Summary of possible relationships between reference, experimental control and test genomes and the resulting abilities of different methods to detect CNVs in the test genome (with respect to the reference genome).

Copy Number Variants in one genome can only be defined with respect to a reference genome. Comparisons to different reference genomes will produce different sets of CNVs for the same test genome. Sequencing based methods directly compare the test genome to the reference genome. For array-based methods however, this comparison is indirect as an experimental control genome is also required. The relationship between the reference genome and this control genome determines which CNVs in the test sample (with respect to the reference genome) are detected.