Open Problems in Extracellular RNA Data Analysis: Insights From an ERCC Online Workshop

Frontiers in Genetics

Bojan Losic¹  Eric L. Van Nostrand²  Bogdan Mateescu³  Brian S. White⁴  Rongshan Yu⁵  Gustavo Stolovitzky⁶  Ryan M. Spengler⁷  Robert R Kitchen⁸  Pieter Mestdagh⁹  Justin Chang^1,10  Joel Rozowsky^1,10  Matthew Roth^1,11  Emily LaPlante^1,11  Aleksander Milosavljevic^1,11  Leonora Balaj^1,12  Roger P. Alexander^1,13  Klaas E. A. Max^1,14  Juan Pablo Tosar^1,15  Karolina Elżbieta Kaczor-Urbanowicz^1,16 

[1] 0Icahn School of Medicine at Mount Sinai, New York, NY, United States;1Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, United States;2Brain Research Institute, University of Zurich, Zurich, Switzerland;3Jackson Laboratory, Bar Harbor, ME, United States;4Department of Computer Science, Xiamen University, Aginome Scientific, Ltd., Xiamen, China;5IBM T.J. Watson Research Center, Yorktown Heights, NY, United States;6School of Medicine and Public Health, University of Wisconsin, Madison, WI, United States;Cardiovascular Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, United States;Center for Medical Genetics, Department of Biomolecular Medicine, Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium;Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States;Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States;Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States;Extracellular RNA Communication Consortium, Phoenix, AZ, United States;Laboratory of RNA Molecular Biology, Rockefeller University, New York, NY, United States;Pasteur Institute of Montevideo and University of the Republic of Uruguay, Montevideo, Uruguay;School of Dentistry, University of California, Los Angeles, Los Angeles, CA, United States;

关键词: extracellular RNA;    RNA-seq;    RNA sequencing;    deconvolulion;    batch variation;    DREAM challenge;   

DOI  :  10.3389/fgene.2021.778416

来源: DOAJ

【 摘 要 】

We now know RNA can survive the harsh environment of biofluids when encapsulated in vesicles or by associating with lipoproteins or RNA binding proteins. These extracellular RNA (exRNA) play a role in intercellular signaling, serve as biomarkers of disease, and form the basis of new strategies for disease treatment. The Extracellular RNA Communication Consortium (ERCC) hosted a two-day online workshop (April 19–20, 2021) on the unique challenges of exRNA data analysis. The goal was to foster an open dialog about best practices and discuss open problems in the field, focusing initially on small exRNA sequencing data. Video recordings of workshop presentations and discussions are available (https://exRNA.org/exRNAdata2021-videos/). There were three target audiences: experimentalists who generate exRNA sequencing data, computational and data scientists who work with those groups to analyze their data, and experimental and data scientists new to the field. Here we summarize issues explored during the workshop, including progress on an effort to develop an exRNA data analysis challenge to engage the community in solving some of these open problems.

【 授权许可】

Unknown