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This Week in Nature: Dec 18, 2014

In Nature Biotechnology this week, a team from Boston Children's Hospital describes a new genome-wide method for detecting DNA double-strand breaks generated by engineered nucleases. By combining high-throughput, genome-wide translocation sequencing with different CRISPR/Cas9 and TALEN gene-editing nucleases, the researchers identified off-target hotspot numbers for the given nucleases and extended the number of known off-targets for certain previously characterized nucleases. They also identified translocations between bona fide nuclease targets on homologous chromosomes, an undesirable collateral effect not previously described.

Meanwhile, in Nature Genetics, a multi-institute team reports the results of its pan-cancer analysis of mutated genetic networks in nearly 4,000 samples from 12 cancer types from The Cancer Genome Atlas. Using a new algorithm designed to find mutated subnetworks more efficiently than existing single-gene pathway and network approaches, the investigators identified 16 significantly mutated subnetworks that comprise well-known cancer signaling pathways, as well as subnetworks with less characterized roles in cancer. Many of the subnetworks exhibit co-occurring mutations across samples and contain genes with rare somatic mutations across multiple cancer types. GenomeWeb has more on this here.

The Scan

Study Links Evolution of Longevity, Social Organization in Mammals

With the help of comparative phylogenetics and transcriptomics, researchers in Nature Communications see ties between lifespan and social organization in mammals.

Tumor Microenvironment Immune Score Provides Immunotherapy Response, Prognostic Insights

Using multiple in situ analyses and RNA sequence data, researchers in eBioMedicine have developed a score associated with immunotherapy response or survival.

CRISPR-Based Method for Finding Cancer-Associated Exosomal MicroRNAs in Blood

A team from China presents in ACS Sensors a liposome-mediated membrane fusion strategy for detecting miRNAs carried in exosomes in the blood with a CRISPR-mediated reporter system.

Drug Response Variants May Be Distinct in Somatic, Germline Samples

Based on variants from across 21 drug response genes, researchers in The Pharmacogenomics Journal suspect that tumor-only DNA sequences may miss drug response clues found in the germline.