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Genomics in the Journals: May 1, 2014

NEW YORK (GenomeWeb) – In Nature Genetics, researchers from Sweden, the UK, and the US explored the potential risks of losing the Y chromosome from a subset of cells circulating in peripheral blood.

By doing array-based genotyping on DNA isolated from peripheral blood samples, the team looked at the incidence — and apparent consequences — of age-related Y chromosome loss in more than 1,150 elderly men.

Researchers detected at least some chromosome Y loss in samples from more than 8 percent of the men tested in the original cohort. That lost Y chromosome mosaicism was associated with both a rise in non-hematological cancer risk and a decrease in mean survival time, they noted — a pattern that held in an independent cohort comprised of hundreds more, slightly younger, men.

"These results illustrate the impact of post-zygotic mosaicism on disease risk, could explain why males are more frequently affected by cancer, and suggest that chromosome Y is important in processes beyond sex determination," co-senior authors Lars Lind and Jan Dumanski, with Uppsala University, and their colleagues wrote, adding that "[loss of chromosome Y] in blood could become a predictive biomarker of male carcinogenesis."

Columbia University's Ian Lipkin and Abdulaziz Alagaili, from the King Saud University and the Saudi Wildlife Authority, led a team of researchers from the US and Saudi Arabia who traced the Middle East respiratory syndrome, or MERS, coronavirus back to a dromedary camel source.

As they reported in mBio, the researchers did direct or culture-based genome sequencing on MERS isolates from several dromedary camel nasal swabs in Saudi Arabia. Their sequence data revealed that the consensus sequence for the camel-carried form of MERS-CoV matches that involved in human infections in the region.

Even so, the team also saw evidence that human cases typically involve just one of the MERS-CoV genotypes present in dromedary camel populations, pointing to a potential bottleneck in the transmission of the virus from camels to humans.

That possibility was supported by preliminary experiments in cultured primate cells, where the study's authors saw infection by only a subset of the genetically diverse MERS-CoVs that they tested.

"The narrow range of MERS viruses in humans and a very broad range in camels may explain in part the why human disease is uncommon: because only a few genotypes are capable of cross-species transmission," first author Thomas Briese, associate director of Columbia University's Center for Infection and Immunity, said in a statement.

A Nature Communications study outlined an analytical tool for interpreting genetic information in light of an individual's ancestry and geographic locale. Researchers from the National Geographic Society's Genographic Consortium and elsewhere developed the Geographic Population Structure, or GPS, tool based on admixture analyses and existing genetic data for populations around the world.

In proof-of-principle analyses included in the paper, the team showed that the GPS tool could accurately trace individuals from three different datasets back to their geographic origin based on information at between 40,000 and 130,000 SNPs with more than 80 percent accuracy.

For individuals from Sardinia, for example, the study's authors applied GPS to match one-quarter of the more than 200 individuals tested back to a specific village of origin, while many more could be traced back to regions near the village where they were born.

"GPS's accuracy and power to infer the biogeography of worldwide individuals down to their country or, in some cases, village, of origin, underscores the promise of admixture-based methods for biogeography and has ramifications for genetic ancestry testing," they wrote.

Researchers from Brigham and Women’s Hospital, Harvard Medical School, the University of Chicago, and elsewhere did an expression quantitative trait locus analysis aimed at better understanding the consequences of carrying various immune gene alleles in cells from the adaptive and innate immune systems — work that they described in Science.

For experiments done through the Immune Variation, or ImmVar, project, the team did array-based gene expression profiling on T lymphocyte and monocyte cells purified out of blood samples from 461 healthy participants of African American, East Asian American, or European American ancestry.

Those cell types were selected to represent both adaptive and innate arms of the immune system, the study authors noted. Their results made it possible to narrow in on nearby and distant variants influencing the expression of genes in those cell types, including some eQTLs that were active in just one of the immune arms.

In the T cells, for example, the researchers saw that cell type-specific eQTLs often involved alleles implicated in autoimmune conditions such as multiple sclerosis, rheumatoid arthritis, and type 1 diabetes. In contrast, alleles associated with Alzheimer's disease and Parkinson's disease appeared more apt to overlap with monocyte-specific eQTLs, they reported.

"This study extends the narrative that many of the effects of disease-related genetic variation are specific to a certain context, such as a given immune cell type," the University of Chicago's Barbara Stranger, a senior author on the study, said in a statement. "Thus, it is clear that further studies must investigate an increasingly complex matrix of cell types and conditions to fully understand the role of human genetic variation in disease."