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This Week in PLOS: Nov 27, 2012

A team from the US, Russia, and Switzerland tracked down human-specific epigenetic marks in neurons from the prefrontal cortex, a brain region involved in higher order cognitive functions. As they report in PLOS Biology, the researchers assessed genome-wide histone H3 trimethyl-lysine 4, or H3K4me3, marks in prefrontal cortex samples from 11 humans, four chimpanzees, and three rhesus macaques. The search uncovered almost 500 sequences with human-specific H3K4me3 levels. Because this epigenetic mark is often associated with transcription start sites, the team suspects that this set of marks includes regulators related to gene expression programs in the human prefrontal cortex.

For more on this study, check out our sister publication GenomeWeb Daily News.

In PLOS One, an international team led by investigators in Portugal and France describes two sequencing-based strategies for uncovering genetic markers that can be used in conservation studies of the Bornean elephant, an endangered Asian elephant subspecies from northern Borneo that's known for its low genetic diversity. Using blood samples from eight Bornean elephants, the researchers examined the feasibility of finding informative markers through low-coverage restriction site associated DNA, or RAD, sequencing with the Illumina GAIIx. Samples from two of the elephants were also assessed through low Roche 454 GS FLX shotgun sequencing. Each technique turned up thousands of apparent SNPs, though the shotgun sequencing approach appeared to have an edge on the microsatellite-marker-finding front. "The approaches used here for marker development in a threatened species demonstrate the utility of high throughput sequencing technologies as a starting point for the development of genomic tools in a non-model species " study authors write, "and in particular for a species with low genetic diversity."

Cepheid's DNA-based tuberculosis test could potentially reduce TB prevalence in southern Africa by nearly 30 percent within the next decade, a study published in PLOS Medicine predicts. Using data for five African countries (Botswana, Lesotho, Namibia, South Africa, and Swaziland), researchers from Harvard School of Public Health, Massachusetts General Hospital, and elsewhere came up with mathematical models assess the cost-effectiveness of standard microscopy-based smear tests for TB and of testing with Xpert MTB/RIF, an automated DNA-based test designed to detect drug resistant TB strains and cases involving co-infection with TB and HIV. The team estimated that implementing the Xpert test would prevent more than 130,000 TB infections in the region over the next decade at a cost of $460 million — a price tag takes into account the estimated expenses of treating TB and HIV infections detected by the test.

The Scan

Study Examines Insights Gained by Adjunct Trio RNA Sequencing in Complex Pediatric Disease Cases

Researchers in AJHG explore the diagnostic utility of adding parent-child RNA-seq to genome sequencing in dozens of families with complex, undiagnosed genetic disease.

Clinical Genomic Lab Survey Looks at Workforce Needs

Investigators use a survey approach in Genetics in Medicine Open to assess technologist applications, retention, and workforce gaps at molecular genetics and clinical cytogenetics labs in the US.

Study Considers Gene Regulatory Features Available by Sequence-Based Modeling

Investigators in Genome Biology set sequence-based models against observational and perturbation assay data, finding distal enhancer models lag behind promoter predictions.

Genetic Testing Approach Explores Origins of Blastocyst Aneuploidy

Investigators in AJHG distinguish between aneuploidy events related to meiotic missegregation in haploid cells and those involving post-zygotic mitotic errors and mosaicism.