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Genome-wide detection of chromosomal imbalances in tumors using BAC microarrays

Abstract

Chromosomal imbalances such as deletions and amplifications are common rearrangements in most tumors1. Specific rearrangements are consistently associated with specific tumor types or stages, implicating the role of the genes in a region of chromosomal imbalance in tumor initiation and progression2. The development of comparative genomic hybridization (CGH)3 has obviated the need to obtain metaphase spreads from tumors, so that the chromosomal imbalances in many solid tumors may be revealed using an extracted genomic DNA sample. However, the resolution of the cytogenetic method remains and the extreme technical difficulty of CGH has restricted its use. Conceptually, DNA microarray4–based CGH is an obvious solution to all of the limitations of conventional CGH. Although arrays have been used for CGH studies5,6,7,8, their success has been limited by poor specific signal-to-noise ratios. Here we demonstrate a microarray-based CGH method that allows reliable detection of chromosomal deletions and amplifications with high resolution. Our microarray system is fundamentally different from most current microarray technologies in that activated DNA is printed on natural glass surfaces while other systems almost exclusively focus on activating the surfaces, a strategy that invariably introduces hybridization backgrounds. The concept of using pre-modification may be generally applied for making arrays of other biological materials, as modifying the substrates will be more controllable in solution than on surfaces.

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Figure 1: Background and spot morphology comparison of a conventional array with that of modified DNA.
Figure 2: Spectrum of chromosomal imbalances in radiation-induced mouse lymphomas.
Figure 3: Comparison of BAC array CGH and SLLP LOH genotyping results.

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Acknowledgements

W.W.C. was a Jane Coffin Childs research fellow. This work was supported by NCI and the Baylor prostate SPORE program. We thank Alec Wang for the cDNA clones and other valuable reagents.

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Correspondence to Allan Bradley.

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Cai, WW., Mao, JH., Chow, CW. et al. Genome-wide detection of chromosomal imbalances in tumors using BAC microarrays. Nat Biotechnol 20, 393–396 (2002). https://doi.org/10.1038/nbt0402-393

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