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BreakDancer: an algorithm for high-resolution mapping of genomic structural variation.

Detection and characterization of genomic structural variation are important for understanding the landscape of genetic variation in human populations and in complex diseases such as cancer. Recent studies demonstrate the feasibility of detecting structural variation using next-generation, short-insert, paired-end sequencing reads. However, the utility of these reads is not entirely clear, nor are the analysis methods with which accurate detection can be achieved. The algorithm BreakDancer predicts a wide variety of structural variants including insertion-deletions (indels), inversions and translocations. We examined BreakDancer's performance in simulation, in comparison with other methods and in analyses of a sample from an individual with acute myeloid leukemia and of samples from the 1,000 Genomes trio individuals. BreakDancer sensitively and accurately detected indels ranging from 10 base pairs to 1 megabase pair that are difficult to detect via a single conventional approach.

Pubmed ID: 19668202


  • Chen K
  • Wallis JW
  • McLellan MD
  • Larson DE
  • Kalicki JM
  • Pohl CS
  • McGrath SD
  • Wendl MC
  • Zhang Q
  • Locke DP
  • Shi X
  • Fulton RS
  • Ley TJ
  • Wilson RK
  • Ding L
  • Mardis ER


Nature methods

Publication Data

September 31, 2009

Associated Grants

  • Agency: NHGRI NIH HHS, Id: HG003079
  • Agency: NCI NIH HHS, Id: P01 CA101937
  • Agency: NHGRI NIH HHS, Id: U54 HG003079

Mesh Terms

  • Algorithms
  • Base Sequence
  • Computer Simulation
  • DNA
  • Genetic Variation
  • Genome, Human
  • Genomics
  • Humans
  • Leukemia, Myeloid, Acute
  • Sequence Analysis, DNA