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This Week in PLOS: Oct 8, 2012

A PLOS Genetics study by researchers from Harvard University and the Max Planck Institute for Evolutionary Anthropology suggests that Neandertal gene flow into European populations happened relatively recently — supporting the theory that Neandertal sequences in non-African populations stem from historical interbreeding between the archaic hominins and modern humans. For its analysis, the team looked at linkage disequilibrium patterns in the genomes of nearly 200 European-American, East Asian, and West African individuals sequenced for the 1000 Genomes Project pilot study. The researchers report that Neandertal gene flow into ancestral European populations probably occurred most recently around 47,000 years ago to 65,000 years ago, with their most conservative estimates placing it within a window from 37,000 years ago to 85,000 years ago.

For more on the study, check out a related news story in our sister publication GenomeWeb Daily News.

A set of blood-based protein biomarkers appears to show promise for predicting individuals' risk of developing an asbestos-related lung cancer called malignant pleural mesothelioma, according to a new PLOS One study. Along with collaborators from several centers in the US, SomaLogic researchers Rachel Ostroff and Michael Mehan compared protein profiles in blood samples from 60 individuals malignant pleural mesothelioma and as many individuals who had been exposed to asbestos, but who had not developed the disease. From the 64 potential biomarkers identified using SomaLogic's proteomic assay, known as SOMAscan, they narrowed in on a 13-marker panel that was subsequently tested and validated with discovery stage samples and samples from additional asbestos-exposed cases and controls. For stage I and stage II cancers, their results suggest that this 13-marker can detect 88 percent of malignant pleural mesothelioma cases with 92 percent accuracy.

Finally, in PLOS Pathogens, an international research group led by investigators in the UK looks at genomic features of an especially aggressive population of Irish potato blight pathogens. The researchers used molecular markers, genome sequence information, and copy number analyses to characterize a Phytophthora infestans lineage known as 13_A2. Their results suggest that the aggressive and invasive lineage appeared in Europe in 2004, quickly spreading to Great Britain where it replaced most of the pathogens from other lineages. Among the most striking features in the13_A2 lineage, the team saw a slew of polymorphisms and variable gene expression profiles during potato infection relative to other P. infestans lineages. The analysis also pointed to conserved pathogen genes in 13_A2 pathogens that may be susceptible to potato resistance genes — information that is expected to help in the quest to breed pathogen-proof potatoes.

The Scan

Study Reveals Details of SARS-CoV-2 Spread Across Brazil

A genomic analysis in Nature Microbiology explores how SARS-CoV-2 spread into, across, and from Brazil.

New Study Highlights Utility of Mutation Testing in Anaplastic Thyroid Cancer

Genetic mutations in BRAF and RAS are associated with patient outcomes in anaplastic thyroid carcinoma, a new JCO Precision Oncology study reports.

Study Points to Increased Risk of Dangerous Blood Clots in COVID-19 Patients

An analysis in JAMA Internal Medicine finds that even mild COVID-19 increases risk of venous thromboembolism.

Y Chromosome Study Reveals Details on Timing of Human Settlement in Americas

A Y chromosome-based analysis suggests South America may have first been settled more than 18,000 years ago, according to a new PLOS One study.