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This Week in Genome Research: Apr 27, 2016

Researchers from Louisiana State University and the Institute for Systems Biology report on a repeat family called Platy-1 that they detected in the genome of the common marmoset, Callithrix jacchus. Starting from a chromosome 3 sequence that stood out during a comparison between the marmoset genome and sequences from humans and other primates, the team used PCR, phylogenetics, and other approaches to trace the history of the suspected non-LTR retrotransposon repeat. Results from the analysis suggest Platy-1 is a short interspersed element that may have started off as an Alu element but became active as a repeat family in New World Monkeys, with nearly 2,300 Platy-1 elements turning up in the common marmoset genome.

A Cold Spring Harbor Laboratory team describes a fragmentation-based protocol for finding copy number variants. The approach — known as "short multiply aggregated sequence homologies," or SMASH — pairs sequencing with random DNA fragmentation. A mapping algorithm then uses multiple mappable tag information to computationally chop long reads into the shorter fragments comprising them before binning these tags to get a look at CNV profiles, the researchers say. "Because fewer reads are necessary relative to [whole-genome sequencing] to give accurate CNV data, SMASH libraries can be highly multiplexed," they write, "allowing large numbers of individuals to be analyzed at low cost."

Spanish researchers present findings from an alternative splicing analysis on tumors from 11 solid cancer types. Using a combination of genome and transcriptome sequences generated for the Cancer Genome Atlas project, the researchers assessed somatic mutations, copy number alterations, and gene expression profiles for RNA-binding proteins suspected of influencing gene splicing and expression. Based on clues for more than 1,300 known or predicted RNA-binding proteins, they put together networks outlining some of the splicing changes that occur in cancers with alterations affecting splicing factors and other RNA-binding proteins.