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Nucleic Acids Research 2005 33(22):e192; doi:10.1093/nar/gni191
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Published online 16 December 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Methods Online

Human and mouse oligonucleotide-based array CGH

Paul van den IJssel, Marianne Tijssen, Suet-Feung Chin1, Paul Eijk, Beatriz Carvalho, Erik Hopmans, Henne Holstege2, Dhinoth Kumar Bangarusamy3, Jos Jonkers2, Gerrit A. Meijer, Carlos Caldas1 and Bauke Ylstra*

Department of Pathology, VU University Medical Center Amsterdam, The Netherlands 1Cancer Genomics Program, Department of Oncology, University of Cambridge Cambridge, UK 2Division of Molecular Biology, The Netherlands Cancer Institute Amsterdam, The Netherlands 3Genome Institute of Singapore, Biomedical Sciences Institutes Singapore

*To whom correspondence should be addressed at Microarray Core Facility, VU University Medical Center, van der Boechorststraat 7-9, 1081 BT Amsterdam, The Netherlands. Tel: +31 20 444 8299; Fax: +31 20 444 8318; Email: b.ylstra{at}vumc.nl

Received July 19, 2005. Revised September 26, 2005. Accepted November 24, 2005.

Array-based comparative genomic hybridization is a high resolution method for measuring chromosomal copy number changes. Here we present a validated protocol using in-house spotted oligonucleotide libraries for array comparative genomic hybridization (CGH). This oligo array CGH platform yields reproducible results and is capable of detecting single copy gains, multi-copy amplifications as well as homozygous and heterozygous deletions as small as 100 kb with high resolution. A human oligonucleotide library was printed on amine binding slides. Arrays were hybridized using a hybstation and analysed using BlueFuse feature extraction software, with >95% of spots passing quality control. The protocol allows as little as 300 ng of input DNA and a 90% reduction of Cot-1 DNA without compromising quality. High quality results have also been obtained with DNA from archival tissue. Finally, in addition to human oligo arrays, we have applied the protocol successfully to mouse oligo arrays. We believe that this oligo-based platform using ‘off-the-shelf’ oligo libraries provides an easy accessible alternative to BAC arrays for CGH, which is cost-effective, available at high resolution and easily implemented for any sequenced organism without compromising the quality of the results.


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