CMT 1A: Microarray MAPH: accurate array-based detection of relative copy number

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BMC Genomics. 2006 Jun 30;7(1):163

Microarray MAPH: accurate array-based detection of relative copy

number in genomic DNA.

Gibbons B, Datta P, Wu Y, Chan A, Armour JA.

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).

CONCLUSIONS: 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.