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This Week in Nature: Mar 2, 2017

In this week's Nature Chemical Biology, researchers from the University of Illinois at Urbana-Champaign describe the use of a new genome-mining tool to study ribosomally synthesized and post-transcriptionally modified peptide (RiPP) natural products. Called RODEO — short for rapid ORF description and evaluation online — the tool combines hidden Markov model-based analysis, heuristic scoring, and machine learning, and was used to identify biosynthetic gene clusters and predict RiPP precursor peptides. In addition to helping expand the knowledge of lasso peptides, RODEO provides a framework for other genome-mining efforts. 

And in Nature Genetics, a Decode Genetics-led group reports on a study highlighting the lack of diversity in non-repetitive sequences in the human reference genome. Using whole-genome sequence data for roughly 15,000 Icelanders, the investigators described nearly 4,000 breakpoint-resolved non-repetitive, non-reference sequence variants with 95 percent of those 200 base pairs or longer also present in chimpanzees, indicating that they are ancestral. Further, 149 variant loci are in linkage disequilibrium with a genome-wide association study catalog marker, suggesting disease relevance. The findings, the authors state, point to the importance of including "variation of all complexity levels when searching for variants that associate with disease." GenomeWeb has more on this study, here.

Also in Nature Genetics, an international research team presents the results of a genome-wide association study that identified common variants associated with macular telangiectasia type 2, a rare neurovascular degenerative retinal disease. By analyzing 476 cases and 1,733 controls of European ancestry, the researchers found genome-wide significant associations at three independent loci, including one known to associate with variation in retinal vascular diameter and two that have been implicated in the glycine/serine metabolic pathway.

The Scan

Cancer Survival Linked to Mutational Burden in Pan-Cancer Analysis

A pan-cancer paper appearing in JCO Precision Oncology suggests tumor mutation patterns provide clues for predicting cancer survival that are independent of other prognostic factors.

Australian Survey Points to Public Support for Genetic Risk Disclosure in Relatives of At-Risk Individuals

A survey in the European Journal of Human Genetics suggests most adult Australians are in favor of finding out if a relative tests positive for a medically actionable genetic variant.

Study Links Evolution of Stony Coral Skeleton to Bicarbonate Transporter Gene

A PNAS paper focuses on a skeleton-related bicarbonate transporter gene introduced to stony coral ancestors by tandem duplication.

Hormone-Based Gene Therapy to Sterilize Domestic Cat

A new paper in Nature Communication suggests that gene therapy could be a safer alternative to spaying domestic cats.