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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
Volume6
Issue1
Pages67-9
Date Published2009 Jan
ISSN1548-7105
KeywordsAlgorithms, Base Sequence, Databases, Nucleic Acid, DNA, Bacterial, Polymorphism, Genetic, Sensitivity and Specificity
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.

URLhttp://dx.doi.org/10.1038/nmeth.1286
DOI10.1038/nmeth.1286
Pubmed

http://www.ncbi.nlm.nih.gov/pubmed/19079253?dopt=Abstract

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