In a paper published online in advance in Genome Research this week, investigators at Washington University in St. Louis report on a method to characterize complex biomes based on in silico karyotyping, with which researchers are able to analyze "a defined representation of all DNA present in a sample." Biome representational in silico karyotyping, or BRISK as the team calls it, uses massively parallel sequencing on 27-mer DNAs per sample to deduce high-resolution karyotypes. With those, researchers can identify "multiple species within a biome." When the team applied BRISK to the biome of human oral mucosa, it found that more than 25 percent of DNA recovered was non-human. The authors add that their "application of BRISK to archival tissue from a nasopharyngeal carcinoma resulted in identification of Epstein-Barr virus infection," which they say substantiates the method's potential use in pathogen discovery.
In another advance online publication, industry researchers describe a "novel next-generation sequencing-based physical mapping technology for construction of bacterial artificial chromosome contigs of complex genomes." This whole-genome profiling approach, the authors write, allows researchers to generate maps for complex plant genomes and "will serve as excellent scaffolds to anchor genetic linkage maps and integrate whole genome sequence data."
A public-private research collaboration between investigators at Signature Genomics and the Cleveland Clinic report in Genome Research this week on the "recurrence, submicroscopic complexity, and potential clinical relevance of copy gains detected by array CGH that are shown to be unbalanced insertions by FISH." When the team found "cryptic, submicroscopic duplications ... at or near the insertion sites in two patients," which they say confounded its clinical interpretation of them, it used FISH, linear amplification, and array-CGH to find them to be, in general, benign alterations. In this way, the team says that duplications such as these can "result in a clinically relevant outcome through the disruption of a gene," and as such, they compel researcher to use "FISH to determine whether copy-number gains detected by array CGH represent tandem duplications or unbalanced insertions."
Investigators at University College London and elsewhere this week report their use of MeDIP-seq to comparatively analyze the methylomes of malignant peripheral nerve sheath tumors, benign neurofibromas, and normal Schwann cells. The team found a "complex landscape" of methylation alterations among the three, and show that "genes associated with CGI shore cDMRs [cancer-associated differentially methylated regions] was able to discriminate between disease phenotypes."