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Personalized copy number and segmental duplication maps using next-generation sequencing.

Despite their importance in gene innovation and phenotypic variation, duplicated regions have remained largely intractable owing to difficulties in accurately resolving their structure, copy number and sequence content. We present an algorithm (mrFAST) to comprehensively map next-generation sequence reads, which allows for the prediction of absolute copy-number variation of duplicated segments and genes. We examine three human genomes and experimentally validate genome-wide copy number differences. We estimate that, on average, 73-87 genes vary in copy number between any two individuals and find that these genic differences overwhelmingly correspond to segmental duplications (odds ratio = 135; P < 2.2 x 10(-16)). Our method can distinguish between different copies of highly identical genes, providing a more accurate assessment of gene content and insight into functional constraint without the limitations of array-based technology.

Pubmed ID: 19718026


  • Alkan C
  • Kidd JM
  • Marques-Bonet T
  • Aksay G
  • Antonacci F
  • Hormozdiari F
  • Kitzman JO
  • Baker C
  • Malig M
  • Mutlu O
  • Sahinalp SC
  • Gibbs RA
  • Eichler EE


Nature genetics

Publication Data

October 29, 2009

Associated Grants

  • Agency: NHGRI NIH HHS, Id: HG004120
  • Agency: NHGRI NIH HHS, Id: P01 HG004120
  • Agency: NHGRI NIH HHS, Id: P01 HG004120-03
  • Agency: NHGRI NIH HHS, Id: R01 HG006004
  • Agency: Howard Hughes Medical Institute, Id:
  • Agency: Howard Hughes Medical Institute, Id:

Mesh Terms

  • Algorithms
  • Chromosome Mapping
  • DNA
  • Gene Dosage
  • Gene Duplication
  • Genome, Human
  • Genomic Library
  • Humans
  • Polymorphism, Genetic
  • Sequence Analysis, DNA