A community challenge to evaluate RNA-seq, fusion detection, and isoform quantification methods for cancer discovery.

Autor:	Creason A; Biomedical Engineering, Oregon Health and Science University, Portland, OR 97239, USA., Haan D; Biomolecular Engineering and UC Santa Cruz Genome Institute, University of California, Santa Cruz, Santa Cruz, CA, USA., Dang K; Sage Bionetworks, Seattle, WA, USA., Chiotti KE; Biomedical Engineering, Oregon Health and Science University, Portland, OR 97239, USA., Inkman M; The Genome Institute, Washington University School of Medicine, 4444 Forest Park Avenue, St. Louis, MO 63110, USA., Lamb A; Sage Bionetworks, Seattle, WA, USA., Yu T; Sage Bionetworks, Seattle, WA, USA., Hu Y; Sage Bionetworks, Seattle, WA, USA., Norman TC; Sage Bionetworks, Seattle, WA, USA., Buchanan A; Biomedical Engineering, Oregon Health and Science University, Portland, OR 97239, USA., van Baren MJ; Biomolecular Engineering and UC Santa Cruz Genome Institute, University of California, Santa Cruz, Santa Cruz, CA, USA., Spangler R; Biomedical Engineering, Oregon Health and Science University, Portland, OR 97239, USA., Rollins MR; Biomedical Engineering, Oregon Health and Science University, Portland, OR 97239, USA., Spellman PT; Biomedical Engineering, Oregon Health and Science University, Portland, OR 97239, USA., Rozanov D; Biomedical Engineering, Oregon Health and Science University, Portland, OR 97239, USA., Zhang J; The Genome Institute, Washington University School of Medicine, 4444 Forest Park Avenue, St. Louis, MO 63110, USA., Maher CA; The Genome Institute, Washington University School of Medicine, 4444 Forest Park Avenue, St. Louis, MO 63110, USA., Caloian C; Computational Biology, Ontario Institute for Cancer Research, Toronto, Canada., Watson JD; Computational Biology, Ontario Institute for Cancer Research, Toronto, Canada., Uhrig S; Division of Applied Bioinformatics, German Cancer Research Center (DKFZ) and Faculty of Biosciences, Heidelberg University, Heidelberg, Germany., Haas BJ; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA., Jain M; Biomolecular Engineering and UC Santa Cruz Genome Institute, University of California, Santa Cruz, Santa Cruz, CA, USA., Akeson M; Biomolecular Engineering and UC Santa Cruz Genome Institute, University of California, Santa Cruz, Santa Cruz, CA, USA., Ahsen ME; Icahn School of Medicine at Mount Sinai, Department of Genetics and Genomic Sciences, One Gustave Levy Place, New York, NY 1498, USA., Stolovitzky G; Icahn School of Medicine at Mount Sinai, Department of Genetics and Genomic Sciences, One Gustave Levy Place, New York, NY 1498, USA; IBM T.J. Watson Research Center, 1101 Kitchawan Road, Route 134, Yorktown Heights, NY 10598, USA., Guinney J; Sage Bionetworks, Seattle, WA, USA., Boutros PC; Computational Biology, Ontario Institute for Cancer Research, Toronto, Canada; Departments of Medical Biophysics and Pharmacology & Toxicology, University of Toronto, Toronto, Canada; Departments of Human Genetics and Urology, University of California, Los Angeles, Los Angeles, CA, USA., Stuart JM; Biomolecular Engineering and UC Santa Cruz Genome Institute, University of California, Santa Cruz, Santa Cruz, CA, USA., Ellrott K; Biomedical Engineering, Oregon Health and Science University, Portland, OR 97239, USA. Electronic address: ellrott@ohsu.edu.
Jazyk:	angličtina
Zdroj:	Cell systems [Cell Syst] 2021 Aug 18; Vol. 12 (8), pp. 827-838.e5. Date of Electronic Publication: 2021 Jun 18.
DOI:	10.1016/j.cels.2021.05.021
Abstrakt:	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. Competing Interests: Declaration of interests The authors declare no competing interests. (Copyright © 2021 The Authors. Published by Elsevier Inc. All rights reserved.)
Databáze:	MEDLINE
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