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Scientists develop strategy to rapidly describe outbreak strains with next-generation DNA sequencing
Date:4/10/2008

Friday, April 11, 2008 In the event of an outbreak or a bioterrorist attack, rapid identification of the genetic changes responsible for virulence or drug resistance is essential to mounting an effective response. Standard DNA sequencing and analysis of a pathogen genome is time-intensive and likely impractical during an emergency. Researchers have now developed a comparative genomics strategy to drastically reduce the time needed to accurately identify unique genetic properties of a potential outbreak strain. This report, which demonstrates the approach using next-generation sequencing technology, is published online today in Genome Research (www.genome.org).

Sanger DNA sequencing, the established technology used to sequence the genomes of many species, including the genomes of humans and hundreds of bacteria, could potentially be used to sequence and analyze a new human pathogen. However, the time required for sequencing and subsequent analysis, or finishing, is such that this approach is not feasible when a rapid response to an outbreak or bioterrorist attack is required. New sequencing technologies are now available, allowing an entire bacterial genome to be sequenced in several hours, but time-intensive finishing steps are still required to determine the complete genome sequence.

In this study, researchers led by Drs. Bernard La Scola and Didier Raoult of the University of the Mediterranean set out to determine whether a rapidly sequenced incomplete genome could be used to quickly characterize an outbreak strain by comparative analysis. In the context of an outbreak, a quick approach may help to identify immediately the genetic determinants responsible for modified virulence or transmission, explains La Scola. The aim of this work was to evaluate the recently available automated pyrosequencing technology without finishing for this purpose.

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Contact: Peggy Calicchia
calicchi@cshl.org
516-422-4012
Cold Spring Harbor Laboratory
Source:Eurekalert

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