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

Nat Methods
Authors
Keywords
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