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This Week in PLOS: Jun 13, 2016

In PLOS Genetics, French and American researchers describe computational efforts to rank the accuracy of functional assays used to classify genetic variants for clinical decision making after targeted-, exome-, or whole-genome sequencing. The team focused on findings from four yeast cell-based functional assays aimed at classifying dozens of variants in BRCA1, a gene that contains variants implicated in enhanced risk of breast and/or ovarian cancer. With the help of a newly developed a probability system, they scrutinized the clinical utility of the resulting variant calls to more clearly distinguish between pathogenic and neutral mutations. In their follow-up analyses, the study's authors saw that the approach "is adapted to experimental systems far beyond the genetic variant assessment, with the probabilistic classification of small interfering RNAs tested for human growth inhibition in high throughput screening."

A team from Sweden and South Africa searches for sites in the genome associated with social parasitism in the Cape bee, Apis mellifera capensis, for another PLOS Genetics paper. The Cape bee sub-species is known for laying its eggs in foreign colonies to take advantage of resources provided by other bees, the researchers say, and are capable of producing diploid females asexually through the fusion of two nuclei from worker bees. To explore the genetic basis of these and other features, the investigators compared genome sequences from 10 Cape bees from sites in Cape Town and Port Elizabeth, South Africa, with genome sequences from A. m. scutellata and A. m. adansonii bees from Pretoria, South Africa, and Nigeria, respectively, uncovering regions of the bee genome that appear to be under positive selection in the socially parasitic Cape sub-species.

Researchers from India present an online resource for bringing together and analyzing genomic data for parasitic helminth worms from the Platyhelminthes, Nematoda, and Acanthocephala phyla that have been collected in northeast India. Authors of the study note that the North-East India Helminth Parasite Information Database, or NEIHPID, which is housed at the North Eastern Hill University's bioinformatics center, contains genome sequencing data for three foodborne trematode parasites from the Platyhelminthes phylum, along with genetic marker and/or morphologic taxonomic data on more than 100 other helminths. "The outcome of the project is a collated compendium of [an] enriched knowledge-base on parasite biology and its impact on human and social well-being," they write, "especially in northeast India."