@article{6243afbccbec436b97c2777075019538,
title = "A community challenge to evaluate RNA-seq, fusion detection, and isoform quantification methods for cancer discovery",
abstract = "The accurate identification and quantitation of RNA isoforms present in the cancer transcriptome is key for analyses ranging from the inference of the impacts of somatic variants to pathway analysis to biomarker development and subtype discovery. The ICGC-TCGA DREAM Somatic Mutation Calling in RNA (SMC-RNA) challenge was a crowd-sourced effort to benchmark methods for RNA isoform quantification and fusion detection from bulk cancer RNA sequencing (RNA-seq) data. It concluded in 2018 with a comparison of 77 fusion detection entries and 65 isoform quantification entries on 51 synthetic tumors and 32 cell lines with spiked-in fusion constructs. We report the entries used to build this benchmark, the leaderboard results, and the experimental features associated with the accurate prediction of RNA species. This challenge required submissions to be in the form of containerized workflows, meaning each of the entries described is easily reusable through CWL and Docker containers at https://github.com/SMC-RNA-challenge. A record of this paper's transparent peer review process is included in the supplemental information.",
keywords = "benchmark, Cancer, Cloud compute, crowd-sourced, DREAM Challenge, evaluation, isoform quantification, RNA fusion, RNA-seq",
author = "{SMC-RNA Challenge Participants} and Allison Creason and David Haan and Kristen Dang and Chiotti, {Kami E.} and Matthew Inkman and Andrew Lamb and Thomas Yu and Yin Hu and Norman, {Thea C.} and Alex Buchanan and {van Baren}, {Marijke J.} and Ryan Spangler and Rollins, {M. Rick} and Spellman, {Paul T.} and Dmitri Rozanov and Jin Zhang and Maher, {Christopher A.} and Cristian Caloian and Watson, {John D.} and Sebastian Uhrig and Haas, {Brian J.} and Miten Jain and Mark Akeson and Ahsen, {Mehmet Eren} and Hongjiu Zhang and Yifan Wang and Yuanfang Guan and Cu Nguyen and Christopher Sugai and Alokkumar Jha and Li, {Jing Woei} and Alexander Dobin and Gustavo Stolovitzky and Justin Guinney and Boutros, {Paul C.} and Stuart, {Joshua M.} and Kyle Ellrott",
note = "Funding Information: The authors would like to acknowledge the work done by Alison Tang and input from Dr. Angela Brooks for working with long-read RNA data, Chris Boniface for his work as a lab consultant, and Dr. Joe Gray for the contribution of the cell lines used for the benchmark dataset creation. The authors would like to acknowledge the support of the National Cancer Institute . This includes funding to UCSC from the ITCR (grant R01CA180778 ), Oregon Health & Science University ( U24CA210957 , U24CA143799 , and HHSN261200800001E ), UCLA ( P30CA016042 ), and Sage Bionetworks ( 5U24CA209923 ). Publisher Copyright: {\textcopyright} 2021 The Authors",
year = "2021",
month = aug,
day = "18",
doi = "10.1016/j.cels.2021.05.021",
language = "English (US)",
volume = "12",
pages = "827--838.e5",
journal = "Cell Systems",
issn = "2405-4712",
publisher = "Cell Press",
number = "8",
}