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This Week in Genome Biology: Dec 16, 2009

In Genome Biology this week, University of Tartu scientists present MEM, or Multi-Experiment Matrix, a web-based tool to search for co-expressed genes across many microarray datasets. Unique features include "automatic detection, characterization and visualization of datasets that includes the strongest co-expression patterns." MEM is available for free.

In a new methods paper, scientists search for genetic interactions in Saccharomyces cerevisae. Igor Ulitsky and Ron Shamir at Tel Aviv University and the University of California, San Francisco's Nevan Krogan have developed a novel method that combines genetic interaction and genomic data to find the approximately 40 percent missing interactions in this model organism. Their results showed almost 190,000 novel interactions.

Scientists led by Jacobs University Bremen's Albert Jeltsch have studied the effect of DNA methylation on autosomal chromosomes and its subsequent effect on phenotypic differences. Looking at methylation of CpG islands on chromosome 21 in white blood cells from healthy people, they saw "novel cases of pronounced differential methylation of alleles," and that this allele-specific methylation is likely to affect about 10 percent of all genes and contribute to allele-specific expression and monoallelic gene silencing, they say.

Scientists have found that assortative mating, or the tendency of two people who share similar ancestry to mate, still persists in Latino populations and has an effect on genomic structure. In a study using 104 "ancestry markers" led by first author Neil Risch at the University of California, San Francisco, they found that in Mexican spouse pairs from Mexico City and the San Francisco Bay Area, there were strong spouse correlations for European and Native American ancestry, but no correlation in African ancestry, they say. In the Puerto Rican pairs sampled from couples from Puerto Rico and New York City, they found spouse correlations for African ancestry and European ancestry but not Native American ancestry. "Ancestry variance is predicted to decline in each generation, but less so under assortative mating," they write. "We used the current observed variances of ancestry to infer even stronger patterns of spouse ancestry correlation in previous generations."

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.