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Nucleic Acids Research 2006 34(2):445-450; doi:10.1093/nar/gkj456
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Published online 26 January 2006

© The Author 2006. 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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BAC to the future! or oligonucleotides: a perspective for micro array comparative genomic hybridization (array CGH)

Bauke Ylstra*, Paul van den IJssel, Beatriz Carvalho, Ruud H. Brakenhoff1 and Gerrit A. Meijer

Department of Pathology, VU University Medical Center PO Box 7057, 1007 MB Amsterdam, The Netherlands 1Department of Otolaryngology/Head-Neck Surgery, VU University Medical Center PO Box 7057, 1007 MB Amsterdam, The Netherlands

*To whom correspondence should be addressed. Tel: +31 20 444 8299; Fax: +31 20 444 8318; Email: b.ylstra{at}vumc.nl

Received October 24, 2005. Revised December 8, 2005. Accepted January 4, 2006.

The array CGH technique (Array Comparative Genome Hybridization) has been developed to detect chromosomal copy number changes on a genome-wide and/or high-resolution scale. It is used in human genetics and oncology, with great promise for clinical application. Until recently primarily PCR amplified bacterial artificial chromosomes (BACs) or cDNAs have been spotted as elements on the array. The large-scale DNA isolations or PCR amplifications of the large-insert clones necessary for manufacturing the arrays are elaborate and time-consuming. Lack of a high-resolution highly sensitive (commercial) alternative has undoubtedly hindered the implementation of array CGH in research and diagnostics. Recently, synthetic oligonucleotides as arrayed elements have been introduced as an alternative substrate for array CGH, both by academic institutions as well as by commercial providers. Oligonucleotide libraries or ready-made arrays can be bought off-the-shelf saving considerable time and efforts. For RNA expression profiling, we have seen a gradual transition from in-house printed cDNA-based expression arrays to oligonucleotide arrays and we expect a similar transition for array CGH. This review compares the different platforms and will attempt to shine a light on the ‘BAC to the future’ of the array CGH technique.


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