High-resolution ROMA CGH and FISH analysis of aneuploid and diploid breast tumors

Hicks, J. B., Muthuswamy, L., Krasnitz, A., Navin, N. E., Riggs, M., Grubor, V., Esposito, D., Alexander, J., Troge, J. E., Wigler, M. H., Maner, S., Lundin, P., Zetterberg, A. (2005) High-resolution ROMA CGH and FISH analysis of aneuploid and diploid breast tumors. Cold Spring Harb Symp Quant Biol, 70. pp. 51-63. ISSN 1943-4456 (Electronic) 0091-7451 (Linking)

URL: http://www.ncbi.nlm.nih.gov/pubmed/16869738
DOI: 10.1101/sqb.2005.70.055

Abstract

Combining representational oligonucleotide microarray analysis (ROMA) of tumor DNA with fluorescence in situ hybridization (FISH) of individual tumor cells provides the opportunity to detect and validate a wide range of amplifications, deletions, and rearrangements directly in frozen tumor samples. We have used these combined techniques to examine 101 aneuploid and diploid breast tumors for which long-term follow-up and detailed clinical information were available. We have determined that ROMA provides accurate and sensitive detection of duplications, amplifications, and deletions and yields defined boundaries for these events with a resolution of <50 kbp in most cases. We find that diploid tumors exhibit fewer rearrangements on average than aneuploids, but rearrangements occur at the same locations in both types. Diploid tumors reflect at least three consistent patterns of rearrangement. The reproducibility and frequency of these events, especially in very early stage tumors, provide insight into the earliest chromosomal events in breast cancer. We have also identified correlations between certain sets of rearrangement events and clinically relevant parameters such as long-term survival. These correlations may enable novel prognostic indicators for breast and other cancers as more samples are analyzed.

Item Type: Paper
Uncontrolled Keywords: Aneuploidy Breast Neoplasms genetics pathology DNA Neoplasm genetics Diploidy Female Gene Expression Profiling Gene Rearrangement Genomics Humans In Situ Hybridization, Fluorescence Oligonucleotide Array Sequence Analysis Prognosis
Subjects: Investigative techniques and equipment
Investigative techniques and equipment > ROMA
diseases & disorders > cancer > cancer types > breast cancer
CSHL Authors:
Communities: CSHL labs > Hicks lab
CSHL labs > Krasnitz lab
CSHL labs > Wigler lab
Depositing User: CSHL Librarian
Date Deposited: 12 Apr 2012 19:31
Last Modified: 01 Mar 2013 19:52
Related URLs:
URI: http://repository.cshl.edu/id/eprint/26198

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