Nat Methods. 2009 Jan;6(1):67-9. Epub 2008 Dec 14.

Sensitive, specific polymorphism discovery in bacteria using massively parallel sequencing.

Nusbaum C, Ohsumi TK, Gomez J, Aquadro J, Victor TC, Warren RM, Hung DT, Birren BW, Lander ES, Jaffe DB.

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Broad Institute of Massachusetts Institute of Technology and Harvard University, 320 Charles Street, Cambridge, MA 02141, USA.

Abstract

Our variant ascertainment algorithm, VAAL, uses massively parallel DNA sequence data to identify differences between bacterial genomes with high sensitivity and specificity. VAAL detected approximately 98% of differences (including large insertion-deletions) between pairs of strains from three species while calling no false positives. VAAL also pinpointed a single mutation between Vibrio cholerae genomes, identifying an antibiotic's site of action by identifying sequence differences between drug-sensitive strains and drug-resistant derivatives.

PMID:: 19079253; [PubMed - indexed for MEDLINE]
PMCID: PMC2613166

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DNA, Bacterial

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