title: CREST maps somatic structural variation in cancer genomes with base-pair resolution.
abstract: We developed 'clipping reveals structure' (CREST), an algorithm that uses next-generation sequencing reads with partial alignments to a reference genome to directly map structural variations at the nucleotide level of resolution. Application of CREST to whole-genome sequencing data from five pediatric T-lineage acute lymphoblastic leukemias (T-ALLs) and a human melanoma cell line, COLO-829, identified 160 somatic structural variations. Experimental validation exceeded 80%, demonstrating that CREST had a high predictive accuracy.
authors.affiliation: Department of Information Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.
authors.forename: Jianmin
authors.initials: J
authors.lastname: Wang
authors.forename: Charles G
authors.initials: CG
authors.lastname: Mullighan
authors.forename: John
authors.initials: J
authors.lastname: Easton
authors.forename: Stefan
authors.initials: S
authors.lastname: Roberts
authors.forename: Sue L
authors.initials: SL
authors.lastname: Heatley
authors.forename: Jing
authors.initials: J
authors.lastname: Ma
authors.forename: Michael C
authors.initials: MC
authors.lastname: Rusch
authors.forename: Ken
authors.initials: K
authors.lastname: Chen
authors.forename: Christopher C
authors.initials: CC
authors.lastname: Harris
authors.forename: Li
authors.initials: L
authors.lastname: Ding
authors.forename: Linda
authors.initials: L
authors.lastname: Holmfeldt
authors.forename: Debbie
authors.initials: D
authors.lastname: Payne-Turner
authors.forename: Xian
authors.initials: X
authors.lastname: Fan
authors.forename: Lei
authors.initials: L
authors.lastname: Wei
authors.forename: David
authors.initials: D
authors.lastname: Zhao
authors.forename: John C
authors.initials: JC
authors.lastname: Obenauer
authors.forename: Clayton
authors.initials: C
authors.lastname: Naeve
authors.forename: Elaine R
authors.initials: ER
authors.lastname: Mardis
authors.forename: Richard K
authors.initials: RK
authors.lastname: Wilson
authors.forename: James R
authors.initials: JR
authors.lastname: Downing
authors.forename: Jinghui
authors.initials: J
authors.lastname: Zhang
mesh_terms: D000465:Algorithms; D000818:Animals; D020137:Base Pair Mismatch; D004273:DNA, Neoplasm / Q000235:genetics*; D016678:Genome / Q000235:genetics*; D006801:Humans; D009369:Neoplasms / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software
chemical_list: D004273:DNA, Neoplasm