, Pejman Mohammadi, François Aguet, Shankara Anand, Kristin Ardlie, Stacey Gabriel, Gad Getz, Aaron Graubert, Kane Hadley, Robert E. Handsaker, Katherine Huang, Seva Kashin, Xiao Li, Daniel G. MacArthur, Samuel R. Meier, Jared L. Nedzel, Duyen T. Nguyen, Ayellet V. Segrè, Ellen Todres, François Aguet, Shankara Anand, Kristin Ardlie, Brunilda Balliu, Alvaro Barbeira, Alexis Battle, Rodrigo Bonazzola, Andrew Brown, Christopher D. Brown, Stephane E. Castel, Donald F. Conrad, Daniel J. Cotter, Nancy J. Cox, Sayantan Das, Olivia M. de Goede, Emmanouil T. Dermitzakis, Jonah Einson, Barbara E. Engelhardt, Eleazar Eskin, Tiffany Eulalio, Nicole M. Ferraro, Elise D. Flynn, Laure Frésard, Eric R. Gamazon, Diego Garrido-Martín, Nicole R. Gay, Gad Getz, Michael J. Gloudemans, Aaron Graubert, Roderic Guigó, Kane Hadley, Andrew R. Hame, Robert E. Handsaker, Yuan He, Paul Hoffman, Farhad Hormozdiari, Lei Hou, Katherine Huang, Hae Kyung Im, Brian Jo, Silva Kasela, Seva Kashin, Manolis Kellis, Sarah Kim-Hellmuth, Alan Kwong, Tuuli Lappalainen, Xiao Li, Xin Li, Yanyu Liang, Daniel G. MacArthur, Serghei Mangul, Samuel R. Meier, Pejman Mohammadi, Stephen B. Montgomery, Manuel Muñoz-Aguirre, Daniel Nachun, Jared L. Nedzel, Duyen T. Nguyen, Andrew B. Nobel, Meritxell Oliva, Yo Son Park, Yong‐Jin Park, Princy Parsana, Abhiram Rao, Ferrán Reverter, John M. Rouhana, Chiara Sabatti, Ashis Saha, Ayellet V. Segrè, Andrew D. Skol, Matthew Stephens, Barbara E. Stranger, Benjamin J. Strober, Nicole A. Teran, Ellen Todres, Ana Viñuela, Gao Wang, Xiaoquan Wen, Fred A. Wright, Valentin Wucher
Abstract
Allele expression (AE) analysis robustly measures cis-regulatory effects. Here, we present and demonstrate the utility of a vast AE resource generated from the GTEx v8 release, containing 15,253 samples spanning 54 human tissues for a total of 431 million measurements of AE at the SNP level and 153 million measurements at the haplotype level. In addition, we develop an extension of our tool phASER that allows effect sizes of cis-regulatory variants to be estimated using haplotype-level AE data. This AE resource is the largest to date, and we are able to make haplotype-level data publicly available. We anticipate that the availability of this resource will enable future studies of regulatory variation across human tissues.