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Genomics in the Journals: Jan 17, 2013

NEW YORK (GenomeWeb News) – A pair of studies by independent research teams reporting in Nature Genetics has implicated fusions between the chromosome 12 genes NAB2 and STAT6 in rare tumors that affect mesenchymal tissue called solitary fibrous tumors.

In the first of these, a University of Michigan and Memorial Sloan-Kettering Cancer Center-led team found a NAB2-STAT6 fusion using whole-exome and transcriptome sequence data generated for a 44-year-old woman with SFT enrolled in the University of Michigan's clinical sequencing program, MI-ONCOSEQ. The same fusion — which brings together a transcriptional repressor-coding gene, NAB2, and STAT6, a gene that encodes a transcriptional activator — showed up in all 27 SFTs that the team subsequently subjected to transcriptome sequencing. Investigators' follow-up experiments in cell line experiments indicated that the newly found fusion spurs cell proliferation, in part, by activating an early growth response pathway.

"These studies establish NAB2-STAT6 as the defining driver mutation of SFT and provide an example of how neoplasia can be initiated by converting a transcriptional repressor of mitogenic pathways into a transcriptional activator," University of Michigan researcher Arul Chinnaiyan and the Memorial Sloan-Kettering Cancer Center's Cristina Antonescu, the study's co-corresponding authors, and their colleagues wrote.

The same fusion was identified in a whole-exome sequencing study by researchers at the Dana-Farber Cancer Institute, Harvard Medical School, the Broad Institute, and elsewhere. That group did exome sequencing on matched tumor and normal samples from 17 individuals with SFTs.

Along with broad chromosome 13 losses in half a dozen of the tumor exomes, that team tracked down more than 22 suspicious somatic mutations per tumor, on average. The investigators also saw seven tumors with NAB2-STAT6 fusions in their initial exome set. When they tested another 53 SFT samples, meanwhile, they found various forms of the NAB2-STAT6 fusion in more than half of the tumors.

A forensic SNP-profiling platform called HIrisPlex shows promise for getting a glimpse at the physical features from long-deceased individuals, according to a study in Investigative Genetics.

Researchers from Poland and the Netherlands extracted DNA from five contemporary bone samples and 21 tooth samples. The tooth set spanned some 800 years and included samples from individuals who died during World War II. Investigators tested each of the samples using HIrisPlex, which looks at two-dozen eye and hair color-related SNPs. Using this approach, they successfully profiled all 24 variants in 23 of the samples. One of these came from Wladyslaw Sikorski, a Polish general who died 70 years ago, the study authors noted. And the HIrisPlex-based approach correctly predicted that the long-dead military man had blue eyes and blond hair, bolstering their confidence in the approach.

"Our findings … highlight the HIrisPlex system as a promising tool in future routine forensic casework involving skeletal remains, including ancient DNA studies, for the prediction of eye and hair color of deceased individuals," corresponding author Wojciech Branicki, a researcher affiliated with Jagiellonian University in Kraków and Kraków's Institute of Forensic Research, and colleagues wrote.

The Max Planck Institute for Evolutionary Anthropology's Mark Stoneking and his colleagues uncovered genetic evidence of gene flow between India and Australia stretching back thousands of years. As they reported online this week in the Proceeding of the National Academy of Sciences, the researchers assessed data at almost 460,000 autosomal SNPs in more than 300 individuals. These included Aboriginal Australians, as well as representatives from populations in New Guinea, India, and Southeast Asia, and individuals with African, European, Chinese, or Gujarati Indian ancestry.

The team's results revealed signs of gene flow between populations in India and Australia going back some 4,230 years, refuting the notion that Australia remained genetically isolated between the continent's initial colonization and the arrival of European populations. The genetic findings were also consistent with shared ancestry for Australian, New Guinean, and the Philippine Mamanwa populations, which appear to have diverged from one another roughly 36,000 years ago, researchers reported. The ancestors of the three populations are believed to have been part of an early out-of-Africa migration via a southerly route.

"This finding supports the view that these populations represent the descendants of an early 'southern route' migration out of Africa," Stoneking said in a statement, "while other populations in the region arrived later by a separate dispersal."

An American Journal of Human Genetics study suggests click-speaking Khoisan populations in southern Africa once had more mitochondrial diversity than previously appreciated.

An international team led by investigators from the Max Planck Institute for Evolutionary Anthropology sequenced the mitochondrial genomes of 500 individuals from Botswana, Namibia, Zambia, and Angola, including representatives from 45 Khoisan populations or Bantu-speaking populations, which have traditionally been more agricultural. Analyses of this maternally inherited genetic information indicated that some individuals from Bantu populations — mainly those based in Zambia — carry a Khoisan-related mitochondrial haplotype that's found only rarely in present-day Khoisan populations. Those involved in the study suspect such patterns may reflect admixture between Bantu individuals and members of a now extinct sub-branch of the Khoisan mitochondrial lineage.

"This is a really important finding, because it demonstrates that we might be able to learn more about the peoples who inhabited sub-Saharan Africa before the Iron Age spread of Bantu-speaking agriculturalists, by studying relic lineages that were taken up by the agriculturalists through intermarriage with indigenous peoples," the study's senior author Brigitte Pakendorf, formerly based at the Max Planck Institute and now at a center in Lyon, explained in a statement."

Genomics In The Journals is a weekly feature pointing readers to select, recently published articles involving genomics and related research.