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GenomeWeb | May 21, 2015

Consortium Reports Results of Challenge to Establish Benchmark for Tumor Mutation Calling

NEW YORK (GenomeWeb) – Next-generation sequencing technologies and bioinformatics pipelines keep improving, yet calling somatic mutations from tumor samples still remains a challenge, as evidenced by recent data from The Cancer Genome Atlas showing that four major genome centers only agreed on 31 percent of SNV calls in lung cancer samples.

To help advance the development of gold standards for somatic mutation calling, an international group including Sage Bionetworks, leading academic institutions from the International Cancer Genome Consortium and TCGA, Annai Systems, and IBM’s DREAM project in 2013 launched the ICGC-TCGA DREAM Somatic Mutation Calling Challenge, a crowdsourced benchmark of algorithms for somatic mutation calling from whole-genome sequencing data. This week, the group reported in a Nature Methods article the initial results of the challenge from 248 analyses of three in silico tumors. Read the full article…