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This Week in PLoS: Jan 11, 2010

Researchers from Baylor report in PLoS One on a new metric, called Minimal Match on Either Side of exon junction, that assesses the quality of exon-junction reads from RNA-Seq data by considering the number of junction reads, mismatches on each read, how close the read is to the center of the junction, and where mismatches on the read occur. They tested out their method on a dataset of mouse brain, liver, and muscle mRNA sequences, finding that their ways was more accurate than the read-counting or logistic regression methods.

Patrick Gillevet and his colleagues characterized the oral fungal microbiome, which they refer to as the "mycobiome," by studying the oral cavities of 20 healthy individuals using a Multitag Pyrosequencing approach. They report in PLoS Pathogens that the most frequent species present were from the Candida genera, followed by Cladosporium, Aureobasidium, and others. Four of predominant genera are pathogenic in humans, the researchers note. "Understanding the relationships between different fungal species as well as between fungi and other members of the oral microbiome will shed light on the pathogenicity of these organisms and may lead to the discovery of novel therapeutic approaches for the prevention and treatment of oral complications," they write.

Italian researchers write in PLoS Biology that they used ultradeep sequencing to study the genomic instability of people with hereditary non-polyposis colorectal cancer. They show that genomic instability may be detected in non-neoplastic tissues from the HNPCC patients, as compared to controls. "The depth of coverage that we reached allowed us to detect genomic instability in neoplastic as well as in nonneoplastic HNPCC samples, offering the first, to our knowledge, evidence of constitutional genomic instability of these individuals," the authors write.

After infecting Drosophila melanogaster with Serratia marcescens, Providencia rettgeri, Enterococcus faecalis, and Lactococcus lactis, researchers led by Andrew Clark looked at the expression of immune system genes as it correlated to the flies' bacterial load. They found an association between bacterial load and genetic variants in genes encoding proteins involved in microbial recognition. "Interactions among genes need to be taken into account when assessing the phenotypic consequences of genetic variation, as signaling cascades such as those in the immune response have the potential to amplify the phenotypic effects of minor genetic variation in individual genes," the researchers add.

The Scan

Suicidal Ideation-Linked Loci Identified Using Million Veteran Program Data

Researchers in PLOS Genetics identify risk variants within and across ancestry groups with a genome-wide association study involving veterans with or without a history of suicidal ideation.

Algorithm Teases Out Genetic Ancestry in Individuals at Biobank Scale

Researchers develop an algorithm known as Rye to tease apart ancestry fractions in admixed individuals at a biobank-scale, applying it to 488,221 UK Biobank participants in Nucleic Acids Research.

Multi-Ancestry Analysis Highlights Comparable Common Variants at Complex Trait-Linked Loci

Researchers in Nature Genetics examine common variants implicated in more than three dozen conditions, estimating genetic effect similarities across ancestry tracts in admixed individuals.

Sick Newborns Selected for WGS With Automated Pipeline

Researchers successfully prioritized infants with potential Mendelian conditions for whole-genome sequencing or rapid whole-genome sequencing, as they report in Genome Medicine.