Detecting Copy Number Changes in Genomic DNA: MAPH and MLPA

Abstract

Publisher Summary Copy number changes, that is, deletions, duplications, and amplifications in genomic DNA are involved in many genetic diseases. However, detection of these rearrangements is rather difficult, mainly because the assay applied should be quantitative. This chapter describes multiplex amplifiable probe hybridization (MAPH) and multiplex ligation-dependent probe amplification (MLPA). These are the new methodologies developed specifically to detect copy number changes in many target sequences simultaneously. The MAPH and MLPA protocols are also outlined in the chapter. For both MAPH and MLPA, the methods of data analysis are effectively identical. The polymerase chain reaction (PCR) products are separated by electrophoresis and each probe is quantified with the relative amount of each product being proportional to the copy number of the locus being tested. The MAPH and MLPA have focused primarily on screening either single genes for exonic deletions and duplications or chromosomal regions for rearrangements. New MLPA/MAPH assays must be developed that will focus not only on specific genes but also on high-resolution analysis of chromosomal regions associated with a range of diseases.