Abstract
Objectives: The aim of this study was to develop and validate a comparative genomic hybridisation (CGH) array that would allow simultaneous targeted analysis of a panel of disease genes and low resolution whole genome analysis. Methods: A bespoke Roche NimbleGen 12x135K CGH array (Roche NimbleGen Inc., Madison, Wisconsin, USA) was designed to interrogate the coding regions of 66 genes of interest, with additional widelyspaced backbone probes providing coverage across the whole genome. We analysed genomic deoxyribonucleic acid (DNA) from 20 patients with a range of previously characterised copy number changes and from 8 patients who had not previously undergone any form of dosage analysis. Results: The custom-designed Roche NimbleGen CGH array was able to detect known copy number changes in all 20 patients. A molecular diagnosis was also made for one of the additional 4 patients with a clinical diagnosis that had not been confirmed by sequence analysis, and carrier testing for familial copy number variants was successfully completed for the remaining four patients. Conclusion: The custom-designed CGH array described here is ideally suited for use in a small diagnostic laboratory. The method is robust, accurate, and cost-effective, and offers an ideal alternative to more conventional targeted assays such as multiplex ligation-dependent probe amplification.
Publication details
- DOI
- 10.18295/2075-0528.1432
- Journal
- Sultan Qaboos University Medical Journal, 13(1), 69-79
- Publisher
- Sultan Qaboos University
- Open access
- Gold open access
- License
- CC BY-ND 4.0
Cite this article
APA 7
Marquis-Nicholson, R., Doherty, E., Lan, J. M., Chuan-Ching, George, A. M., Thrush, A., & Love, D. R. (2025). Array-based Identification of Copy Number Changes in a Diagnostic Setting: Simultaneous gene-focused and low resolution whole human genome analysis. Sultan Qaboos University Medical Journal, 13(1), 69-79. https://doi.org/10.18295/2075-0528.1432
MLA 9
Marquis-Nicholson, Renate, et al. "Array-based Identification of Copy Number Changes in a Diagnostic Setting: Simultaneous gene-focused and low resolution whole human genome analysis." Sultan Qaboos University Medical Journal, vol. 13, no. 1, 2025, pp. 69-79. https://doi.org/10.18295/2075-0528.1432.
Chicago (author–date)
Marquis-Nicholson, Renate, Elaine Doherty, Jennifer M. Lan, Chuan-Ching, Alice M. George, Anthony Thrush, and Donald R. Love. 2025. "Array-based Identification of Copy Number Changes in a Diagnostic Setting: Simultaneous gene-focused and low resolution whole human genome analysis." Sultan Qaboos University Medical Journal 13 (1): 69-79. https://doi.org/10.18295/2075-0528.1432.
Harvard
Marquis-Nicholson, R., Doherty, E., Lan, J. M., Chuan-Ching, George, A. M., Thrush, A. and Love, D. R. (2025) 'Array-based Identification of Copy Number Changes in a Diagnostic Setting: Simultaneous gene-focused and low resolution whole human genome analysis', Sultan Qaboos University Medical Journal, 13(1), pp. 69-79. doi:10.18295/2075-0528.1432.
Vancouver
Marquis-Nicholson R, Doherty E, Lan JM, Chuan-Ching, George AM, Thrush A, et al. Array-based Identification of Copy Number Changes in a Diagnostic Setting: Simultaneous gene-focused and low resolution whole human genome analysis. Sultan Qaboos University Medical Journal. 2025;13(1):69-79. doi:10.18295/2075-0528.1432
IEEE
R. Marquis-Nicholson, E. Doherty, J. M. Lan, Chuan-Ching, A. M. George, A. Thrush, and D. R. Love, "Array-based Identification of Copy Number Changes in a Diagnostic Setting: Simultaneous gene-focused and low resolution whole human genome analysis," Sultan Qaboos University Medical Journal, vol. 13, no. 1, pp. 69-79, 2025, doi: 10.18295/2075-0528.1432.