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Genomics in the Journals: Sep 19, 2013

NEW YORK (GenomeWeb News) – In Nature Genetics, a team from Germany, Belgium, and Sweden described a de novo gain-of-function mutation in the voltage-gated sodium ion channel gene SCN11A that appears to produce a congenital condition characterized by the inability to feel pain, tissue damage, gastrointestinal ailments, and other features.

The researchers started by doing exome sequencing on a German girl born with such congenital defects in pain perception, along with both her unaffected parents. Sifting through these protein-coding sequences, they found a heterozygous, non-synonymous alteration in SCN11A, pointing to a potential role for sodium channel glitches in some sporadic pain perception cases.

By sequencing the coding portions of SCN11A in another 58 individuals with pain perception problems, the group detected the same missense mutation in a Swedish boy with the same type of so-called early-onset sensory loss. Follow-up experiments in mice indicated that the de novo change to SCN11A leads to an inappropriate boost in activity by the ion channel containing the protein it encodes.

Based on findings from the study, its authors argued that "SCN11A channelopathy should be considered in individuals with a congenital insensitivity to pain, muscular hypotonia, and gastrointestinal disturbances."

The University of Lausanne's Carlo Rivolta and colleagues from several international centers did whole-genome sequencing on more than a dozen individuals as part of their effort to find new contributors to an eye condition called autosomal recessive retinitis pigmentosa risk — work they described in the early, online version of the Proceedings of the National Academy of Sciences.

The researchers sequenced the genomes of eight North American individuals with ARRP and eight Japanese individuals with ARRP during the search for culprits in the progressive condition, which can eventually lead to blindness. In the process, they found new mutations in several known ARRP risk genes as well as rearrangements and mutations in sequences not previously linked to the disease.

The latter set of alterations included a frameshift mutation in an enzyme-coding gene called NEK2. That gene also appeared to affect retinal function in follow-up zebrafish experiments, prompting the study's authors to propose that "NEK2 is a disease gene and … the retinal phenotype that results from its deficiency may represent a newly recognized ciliopathy."

Elevated blood levels of a metabolite known as 2-aminoadipic acid, or 2-AAA, may portend type 2 diabetes development, even a decade or more before the disease appears, according to a Journal of Clinical Investigation study.

Following from earlier research pointing to metabolite shifts in individuals who went on to develop type 2 diabetes, researchers from Vanderbilt University and elsewhere used a combination of liquid chromatography and triple quadrupole tandem mass spectrometry to assess metabolite patterns in blood samples from initially diabetes-free Framingham Heart Study participants who were diagnosed with the disease over 12 years of the study.

The team uncovered an association between blood 2-AAA concentrations and diabetes risk by comparing metabolite profiles in samples from 188 individuals diagnosed with type 2 diabetes some eight years or more after being first examined for the study with those in as many matched controls.

A similar hike in 2-AAA levels in blood samples from individuals who eventually developed type 2 diabetes was detected in a replication study based on data for another 162 cases and 162 controls from the Malmö Diet and Cancer Study, the group reported, suggesting the metabolite might ultimately make a feasible biomarker for the disease.

"These data highlight a metabolite not previously associated with diabetes risk that is increased up to 12 years before the onset of overt disease," Vanderbilt researchers Robert Gerszten and Thomas Wang, the study's co-corresponding authors, and their colleagues wrote. "Our findings suggest that 2-AAA is a marker of diabetes risk and a potential modulator of glucose homeostasis in humans."

A Nature Communications study highlighted findings from a genome sequencing study of the mulberry tree Morus notabilis.

Researchers from China and elsewhere used Illumina sequencing to tackle the 357 million or so bases in the M. notabilis genome. The resulting 330 million base draft genome assembly houses an estimated 29,338 protein-coding genes, they reported, along with a raft of repeat sequences.

Together with transcriptome sequences, which were used to help annotate the genome, the newly available genome offered clues about the mulberry tree's biology, evolution, and relationships with other plants in the Rosaceae family.

It is also providing information on the deciduous tree's ongoing interaction with silkworms, which have been supplied with mulberry leaves as a food source since the early stages of silkworm domestication thousands of years ago. For instance, the team noted that several microRNAs predicted from the mulberry sequence match miRNAs detected in the silkworm tissues.

"As a model system for studies of plant-herbivore relationships, the availability of the mulberry and silkworm genome sequences offers a unique opportunity to gain insights into such biological partnerships prevalent in most terrestrial habitats."

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