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Nat Methods. 2011 Jun 12;8(8):652-4. doi: 10.1038/nmeth.1628.

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

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  • 1Department of Information Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.

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.

PMID:
21666668
[PubMed - indexed for MEDLINE]
PMCID:
PMC3527068
Free PMC Article

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