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

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.

Pubmed ID: 21666668


  • Wang J
  • Mullighan CG
  • Easton J
  • Roberts S
  • Heatley SL
  • Ma J
  • Rusch MC
  • Chen K
  • Harris CC
  • Ding L
  • Holmfeldt L
  • Payne-Turner D
  • Fan X
  • Wei L
  • Zhao D
  • Obenauer JC
  • Naeve C
  • Mardis ER
  • Wilson RK
  • Downing JR
  • Zhang J


Nature methods

Publication Data

August 29, 2011

Associated Grants

  • Agency: NCI NIH HHS, Id: P30 CA021765
  • Agency: NCI NIH HHS, Id: P30 CA021765

Mesh Terms

  • Algorithms
  • Animals
  • Base Pair Mismatch
  • DNA, Neoplasm
  • Genome
  • Humans
  • Neoplasms
  • Polymorphism, Single Nucleotide
  • Sequence Alignment
  • Sequence Analysis, DNA
  • Software