Multiplex Ligation-Dependent Probe Amplification (MLPA) and Methylation-Specific (MS)-MLPA

This chapter reviews the use of multiplex ligation-dependent probe amplification (MLPA) in the quantification of genomic copy-number changes, detection of specific point mutations and methylation changes, and mRNA profiling. Although emphasis is on the detection of MLPA amplification products by capillary electrophoresis, alternative detection methods such as bead and array hybridization are also discussed. As compared to FISH, MLPA has the advantage of being a multiplex technique in which very small (50–70 nt) sequences are detected. Most aberrations disrupting a single gene are too small to be detected by FISH. Moreover, MLPA can be used on purified DNA. Compared to array-based comparative genomic hybridization, MLPA is a low-cost and technically uncomplicated technique. Although MLPA is not suitable for genome-wide research screening, it is a good alternative to array-based techniques for many routine diagnostic applications. Procedures for the design and use of ‘‘home-made’’ synthetic MLPA probes for temporary research applications are described. The approximately 300 probe sets now commercially available are dedicated to applications ranging from the relatively common to the very rare, such as hereditary pancreatitis, antithrombin deficiency, and Birt–Hogg–Dube syndrome.