title: Sensitive, specific polymorphism discovery in bacteria using massively parallel sequencing.
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.
authors.affiliation: Broad Institute of Massachusetts Institute of Technology and Harvard University, 320 Charles Street, Cambridge, MA 02141, USA.
authors.forename: Chad
authors.initials: C
authors.lastname: Nusbaum
authors.forename: Toshiro K
authors.initials: TK
authors.lastname: Ohsumi
authors.forename: James
authors.initials: J
authors.lastname: Gomez
authors.forename: John
authors.initials: J
authors.lastname: Aquadro
authors.forename: Thomas C
authors.initials: TC
authors.lastname: Victor
authors.forename: Robert M
authors.initials: RM
authors.lastname: Warren
authors.forename: Deborah T
authors.initials: DT
authors.lastname: Hung
authors.forename: Bruce W
authors.initials: BW
authors.lastname: Birren
authors.forename: Eric S
authors.initials: ES
authors.lastname: Lander
authors.forename: David B
authors.initials: DB
authors.lastname: Jaffe
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D004269:DNA, Bacterial / Q000032:analysis* / Q000235:genetics*; D030561:Databases, Nucleic Acid; D011110:Polymorphism, Genetic / Q000235:genetics*; D012680:Sensitivity and Specificity
chemical_list: D004269:DNA, Bacterial