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Genomics in the Journals: Jun 26, 2014

NEW YORK (GenomeWeb) – In Nature Genetics, researchers from Singapore, the US, and Japan outlined the recurrent protein-coding mutations they detected in nasopharyngeal cancer through whole-exome sequencing, targeted sequencing, transcriptomics, and SNP-based copy number analyses. The cancer, which affects epithelial tissue in the nasal passage and pharynx, is known to occur at higher-than-usual rates in southern China, parts of Southeast Asia, and northern Africa, they noted.

To better understand its genetics, the team started by doing exome sequencing on matched tumor and normal samples from 56 individuals with nasopharyngeal cancer and on five cell lines developed from other tumor samples. For all but six of the primary tumor samples, the investigators used arrays to assess copy number patterns — an approach they applied to two non-sequenced tumor samples as well. They also did RNA sequencing on four tumors to get a glimpse of nasopharyngeal cancer gene expression patterns.

After targeted sequencing on the possible cancer driver genes in 61 more matched tumor-normal samples and five nasopharyngeal cancers for which corresponding control samples weren't available, the investigators were left with nine recurrently mutated genes.

The data also revealed recurrent glitches in chromatin modification pathways, along with pathways involved in autophagy and cell signaling. These "pathway derangements" pointed to possible treatment targets, the study authors argued, noting that drugs targeting ERBB-PI3K pathway components are already being tested in other cancer types.


In another study appearing in Nature Genetics, the Wellcome Trust Sanger Institutes' Stephan Schiffels and Richard Durbin applied a new computational method to explore long-term human population histories.

The approach — known as the multiple sequentially Markovian coalescent, or MSMC model — was designed to discern not only extremely old population separations, but also those occurring within the past 20,000 to 30,000 years, a period that's tricky to see with other population analysis methods such as the pairwise sequential Markovian coalescent (PSMC) model.

Using MSMC to assess mutations from multiple members of nine modern-day human populations, the researchers were able to get a sense of historical population sizes and scaled splits for these populations. With the help of mutation rate and generation time data, for example, they saw a split between non-African and Yoruba African populations going back more than 100,000 years.

Though they noted that ancient population structures within Africa may complicate this picture, the study authors argued that such findings seem to agree with patterns predicted from mitochondrial sequence data.


A PLOS One study suggests Neanderthals may have consumed somewhat more plant material than previously believed. Researchers from Spain and the US used gas chromatography and mass spectrometry approaches to scrutinize compounds present in 50,000-year-old fecal samples from Neanderthals living at a site called El Salt in Spain.

The team tested five different sediment samples taken at various levels at the El Salt site. Along with compounds produced by the gut bacteria that help break down cholesterol, the analysis uncovered metabolites that seem to correspond with digestion of plant material.

While the available data indicated that Neanderthals mainly consumed meat, authors of the study argued that the results are consistent with consumption of at least some vegetables or other plants by Stone Age human relatives.

"[O]ur results … have implications regarding digestive systems and gut microbial evolution," they wrote, noting that additional studies will help in interpreting the current results within a larger framework of human evolution.


Considering mutation rates at loci used for variable number tandem repeat testing can help in determining whether strains of the foodborne pathogen Salmonella enterica Typhimurium are involved in a given outbreak, according to a study in the Journal of Bacteriology.

A group of Australian researchers took a closer look at five sites in the S. Tymphimurium genome that are commonly used for multi-locus variable number tandem repeat analysis (MLVA).

Based on MLVA profiles for bugs generated by passaging a single isolate over tens of thousands of generations in the lab — together with MLVA profiles and/or genome sequence information on hundreds more Tasmanian isolates and an isolate grown in mice — the researchers determined that three of the loci are prone to mutation during the passage process.

Consequently, they argued that variation at one of the three loci may appear in isolates that have stemmed from the same transmission cluster. Still, their findings also highlighted the high level of stability present at the five MLVA sites over as many as 1,000 passages, suggesting lab-induced mutation is unlikely to interfere with analyses of isolates from a given source.

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