title: Large-insert genome analysis technology detects structural variation in Pseudomonas aeruginosa clinical strains from cystic fibrosis patients.
abstract: Large-insert genome analysis (LIGAN) is a broadly applicable, high-throughput technology designed to characterize genome-scale structural variation. Fosmid paired-end sequences and DNA fingerprints from a query genome are compared to a reference sequence using the Genomic Variation Analysis (GenVal) suite of software tools to pinpoint locations of insertions, deletions, and rearrangements. Fosmids spanning regions that contain new structural variants can then be sequenced. Clonal pairs of Pseudomonas aeruginosa isolates from four cystic fibrosis patients were used to validate the LIGAN technology. Approximately 1.5 Mb of inserted sequences were identified, including 743 kb containing 615 ORFs that are absent from published P. aeruginosa genomes. Six rearrangement breakpoints and 220 kb of deleted sequences were also identified. Our study expands the "genome universe" of P. aeruginosa and validates a technology that complements emerging, short-read sequencing methods that are better suited to characterizing single-nucleotide polymorphisms than structural variation.
authors.affiliation: Genome Center, University of Washington, Seattle, WA 98195, USA. hhayden@u.washington.edu
authors.forename: Hillary S
authors.initials: HS
authors.lastname: Hayden
authors.forename: Will
authors.initials: W
authors.lastname: Gillett
authors.forename: Channakhone
authors.initials: C
authors.lastname: Saenphimmachak
authors.forename: Regina
authors.initials: R
authors.lastname: Lim
authors.forename: Yang
authors.initials: Y
authors.lastname: Zhou
authors.forename: Michael A
authors.initials: MA
authors.lastname: Jacobs
authors.forename: Jean
authors.initials: J
authors.lastname: Chang
authors.forename: Laurence
authors.initials: L
authors.lastname: Rohmer
authors.forename: David A
authors.initials: DA
authors.lastname: D'Argenio
authors.forename: Anthony
authors.initials: A
authors.lastname: Palmieri
authors.forename: Ruth
authors.initials: R
authors.lastname: Levy
authors.forename: Eric
authors.initials: E
authors.lastname: Haugen
authors.forename: Gane K S
authors.initials: GK
authors.lastname: Wong
authors.forename: Mitch J
authors.initials: MJ
authors.lastname: Brittnacher
authors.forename: Jane L
authors.initials: JL
authors.lastname: Burns
authors.forename: Samuel I
authors.initials: SI
authors.lastname: Miller
authors.forename: Maynard V
authors.initials: MV
authors.lastname: Olson
authors.forename: Rajinder
authors.initials: R
authors.lastname: Kaul
mesh_terms: D001483:Base Sequence; D003550:Cystic Fibrosis / Q000382:microbiology*; D016172:DNA Fingerprinting / Q000379:methods*; D004252:DNA Mutational Analysis / Q000379:methods*; D014644:Genetic Variation; D016680:Genome, Bacterial; D006801:Humans; D008969:Molecular Sequence Data; D016254:Mutagenesis, Insertional; D011550:Pseudomonas aeruginosa / Q000235:genetics* / Q000302:isolation & purification; D011995:Recombination, Genetic; D017384:Sequence Deletion