Flowchart illustrating some of the factors that need to be considered when attempting to assess copy number variation. Hexagons are used to designate choices, and rounded rectangles indicate the major techniques that are discussed further in this review. Note the arrow from the bottom of the whole-genome scan that leads back to targeted analysis. This emphasises the fact that copy number variants identified through whole-genome scans can be confirmed or tested directly in large cohorts of individuals using targeted analyses. Abbreviations: BACs, bacterial artificial chromosomes; CGH, comparative genomic hybridisation; MAPH, multiplex amplifiable probe hybridisation; MLPA, multiplex ligation-dependent probe amplification; PCR, polymerase chain reaction; QMPSF, quantitative multiplex PCR of short fluorescent fragments; qPCR, quantitative PCR; SNP, single nucleotide polymorphism.