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This Week in Genome Biology: Nov 2, 2016

Studies by independent research teams describe epigenetic patterns associated with gestational age at birth. For the first of these studies, a Norwegian-led team took advantage of a mother and childbirth cohort from Norway, exploring relationships between gestational age — based on ultrasound measurements and mothers' last menstrual period — and array-based methylation patterns in cord blood samples from more than 1,700 newborns. The search led to nearly 5,500 cytosine methylation sites associated with ultrasound-based gestational age. For their part, researchers from Emory University and elsewhere narrowed in on 148 gestational age-associated cytosine methylation markers based on cord blood and blood spot samples for infants from half a dozen datasets before validating the predictive prowess of these markers in samples from more than 1,000 additional infants.

A French team reports on a new computational strategy for translating gene expression patterns into estimate cell population representation in a given sample. The approach — known as the Microenvironment Cell Populations-counter, or MCP-counter — uses transcriptome data to quantify the relative representation of immune or stromal cell populations in a mixed sample based on transcriptomic markers gleaned from available expression datasets, the researchers say. In proof-of-principle experiments, they used MCP-counter to investigate immune cell infiltration in dozens of healthy tissue or cancer samples. The authors argue that the approach "should help to unravel the role of immune and stromal populations in cancer and other diseases and to decipher the interplay between these populations."

Finally, researchers from the Donald Danforth Plant Science Center and elsewhere present findings from a genome sequencing study of Dichanthelium oligosanthes, a panicoid grass that performs so-called C3 photosynthesis. Along with anatomical, physiological, and biochemical analyses of the grass, the team used short read sequencing to produce a draft nuclear genome assembly spanning almost 590 million bases and a choloroplast genome that was more than 140,000 bases. It also performed a comparative transcriptomic analysis using leaf expression data for D. oligosanthes and C4 photosynthetic grasses such as Sorghum bicolor. "This genome will not only provide a better C3 species for comparisons with C4 panicoid grasses," the investigators note, "but also highlights the power of using high-throughput sequencing to address questions in evolutionary biology."