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Genomics In The Journals: Mar 22, 2012

NEW YORK (GenomeWeb News) – Two independent teams have published studies in Nature Genetics implicating the SWI/SNF chromatin-remodeling complex in a developmental condition known as Coffin-Siris syndrome.

For the first of these, a group from the Netherlands tracked down de novo truncating mutations in ARID1B through exome sequencing experiments on five individuals, including one affected parent-child trio and two unrelated individuals with CSS. The investigators found ARID1B mutations in the exomes of all three affected individuals. When they went on to do array-based screening for copy number alterations in 2,000 more individuals with intellectual disability, the investigators found three individuals with deletions affecting the ARID1B gene, which codes for a SWI/SNF complex sub-unit.

In another Nature Genetics study, researchers from Japan and the US found mutations in ARID1B, as well as five other SWI/SNF complex sub-unit genes, contributing to CSS. That team initially detected de novo mutations in the SMARCB1 gene in two of the five CSS cases that they tested by exome sequencing. When they subsequently screened 23 more individuals with the condition, focusing on 15 genes coding for SWI-SNF complex components, that team found another 20 affected individuals who had germline mutations affecting ARID1A, ARID1B, SMARCB1, SMARCA2, SMARCA4, or SMARCE1.

A BMC Evolutionary Biology study of mouse mitochondrial DNA phylogeny has found further evidence that centuries old house mouse migration patterns in the North Atlantic mirror those of Norwegian Vikings.

Past studies have shown that Vikings carried mice from specific clades with them when they colonized parts of the British Isles in the 8th to 10th century. Now, an international team has used mitochondrial haplotype patterns found using ancient mouse samples to show that this occurred in other areas as well. For instance, their results suggest that mice originating in Norway moved into Iceland in around the 10th century and have been there ever since. On the other hand, it seems mice that were introduced to Greenland via Viking travels have since become extinct and replaced by a mouse clade from Denmark belonging to a different sub-species.

The researchers did not see signs of mice introduced by Vikings at early settlements in Newfoundland, Cornell researcher Jeremy Searle, the study's senior author, explained in a statement. "We found no evidence of house mice from the Viking period in Newfoundland. If mice did arrive in Newfoundland, then like the Vikings, their presence was fleeting and we found no genetic evidence of it."

Norwegian and German researchers who developed software called LDsnpR for linking SNPs to genes based not only on their actual location but also on pairwise linkage disequilibrium patterns argue that this sort of SNP binning influences the information that can be gleaned from genome-wide association studies. As they report in the American Journal of Human Genetics, the group found that including linkage disequilibrium-based SNP binning information altered the way genes were ranked when using non-imputed and imputed data from some published bipolar disorder studies.

Based on their analyses, the study's authors concluded that "ignoring [linkage disequilibrium] can result in the misinterpretation of the GWAS findings and have an impact on subsequent genetic and functional studies."

University of Minnesota law professor and bioethicist Susan Wolf and co-authors from several sites in the US and Canada address the return of participant research results and incidental findings for genomic analyses done using biobank or other archived data in Genetics in Medicine. The group set out a list of 10 recommendations for new and existing biobanks that stemmed from a two-year, National Institutes of Health-funded analysis. They argue that biobanks need to consider issues surrounding incidental findings and individual result return at each stage of the biobanking process. In situations where participants can be re-identified, the team explained, that may mean coming up with a system for communicating validated and clinically actionable information to biobank participants, even when the findings fall outside of the specific focus of a given study.

"We suggest that findings that are analytically valid, reveal an established and substantial risk of a serious health condition, and are clinically actionable should generally be offered to consenting contributors," Wolf and her colleagues wrote.

"Considering the entire biobank research system is essential, including the three major actors: primary researchers or collection sites, the biobank itself, and secondary researchers," they concluded. "All have the potential to generate returnable [incidental findings] and [individual research results]."

A team from Singapore, the UK, and the US has shown that knocking out a gene called TRIM28 in mouse eggs has a dramatic effect on the epigenetic patterns that occur during the so-called oocyte-to-embryo transition after fertilization — work that they describe in Science. Though mouse zygotes formed from normal sperm cells combined with maternal germ line cells lacking TRIM28 start expressing the paternal version of the gene at the four-cell stage, researchers reported, embryos don't develop normally without maternal copies of the gene.

"Our findings illustrate the exquisite temporal and spatial balance between maternal and zygotic factors in the early embryo that are required to maintain epigenetic states," corresponding author Daniel Messerschmidt, from Singapore's Institute of Medical Biology, and colleagues wrote. "Perturbing this balance can cause a wide spectrum of phenotypic variability."

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

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