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Genomics in the Journals: Nov 29, 2013

NEW YORK (GenomeWeb News) – In the early, online edition of the Proceedings of the National Academy of Sciences, an Uppsala University team reported on findings from a computational study of retrovirus phylogeny in host genomes.

Using data for almost 90,000 retroviruses that have worked their way into dozens of vertebrate host genomes, the researchers assessed relationships between viruses in a genus called Gammaretrovirus. They also considered the predicted distribution and diversity of these and related "class I" endogenous retroviruses.

Results of the in silico computational analysis suggest that endogenous retroviruses have a long history of switching hosts — in particular, hopping back and forth between different mammalian species. Based on the retrovirus diversity detected in the study, those involved in the work also cautioned that there may be far more undetected endogenous retroviruses than were previously estimated.

"This study demonstrates the potential of the genomic record as an important resource for improving understanding of the long term co-evolution among retroviruses and host species," senior author Patric Jern, a biochemistry and microbiology researcher at Uppsala University, said in a statement.

An international team led by investigators at the University of Copenhagen and the University of California at Berkeley did exome sequencing on thousands of Danes in an effort to unearth relatively rare protein-coding variants contributing to type 2 diabetes.

As they reported in the American Journal of Human Genetics, the researchers deeply sequenced protein-coding portions of the genome in 1,000 Danish individuals with diabetes and as many unaffected Danes.

When they sifted through sequences from these cases and controls to look for individual variants or clusters of low-frequency variants that were over-represented in type 2 diabetes, though, investigators did not detect small sets of genes that were significantly more prone to such variation in affected individuals.

"[No] gene showed a significant association with disease risk after we corrected for the number of genes analyzed," senior authors Rasmus Nielsen with UC Berkeley, and the University of Copenhagen's Oluf Pedersen, and their colleagues wrote. "Thus, we could reject a model for the genetic architecture of type 2 diabetes where rare non-synonymous variants clustered in a modest number of genes (fewer than 20) are responsible for the majority of disease risk."

Mutations to the transcription factor-coding gene GSC can contribute to a rare, autosomal recessive developmental condition characterized by short stature and a specific set of face, ear, and other skeletal features, according to another AJHG study.

A team from the UK, Netherlands, Egypt, and Canada used a combination of molecular karyotyping and exome sequencing to explore the genetic basis of "short stature, auditory canal atresia, mandibular hypoplasia, and skeletal abnormalities," or SAMS.

By doing whole-exome sequencing on a child with SAMS and his unaffected parents and brother, the researchers detected a GSC deletion suspected of causing the skeletal condition. Similar alterations to GSC were subsequently detected in three more children with SAMS through array-based karyotyping and targeted sequencing experiments.

The group's follow-up work on developing mouse embryos supported the notion that GSC contributes to skeletal development. Localization patterns in the developing mice indicated that the Goosecoid protein encoded by GSC acts as an effector in a regulatory pathway that mediates bone and cartilage-related differentiation and growth during mammalian development.

Based on results of their analyses, the study's authors argued that Goosecoid likely has a key role in development in humans and other mammals, contributing to everything from face and skull features to joint development.

Researchers from Brazil used a mitochondrial DNA markers and selected genomic sequences to assess relationships between wild cat species from the Leopardus genus in that country — work that they described in Current Biology.

By combing through such sequence data for more than 200 wild cats in Brazil, the team saw signs of historical mixing between housecat-sized wild cats called tigrina from the northeast area of Brazil and the so-called Pampas cat, L. colocolo. Admixture appears to have been more recent and ongoing between tigrinas from the southern portion of the country and another wild cat species called L. geoffroyi, or Geoffrey's cat, on the other hand.

In the process, the investigators also identified two apparently distinct types of tigrina living in northeastern Brazil and southern parts of the country. The populations were previously thought to inter-breed with one another, they explained. But the current analysis points to a lack of gene flow between the northeastern tigrina, L. tigrinus, and the southern species, now designated as L. guttulus.

"[A]ll four species are threatened, and we need to understand as much as possible regarding their genetics, ecology, and evolution to be able to design adequate conservation strategies on their behalf," the study's senior Eduardo Eizirik, with the Pontifical Catholic University of Rio Grande do Sul in Brazil, said in a statement.