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

Nat Methods

Authors	Chad Nusbaum Toshiro Ohsumi James Gomez John Aquadro Thomas Victor Robert Warren Deborah Hung Bruce Birren Eric Lander David Jaffe
Keywords	Base Sequence Algorithms Sensitivity and Specificity Polymorphism, Genetic Databases, Nucleic Acid DNA, Bacterial
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.
Year of Publication	2009
Journal	Nat Methods
Volume	6
Issue	1
Pages	67-9
Date Published	2009 Jan
ISSN	1548-7105
URL
DOI	10.1038/nmeth.1286
PubMed ID	19079253
PubMed Central ID	PMC2613166
Links
Grant list	R01 HG003474-03 / HG / NHGRI NIH HHS / United States R01 HG003474 / HG / NHGRI NIH HHS / United States R01 HG003474-02 / HG / NHGRI NIH HHS / United States R01 HG003474-01A1 / HG / NHGRI NIH HHS / United States R01 HG003474-04 / HG / NHGRI NIH HHS / United States