Editor's Note: Some of the articles described below are not yet available at the PNAS site, but they are scheduled to be posted some time this week.
In the early, online edition of the Proceedings of the National Academy of Sciences, an international team led by investigators at Cold Spring Harbor Lab and the University of Cambridge presents results from an effort to sequence the genome and transcriptome of the free-living regenerative flatworm Macrostomum lignano. Given the complex and repeat-rich nature of the sequence, the researchers put together two flatworm genome assemblies, one produced with short reads alone and another that included Pacific Biosciences single-molecule, real-time reads. With the help of transcript reads, they uncovered almost 20,000 protein-coding genes in the flatworm, while comparisons with nearly two dozen other species pointed to potential contributors to pluripotency and regeneration. GenomeWeb has more on the study, here.
A Korean group describes gastric cancer alterations that appear to influence tumor susceptibility to certain drugs. Using array comparative genomic hybridization, the researchers searched for recurrent copy number changes in tumor and normal samples from 103 individuals with gastric cancer. For 55 of these individuals, they also did exome sequencing to uncover tumor-associated mutations. Together, the results suggest that almost one-fifth of gastric cancer cases involved BCL2L1 amplifications that may respond to a BCL2L1 inhibitor. And almost 11 percent of the tumors contained DLC1 gene mutations that prompt activation of a Rho-ROCK signaling pathway, leading the study's authors to subject such cells to a ROCK inhibitor that appeared to curb cell growth.
Finally, researchers from Cold Spring, the New York Genome Center, and Albert Einstein College of Medicine explore transmission patterns for disruptive de novo mutations implicated in autism spectrum disorder. Based on existing whole-exome sequence data for thousands of children with ASD and their unaffected parents and/or siblings, the team found evidence that the ASD-related genes are less prone to disruptive mutations in general than other genes, suggesting they are under negative selection. Nevertheless, the analysis uncovered new details about transmission of genes with higher or lower 'likely gene-disruptive' loads, highlighting differences in mutational load in ASD-affected individuals at each end of the intelligence quotient spectrum.