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Genomics In The Journals: Feb 23, 2012

NEW YORK (GenomeWeb News) – In BMC Genomics, Texas researchers describe the insights gained by sequencing the genome of the Quarter Horse, which has been bred for speed over short distances. By comparing the 59.6 billion base genome sequence to the publicly available horse reference genome, generated for a Thoroughbred mare in 2009, the team tracked down more than three million SNPs, 193,000 small insertions and deletions, and almost 300 copy number alterations. Among sequences containing variants in the Quarter Horse, they saw an over-representation of genes involved in sensory perception, immune function, and signal transduction.

An American and Australian-led team estimates the proportion of schizophrenia risk that can be explained by common variants in a Nature Genetics study. Based on data for more than 900,000 imputed SNPs in the genomes of 9,087 individuals with the condition and 12,171 individuals without, the researchers estimate that common SNPs can account for roughly 23 percent of variability in schizophrenia risk. Analyses of the data, collected through the International Schizophrenia Consortium, the Molecular Genetics of Schizophrenia Collaboration, and other studies, indicate that much of the schizophrenia-related genetic variation falls in a few thousand genes expressed in the central nervous system.

"These results are consistent with a polygenic genetic architecture and imply more individual SNP associations will be detected for this disease as sample size increases," University of Queensland researchers Peter Visscher and Naomi Wray, the study's senior authors, and colleagues wrote.

Researchers from the Universities of Illinois, Oxford, and California used high-throughput sequencing to get a peek at the speciation process in the thermoacidophilic archaea Sulfolobus islandicus — work that they describe in PLoS Biology. By sequencing a dozen S. islandicus strains from a hot spring in Russia and looking at gene flow and homologous recombination patterns in the microbes, the team identified two genetically diverging S. islandicus groups. Within each group, microbes were sharing more genes with one another than with the other group, they found, an apparent step en route to speciation. Divergence between the groups was particularly pronounced in certain regions of the genome, the authors added, hinting that "certain genomic regions are more prone to become differentiated between species than others."

"These data support a model where species do not require physical barriers to gene flow but are maintained by ecological differentiation," University of Illinois microbiology and genomic biology researcher Rachel Whitaker, the study's senior author, and colleagues explained.

A Journal of Clinical Investigation study suggests mutations in a replication-related gene can cause an autosomal recessive disorder that affects growth and immune function. The University of London-led team did genotyping and targeted exome sequencing in eight affected individuals from the Irish Traveler population to explore the genetics behind a form of familial glucocorticoid deficiency characterized by slow growth, chromosomal breakage, and a shortage of certain natural killer cells in the innate immune system. The search led to a truncating mutation in MCM4, a helicase gene involved in DNA replication, with downstream effects on natural kill cell function.

Researchers from Rockefeller University and elsewhere reached similar conclusions in their own JCI study. That team did linkage analysis, fine mapping, and more on six related individuals from the nomadic Irish population who were affected by an autosomal recessive condition involving growth delays, natural killer cell deficiency, a propensity for viral infections, and other symptoms. Again, they traced the trouble to a splice-site mutation in MCM4 that appears to alter the function of the resulting protein in some tissues, leading to genomic instability.

In an accompanying commentary article, University of Pennsylvania pediatrics researcher Jordan Orange credits the two teams with defining "a new genetic syndrome that establishes the importance of mature [natural killer] cells in human host defense and suggests novel molecular requirements in [natural killer] cell maturation."

"The further definition of human [natural killer] cell deficiency and its genetic roots also define the clinical relevance of this diagnosis and the need for continued research if we are to develop therapeutics that benefit affected patients," Orange adds.

A group led by investigators at the University of California at San Francisco and the La Jolla, Calif.-based biotherapeutics company Intellikine used ribosome profiling to track the translational patterns associated with aberrant signaling by the enzyme mTOR, a protein synthesis regulator, in prostate cancer. As they report in the early, online version of Nature, the researchers found that "oncogenic mTOR" was associated with the enhanced translation of messenger RNAs for genes involved in cell proliferation, metabolism, invasion, and other processes contributing to cancer formation and metastasis. On the other hand, the presence of their mTOR inhibitor INK128 seemed to curb these effects.

"Together, these findings extend our understanding of how the 'cancerous' translation machinery steers specific cancer cell behavior, including metastasis, and may be therapeutically targeted," the study's authors write.

Genomics In The Journals is a weekly feature pointing readers to select, recently published articles involving genomics and related research.

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