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This Week in PLoS: Mar 29, 2010

In PLoS One this week, researchers from six US institutions report the results of their genome-wide association study that identifies GPC5 as a novel genetic locus that is protective against sudden cardiac arrest. Using a case-control design with participants from the Oregon Sudden Unexpected Death Study, and, while no SNPs identified reached genome-wide significance, the minor allele of GPC5 showed an association with a lower risk of SCA. "In a combined Cox proportional hazards model analysis that adjusted for race, the minor allele exhibited a hazard ratio of 0.85," the authors write. The team validated the association of GPC5 in two other cohorts, though they write that the mechanism behind the observed association will require further investigation.

A team of investigators describes their approach for predicting transcription factor binding sites in mammalian regulatory networks in PLoS One this week. By integrating existing methods for "regulatory network reverse engineering from mRNA expression data, linearly and non-linearly conserved regulatory region discovery, and [transcription factor binding site] TFBS evaluation and discovery," the authors constructed a test set of high-likelihood interactions in order to create realistic prediction-accuracy estimates. They biochemically validated TFBS predictions made for transcription- and co-factors using a known binding motif.

Researchers in the UK present evidence for large, complex networks of short silencing RNAs in plants; they developed a network by predicting targets of ssRNA populations derived from high-throughput sequencing experiments and also identified protein families that act as "hubs" within it. "Comparison of the repetition of genomic sub-sequences of ssRNA length between Arabidopsis and E.coli suggest that the network structure is made possible by the underlying repetitiveness in the genome sequence," the authors write, adding that their results elicit the existence of a robust ssRNA interaction network that could have a "massive effect on the regulation of gene expression via mediation of transcript levels."

In PLoS Computational Biology, an international research team reports their elucidation of a human-specific de novo protein-coding gene that is associated with human brain functions. Using a computational approach that gleaned data from various genome-wide association studies and linkage analyses of nicotine addiction, the team deciphered FLJ33706 as human-specific; using real-time PCR and other methods, they verified the gene's mRNA and protein expression in the brain. The team's immunohistochemical evaluation in normal human brain cortex showed that the FLJ33706 protein is localized in neurons. "FLJ33706 provided the strongest evidence so far that human-specific de novo genes can have protein-coding potential and differential protein expression, and be involved in human brain functions," the authors say.

The Scan

Ancient Greek Army Ancestry Highlights Mercenary Role in Historical Migrations

By profiling genomic patterns in 5th century samples from in and around Himera, researchers saw diverse ancestry in Greek army representatives in the region, as they report in PNAS.

Estonian Biobank Team Digs into Results Return Strategies, Experiences

Researchers in the European Journal of Human Genetics outline a procedure developed for individual return of results for the population biobank, along with participant experiences conveyed in survey data.

Rare Recessive Disease Insights Found in Individual Genomes

Researchers predict in Genome Medicine cross-population deletions and autosomal recessive disease impacts by analyzing recurrent nonallelic homologous recombination-related deletions.

Genetic Tests Lead to Potential Prognostic Variants in Dutch Children With Dilated Cardiomyopathy

Researchers in Circulation: Genomic and Precision Medicine found that the presence of pathogenic or likely pathogenic variants was linked to increased risk of death and poorer outcomes in children with pediatric dilated cardiomyopathy.