July 20, 2016

A challenge to the community to improve RNA sequencing data

rna-seq

A new DREAM Challenge was launched on June 30 focusing on the abnormal RNA molecules in cancer cells. The ICGC-TCGA DREAM SMC-RNA Challenge is an international effort designed to improve standard methods for identifying cancer-associated rearrangements in RNA sequencing (RNA-seq) data, providing new tools for cancer researchers. Improved RNA sequencing data will allow researchers to better understand cancer leading to new and better-personalized approaches to cancer treatment.

The Challenge is open to the entire research community, and anyone interested in participating is encouraged to register at https://synapse.org/SMC_RNA.

DREAM (Dialogue on Reverse Engineering Assessment and Methods) Challenges are a not-for-profit community effort that pose fundamental questions about systems biology and translational medicine to the wider research community. Designed and run by researchers from a variety of organizations, the Challenges invite participants to submit solutions to problems posed while working together in collaboration. The SMC series of DREAM Challenges have been running since 2013, and focus on key questions in cancer genomics. The SMC Challenges are led by Challenge Director Dr. Paul Boutros, a Principal Investigator at OICR, which serves as the central coordinating site.

To motivate participants and foster collaboration the DREAM Challenges use Sage Bionetwork’s Synapse platform, which provides leaderboards, discussion forums and the ability for teams to dynamically form and re-form as the Challenge proceeds. The SMC-RNA Challenge is unique in that it is entirely cloud-based, running on a series of academic cloud pilots created by the U.S. National Cancer Institute, which is co-funding this Challenge. A manuscript describing the challenge design and results, along with the winning model will be submitted to Nature Biotechnology for publication.

The SMC Challenges are led by Challenge Director Dr. Paul Boutros, a Principal Investigator at OICR, which serves as the central coordinating site.

Results from an earlier SMC DREAM Challenge were published last May in the journal Nature Methods. These results provided a new gold standard for defining the most accurate methods for identifying somatic mutations in cancer genomes. It is hoped that the SMC-RNA Challenge will provide the same for RNA sequencing data.