Methods to detect and analyze copy number variations at the genome-wide and locus-specific levels

Copy number variations (CNVs) have effects on phenotypes by altering transcription levels of genes and may have major impacts on protein sequence, structure and function. Therefore, CNV screening and analysis focused on the identification of CNV-genetic disease relations are actively progressing. CNVs can be detected and analyzed by various methodologies at the genome-wide and locus-specific levels. The genome-wide analysis of CNVs has been enhanced by bioinformatic tools for long-range sequence analysis, and comparative genome hybridization using microarrays containing either single nucleotide polymorphisms or bacterial artificial chromosome clones that represent the whole genome. RFLP followed by Southern blot analysis, quantitative real-time PCR, pyrosequencing, ligation detection reaction and the invader assay have become the main tools for locus-specific analysis so far. In this review, we present a brief principle, application history, and strengths and weaknesses of the methods used to detect CNVs at the genome-wide and locus-specific levels.