A community challenge to evaluate RNA-seq, fusion detection, and isoform quantification methods for cancer discovery.
Cancer
Cloud compute
DREAM Challenge
RNA fusion
RNA-seq
benchmark
crowd-sourced
evaluation
isoform quantification
Journal
Cell systems
ISSN: 2405-4720
Titre abrégé: Cell Syst
Pays: United States
ID NLM: 101656080
Informations de publication
Date de publication:
18 08 2021
18 08 2021
Historique:
received:
01
10
2019
revised:
15
09
2020
accepted:
25
05
2021
pubmed:
20
6
2021
medline:
7
4
2022
entrez:
19
6
2021
Statut:
ppublish
Résumé
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.
Identifiants
pubmed: 34146471
pii: S2405-4712(21)00207-6
doi: 10.1016/j.cels.2021.05.021
pmc: PMC8376800
mid: NIHMS1710731
pii:
doi:
Substances chimiques
Protein Isoforms
0
RNA
63231-63-0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
827-838.e5Subventions
Organisme : NCI NIH HHS
ID : U24 CA180922
Pays : United States
Organisme : NCI NIH HHS
ID : U24 CA209923
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM109031
Pays : United States
Organisme : NCI NIH HHS
ID : U24 CA143799
Pays : United States
Organisme : NCI NIH HHS
ID : P30 CA016042
Pays : United States
Organisme : NCI NIH HHS
ID : U24 CA210957
Pays : United States
Organisme : NCI NIH HHS
ID : R01 CA180778
Pays : United States
Organisme : NCI NIH HHS
ID : R50 CA211461
Pays : United States
Organisme : CCR NIH HHS
ID : HHSN261200800001C
Pays : United States
Organisme : NCI NIH HHS
ID : HHSN261200800001E
Pays : United States
Organisme : NCI NIH HHS
ID : U24 CA210990
Pays : United States
Investigateurs
Hongjiu Zhang
(H)
Yifan Wang
(Y)
Yuanfang Guan
(Y)
Cu Nguyen
(C)
Christopher Sugai
(C)
Alokkumar Jha
(A)
Jing Woei Li
(JW)
Alexander Dobin
(A)
Informations de copyright
Copyright © 2021 The Authors. Published by Elsevier Inc. All rights reserved.
Déclaration de conflit d'intérêts
Declaration of interests The authors declare no competing interests.
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