In PLoS Biology this week, investigators at China's BGI describe "the DNA methylome of human peripheral blood mononuclear cells" from the same Han Chinese individual whose genome the institute published in Nature in 2008. Using whole-genome bisulfite sequencing, the team "found that 68.4 percent of CpG sites and [less than] 0.2 percent of non-CpG sites were methylated" in the PBMC sequence. In addition, the BGI team reports "20 distinct genomic features" of the PBMC epigenome — "including regulatory, protein-coding, non-coding, RNA-coding, and repeat sequences," and allele-specific methylation, which they identified by integrating data from the individuals' PBMC methylome and whole genome.
Researchers at Australia's University of Adelaide and their colleagues report in PLoS Biology that they cloned and sequenced the ancient mitochondrial DNA of 21 individuals from a Linear Pottery Culture — "5,500-4,900 calibrated B.C." — graveyard in Germany. Using their own "SNP multiplex PCR systems to generate new mitochondrial and Y-chromosomal data," as well as published data for Western Eurasian populations, the Adelaide-led team found "that the LBK population shared an affinity with the modern-day Near East and Anatolia, supporting a major genetic input from this area during the advent of farming in Europe," though it also showed "a clearly distinct distribution of mitochondrial haplogroup frequencies" from other early Neolithic populations.
In PLoS One this week, Norwegian researchers show that there are "distinct genetic differences" between colorectal cancer tumors from young and elderly patients. More specifically, in patients under 50, the researchers found no PIK3CA mutations and more frequent TP53 mutations than in older CRC patients. Although the "total gene mutation index was lowest in tumors from the youngest patients," the authors write, "the genome complexity, assessed as copy number aberrations, was highest in tumors" from this group. Based on their tumor mutation characterizations, the researchers suggest that "mutation testing for prediction of EGFR treatment response may be restricted to KRAS and BRAF" in CRC patients over 70.
In another paper published in PLoS One this week, a team led by investigators at the University of Illinois, Urbana-Champaign, reports its characterization of the fecal microbiomes of three different non-human primates, which "revealed that the gut microbiota of these primates are distinct and reflect host phylogeny." The researchers suggest that in addition to dietary influences, the fecal microbiomes of wild primates could be species specific. They add that their study provides the "framework for comparative microbiome analysis between human and non-human primates as well as a comparative evolutionary understanding of the human microbiome."