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This Week in Genome Biology: Dec 3, 2014

Researchers from Norway and the UK retraced the history of an extensively drug-resistant case of Mycobacterium tuberculosis that cropped up in a single individual. By sequencing nine samples collected from the individual over three-and-a-half years, the team identified several M. tuberculosis lineages that appeared to compete with and replace one another following exposure to various tuberculosis treatments. The study's authors saw the advent of drug-dodging mutations in multiple clones, with resistant clones generally out-competing those susceptible to treatment. "We observed both rapid acquisitions of resistance to antimicrobial compounds mediated by individual mutations," they write, "as well as a gradual increase in fitness in the presence of antibiotics, likely driven by stable gene expression reprogramming."

A Broad Institute-led team describes the deep RNA sequencing strategy it developed to sequence and assemble Lassa virus and Ebola virus genomes from clinical and biological source samples. With the help of hybrid selection strategy and targeted RNase H enzyme step that digests ribosomal RNA and other contaminants, the researchers successfully enriched for RNA from the Lassa and Ebola genomes, making it possible to get unbiased, deep coverage of the viral sequences. For more on the sequencing approaches used, check out this GenomeWeb feature story.

In a commentary article in Genome Biology, researchers based at Redeemer's University and the University of Ibadan, both in Nigeria, outline existing initiatives aimed at increasing the availability of genomics infrastructure and staff within Africa — advances that they argue will help in controlling infectious disease on the continent and beyond. In particular, the team pointed to the H3Africa consortium, funded by the Wellcome Trust, and the National Institute of Health, and to the World Bank-funded African Center of Excellence for Genomics and Infectious Diseases (ACEGID). "The initial success of the H3Africa and ACEGID initiatives has shown that well though through and articulated programs can enable African scientists to purse high-impact projects," they write. "This work will not only bring regional academic and research success for African science, but will also contribute to the improvement of global public health."

The Scan

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.

Team Presents Cattle Genotype-Tissue Expression Atlas

Using RNA sequences representing thousands of cattle samples, researchers looked at relationships between cattle genotype and tissue expression in Nature Genetics.

Researchers Map Recombination in Khoe-San Population

With whole-genome sequences for dozens of individuals from the Nama population, researchers saw in Genome Biology fine-scale recombination patterns that clustered outside of other populations.

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.