1. ¹Department of Cytogenetics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
2. ²Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu/Estonia Biocentre, Tartu, Estonia

Correspondence: Dr PC Patsalis, Department of Cytogenetics, The Cyprus Institute of Neurology and Genetics, PO Box 23462, 1683 Nicosia, Cyprus. Tel: +357 22 39 26 95; Fax: +357 22 39 27 93; E-mail: patsalis@cing.ac.cy

Received 6 July 2006; Revised 28 September 2006; Accepted 12 October 2006; Published online 22 November 2006.

Abstract

Array-based genome-wide screening methods were recently introduced to clinical practice in order to detect small genomic imbalances that may cause severe genetic disorders. The continuous advancement of such methods plays an extremely important role in diagnostic genetics and medical genomics. We have modified and adapted the original multiplex amplifiable probe hybridization (MAPH) to a novel microarray format providing an important new diagnostic tool for detection of small size copy-number changes in any locus of human genome. Here, we describe the new array-MAPH diagnostic method and show proof of concept through fabrication, interrogation and validation of a human chromosome X-specific array. We have developed new bioinformatic tools and methodology for designing and producing amplifiable hybridization probes (200–600 bp) for array-MAPH. We designed 558 chromosome X-specific probes with median spacing 238 kb and 107 autosomal probes, which were spotted onto microarrays. DNA samples from normal individuals and patients with known and unknown chromosome X aberrations were analyzed for validation. Array-MAPH detected exactly the same deletions and duplications in blind studies, as well as other unknown small size deletions showing its accuracy and sensitivity. All results were confirmed by fluorescence in situ hybridization and probe-specific PCR. Array-MAPH is a new microarray-based diagnostic tool for the detection of small-scale copy-number changes in complex genomes, which may be useful for genotype–phenotype correlations, identification of new genes, studying genetic variation and provision of genetic services.