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This Week in Genome Research: Jun 10, 2009

This week in Genome Research, scientists at the University Hospital Regensburg in Germany have used a "novel approach that is based on the separation of a genome into methylated and unmethylated fractions" to scan for differential DNA methylation in human conventional CD4+ T cells and CD4+CD25+ regulatory T cells. They found more than 100 differentially methylated regions in mostly cell-type specific genes, the majority of which were found at promoter-distal sites. These sites also were found to have differential patterns of histone H3 lysine 4 methylation.

A consortium has published the collaborative consensus coding sequence (CCDS) project. In trying to identify the complete protein-coding set for the human and mouse reference genomes, the work, led by NCBI's David Lipman, identified 20,159 human and 17,707 mouse consensus coding regions from 17,052 human and 16,893 mouse genes.

Lead author Evan Eichler and his team have published a method for rapid, targeted CNV genotyping for rare variants in neurocognitive disease. Using the Illumina BeadXpress SNP genotyping assay and a customized algorithm, the Snp-Conditional OUTlier detection (SCOUT), they were able to detect both rare and common CNVs in large sample collections. The method, they say is "customizable, cost-effective, highly parallelized, and largely automated," and was able to identify known pathogenic variants and potentially pathogenic rearrangements in a large sample size of children with intellectual disability.

Jinchuan Xing at the Eccles Institute of Human Genetics at the University of Utah was first author on a paper that looked at more than 8,000 structural variants to identify mobile element-associated SVs as small as 100 bp and specific to the HuRef genome. The scientists found 706 mobile element insertions and 140 mobile element-associated deletions. This first look genome-wide showed that 10 percent of the HuRef-specific indels larger than 100 bp are caused by mobile element-associated events, they say in the abstract.