Methylation-Specific MLPA (MS-MLPA): simultaneous detection of CpG methylation and copy number changes of up to 40 sequences

• Published in: Nucleic acids research 2005-01, Vol.33 (14), p.e128-e128
• Main Authors: Nygren, Anders O. H., Ameziane, Najim, Duarte, Helena M. B., Vijzelaar, Raymon N. C. P., Waisfisz, Quinten, Hess, Corine J., Schouten, Jan P., Errami, Abdellatif
• Format: Article
• Language: English
• Subjects: Acute Disease; Angelman Syndrome - genetics; Cell Line, Tumor; CpG Islands; DNA Methylation; Gene Dosage; Humans; Leukemia, Myeloid - diagnosis; Leukemia, Myeloid - genetics; Methods Online; Molecular Diagnostic Techniques; Paraffin Embedding; Polymerase Chain Reaction - methods; Prader-Willi Syndrome - genetics; Sequence Analysis, DNA; Sulfites - chemistry
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gni127

Copy number changes and CpG methylation of various genes are hallmarks of tumor development but are not yet widely used in diagnostic settings. The recently developed multiplex ligation-dependent probe amplification (MLPA) method has increased the possibilities for multiplex detection of gene copy number aberrations in a routine laboratory. Here we describe a novel robust method: the methylation-specific MLPA (MS-MLPA) that can detect changes in both CpG methylation as well as copy number of up to 40 chromosomal sequences in a simple reaction. In MS-MLPA, the ligation of MLPA probe oligonucleotides is combined with digestion of the genomic DNA–probe hybrid complexes with methylation-sensitive endonucleases. Digestion of the genomic DNA–probe complex, rather than double-stranded genomic DNA, allowed the use of DNA derived from the formalin treated paraffin-embedded tissue samples, enabling retrospective studies. To validate this novel method, we used MS-MLPA to detect aberrant methylation in DNA samples of patients with Prader–Willy syndrome, Angelman syndrome or acute myeloid leukemia.