In this week's Nature, researchers from Washington University report on the discovery of a new genetic risk variant for Alzheimer's disease. The team conducted whole-exome sequencing on DNA from 29 affected individuals and 11 unaffected people, from 14 families with histories of late-onset Alzheimer's disease. It discovered a rare variant in the phospholipase D3, or PLD3, gene that was associated with a significantly greater risk of the disease. Cell culture testing showed that higher levels of the PLD3 protein reduced amyloid-beta, which accumulates in the brains of Alzheimer's disease patients, whereas lower levels of PLD3 increased amyloid-beta.
GenomeWeb Daily News has more on this study here.
Meanwhile, in Nature Methods, investigators from the University of Toronto highlight the presence of DNase I cleavage bias in transcription factor footprint identification. The sequencing of DNase I hypersensitive sites, or DNase-seq, is widely used to identify cis-regulatory elements across the genome. In an analysis of genome-wide binding sites of 36 transcription factors, the group found that footprinting data from DNase-seq was informative for some of them, but uninformative for many others. The researchers determined that "intrinsic DNase I cutting biases, a factor that had not been adequately accounted for in previous footprinting studies, can be incorrectly interpreted as patterns induced by TF binding."