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This Week in Genome Biology: Dec 2, 2015

A team from Weill Cornell Medicine, New York-Presbyterian Hospital, and Memorial Sloan-Kettering Cancer Center presents a sequencing-centered method for finding microbial community members present in low abundance in small clinical samples. The team sequenced 27 gastric biopsy samples collected with an endoscope from 22 individuals with active Helicobacter pylori infections and no prior treatment for the bug. Along with a multitude of reads that mapped to the human genome, the samples contained bacterial reads that were classified with the help of multiple mapping and filtering strategies, uncovering microbial communities that clustered the stomach biopsy samples into three groups. The investigators used a similar approach to identify H. pylori and other microbes in gastric samples generated for the Cancer Genome Atlas project.

Researchers from the US, Czech Republic, and China describe a geminivirus vector-based effort to make heritable modifications to the tomato plant genome. With the help of the geminivirus vector, the researchers placed a stronger-than-usual promoter upstream of an anthocyanin biosynthesis gene, boosting the expression of tomato pigments in the plants. Their results suggest the insertion was successful more than two-thirds of the time, producing modifications far more frequently than methods that use Agrobacterium bacteria for DNA delivery during gene targeting, with no ongoing off-target effects.

Finally, a French-led team introduces a pipeline called HiC-Pro for dealing with data from Hi-C experiments, demonstrating the approach using data from two public datasets representing Hi-C experiments on the same human cell line. Starting with raw sequencing reads, the authors say, the approach produces normalized contact maps with user-defined levels of resolution — from intra- and inter-chromosomal maps to allele-specific interactions informed by additional phased genotype data. "When phased genotypes are available, HiC-Pro is able to distinguish allele-specific interactions," they write, "and to build both maternal and paternal contact maps."