A Mayo Clinic-led team of investigators has developed a pipeline for individualized disease module construction, which they report in this week's Genome Research. The pipeline starts with the analysis of an individuals' protein-protein interactions, which are then annotated, examined for the shortest path between diseased genes and for disease activity, and compared against random distribution to yield a collection of significant paths that make up a person's individualized disease network. They applied their pipeline to a cohort of 90 breast cancer patients from the TCGA BRCA Project to find that the importance of cancer genes like TP53 and PIK3CA varies across patients and that a combinatorial screen could further identify target therapy genes for individual patients. "As the first analysis of de novo individualized disease modules, we illustrate the power of individualized disease modules for precision medicine by providing deep novel insights on the activity of diseased genes in individuals," Mayo's Hu Li and colleagues wrote.
Catherine Farrell from National Center for Biotechnology Information and her colleagues describe a new functional element dataset housed by the agency, called RefSeqFE. RefSeqFE contains experimentally validated data on gene regulatory elements, replication origins, genomic instability and recombination regions, and gene regulatory and recombination partner interactions within humans and mice. "The dataset has multiple uses, ranging from basic functional discovery, to genetic variant interpretation, to use as experimentally validated reference standards in multiple bioinformatic and epigenomic studies," Farrell and her colleagues write at Genome Research. "Furthermore, the activity-supported interactions can be used as reference standards for gene regulatory or recombination interaction."
A team from Germany and China has uncovered evidence within Schizosaccharomyces pombe that supports the "genomic shock hypothesis." That hypothesis says that hybridization could lead to the reawakening of transposable elements that were dormant in the parent lineages. The team here conducted long-read sequencing of 37 S. pombe samples representing 31 strains with a range of ancestral admixture proportions to characterize their repertoire of transposable elements. They found that the number of long terminal repeat retrotransposons varied widely, but were in concert with the degree of genomic admixture. "Our results are consistent with the idea that hybridization of two closely related S. pombe lineages, Sp and Sk (Dxy ~ 0.005), activated TE proliferation in the admixed genomes," they write.