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This Week in Genome Research: Sep 5, 2012

Investigators in the UK report in Genome Research on next-generation sequencing methods for analyzing DNA methylation patterns found in blood spots from newborns that have been collected on Guthrie cards. Using a bisulfite conversion-based array and a MeDIP-seq approach, the researchers write that they identified "temporally stable epialleles that are present at birth in humans." As Vardhman Rakyam from the Queen Mary University of London tells our sister publication In Sequence, Guthrie cards could be a resource to help researchers understand disease risk. "If we could use genetics and epigenetics at birth, that could provide an interesting and potentially useful avenue for prediction," he says.

Also in Genome Research, researchers led by the University of California, Berkeley's Jillian Banfield present their metagenomic methods to track the microbial community makeup of fecal samples collected over the course of a month from a premature infant. They write that they were able to generate eight complete or nearly complete genomes and nine partial genomes, and that 96 percent of their reads could be assembled into scaffolds larger than 500 basepairs and binned. "Time-series based binning proved to be both accurate and sensitive because sample compositions varied, and genomes had unique abundance patterns," Banfield and her colleagues write. "This approach should be generally applicable for the binning of metagenomic data collected over a time course, even for more complex environments." They add that they could see the relative abundance of three Staphylococcus epidermidis strains change over time as well as see Propionibacterium acnes decline while then seeing the rise of other Propionibacterium and Peptoniphilus species.

Finally, Rob Knight at the University of Colorado and his colleagues report on their examination of early human gut microbe succession. Focusing on Clostridium cluster XIVa Knight and his team "identified genes likely selected during adaptation to pioneer/opportunistic lifestyles as those for which early succession association and not phylogenetic relationships explain genomic abundance." The researchers add that these genes show possible ways how opportunistic bacteria tolerate stressors and that the genes could be biomarkers for early succession or disturbance.

The Scan

Myotonic Dystrophy Repeat Detected in Family Genome Sequencing Analysis

While sequencing individuals from a multi-generation family, researchers identified a myotonic dystrophy type 2-related short tandem repeat in the European Journal of Human Genetics.

TB Resistance Insights Gleaned From Genome Sequence, Antimicrobial Response Assays

Researchers in PLOS Biology explore M. tuberculosis resistance with a combination of sequencing and assays looking at the minimum inhibitory concentrations of 13 drugs.

Mendelian Disease Genes Prioritized Using Tissue-Specific Expression Clues

Mendelian gene candidates could be flagged for further functional analyses based on tissue-specific transcriptome and proteome profiles, a new Journal of Human Genetics paper says.

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.