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

• Published in: Nature protocols Vol. 3; no. 5; pp. 849 - 865
• Main Authors: Patsalis, Philippos C, Kousoulidou, Ludmila, Männik, Katrin, Sismani, Carolina, ilina, Olga, Parkel, Sven, Puusepp, Helen, Tõnisson, Neeme, Palta, Priit, Remm, Maido, Kurg, Ants
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 01-05-2008; Nature Publishing Group
• Subjects: Analytical Chemistry; Biological Techniques; Biomedical and Life Sciences; Cloning; Comparative genomic hybridization; Computational Biology/Bioinformatics; Copy number variations; Deoxyribonucleic acid; DNA; DNA - metabolism; Genetic testing; Genetics; Genomes; Genomics; Genomics - methods; Hybridization; Identification and classification; Innovations; Life Sciences; Microarray Analysis - methods; Microarrays; Molecular Probe Techniques; Molecular Probes - metabolism; Nucleic Acid Hybridization - methods; Organic Chemistry; Probes; protocol; Software; Cyprus
• ISSN: 1754-2189; 1750-2799
• DOI: 10.1038/nprot.2008.49

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.