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.
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Acknowledgements
This work was funded by the grants 30/2001 from the Cyprus RPF, QLRT-2001-01810 from the EURO-MRX EU, 5467 from the Estonian Science Foundation, by 0182649s04 from the Estonian Ministry of Education and Research and by 070191/Z/03/Z from the Wellcome Trust International Senior Research Grant. We thank D Andreou, C Tryfonos, E Hadjiyanni, C Pitta, C Antoniades, S Bashiardes and G Slavin for their contribution. Many thanks to Professor J Vermeesch, Dr K Õunap and Dr R Žordania for the provision of DNA samples and the Wellcome Trust Sanger Institute for the provision of BAC/PAC clones.
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Supplementary Information accompanies the paper on European Journal of Human Genetics website (http://www.nature.com/ejhg)
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Patsalis, P., Kousoulidou, L., Männik, K. et al. Detection of small genomic imbalances using microarray-based multiplex amplifiable probe hybridization. Eur J Hum Genet 15, 162–172 (2007). https://doi.org/10.1038/sj.ejhg.5201738
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DOI: https://doi.org/10.1038/sj.ejhg.5201738
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