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Nucleic Acids Research 2004 32(19):e146; doi:10.1093/nar/gnh142
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Published online 28 October 2004

Nucleic Acids Research, Vol. 32 No. 19 © Oxford University Press 2004; all rights reserved

Genomic profiling by DNA amplification of laser capture microdissected tissues and array CGH

Joana Cardoso1,2, Lia Molenaar1,2, Renée X. de Menezes3, Carla Rosenberg4, Hans Morreau5, Gabriela Möslein6, Riccardo Fodde1 and Judith M. Boer2,*

1 Department of Pathology, Josephine Nefkens Institute, Erasmus University Medical Center, Rotterdam, The Netherlands, 2 Center for Human and Clinical Genetics, 3 Department of Medical Statistics, 4 Department of Molecular and Cellular Biology and 5 Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands and 6 Department of Surgery, Heinrich Heine University, Düsseldorf, Germany

* To whom correspondence should be addressed at Center for Human and Clinical Genetics, Leiden University Medical Center, Wassenaarseweg 72, 2333 AL Leiden, The Netherlands. Tel: +31 71 527 6611; Fax: +31 71 527 6075; Email: j.m.boer{at}lumc.nl

Received August 24, 2004; Revised September 21, 2004; Accepted September 30, 2004

Comparative genomic hybridization by means of BAC microarrays (array CGH) allows high-resolution profiling of copy-number aberrations in tumor DNA. However, specific genetic lesions associated with small but clinically relevant tumor areas may pass undetected due to intra-tumor heterogeneity and/or the presence of contaminating normal cells. Here, we show that the combination of laser capture microdissection, {phi}29 DNA polymerase-mediated isothermal genomic DNA amplification, and array CGH allows genomic profiling of very limited numbers of cells. Moreover, by means of simple statistical models, we were able to bypass the exclusion of amplification distortions and variability prone areas, and to detect tumor-specific chromosomal gains and losses. We applied this new combined experimental and analytical approach to the genomic profiling of colorectal adenomatous polyps and demonstrated our ability to accurately detect single copy gains and losses affecting either whole chromosomes or small genomic regions from as little as 2 ng of DNA or 1000 microdissected cells.


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