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This Week in Genome Research: Feb 20, 2013

The University of Washington's Jay Shendure and colleagues describe an approach for finding low frequency variants, while reining in sequence errors. This "single molecule molecular inversion probe," or smMIP, assay combines single molecule tagging with molecular inversion probe-based multiplexed targeted capture, they say. In their Genome Research study, for instance, investigators used smMIP on eight cell lines and 45 clinical cancer samples, targeting 33 clinically informative genes apiece. The approach picked up mutations at down to the 1 percent frequency level with 83 percent sensitivity, prompting those involved to argue that "smMIP will be broadly adoptable as a practical and effective method for accurately detecting low frequency mutations in both research and clinical settings."

For more on the method, check out the latest issue of our sister publication, In Sequence.

Complex breakpoints are common in cancer genomes, according to a study by researchers at the University of Virginia and elsewhere. Using a paired-end mapping algorithm called HYDRA-MULTI, the team tallied up breakpoints in 64 cancer samples using matched tumor and normal sequence data generated for The Cancer Genome Atlas. From mapping patterns for nearly 6,200 somatic structural variant breakpoints, the investigators determined that three-quarters of the tumor genomes housed one or more complex clusters of breakpoints. Their subsequent analyses suggest that many of the complex rearrangements found in the cancer genomes appeared through lone mutational events — apparently involving a combination of double-strand breaks and non-homologous repair.

Researchers from the Massachusetts General Hospital and Harvard Medical School performed deep sequencing on small RNAs from Caenorhabditis elegans and a few nematode worms from the same genus to explore the evolutionary history of small regulatory RNAs. When it sifted through microRNA, small interfering RNA, and piwi-interacting RNA profiles in the worms, the team saw relatively little conservation at specific siRNAs or piRNAs. On the other hand, C. elegans and the three other worms shared conservation across dozens of miRNA families and in broader features of the siRNA and piRNA pathways.