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JCVI-NYU Tooth Decay Study to Employ Enrichment Gene Sequencing

By Alex Philippidis

NEW YORK (GenomeWeb News) — Researchers from the J. Craig Venter Institute and New York University College of Dentistry will use a JCVI-developed genome sequencing method to identify microbes associated with tooth decay, under a four-year study to be funded through an NIH grant.

Scott Peterson, JCVI's director of functional genomics research technology, serves as principal investigator for the grant, while the PI on a subcontract of the grant awarded to NYUCD is Walter Bretz, associate professor of cariology & comprehensive care at the dental college. Bretz told GenomeWeb Daily News the approximately $3.6 million NIH grant will allow NYU and JCVI to speed up the process of sequencing oral bacteria through the enrichment of genomic DNA.

"In this case, you utilize all the dead bugs that come to surface, and you reach a plateau where you no longer can recover additional unknown species," Bretz said. "And with the enrichment methods, you can allow for the surfacing of all the bacteria, including some that you may have not detected through the traditional brute-force sequencing."

Enrichment gene sequencing will be used to study samples to be drawn from 100 pairs of twins ages 6 to 18, and selected from a database of 1,500 twin pairs developed by Bretz for the Twins Institute for Genetics Research in Montes Claros, Brazil.

The twins are being studied, Bretz said, because they live together and have similar dietary habits and health practices, yet one twin may be further along in the development of tooth decay or dental caries than the other. Researchers believe the answer lies with the thousands of microbes in the oral cavity or mouth of each twin.

"Our study endeavors to define the relative abundance of many species comprising the dental plaque microbiome in 60- 70 twin pairs discordant for dental caries in association and longitudinal studies," according to the abstract of the project grant.

Samples will undergo 16s rDNA sequencing using Roche 454 sequencing, as well as metagenomic analysis designed to find "the 20 or 30 of the bacteria that become the most informative in terms of health or disease," Bretz said.

According to the grant abstract, the functional relevance of differentially abundant species, strains, and genes "will be determined by conducting targeted meta-transcriptomic studies."

NYUCD will be responsible for coordinating research with the Twins Institute, as well as perform clinical examinations after obtaining microbiological samples and blood samples for "discordant" twins where one has dental caries and the other doesn't. Samples will be analyzed at JCVI.

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