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This Week in Genome Research: Jun 21, 2017

An international team led by investigators at the Wellcome Trust Sanger Institute in the UK takes a look at population genomics and genome dynamics in Chlamydia trachomatis, a bacterial species notorious for its role in sexually transmitted infections and infections that can lead to blindness. Using genome sequence data for 563 C. trachomatis isolates, including more than 450 not described in previous studies, the researchers delineated two key evolutionary phases in the pathogen's history and performed analyses that refined the timeline for its diversification. "Temporal analysis indicates that lineages have recently expanded in the space of thousand of years, rather than the millions of years previously thought," they write, "a finding that dramatically changes our understanding of this pathogen's history."

A population genomics study of the opportunistic fungal pathogen Cryptococcus neoformans explores selective pressures in the environment that appear to have bumped up fungal virulence in humans as well. For that study, researchers from the Broad Institute and elsewhere did genome sequencing on nearly 400 C. neoformans isolates from African-specific and global lineages, using phylogenetics, comparative genomics, phenotypic analyses, and a genome-wide association approach to get a closer look at C. neoformans relationships, virulence, responses to selection, and more. The study's authors say their data "highlight the complex evolutionary interplay between adaptation to natural environments and opportunistic infections, and that selection on specific pathways may predispose isolates to human virulence."

A team from the US, UK, Germany, and Canada describe a non-coding mutation identified in individuals with an autosomal recessive microcephaly-micromelia syndrome (MMS) that has so far been found in just one First Nations population in northern Saskatchewan. With the help of RNA sequencing — combined with genome, exome, or targeted sequencing — the researchers narrowed in on a non-coding variant that altered splicing of DONSON, a gene suspected of contributing to embryonic development based on their follow-up mouse experiments and gene expression analyses.

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.