Cell types of origin of the cell-free transcriptome
Sevahn K. Vorperian(Stanford University), Mira N. Moufarrej(Stanford University), Overall Project Direction and Coordination(Stanford University), Robert C. Jones(Chan Zuckerberg Initiative (United States)), Jim Karkanias(Howard Hughes Medical Institute), Mark A. Krasnow(Howard Hughes Medical Institute), Angela Oliveira Pisco(Chan Zuckerberg Initiative (United States)), Stephen R. Quake(Chan Zuckerberg Initiative (United States)), Julia Salzman(Chan Zuckerberg Initiative (United States)), Nir Yosef(Ragon Institute of MGH, MIT and Harvard), Donor Recruitment(Donor Network West), Bryan Bulthaup(Donor Network West), Phillip Brown(Donor Network West), William Harper(Donor Network West), Marisa Hemenez(Donor Network West), Ravikumar Ponnusamy(Donor Network West), Ahmad Salehi(Donor Network West), Bhavani A. Sanagavarapu(Donor Network West), Eileen Spallino(Donor Network West), Surgeons(University of California, San Francisco), Ksenia A. Aaron(Donor Network West), Waldo Concepcion(Donor Network West), James M. Gardner(University of California, San Francisco), Burnett S. Kelly(California Department of Health Care Services), Nikole Neidlinger(Donor Network West), Zifa Wang(Donor Network West), Logistical coordination(Stanford University), Sheela Crasta(Chan Zuckerberg Initiative (United States)), Saroja Kolluru(Chan Zuckerberg Initiative (United States)), Maurizio Morri(Chan Zuckerberg Initiative (United States)), Serena Y. Tan(Stanford University), Kyle J. Travaglini(Stanford University), Chenling Xu(University of California, Berkeley), Organ Processing(University of California, San Francisco), Marcela Alcántara‐Hernández(Stanford University), Nicole Almanzar(Stanford University), Jane Antony(Stanford University), Benjamin Beyersdorf(Stanford University), Deviana Burhan(University of California, San Francisco), Kruti Calcuttawala(Stanford University), Matthew M. Carter(Stanford University), Charles K. F. Chan(Stanford University), Charles Chang(Stanford University), Stephen Chang(Stanford University), Alex Colville(Stanford University), Rebecca N. Culver(Stanford University), Ivana Cvijović(Stanford University), Gaetano D’Amato(Stanford University), Camille Ezran(Stanford University), Francisco X. Galdos(University of California, San Francisco), Astrid Gillich(Stanford University), William R. Goodyer(University of California, San Francisco), Yan Hang(Stanford University), Alyssa Hayashi(University of California, San Francisco), Sahar Houshdaran(University of California, San Francisco), Xianxi Huang(Shantou University), Juan C. Irwin(University of California, San Francisco), SoRi Jang(Stanford University), Júlia Vallvé-Juanico(University of California, San Francisco), Aaron M. Kershner(Stanford University), Soochi Kim(Stanford University), Bernhard Kiss(Stanford University), William Kong(University of California, San Francisco), Maya E. Kumar(Stanford University), Angera H. Kuo(Stanford University), Rebecca Leylek(Stanford University), Baoxiang Li(Stanford University), Gabriel B. Loeb(University of California, San Francisco), Wan-Jin Lu(Stanford University), Sruthi Mantri(Stanford University), Maxim Markovic(Stanford University), Patrick L. McAlpine(Chan Zuckerberg Initiative (United States)), Antoine de Morrée(University of California, San Francisco), Karim Mrouj(Stanford University), Shravani Mukherjee(Stanford University), Tyler Muser(Stanford University), Patrick Neuhöfer(Stanford University), Thi D. Nguyen(University of California, San Francisco), Kimberly Perez(Stanford University), Ragini Phansalkar(Stanford University), Nazan Puluca(Stanford University), Zhen Qi(University of California, San Francisco), Poorvi Rao(University of California, San Francisco), Hayley M. Raquer-McKay(University of California, San Francisco), Nicholas Schaum(Stanford University), Bronwyn Scott(Stanford University), Bobak Seddighzadeh(University of California, San Francisco), Joe M. Segal(University of California, San Francisco), Sushmita Sen(University of California, San Francisco), Shaheen S. Sikandar(Stanford University), Sean P. Spencer(Stanford University), L.C. Steffes(Stanford University), Varun Ramanan Subramaniam(Stanford University), Aditi Swarup(Stanford University), Michael Swift(University of California, San Francisco), Will Van Treuren(Stanford University), Emily Trimm(University of California, San Francisco), Stefan Veizades(University of California, San Francisco), Sivakamasundari Vijayakumar(University of California, San Francisco), Kim Chi Vo(University of California, San Francisco), Sevahn K. Vorperian(University of California, San Francisco), Wanxin Wang(University of California, San Francisco), H Weinstein(University of California, San Francisco), Juliane Winkler(University of California, San Francisco), Ting-Hsuan Wu(Chan Zuckerberg Initiative (United States)), Jamie Xie(University of California, San Francisco), Andrea R. Yung(Chan Zuckerberg Initiative (United States)), Yue Zhang(Chan Zuckerberg Initiative (United States)), Sequencing(Chan Zuckerberg Initiative (United States)), Angela M. Detweiler(Chan Zuckerberg Initiative (United States)), Honey Mekonen(Chan Zuckerberg Initiative (United States)), Norma Neff(Chan Zuckerberg Initiative (United States)), Rene Sit(Chan Zuckerberg Initiative (United States)), Michelle Tan(Chan Zuckerberg Initiative (United States)), Jia Yan(Chan Zuckerberg Initiative (United States)), Histology(Stanford University), Gregory R. Bean(Chan Zuckerberg Initiative (United States)), Vivek Charu(University of California, Berkeley), Erna Forgó(Chan Zuckerberg Initiative (United States)), Brock A. Martin(Stanford University), Michael G. Ozawa(Chan Zuckerberg Initiative (United States)), Oscar Silva(Chan Zuckerberg Initiative (United States)), Angus Toland(Stanford University), Venkata N. P. Vemuri(Chan Zuckerberg Initiative (United States)), Data Analysis(University of California, Berkeley), Shaked Afik(Chan Zuckerberg Initiative (United States)), Kyle Awayan(Chan Zuckerberg Initiative (United States)), Rob Bierman(Stanford University), Olga Botvinnik(Chan Zuckerberg Initiative (United States)), Ashley Byrne(Chan Zuckerberg Initiative (United States)), Michelle Chen(Chan Zuckerberg Initiative (United States)), Roozbeh Dehghannasiri(Stanford University), Adam Gayoso(University of California, Berkeley), Alejandro A. Granados(Chan Zuckerberg Initiative (United States)), Qiqing Li(Chan Zuckerberg Initiative (United States)), Gita Mahmoudabadi(Chan Zuckerberg Initiative (United States)), Aaron McGeever(Chan Zuckerberg Initiative (United States)), Julia Olivieri(Chan Zuckerberg Initiative (United States)), Madeline Park(Chan Zuckerberg Initiative (United States)), Neha Ravikumar(University of California, Berkeley), Geoff Stanley(University of California, Berkeley), Weilun Tan(Chan Zuckerberg Initiative (United States)), Alexander J. Tarashansky(Chan Zuckerberg Initiative (United States)), Rohan Vanheusden(Chan Zuckerberg Initiative (United States)), Peter Wang(Stanford University), Sheng Wang(VA Palo Alto Health Care System), Galen Xing(Chan Zuckerberg Initiative (United States)), Chenling Xu(University of California, Berkeley), Nir Yosef(Ragon Institute of MGH, MIT and Harvard), Expert Cell Type Annotation(University of California, San Francisco), Rebecca N. Culver(University of California, San Francisco), Les Dethlefsen(Stanford University), Po-Yi Ho(Stanford University), Shixuan Liu(Stanford University), Jonathan S. Maltzman(University of California, San Francisco), Ross J. Metzger(University of California, San Francisco), Koki Sasagawa(Stanford University), Rahul Sinha(Stanford University), Hanbing Song(University of California, San Francisco), Bruce Wang(University of California, San Francisco), Tissue Expert Principal Investigators(University of California, San Francisco), Steven E. Artandi(Stanford University), Philip A. Beachy(Stanford University), Michael F. Clarke(University of California, San Francisco), Linda C. Giudice(University of California, San Francisco), Franklin W. Huang(San Francisco VA Medical Center), Kerwyn Casey Huang(Stanford University), Juliana Idoyaga(Cardiovascular Institute of the South), Seung K. Kim(Stanford University), Christin S. Kuo(Chan Zuckerberg Initiative (United States)), Patricia K. Nguyen(University of California, San Francisco), Thomas A. Rando(Stanford University), Kristy Red-Horse(Stanford University), Jeremy F. Reiter(University of California, San Francisco), David A. Relman(VA Palo Alto Health Care System), Justin L. Sonnenburg(Stanford University), Albert Y. Wu(Stanford University), Sean M. Wu(Cardiovascular Institute of the South), Tony Wyss‐Coray(Stanford University), Stephen R. Quake(Chan Zuckerberg Initiative (United States))
Cited by 100Open Access
Abstract
Cell-free RNA from liquid biopsies can be analyzed to determine disease tissue of origin. We extend this concept to identify cell types of origin using the Tabula Sapiens transcriptomic cell atlas as well as individual tissue transcriptomic cell atlases in combination with the Human Protein Atlas RNA consensus dataset. We define cell type signature scores, which allow the inference of cell types that contribute to cell-free RNA for a variety of diseases.
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