Human Genetics

, Volume 114, Issue 5, pp 464–467

Detection of DNA copy number abnormality by microarray expression analysis

  • Xiaofeng Zhou
  • Steven W. Cole
  • Shen Hu
  • David T. W. Wong
Original Investigation

DOI: 10.1007/s00439-004-1087-9

Cite this article as:
Zhou, X., Cole, S.W., Hu, S. et al. Hum Genet (2004) 114: 464. doi:10.1007/s00439-004-1087-9

Abstract

Gene copy-number abnormalities (CNAs) are characteristic of solid tumors and are found in association with developmental abnormalities and/or mental retardation. The ultimate impact of CNAs is exerted by the altered expression of encoded genes. We have utilized high-density oligonucleotide arrays from Affymetrix to identify DNA CNAs via their impact on mRNA expression levels. In these studies, we have used three different trisomic cell lines (trisomy 9, trisomy 18, trisomy 21) as models of CNAs and have compared mRNA expression in those trisomic cells with that observed in diploid cell lines of matched tissue origin. Our data clearly show that genes from CNA chromosome regions are substantially over-represented (P<0.000001 by chi-square analysis) in the differentially expressed subset from comparisons of all three trisomic cell lines with normal matching cells. In addition, we have been able to detect the origin of the duplication by a statistical scan for over-expressed genes. These data show that microarray detection of differential mRNA expression can be used to identify significant DNA CNAs.

Copyright information

© Springer-Verlag 2004

Authors and Affiliations

  • Xiaofeng Zhou
    • 1
  • Steven W. Cole
    • 2
  • Shen Hu
    • 1
  • David T. W. Wong
    • 1
    • 3
    • 4
    • 5
    • 6
  1. 1.Laboratory of Head and Neck Cancer Research, Dental Research Institute, School of DentistryUniversity of California at Los AngelesLos AngelesUSA
  2. 2.Division of Hematology-Oncology, Department of Medicine, David Geffen School of MedicineUniversity of California at Los AngelesLos AngelesUSA
  3. 3.Division of Oral Biology & Medicine, School of DentistryUniversity of California at Los AngelesLos AngelesUSA
  4. 4.Jonsson Comprehensive Cancer CenterUniversity of California at Los AngelesLos AngelesUSA
  5. 5.Molecular Biology InstituteUniversity of California at Los AngelesLos AngelesUSA
  6. 6.UCLA School of DentistryLos AngelesUSA