The Wellcome Trust Sanger Institute's Michael Stratton and colleagues from centers around the world describe fusions involving mitochondrial and nuclear genes that they detected in cancerous or neoplastically transformed cells. Using genome sequence data for matched tumor and normal samples from 559 individuals, together with sequences from 28 cancer cell lines, the team found 25 examples of somatic mitochondrial transfer in the nucleus of a dozen tumor samples, producing mitochondrial-nuclear DNA fusions that tended to coincide with a rise in nuclear DNA rearrangements.
Genomic imprinting may play a relatively minor role in mediating tissue-specific gene expression levels, according to research by a New York Genome Center- and University of California, San Francisco-led team. The researchers assessed imprinting in nearly 1,600 tissue samples collected from 178 individuals enrolled in the Genotype Tissue Expression, or GTEx, project. Based on the allelic expression profiles present in samples from different tissue types, they found frequent signs of tissue- and gender-specific imprinting. But this imprinting appeared to have subtle effects on expression differences detected between tissues.
A team from the US and Spain introduce a database designed to improve metagenomic sequence searches and analyses in Genome Research. Using data from GenBank and the 1000 Genomes Project, the researchers put together a collection of extracted sequence that revealed reference-free human reads in shotgun metagenomic sequence data — an approach they demonstrated using samples from the Human Microbiome Project. "Left unidentified, human reads can complicate and slow down further analysis," the study's authors note, "and lead to inaccurately labeled microbial taxa and ultimately lead to privacy concerns as more human genome data is collected."