Array-MAPH: a methodology for the detection of locus copy-number changes in complex genomes.
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.
Kousoulidou
Ludmila
L
Department of Cytogenetics, The Cyprus Institute of Neurology & Genetics, Nicosia, Cyprus.
Männik
Katrin
K
Sismani
Carolina
C
Zilina
Olga
O
Parkel
Sven
S
Puusepp
Helen
H
Tõnisson
Neeme
N
Palta
Priit
P
Remm
Maido
M
Kurg
Ants
A
Patsalis
Philippos C
PC
D004247:DNA / Q000378:metabolism*; D023281:Genomics / Q000379:methods*; D046228:Microarray Analysis / Q000379:methods*; D015336:Molecular Probe Techniques; D015335:Molecular Probes / Q000378:metabolism; D009693:Nucleic Acid Hybridization / Q000379:methods*; D012984:Software
D015335:Molecular Probes; D004247:DNA