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Detection of DNA copy number abnormality by microarray expression analysis

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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.

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References

  • Albertson DG, Pinkel D (2003) Genomic microarrays in human genetic disease and cancer. Hum Mol Genet (in press)

  • Capone GT (2001) Down syndrome: advances in molecular biology and the neurosciences. J Dev Behav Pediatr 22:40–59

    CAS  PubMed  Google Scholar 

  • Efron B Tibshirani RJ (1993) An introduction to the bootstrap. Chapman & Hall, New York

  • Fleiss JL (1981) Statistical methods for rates and proportions. Wiley, New York

  • Forozan F, Karhu R, Kononen J, Kallioniemi A, Kallioniemi OP (1997) Genome screening by comparative genomic hybridization. Trends Genet 13:405–409

    Article  CAS  PubMed  Google Scholar 

  • Kashiwagi H, Uchida K (2000) Genome-wide profiling of gene amplification and deletion in cancer. Hum Cell 13:135–141

    CAS  PubMed  Google Scholar 

  • Popescu NC, Zimonjic DB (1997) Molecular cytogenetic characterization of cancer cell alterations. Cancer Genet Cytogenet 93:10–21

    Article  CAS  PubMed  Google Scholar 

  • Schwab M (1999) Oncogene amplification in solid tumors. Semin Cancer Biol 9:319–325

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

This work was supported in part by NIH PHS grants R21 CA94216 (to D. Wong), R21 AI49135, and R01 AI52737 (to S. Cole), and NIH training grant DE07296-07 and a CRFA fellowship (to X. Zhou). The Affymetrix U133A array hybridization and scanning were performed in the UCLA DNA microarray facility.

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Correspondence to David T. W. Wong.

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Zhou, X., Cole, S.W., Hu, S. et al. Detection of DNA copy number abnormality by microarray expression analysis. Hum Genet 114, 464–467 (2004). https://doi.org/10.1007/s00439-004-1087-9

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  • DOI: https://doi.org/10.1007/s00439-004-1087-9

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