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Nat Methods DOI:10.1038/nmeth.1286

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

Publication TypeJournal Article
Year of Publication2009
AuthorsNusbaum, C, Ohsumi, TK, Gomez, J, Aquadro, J, Victor, TC, Warren, RM, Hung, DT, Birren, BW, Lander, ES, Jaffe, DB
JournalNat Methods
Date Published2009 Jan
KeywordsAlgorithms, Base Sequence, Databases, Nucleic Acid, DNA, Bacterial, Polymorphism, Genetic, Sensitivity and Specificity

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.


Alternate JournalNat. Methods
PubMed ID19079253
PubMed Central IDPMC2613166
Grant ListR01 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