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An MLPA ‐Based Strategy for Discrete CNV Genotyping: CNV ‐mi RNA s as an Example
Author(s) -
MarcinkowskaSwojak Malgorzata,
Uszczynska Barbara,
Figlerowicz Marek,
Kozlowski Piotr
Publication year - 2013
Publication title -
human mutation
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.981
H-Index - 162
eISSN - 1098-1004
pISSN - 1059-7794
DOI - 10.1002/humu.22288
Subject(s) - biology , copy number variation , genotyping , multiplex ligation dependent probe amplification , computational biology , genetics , multiplex , international hapmap project , human genome , genome , genotype , gene , exon
ABSTRACT Copy number variation ( CNV ) has become well recognized in recent years. It has been estimated that common CNV s account for approximately 10% of the human genome and that they overlap hundreds of genes and other functional genetic elements. Although substantial progress in genome‐wide CNV analysis has been made recently, there is still a need for a method that allows precise genotyping of selected CNV s. Here, we describe a novel strategy for CNV genotyping, taking advantage of the general 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 mi RNA genes. Extensive quality control analysis demonstrated high reproducibility and reliability of the genotypes determined using our method. Detailed analysis of identified CNV s revealed that they are highly differentiated among the H ap M ap populations. The main advantages of the developed 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 strategy attractive for large‐scale genetic analyses.