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This Week in PLOS: Sep 17, 2018

In PLOS Genetics, a University of Lausanne-led team takes a look at intra-tumor heterogeneity patterns with a clonal phylogeny analysis of thousands of cancer from 32 tumor types. The team computationally inferred the clonal compositions based on somatic mutation and copy number profiles for 5,593 tumors assessed through the Cancer Genome Atlas. Although the results pointed to enhanced within-tumor heterogeneity in tumors marked by rampant mutations and copy number changes, for example, the authors note that "extremely unstable tumors associated with DNA repair deficiencies or high chromosomal instability are not the most intrinsically heterogeneous."

Korean and Japanese researchers reporting in PLOS One present an analysis aimed at untangling the advent and dispersal of Thoroughbred racehorses. The team did mitochondrial genome sequencing on 14 Thoroughbreds and two Przewalski's horse. By comparing the mitochondrial genomes to one another and to mitochondrial sequences for more than 150 horses representing dozens of horse breeds around the world, authors of that study saw "multiple maternal origins" for racehorses, which appear to be related to horses from Europe, the Middle East, and Asia. "[T]here was no apparent correlation between geographic origin or breed and the evolution of global horses," they write, noting that "the population expansion of modern horses, including Thoroughbreds, occurred approximately 5,500 to 11,000 years ago."

A team from the University of Victoria, Fisheries and Oceans Canada, and elsewhere explore genomic and transcriptomic features in the Arctic charr, Salvelinus alpinus, a member of the Salmonidae family found in frigid waters. The researchers established a new genetic map for Arctic charr based on data for Nauyuk Lake and Tree River strains, before using long and short read sequencing approaches to put together a 1.5 billion base genome assembly spanning some 70 percent of the predicted Arctic charr genome. Together with transcript data for a dozen Arctic charr tissues, the genome led to thousands of genes, repetitive elements appearing across more than half of the genome, and gene expression profiles shared with other salmonid species. 

The Scan

New Study Investigates Genomics of Fanconi Anemia Repair Pathway in Cancer

A Rockefeller University team reports in Nature that FA repair deficiency leads to structural variants that can contribute to genomic instability.

Study Reveals Potential Sex-Specific Role for Noncoding RNA in Depression

A long, noncoding RNA called FEDORA appears to be a sex-specific regulator of major depressive disorder, affecting more women, researchers report in Science Advances.

New mRNA Vaccines Offer Hope for Fighting Malaria

A George Washington University-led team has developed mRNA vaccines for malaria that appear to provide protection in mice, as they report in NPJ Vaccines.

Unique Germline Variants Found Among Black Prostate Cancer Patients

Through an exome sequencing study appearing in JCO Precision Oncology, researchers have found unique pathogenic or likely pathogenic variants within a cohort of Black prostate cancer patients.