SURVEY AND SUMMARY BAC to the future! or oligonucleotides: a perspective for micro array comparative genomic hybridization (array CGH)

The array CGH technique (Array Comparative Genome Hybridization) has been developed to detect chromosomal copy number changes on a genomewide 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. ARRAY CGH IMPROVES SPATIAL RESOLUTION Classical comparative genomic hybridization provided the possibility for detecting chromosomal copy number changes in cell and tissue samples, similar to karyotyping, without the need of culturing (1). Even formalin-fixed paraffin-embedded (FFPE) archival material could be analyzed, allowing for the exploration of large clinical tissue archives (2–4). Yet, resolution was limited and analysis required a high level of cytogenetic expertise. Array CGH was introduced in the late nineties (4) and overcame these two major drawbacks. Several excellent reviews have been written on the applications and current status of array CGH of which we highly recommend Pinkel and Alberston (5), among others (6–9). The first array CGH platforms generally used large-insert clones, such as BAC (Bacterial Artificial Chromosomes), YAC (Yeast Artificial Chromosomes) or PAC (P1-derived Artificial Chromosomes) clones. Later, also the shorter cosmids and fosmids clones were introduced as spotted elements (5), as well as 130–600 bp single-stranded DNA molecules (10). Several laboratories used cDNA arrays, initially designed for expression profiling, as an alternative for measuring chromosomal copy number changes (2). Even though this approach certainly has yielded valuable information, it cannot compete with the current platforms in terms of its maximal achievable resolution. Advantages and disadvantages of the cDNA platform for array CGH are discussed in further detail by Davies et al. (8). Until recently, commercial alternatives have had very limited resolution, 3 Mb or less which is comparable with conventional CGH (1,11,12). As a result of the lack of widely accessible platforms, the possibilities of oligonucleotides as spotted elements on the arrays have been successfully explored. Oligonucleotide array CGH (oaCGH) now offers genome-covering resolution. To our knowledge, we are the only group that developed both oaCGH (13–15) as well as BAC-based array CGH (16–20), without a commercial *To whom correspondence should be addressed. Tel: +31 20 444 8299; Fax: +31 20 444 8318; Email: [email protected] 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 [email protected] Nucleic Acids Research, 2006, Vol. 34, No. 2 445–450 doi:10.1093/nar/gkj456 Published online January 26, 2006