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This Week in PNAS: Oct 27, 2015

Editor's Note: Some of the articles described below are not yet available at the PNAS site, but they are scheduled to be posted some time this week.

In the early, online edition of the Proceedings of the National Academy of Sciences, researchers from the US and the UK describe findings from an effort to sequence the mitochondrial genomes of two Pleistocene era infants found in what is now Alaska. The team did targeted capture-assisted Ion Torrent sequencing on mitochondrial DNA in two samples obtained from central Alaska's Upward Sun River Site, each believed to be roughly 11,500 years old. When they compared hypervariable mitochondrial sequences to one another and to existing mitochondrial genomes, the study's authors found that the infants belonged to the C1b and B2 mitochondrial haplogroups, respectively, though neither coincided with mitochondrial lineages found in northern regions nowadays. "The ancient mitochondrial genomes of the two contemporaneous Upward Sun River infant burials provide an important anchor between modern patterns of genetic variation and the inferences that may be drawn from retrospective population genetic analyses," they write.

An American and German team did whole-genome sequencing on matched tumor and normal samples from a 59-year-old Hispanic man with an aggressive form of prostate adenocarcinoma, exploring the feasibility of finding individual driver genes using unbiased computational and experimental validation methods. Among the more than 4,800 single nucleotide variants, 867 copy number changes, 356 small insertions and deletions, and four structural glitches they detected in the tumor, the researchers narrowed in on a novel mutation in the tumor suppressor gene PTEN that appeared to boost the pro-tumor activity of the resulting protein product — a gain of function role they verified through subsequent cellular assays.

Human Longevity's J. Craig Venter and colleagues point out that library preparation methods can impact the taxonomic groups and microbial genes identified through metagenomic sequencing on human microbiomes. The group did a head-to-head comparison of microbial community patterns in human stool samples tested by metagenomic sequencing with the help of Illumina Nextera XT, TruSeq Nano PCR-free, KAPA Biosciences Hyper Prep PCR and KAPA PCR-free library prep kits. Analyses on the sequences uncovered distinct taxonomic representatives depending on the kit used and pointed variable error profile biases, read losses, and so on. Based on their analyses, the study's authors argued in favor of PCR-free approaches to diminish PCR-related bias and noted that "the inclusion of a known-input cell spike-in control provides accurate quantitation of organisms in clinical samples."