CREST maps somatic structural variation in cancer genomes with base-pair resolution
- 12 June 2011
- journal article
- research article
- Published by Springer Science and Business Media LLC in Nature Methods
- Vol. 8 (8), 652-654
- https://doi.org/10.1038/nmeth.1628
Abstract
This algorithm uses the soft-clipped, unaligned parts of a sequence read to map structural variation in cancer genomes with high predictive accuracy. 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.Keywords
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