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High-resolution cDNA microarray CGH mapping of genomic imbalances in osteosarcoma using formalin-fixed
M Zielenska1, P Marrano, P Thorner
1Department of Laboratory Medicine and Pathobiology, University of Toronto, Princess Margaret Hospital and The Ontario Cancer Institute, Ont, Canada.
Cytogenetic and Genome Research
|August 12, 2004
Summary
Array comparative genomic hybridization (CGH) using cDNA microarrays identified chromosomal imbalances in osteosarcoma (OS) FFPE tissues. Chromosomes X, 1, 12, and 17 showed the most significant genomic alterations in OS.
Area of Science:
- Genomic instability in cancer
- Molecular oncology
- Cytogenetics
Background:
- Formalin-fixed paraffin-embedded (FFPE) tumor tissue is valuable for retrospective genomic studies.
- Comparative genomic hybridization (CGH) has provided cytogenetic information on osteosarcoma (OS), but metaphase CGH has limited resolution.
- Array CGH offers improved detection and delineation of copy number aberrations, but high costs and limited array density have hindered comprehensive profiling of tumors like OS.
Purpose of the Study:
- To investigate chromosomal imbalances in osteosarcoma (OS) using a cDNA/EST microarray-based CGH approach.
- To precisely map copy number alterations in FFPE OS samples.
- To identify recurrent genomic aberrations associated with osteosarcoma development.
Main Methods:
- CGH analysis was performed on eight OS FFPE samples using a microarray with 18,980 human cDNAs.
- The microarray covered all autosomal chromosomes and the X chromosome.
- Interphase fluorescence in situ hybridization (FISH) was used to validate specific findings, including X chromosome gain/amplification.
Main Results:
- Chromosomes 1, 12, 17, and X exhibited the most frequent chromosomal imbalances in the analyzed OS samples.
- Gain/amplification of the X chromosome was detected in 4 out of 8 OS cases.
- Gain/amplification of 17p11.2 was frequently observed alongside a distal deletion in the p53 gene region.
Conclusions:
- cDNA microarray-based CGH is effective for profiling genomic imbalances in FFPE osteosarcoma.
- Recurrent copy number alterations, particularly involving chromosome X and the p53 locus, are significant in osteosarcoma.
- Further investigation into the role of these genomic aberrations in OS oncogenesis is warranted.
