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

2011; Nature Portfolio; Volume: 8; Issue: 8 Linguagem: Inglês

10.1038/nmeth.1628

1548-7105

Jianmin Wang, Charles G. Mullighan, John Easton, Stefan Roberts, Susan L. Heatley, Jing Ma, Michael Rusch, Ken Chen, Christopher Harris, Li Ding, Linda Holmfeldt, Debbie Payne-Turner, Xian Fan, Lei Wei, David Zhao, John C. Obenauer, Clayton W. Naeve, Elaine R. Mardis, Richard K. Wilson, James R. Downing, Jinghui Zhang,

Genomics and Phylogenetic Studies

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.