Biomedical Engineering, Oregon Health and Science University, Portland, OR 97239, USA.
Biomolecular Engineering and UC Santa Cruz Genome Institute, University of California, Santa Cruz, Santa Cruz, CA, USA.
Cell Syst. 2021 Aug 18;12(8):827-838.e5. doi: 10.1016/j.cels.2021.05.021. Epub 2021 Jun 18.
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.
准确识别和定量癌症转录组中存在的 RNA 异构体对于从推断体细胞变异的影响到通路分析、生物标志物开发和亚型发现等各种分析都至关重要。ICGC-TCGA DREAM 体细胞突变调用 RNA（SMC-RNA）挑战赛是一项众包努力，旨在对批量癌症 RNA 测序（RNA-seq）数据中 RNA 异构体定量和融合检测方法进行基准测试。该挑战赛于 2018 年结束，在 51 个合成肿瘤和 32 个带有融合构建体的细胞系上，对 77 个融合检测条目和 65 个异构体定量条目进行了比较。我们报告了用于构建此基准的条目、排行榜结果以及与准确预测 RNA 物种相关的实验特征。该挑战赛要求提交的内容采用容器化工作流程的形式，这意味着通过 CWL 和 Docker 容器（位于 https://github.com/SMC-RNA-challenge）可以轻松重用描述的每个条目。本文的透明同行评审过程记录包含在补充信息中。
