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This Week in Nature: Dec 12, 2013

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."

The Scan

Positive Framing of Genetic Studies Can Spark Mistrust Among Underrepresented Groups

Researchers in Human Genetics and Genomics Advances report that how researchers describe genomic studies may alienate potential participants.

Small Study of Gene Editing to Treat Sickle Cell Disease

In a Novartis-sponsored study in the New England Journal of Medicine, researchers found that a CRISPR-Cas9-based treatment targeting promoters of genes encoding fetal hemoglobin could reduce disease symptoms.

Gut Microbiome Changes Appear in Infants Before They Develop Eczema, Study Finds

Researchers report in mSystems that infants experienced an enrichment in Clostridium sensu stricto 1 and Finegoldia and a depletion of Bacteroides before developing eczema.

Acute Myeloid Leukemia Treatment Specificity Enhanced With Stem Cell Editing

A study in Nature suggests epitope editing in donor stem cells prior to bone marrow transplants can stave off toxicity when targeting acute myeloid leukemia with immunotherapy.