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This Week in Genome Research: Jul 11, 2013

An international team led by investigators at Pfizer Oncology, BGI-Shenzhen, the University of Copenhagen, and Eli Lilly and Company used whole-genome sequencing to track down recurrent genetic glitches in the liver cancer hepatocellular carcinoma — particularly forms of the disease involving hepatitis B virus infection. As they report online in Genome Research, the researchers found that the tumor suppressor gene TP53 was mutated in more than one-third of tumors when they sequenced tumor and matched normal samples from 88 individuals with HCC. An oncogene called beta catenin was often altered, too, they found, as were other components of the beta catenin pathway and a signaling pathway that includes JAK1 and STAT gene products.

Researchers from the University of Washington, the University of British Columbia, and elsewhere describe a genetic resource comprised of more than 2,000 mutated Caenorhabditis elegans strains. For the Million Mutation Project, the group performed random mutagenesis on each C. elegans strain before using whole-genome sequencing to tally up the mutations introduced in the roundworms during that process. The resulting collection, available through the Caenorhabditis Genetics Center, includes 2,007 mutated strains C. elegans containing some 800,000 or more single nucleotide changes and more than 16,000 small insertions, deletions, or copy number changes. It also houses data on several dozen wild C. elegans isolates, study authors note.

University of Washington genome sciences researcher Evan Eichler and colleagues scrutinized copy number variant patterns across almost 100 great ape and human genomes, focusing on the diversity of these variants in various lineages, the frequency with which they occur, and their relationship to single nucleotide changes. Using genome sequence data for 97 sequenced great apes and humans, the team tracked down 340 deletions and more than 400 duplications that appear to have become fixed in the genomes of hominids in general. But the investigators also identified deletion and duplication patterns that are specific to given lineages within the hominid family tree, including human-specific deletion events and a higher-than-usual rate of deletion in the chimpanzee lineage.