Research community comes together to provide new 'gold standard' for genomic data analysis | EurekAlert! Science News

"Cancer research leaders at the Ontario Institute for Cancer Research, Oregon Health & Science University, Sage Bionetworks, the distributed DREAM (Dialog for Reverse Engineering Assessment and Methods) community and The University of California Santa Cruz published the first findings of the ICGC-TCGA-DREAM Somatic Mutation Calling (SMC) Challenge (The Challenge: https://www.synapse.org/#!Synapse:syn312572) today in the journal Nature Methods. These results provide an important new benchmark for researchers, helping to define the most accurate methods for identifying somatic mutations in cancer genomes. The results could be the first step in creating a new global standard to determine how well cancer mutations are detected. The Challenge, which was initiated in November 2013, was an open call to the research community to address the need for accurate methods to identify cancer-associated mutations from whole-genome sequencing data. Although genomic sequencing of tumour genomes is exploding, the mutations identified in a given genome can differ by up to 50 per cent just based on how the data is analyzed. Research teams were asked to analyze three in silico (computer simulated) tumour samples and publicly share their methods. The 248 separate analyses were contributed by teams around the world and then analyzed and compared by Challenge organizers. When combined, the analyses provide a new ensemble algorithm that outperforms any single algorithm used in genomic data analysis to date. The authors of the paper also report a computational method, BAMSurgeon (developed by co-lead author Adam Ewing, a postdoctoral fellow in the lab of Dr. David Haussler at UC Santa Cruz), capable of producing an accurate simulation of a tumour genome ..."