In PLOS Genetics, a team from the Massachusetts Institute of Technology and Ariad Pharmaceuticals introduce an inherited disease genetics-focused approach for finding genes and variants involved in cancer development and progression. The researchers relied on a computational method for comparing variants from a large database of variants identified in inherited disease studies with variants present in various cancer types. In an analysis of nearly 7,400 exome sequences for tumors profiled for The Cancer Genome Atlas project, for example, they found that melanoma samples contained recurrent, activating mutations in SOS1, a gene implicated in Noonan syndrome.
Korean researchers reporting in PLOS One describe findings from a genome re-sequencing and comparative genomics study of melon plants from four accessions in relation to their vulnerability to powdery mildew fungus. From sequences spanning nearly 83 percent of the powdery mildew genome, on average, the team tracked down some 7.4 million SNPs, 1.9 million small insertion and deletions, and nearly 183,000 structural variant candidates. With these variants, the group began defining disease-related quantitative trait loci in the plants, including SNPs and indels associated with defense against powdery mildew and other pathogens.
An adenovirus found in Antarctic penguins appears to represent a previously unobserved species in the Siadenovirus genus, according to another PLOS One paper by another Korean team. The researchers did targeted sequencing on multiple organ samples from 78 Chinstrap, Gentoo, or Adelie penguin carcasses collected on King George Island from 2008 to 2013, identifying adenoviruses in more than one-quarter of the penguins and in all but two of the organ types tested. They also sequenced complete adenovirus genomes — spanning between 24,630 and 24,662 bases — from two Chinstrap penguins and two Gentoo penguins. When the investigators compared predicted amino acid sequences from the penguin adenoviruses to those from other adenoviruses, though found that the penguin viruses clustered together in a group near an adenovirus found in turkeys.