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This Week in PLoS: Jul 20, 2009

An interview with Pat Brown in PLoS Genetics this week takes a look at his role in developing microarrays, the creation of PLoS, and more. About his motivation behind open access publishing: "I want to LITERALLY overthrow the scientific publishing establishment," he says. "PLoS is just part of a longer range plan. The idea is to completely change the way the whole system works for scientific communication."

Also in PLoS Genetics, scientists performed the first GWAS for hypertension and blood pressure in an African American population, "a population group in the United States that is disproportionately affected by hypertension and associated complications, including stroke and kidney diseases," they say in the abstract. Scanning for 800,000 SNPs in 1,017 African Americans from Washington, D.C., they identified associations for systolic BP in or near the genes PMS1, SLC24A4, YWHA7, IPO7, and CACANA1H.

In PLoS One, scientists at CombiMatrix used miRNA expression patterns to classify tumor cells. Employing a pan-human, high-density microarray, they were able to classify five types of human cancer — prostate, colon, ovarian, breast, and lung — according to miRNA expression patterns. They say that there are enough miRNAs in one milliliter of serum to detect miRNA expression patterns without amplification.

Finally, U.S. Army Medical Research scientists published a method to predict protein structure in this week's issue of PLoS One. Their PSPP (protein structure prediction pipeline) is a "standalone protein structure prediction software package suitable for high-throughput structural genomic applications." The software does comparative modeling, fold recognition, and ab initio, and can be deployed on a user's own high-performance computing cluster.

The Scan

Expanded Genetic Testing Uncovers Hereditary Cancer Risk in Significant Subset of Cancer Patients

In Genome Medicine, researchers found pathogenic or likely pathogenic hereditary cancer risk variants in close to 17 percent of the 17,523 patients profiled with expanded germline genetic testing.

Mitochondrial Replacement Therapy Embryos Appear Largely Normal in Single-Cell 'Omics Analyses

Embryos produced with spindle transfer-based mitochondrial replacement had delayed demethylation, but typical aneuploidy and transcriptome features in a PLOS Biology study.

Cancer Patients Report Quality of Life Benefits for Immune Checkpoint Inhibitors

Immune checkpoint inhibitor immunotherapy was linked in JAMA Network Open to enhanced quality of life compared to other treatment types in cancer patients.

Researchers Compare WGS, Exome Sequencing-Based Mendelian Disease Diagnosis

Investigators find a diagnostic edge for whole-genome sequencing, while highlighting the cost advantages and improving diagnostic rate of exome sequencing in EJHG.