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Genomics In The Journals: Jun 9, 2011

By a GenomeWeb staff reporter

NEW YORK (GenomeWeb News) – In Lancet Infectious Diseases, a UK research group describes how it used whole-genome sequencing to find a methicillin-resistant Staphylococcus aureus isolate that contains a previously unknown version of mecA — a gene contributing to beta-lactam antibiotic response. The team originally detected the bug in milk samples from British dairy cows and subsequently found it in human samples from Scotland, England, and Denmark. Based on their findings, those involved in the study argue that it may be necessary to tweak diagnostic strategies to include tests for the newly identified isolate.

"[W]hen existing PCR or monoclonal antibody methods are used as the only method to detect MRSA, or when these methods are used to confirm provisional detection of MRSA, then [the new mecA homologue-containing version of] S. aureus will be wrongly diagnosed as methicillin susceptible," University of Cambridge veterinary medicine researcher Mark Holmes, senior author on the study, and his co-authors wrote. "The use of new PCR primers such as those described in this paper, and the production of new monoclonal antibodies, would address this problem."

A Cold Spring Harbor Laboratory-led team reports on autism-associated de novo and inherited rare copy number changes that they found in families that had just one child with autism spectrum disorder. By doing comparative genomic hybridization analyses with NimbleGen HD2 2.1 million probe arrays in nearly 1,500 trios from the Simons Simplex Collection, the researchers identified dozens of rare de novo copy number changes and found evidence that copy number changes, especially duplications, can be transmitted from parents to affected children in a small subset of cases. The findings appear in Neuron.

"We confirm a major contribution from de novo deletions and duplications but also find evidence of a role for inherited 'ultrarare' duplications," CSHL researcher Michael Wigler, senior author on the study, and co-authors wrote. "The functions of the genes in the regions of de novo variation point to a great diversity of genetic causes but also suggest functional convergence."

Indeed, in the same issue of the journal, Wigler and other researchers from Columbia University and CSHL describe how they used a gene interaction analysis approach — dubbed network-based analysis of genetic associations (NETBAG) — to investigate functional connections between genes harboring 75 of these de novo copy number changes. The network approach indicated that copy number alterations in ASD tend to cluster in genes from pathways involved in brain-related processes such as synapse development and maturation. It also provides evidence hinting that stronger functional alterations are needed to produce ASD in females, the team noted, perhaps explaining why the condition is more common in males.

In a third Neuron study, another American research team describes its own efforts to track down de novo, recurrent copy number changes in families from the Simons Simplex Collection using Illumina IMV1 or IMV3 Duo Bead microarrays. That group genotyped blood, cell line, or saliva samples from nearly 4,500 individuals from 1,174 ASD-affected families. Among the six rare, recurrent copy number change-containing loci they detected: a duplication on chromosome 7 that affects a gene known to be deleted in extremely social individuals with a syndrome known as Williams-Beuren.

In Science Translational Medicine, meanwhile, researchers from the Baylor College of Medicine and elsewhere report on findings from a protein interaction network that they developed to study ASD. The protein interactome — established using a yeast two-hybrid screen that relied on a library of human complementary DNA sequences corresponding to dozens of ASD-associated genes — uncovered hundreds of interaction partners for these genes, the researchers explained, and points to overlapping proteins and pathways within the genetically heterogeneous condition. The team also tracked down new deletions on chromosome 16 and 15 and a new duplication on the X-chromosome in individuals with idiopathic ASD that affect genes within the interactome.

"Uncovering functional relationships among diverse ASD-related proteins is a first step toward the ultimate goal of developing therapies that might benefit multiple functionally or mechanistically related ASDs," senior author Huda Zoghbi, a researcher affiliated with Baylor College of Medicine and Texas Children's Hospital's Jan and Dan Duncan Neurological Research Institute, and her co-authors wrote.

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

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