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This Week in PNAS: May 28, 2019

Researchers in Belgium outline a machine learning method aimed at detecting variants that are pathogenic when present in pairs. The tool — known as the Variant Combinations Pathogenicity Predictor (VarCoPP) — brings together insights from the variants, genes, and gene pairs to find such pathogenic variant combinations, the team explains. After training and testing VarCoPP with data from the 1000 Genomes Project and pathogenic variant combinations previously reported in the Digenic Diseases Database (DIDA), the authors validated the tool on almost two dozen pathogenic variant combinations reported in studies that came out after the latest DIDA update, demonstrating that VarCoPP picks up pathogenic combinations accurately and precisely. "[T]he VarCoPP has been designed to act as an interpretable method that can provide explanations on why a bilocus combination is predicted as pathogenic and which biological information is important for that prediction," they write.

A team from the US and Israel explores adaptations and genomic divergence in Drosophila simulans fruit flies found on ecologically distinct slopes of Israel's Evolution Canyon. Using pooled sequencing, the researchers generated genome sequences for representatives from D. simulans lines originating at distinct Evolution Canyon slope sites, identifying millions of SNPs used for their subsequent selection and divergence analyses, as well as comparisons with features previously reported in D. melanogaster fruit flies. "Our results show even deeper interslope divergence in D. simulans than in D. melanogaster," they report, "with extensive signatures of selective sweeps present in flies from both slopes but enhanced in the population from the hotter and drier south-facing slope." 

Researchers from the US, Germany, and Russia share findings from a bat evolutionary analysis focused on phylogeny and selection patterns across 18 bat species. The team began by generating new transcriptome sequences for the African hammer-headed bat, Hypsignathus monstrosus, and the Egyptian fruit bat, Rousettus aegyptiacus. Together with available genome and transcriptome data for another 16 bat species, the transcriptomes helped to untangle bat gene alignments, develop a bat phylogenetic tree, and search for signs of positive selection in the bat genomes. For example, the latter analysis highlights 181 genes showing signs of positive selection, including those involved in processes ranging from immune system responses to collagen formation, the investigators note.

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.