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This Week in PLoS: Jan 18, 2010

In PLoS ONE this week, Eric Schadt and his colleagues quantified the extent of population stratification in Caucasian American, African American, and Hispanic American populations. After genotyping and measuring gene expression in liver tissue from nearly 1,100 individuals, the team came up with a method for detecting this population stratification and also examined how it affects expression quantitative trait loci in genome-wide association studies.

A Canadian research team reports that they have integrated gene expression, DNA methylation, copy number, and SNP data from human breast cancer cell lines to explore the interplay between genomic and epigenetic changes during breast cancer metastasis. "Our integrated report … provides an algorithm to logically assess prospective gene targets that are epigenetically regulated and those that are altered by copy number (but are not epigenetically modified) thus allowing us to refine the epigenetic signatures of breast cancer," they write.

In PLoS Genetics, French researchers Sara Vieira-Silva and Eduardo Rocha examine the relationship between microbial growth rate and genomic traits, developing a method to predict maximal growth rate based on genome fragments that they then applied to metagenomic samples from three environments. "Growth rates have been a key variable in microbial physiology studies in the last century," the duo writes, "and we show how intimately they are linked with genome organization and prokaryotic ecology."

Another French research team experimentally tested the evolution of symbiotic bacteria of legume roots from pathogenic bacteria in a PLoS Biology paper. To explore this, the team assessed a symbiotic plasmid-containing pathogenic bacterial species called Ralstonia solanacearum, demonstrating that both gene transfer and genome adaptation caused by plant selection contribute to the evolution of rhizobial bacteria.

The Scan

Single-Cell Sequencing Points to Embryo Mosaicism

Mosaicism may affect preimplantation genetic tests for aneuploidy, a single-cell sequencing-based analysis of almost three dozen embryos in PLOS Genetics finds.

Rett Syndrome Mouse Model Study Points to RNA Editing Possibilities

Investigators targeted MECP2 in mutant mouse models of Rett syndrome, showing in PNAS that they could restore its expression and dial down symptoms.

Investigators Find Shared, Distinct Genetic Contributors to Childhood Hodgkin Lymphoma

An association study in JAMA Network Open uncovers risk variants within and beyond the human leukocyte antigen locus.

Transcriptomic, Epigenetic Study Appears to Explain Anti-Viral Effects of TB Vaccine

Researchers report in Science Advances on an interferon signature and long-term shifts in monocyte cell DNA methylation in Bacille Calmette-Guérin-vaccinated infant samples.