An MLPA-based strategy for discrete CNV genotyping: CNV-miRNAs as an example.

Copy number variation (CNV) has become well recognized in recent years. It has been estimated that common CNVs account for approximately 10% of the hu- man genome and that they overlap hundreds of genes and other functional genetic elements. Although substantial progress in genome-wide CNV analysis has been made re- cently, there is still a need for a method that allows precise genotyping of selected CNVs. Here, we describe a novel strategy for CNV genotyping, taking advantage of the gen- eral principles of the multiplex ligation-dependent probe amplification (MLPA) method and short oligonucleotide probes, allowing easy custom design and generation of assays for almost any genomic region of interest. As a proof-of-concept, we developed two assays covering 17 candidate CNV regions that overlap human miRNA genes. Extensive quality control analysis demonstrated high reproducibility and reliability of the genotypes de- termined using our method. Detailed analysis of identified CNVs revealed that they are highly differentiated among the HapMap populations. The main advantages of the de- veloped strategy include the simplicity of the assay design, its flexibility in terms of the selection of genomic regions, and its low cost (<$1-$10/genotype, depending on scale of experiment). These advantages make the presented strat- egy attractive for large-scale genetic analyses. Hum Mutat 34:763-773, 2013. C � 2013 Wiley Periodicals, Inc.