In PLoS Genetics this week, researchers report that their combination of somatic and germline mutation analyses has revealed allelic selection of amplicons in glioblastoma. In examining the tumor and normal-tissue genomes of 178 glioblastoma patients from The Cancer Genome Atlas, the team found that "SNP alleles that are most significantly overrepresented in amplicons tend to occur in genes involved with regulation of kinase and transferase activity, and many of these genes are known contributors to gliomagenesis."
A trio of investigators at the Max-Planck Institute for Biochemistry describe their use of "large-scale and high-resolution proteomics combined with gene copy number analysis to investigate in a global manner to what extent these genomic changes have a proteomic output and therefore the ability to affect cellular transformation," in PLoS Genetics this week. Proteins encoded by amplified oncogenes tend to be overexpressed, the authors write, adding that the "regulation of biological processes and molecular complexes is independent of general copy number changes."
Over in PLoS One, researchers at Iowa State University "present an effective strategy for pursuing a systems biology approach that utilizes an evolutionary comparative framework between two model organisms, fly and mouse." The investigators set out to determine whether a "seed network derived from studies of retinal cell determination in the fly, Drosophila melanogaster" would be useful to identify "candidate genes for their role in mouse retinal development." Their study identified 46 genes correlated with the seed network members.
This week, PLoS added two new topics to PLoS Currents, "an open-access publication forum for the extremely rapid communication of new research findings, which minimizes the delay between submission and publication." In an introduction to PLoS Currents: Evidence on Genomic Tests, the Centers for Disease Control's Muin Khoury and his colleagues write that the new forum "is intended to complement other efforts to evaluate genomic applications, both ongoing and planned, by using carefully targeted approaches." The authors say that Evidence on Genomic Tests "will publish brief, structured summaries of essential evidence for the validity and utility of genomic tests," for an intended audience of genetics researchers, public health professionals, health care practitioners, and "decision-makers."