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DREAM Challenge Encourages Development of New Tools to Identify RNA Species in Cancer Cells

NEW YORK (GenomeWeb) – The University of California, Santa Cruz announced today that it has launched a DREAM challenge to develop algorithms that can detect abnormal RNA sequences in cancer cells.

DREAM — short for Dialogue for Reverse Engineering Assessments and Methods — was founded in 2006 by Columbia University's Andrea Califano and Mount Sinai's Gustavo Stolovitzky, and is coordinated by the Ontario Institute for Cancer Research.

UCSC's DREAM challenge is called Somatic Mutation Calling RNA (SMC-RNA) — contestants may submit algorithms designed to detect rearrangements in RNA-seq data, as well as for detecting and quantifying mRNA fusions and isoforms, via the National Cancer Institute Cancer Genomics Cloud Pilots.

The cloud pilots are a computing network for storing and analyzing genomic data that was developed by the Broad Institute, the Institute for Systems Biology, and Seven Bridges Genomics under a 2014 NCI initiative.

According to UCSC, the algorithms will be specifically evaluated using both in silico and spiked-in data and judged based on their ability to estimate abundances of a set of known RNA isoforms and to predict the presence of novel gene fusions.

"Predicting RNA species in a cancer cell is a particularly challenging task," UCSC Professor and challenge leader Josh Stuart said in a statement. "RNA expression reflects much of the deranged complexity of the underlying cancer cell DNA and then adds another level of derangement on top of that." 

Contestants can register for the challenge at the Sage Bionetworks Synapse platform website, which will also feature a leaderboard and offer teams the chance to form and reform as the challenge proceeds. 

Individuals and teams who submit final models will be invited to participate as consortium coauthors on an overview paper of the challenge that will be submitted to Nature Biotechnology. Top performers will receive travel awards and speaking invitations to the 2017 DREAM conference.