Computational methods for discovering structural variation with next-generation sequencing

Paul Medvedev, Monica Stanciu, Michael Brudno

Research output: Contribution to journalArticlepeer-review

430 Scopus citations


In the last several years, a number of studies have described large-scale structural variation in several genomes. Traditionally, such methods have used whole-genome array comparative genome hybridization or single-nucleotide polymorphism arrays to detect large regions subject to copy-number variation. Later techniques have been based on paired-end mapping of Sanger sequencing data, providing better resolution and accuracy. With the advent of next-generation sequencing, a new generation of methods is being developed to tackle the challenges of short reads, while taking advantage of the high coverage the new sequencing technologies provide. In this survey, we describe these methods, including their strengths and their limitations, and future research directions.

Original languageEnglish (US)
Pages (from-to)S13
JournalNature methods
Issue number11S
StatePublished - Nov 2009

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Biochemistry
  • Molecular Biology
  • Cell Biology


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