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Nucleic Acids Research 2005 33(18):e159; doi:10.1093/nar/gni161
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Published online 12 October 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

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Rapid detection of genomic imbalances using micro-arrays consisting of pooled BACs covering all human chromosome arms

Jeroen Knijnenburg, Marja van der Burg, Philomeen Nilsson1, Hans Kristian Ploos van Amstel1, Hans Tanke and Károly Szuhai*

Department of Molecular Cell Biology, Leiden University Medical Center Wassenaarseweg 72, 2333 AL Leiden, The Netherlands 1Department of Medical Genetics, Utrecht Medical Center Lundlaan 6, 3584 EA Utrecht, The Netherlands

*To whom correspondence should be addressed. Tel: 31 71 5276194; Fax: 31 71 5276180; Email: k.szuhai{at}lumc.nl

Received August 12, 2005. Revised September 27, 2005. Accepted September 27, 2005.

A strategy is presented to select, pool and spot human BAC clones on an array in such a way that each spot contains five well performing BAC clones, covering one chromosome arm. A mini-array of 240 spots was prepared representing all human chromosome arms in a 5-fold as well as some controls, and used for comparative genomic hybridization (CGH) of 10 cell lines with aneusomies frequently found in clinical cytogenetics and oncology. Spot-to-spot variation within five replicates was below 6% and all expected abnormalities were detected 100% correctly. Sensitivity was such that replacing one BAC clone in a given spot of five by a BAC clone from another chromosome, thus resulting in a change in ratio of 20%, was reproducibly detected. Incubation time of the mini-array was varied and the fluorescently labelled target DNA was diluted. Typically, aneusomies could be detected using 30 ng of non-amplified random primed labelled DNA amounts in a 4 h hybridization reaction. Potential application of these mini-arrays for genomic profiling of disseminated tumour cells or of blastomeres for preimplantation genetic diagnosis, using specially designed DNA amplification methods, are discussed.


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