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Open Access Methodology article

Microarray MAPH: accurate array-based detection of relative copy number in genomic DNA

Brian Gibbons1, Parikkhit Datta1, Ying Wu2, Alan Chan2 and John AL Armour1*

Author Affiliations

1 Institute of Genetics, University of Nottingham, QMC, Nottingham NG7 2UH, UK

2 PamGene International B.V., P.O. Box 1345, 5200 BJ 's-Hertogenbosch, The Netherlands

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BMC Genomics 2006, 7:163  doi:10.1186/1471-2164-7-163

Published: 30 June 2006

Abstract

Background

Current methods for measurement of copy number do not combine all the desirable qualities of convenience, throughput, economy, accuracy and resolution. In this study, to improve the throughput associated with Multiplex Amplifiable Probe Hybridisation (MAPH) we aimed to develop a modification based on the 3-Dimensional, Flow-Through Microarray Platform from PamGene International. In this new method, electrophoretic analysis of amplified products is replaced with photometric analysis of a probed oligonucleotide array. Copy number analysis of hybridised probes is based on a dual-label approach by comparing the intensity of Cy3-labelled MAPH probes amplified from test samples co-hybridised with similarly amplified Cy5-labelled reference MAPH probes. The key feature of using a hybridisation-based end point with MAPH is that discrimination of amplified probes is based on sequence and not fragment length.

Results

In this study we showed that microarray MAPH measurement of PMP22 gene dosage correlates well with PMP22 gene dosage determined by capillary MAPH and that copy number was accurately reported in analyses of DNA from 38 individuals, 12 of which were known to have Charcot-Marie-Tooth disease type 1A (CMT1A).

Conclusion

Measurement of microarray-based endpoints for MAPH appears to be of comparable accuracy to electrophoretic methods, and holds the prospect of fully exploiting the potential multiplicity of MAPH. The technology has the potential to simplify copy number assays for genes with a large number of exons, or of expanded sets of probes from dispersed genomic locations.