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Genomics in the Journals: Feb 6, 2014

NEW YORK (GenomeWeb News) – In Nature Genetics, a UK-led group described the diverse mutation patterns it detected within and between tumors from 10 individuals with the kidney cancer clear cell renal carcinoma.

By using multi-region exome sequencing to assess patients' tumor and matched normal samples, the researchers determined that intra-tumor heterogeneity is widespread in ccRCC, turning up in all 10 tumors tested and increasing as more and more biopsies from the same tumor were analyzed.

As many as three-quarters of ccRCC driver mutations are present in just a subset of clones within each tumor, the team found. Even so, one gene was mutated with particular frequency: in all 10 tumors, VHL gene alterations appeared at the "trunk" of phylogenetic trees constructed to consider the mutational relationships between sub-clones. Chromosome 3 losses were also ubiquitous amongst the tumors.

A comparison of sub-clones from each tumor also highlighted the shift in mutation process at play as ccRCC tumors persist and progress, the study's authors noted, explaining that "sub-clonal driver events in solid tumors may provide an explanation for the inevitable acquisition of resistance to targeted therapeutics in advanced disease."

"The regional isolation of tumor clades in ccRCC, together with extensive evidence of parallel evolution of tumor sub-clones, raises important questions regarding how tumors can be optimally sampled," they added, "and whether future evolutionary tumor branches might be predictable and ultimately targetable."

A new strain of influenza A has turned up in China over the past few months, according to a paper published in the Lancet. Chinese researchers used RT-PCR and Sanger sequencing to type and characterize a flu virus isolate collected from a 73-year-old woman who was admitted to a hospital in China's Jiangxi province in late November of last year and died shortly after.

Their results indicated that the virus, a new form of influenza A H10N8 known as JX346, is comprised of various reassorted avian influenza A genes.

For instance, its haemagglutinin gene belongs to a Eurasian flu lineage and shares features with a H10N3 strain previously detected in ducks. On the other hand, the virus' neuraminase gene was from a North American avian lineage and resembled influenza H10N8 and H3N8 strains detected in Korea and Japan, respectively. Meanwhile, its internal genes shared features with an influenza A H9N2 strain believed to be circulating in Chinese poultry.

The case described in the study represents the first reported instance of human infection by an avian influenza A H10N8 strain, the study's authors noted, though a second case has been detected since the paper was submitted. Mutations in the virus' PB2 gene are suspected of helping it infect humans and other mammals.

"A second case of H10N8 was identified in Jiangxi Province, China on January 26, 2014," co-author Mingbin Liu, with Nanchang City Center for Disease Control and Prevention, noted in a statement. "This is of great concern because it reveals that the H10N8 virus has continued to circulate and may cause more human infections in the future."

Members of a large team of researchers from around the world used permafrost soil sequencing to take a look back at the plants that inhabited sites in the Artic over the past 50,000 years or so — work they reported in Nature.

The team did mass spectrometry-based radiocarbon dating on 242 permafrost samples collected at more than 20 Arctic sites, using targeted, trnL plastid gene and internal transcribed spacer sequencing to look back at the plant life at the locales over several stretches of time: from 25,000 to 50,000 years ago (in the period before the Last Glacial Maximum), during the LGM itself, which occurred between 15,000 and 25,000 years ago, and in the 15,000 years since the LGM.

The DNA barcoding data indicated that protein-dense, non-grassy, herbaceous vascular plants known as forbs were the most common plant type in the Arctic through the LGM and up until roughly 10,000 years ago, when grasses, sedges, and rushes — together called graminoids — as well as woody plant types became more dominant.

By adding in a DNA-based analyses of ancient coprolite samples and nematode worm communities in present-day soils, investigators were able to get new clues about the ancient diets of large animals, or "megafauna," such as woolly mammoths, woolly rhinos, bison, and horses that once lived in the region.

"Our analyses indicate that both graminoids and forbs would have featured in megafaunal diets," researchers wrote, noting that "a diet rich in forbs may help to explain how numerous large animals were sustained; forbs may be more nutrient-rich and more easily digested."

A Current Biology study outlined findings from a genome sequencing study of the clonal raider ant, Cerapachys biroi, a species that organizes itself in colonies mainly comprised of asexual worker ants with no queen.

Researchers based in the US, Denmark, and China used a combination of Illumina and Roche 454 sequencing to tackle the ant's genome, generating sequence that they used to put together a 214 million base genome assembly.

Together with transcriptome sequences generated for tissues from ants at various stages of development and social behavior, the genome sequence made it possible for the team to annotate nearly 17,300 predicted protein-coding genes. That set included genes resembling those implicated in labor roles in other social insects, the group noted.

Additional cytological and restriction site-associated sequencing experiments also helped in untangling the asexual ant's automixis-based mode of reproduction and factors influencing its sex determination, study authors reported, noting that "the unique biology of C. biroi makes the species a promising new model system to study the molecular underpinnings of social evolution and behavior."