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Human Genetics

, Volume 119, Issue 1–2, pp 185–198 | Cite as

Identification of large-scale human-specific copy number differences by inter-species array comparative genomic hybridization

  • Violaine Goidts
  • Lluis Armengol
  • Werner Schempp
  • Jeffrey Conroy
  • Norma Nowak
  • Stefan Müller
  • David N. Cooper
  • Xavier Estivill
  • Wolfgang Enard
  • Justyna M. Szamalek
  • Horst Hameister
  • Hildegard Kehrer-SawatzkiEmail author
Original Investigation

Abstract

Copy number differences (CNDs), and the concomitant differences in gene number, have contributed significantly to the genomic divergence between humans and other primates. To assess its relative importance, the genomes of human, common chimpanzee, bonobo, gorilla, orangutan and macaque were compared by comparative genomic hybridization using a high-resolution human BAC array (aCGH). In an attempt to avoid potential interference from frequent intra-species polymorphism, pooled DNA samples were used from each species. A total of 322 sites of large-scale inter-species CND were identified. Most CNDs were lineage-specific but frequencies differed considerably between the lineages; the highest CND frequency among hominoids was observed in gorilla. The conserved nature of the orangutan genome has already been noted by karyotypic studies and our findings suggest that this degree of conservation may extend to the sub-microscopic level. Of the 322 CND sites identified, 14 human lineage-specific gains were observed. Most of these human-specific copy number gains span regions previously identified as segmental duplications (SDs) and our study demonstrates that SDs are major sites of CND between the genomes of humans and other primates. Four of the human-specific CNDs detected by aCGH map close to the breakpoints of human-specific karyotypic changes [e.g., the human-specific inversion of chromosome 1 and the polymorphic inversion inv(2)(p11.2q13)], suggesting that human-specific duplications may have predisposed to chromosomal rearrangement. The association of human-specific copy number gains with chromosomal breakpoints emphasizes their potential importance in mediating karyotypic evolution as well as in promoting human genomic diversity.

Keywords

Segmental Duplication Lymphoblastoid Cell Line Copy Number Gain AQP7 Gene Primate Genome 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgements

We thank Antje Kollak, Helene Spöri and Stefanie Raith for technical assistance. This research was funded by the Deutsche Forschungsgemeinschaft (DFG KE 724/2-1). L.A. and X.E. are supported by Genome Spain and the “Generaliyay de Catalunya”.

Supplementary material

439_2005_130_MOESM1_ESM.pdf (1.3 mb)
Supplementary material

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Copyright information

© Springer-Verlag 2006

Authors and Affiliations

  • Violaine Goidts
    • 1
  • Lluis Armengol
    • 2
  • Werner Schempp
    • 3
  • Jeffrey Conroy
    • 4
  • Norma Nowak
    • 4
  • Stefan Müller
    • 5
  • David N. Cooper
    • 6
  • Xavier Estivill
    • 2
    • 7
  • Wolfgang Enard
    • 8
  • Justyna M. Szamalek
    • 1
  • Horst Hameister
    • 1
  • Hildegard Kehrer-Sawatzki
    • 1
    Email author
  1. 1.Department of Human GeneticsUniversity of UlmUlmGermany
  2. 2.Program in Genes and Disease, Center for Genomic RegulationBarcelona Biomedical Research ParkBarcelonaSpain
  3. 3.Institute of Human Genetics and AnthropologyUniversity of FreiburgFreiburgGermany
  4. 4.Department of Cancer GeneticsRoswell Park Cancer InstituteBuffaloUSA
  5. 5.Institute of Anthropology und Human GeneticsLudwig-Maximilian-UniversityMünchenGermany
  6. 6.Institute of Medical GeneticsCardiff UniversityCardiffUK
  7. 7.Life and Health Science DepartmentPompeu Fabra UniversityBarcelonaSpain
  8. 8.Max-Planck Institute for Evolutionary AnthropologyLeipzigGermany

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