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Genomics In The Journals: Feb 10, 2011

By a GenomeWeb staff reporter

NEW YORK (GenomeWeb News) – St. Jude Children's Research Hospital researcher Mary Relling and her co-authors reported online in Nature Genetics that they have detected a pattern of genomic variation that's not only more common in individuals of Native American descent, but which coincides with risk of relapse in children afflicted with acute lymphoblastic leukemia — findings that they say may help explain some of the known ancestry-related differences in the survival rate for children with the disease.

"Ancestry-related differences in relapse risk were abrogated by the addition of a single extra phase of chemotherapy," they wrote, "indicating that modifications to therapy can mitigate the ancestry-related risk of relapse."

In a Journal of Clinical Investigation paper this week, an American research team reported that it found gene expression signatures in Plasmodium falciparum that occur when the malaria parasite infects pregnant women or children, respectively. Using a so-called not-so-random primer approach coupled with RNA sequencing, the researchers characterized expression patterns in parasites from patient samples, identifying at least a dozen genes that are more highly expressed when the parasite infects pregnant women and eight genes whose expression is ramped up when it infects children.

A California team published a study online in Nature describing their efforts to explain a known association between a so-called 'gene desert' on chromosome 9 and coronary artery disease. By looking at long distance interactions in the genome, they found nearly three-dozen enhancers in the chromosome 9 region, which has also been linked to type 2 diabetes. These enhancers help ramp up the expression of other genes, they found — activity that seems to get altered when certain variants are present in the region.

In another Nature paper, University of Rochester researchers Chenguang Gong and Lynne Maquat tracked down ties between Alu elements — repetitive sequences that have expanded in some primates, including humans — and long non-coding RNA activity. Their results suggest Alu elements and lncRNAs interact to influence the degradation of messenger RNAs in concert with Staufen-1 and other proteins.

"Previously, no one knew what Alu elements and long non-coding RNAs did, whether they were junk or if they had any purpose," Maquat said in a statement. "Now, we've shown that they actually have important roles in regulating protein production."

In its second installment of articles celebrating a decade of human genomics, Science features perspectives pieces by University of Pennsylvania bioethicist Arthur Caplan, Pacific Biosciences CSO Eric Schadt, BGI Executive Director Jun Wang, Decode Genetics President and CEO Kari Stefansson, Harvard University researcher Pardis Sabeti, Duke University researcher Charmaine Royal, University of Geneva researcher Emmanouil Dermitzakis, and Archbishop Desmond Tutu.

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

The Scan

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