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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.

SUBMITTER: Wang J

PROVIDER: S-EPMC3527068 | biostudies-literature | 2011 Jun

REPOSITORIES: biostudies-literature

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CREST maps somatic structural variation in cancer genomes with base-pair resolution.

Wang Jianmin J Mullighan Charles G CG Easton John J Roberts Stefan S Heatley Sue L SL Ma Jing J Rusch Michael C MC Chen Ken K Harris Christopher C CC Ding Li L Holmfeldt Linda L Payne-Turner Debbie D Fan Xian X Wei Lei L Zhao David D Obenauer John C JC Naeve Clayton C Mardis Elaine R ER Wilson Richard K RK Downing James R JR Zhang Jinghui J

Nature methods 20110612 8

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 CRE ...[more]

PMID: 21666668

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