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This Week in PNAS: Dec 29, 2010

In this week's PNAS Early Edition, the Broad Institute's David Jaffe and his colleagues describe ALLPATHS-LG, a genome assembly algorithm that uses data from massively parallel sequencers. Using ALLPATHS-LG on Illumina data, Jaffe et al. found that their assembly accuracy was higher than that achieved with capillary-based sequencing.

In another PNAS paper published online in advance this week, researchers at Switzerland's University of Basel show that the ultraconserved RNA 338 is aberrantly expressed in a both murine and human hepatocellular carcinoma cell lines, and suggest that its associated 590-base pair RNA gene, TUC338, may play a role in the pathobiology of hepatocellular carcinoma. Transcribed ultraconserved non-coding RNAs, the authors write, represent "a unique class of genes involved in [hepatocellular carcinoma]."

A team led by investigators at the National Institute of Allergy and Infectious Diseases reports that "genetic susceptibility to systemic lupus erythematosus protects against cerebral malaria in mice" in PNAS this week. As immune mechanisms appear to protect lupus-prone mice during parasitic infections – due to "a deficiency in FcγRIIB or overexpression of Toll-like receptor 7" – these animals show improved survival in malarial infections, the authors write.

Researchers at the University of New Mexico School of Medicine and their collaborators show that "methylation of histone H3 lysine 36 enhances DNA repair by non-homologous end-joining." More specifically, when screening for histone methylation post-DNA double-strand break induction using ionizing radiation, the team identified H3K36me2 as "the major event." In human cell system experiments, the researchers saw that "the DNA repair protein Metnase ... localized to an induced DSB and directly mediated the formation of H3K36me2 near the induced DSB." H3K36 dimethylation "improved the association of early DNA repair components, including NBS1 and Ku70, with the induced DSB and enhanced DSB repair," the authors write.

The Scan

Genetic Risk Factors for Hypertension Can Help Identify Those at Risk for Cardiovascular Disease

Genetically predicted high blood pressure risk is also associated with increased cardiovascular disease risk, a new JAMA Cardiology study says.

Circulating Tumor DNA Linked to Post-Treatment Relapse in Breast Cancer

Post-treatment detection of circulating tumor DNA may identify breast cancer patients who are more likely to relapse, a new JCO Precision Oncology study finds.

Genetics Influence Level of Depression Tied to Trauma Exposure, Study Finds

Researchers examine the interplay of trauma, genetics, and major depressive disorder in JAMA Psychiatry.

UCLA Team Reports Cost-Effective Liquid Biopsy Approach for Cancer Detection

The researchers report in Nature Communications that their liquid biopsy approach has high specificity in detecting all- and early-stage cancers.