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This Week in Genome Biology: Oct 5, 2016

German and Swiss researchers describe apparent ties between rare CNVs and gene signatures associated with survival in human cancer in Genome Biology. Starting with expression and copy number data for 768 cancer cell lines from the Cancer Cell Line Encyclopedia, the team came up with a so-called cancer cell transcriptional regulatory network model that was subsequently used to drill down into copy number alteration interactions with survival signature genes in tumors from half a dozen tissue types. Based on these analyses, the investigators argue that survival predictions may be improved by including some copy number interactions, though they note that "rare patient-specific [copy number alterations] often have stronger effects on signature genes than frequent gene [copy number alterations]."

A team led by investigators at the US Department of Agriculture's Agricultural Research Service presents findings from a new draft genome assembly for the Mediterranean fruit fly, Ceratitis capitata. Using DNA from inbred adult C. capitata flies, also known as medflies, the researchers sequenced and assembled a 479-million-basepair genome assembly that contained 14,162 protein-coding genes, more than 100 pseudogenes, and almost 23,100 messenger RNA transcripts. With the help of RNA sequencing and comparative proteomics, they also detected apparent expansions in gene families involved in chemoreception, insecticide response, and other processes that may contribute to medfly invasiveness and interactions with the fruits and vegetables it infests.

Finally, researchers from the UK, US, Germany, and Belgium explore components of the fecal microbiome that may correspond to visceral fat patterns in thousands of twins from the TwinsUK cohort. The team profiled members of gut microbial communities using 16S ribosomal RNA sequence data on fecal samples from 3,666 twins who had been measured for several adiposity traits. As in past studies, investigators saw diminished microbial diversity in gut microbiomes of heavier individuals. But their analysis hinted that particular adiposity phenotypes such as visceral fat patterns may be linked to distinct gut microbial patterns that may be partly mediated by host genetics.