Protocol abstract


Nature Protocols 3, 849 - 865 (2008)
Published online: 24 April 2008 | doi:10.1038/nprot.2008.49

Subject Categories: Genetic analysis | Genomics and proteomics | Nucleic acid based molecular biology

Array-MAPH: a methodology for the detection of locus copy-number changes in complex genomes

Ludmila Kousoulidou1, Katrin Männik2, Carolina Sismani1, Olga Z caronilina2, Sven Parkel2, Helen Puusepp2, Neeme Tõnisson2, Priit Palta2, Maido Remm2, Ants Kurg2 & Philippos C Patsalis1


High-throughput genome-wide screening methods to detect subtle genomic imbalances are extremely important for diagnostic genetics and genomics. Here, we provide a detailed protocol for a microarray-based technique, applying the principle of multiplex amplifiable probe hybridization (MAPH). Methodology and software have been developed for designing unique PCR-amplifiable sequences (400–600 bp) covering any genomic region of interest. These sequences are amplified, cloned and spotted onto arrays (targets). A mixture of the same sequences (probes) is hybridized to genomic DNA immobilized on a membrane. Bound probes are recovered and quantitatively amplified by PCR, labeled and hybridized to the array. The procedure can be completed in 4–5 working days, excluding microarray preparation. Unlike array-comparative genomic hybridization (array-CGH), test DNA of specifically reduced complexity is hybridized to an array of identical small amplifiable target sequences, resulting in increased hybridization specificity and higher potential for increasing resolution. Array-MAPH can be used for detection of small-scale copy-number changes in complex genomes, leading to genotype–phenotype correlations and the discovery of new genes.

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

Correspondence to: Philippos C Patsalis1 e-mail: patsalis@cing.ac.cy

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