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This Week in Genome Research: Feb 3, 2016

A team from MIT and Harvard describe a single-cell sequencing strategy for detecting large, somatic copy number variants spanning a million bases or more. After looking at the sensitivity and specificity of existing low-coverage single-cell sequencing methods for megabase CNV detection, the researchers came up with their own tweaks to bump up the sensitivity of their analytical methods. In individual cells from postmortem human brain and skin tissues from multiple individuals, for example, the study's authors saw large, somatic CNVs in nearly one-tenth of cells. "We conclude that large CNVs can be tolerated in subpopulations of cells," the team writes, "and that particular CNVs are relatively prevalent within and across individuals."

Researchers from the University of California, Berkeley, and Oklahoma State University explore regulatory features related to speciation in the house mouse using offspring from a cross between two subspecies, Mus musculus musculus and M. m. domesticus. Using RNA sequencing and comparisons between expression and allele-specific reads in testis tissue from sterile and fertile male M. m. musculus-M. m. domesticus hybrids, the team searched for speciation-related cis and trans regulatory elements as well as expression shifts associated with sterility.  

Finally, South Korean researchers present a method called multiplex Digenome-seq, designed to detect genome-wide target specificities for as many as 11 CRISPR-Cas9 nucleases at once. The approach involves computational detection of in vitro cleavage patterns after whole-genome sequencing of cell-free DNA that had been digested with single guide RNA and subjected to Cas9 nucleases, the team explains. The group's results suggest multiplex Digenome-seq compares favorably to other sequencing-based target detection methods, picking up off-target sites that may not have otherwise been detected. And after profiling hundreds of CRISPR-Cas9 cleavage sites with the approach, the authors came up with target selection guidelines aimed at dialing down off-target activity.