Genome-wide comparison of differences in the integration sites of interspersed repeats between closely related genomes

Nucleic Acids Res. 2002 Jul 15;30(14):e71. doi: 10.1093/nar/gnf071.


A technique for genome-wide detection of differences in the integration site positions of interspersed repeats in related genomes (DiffIR) is described. The technique is based on a whole- genome selective PCR amplification of the repeats' flanking regions followed by a differential hybridization screening of the arrayed library of the selected amplicons. The technique was successfully applied to the comparison of the integration sites in the human and chimpanzee genomes, allowing us to discover 11 new human-specific integrations of human endogenous retrovirus, K family (HML-2) long terminal repeats.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • DNA / chemistry
  • DNA / genetics
  • Endogenous Retroviruses / genetics*
  • Genome
  • Genome, Human*
  • Humans
  • Molecular Sequence Data
  • Nucleic Acid Amplification Techniques
  • Pan troglodytes / genetics
  • Sequence Analysis, DNA
  • Terminal Repeat Sequences / genetics*
  • Virus Integration / genetics*


  • DNA

Associated data

  • GENBANK/AF493416
  • GENBANK/AF493417
  • GENBANK/AF493418
  • GENBANK/AF493419
  • GENBANK/AF493420
  • GENBANK/AF493421
  • GENBANK/AF493422
  • GENBANK/AF493423
  • GENBANK/AF493424
  • GENBANK/AF493425
  • GENBANK/AF493426