Figure 2. Methods for genome-wide identification of copy number variations (CNVs). (A) Test and reference DNA samples are labeled with different fluorescent dyes (cyanine-3 and cyanine-5, respectively) to identify CNVs using array-comparative genomic hybridization (array-CGH). The mixture of labeled DNAs (reference and test) is hybridized onto the whole-genome microarray. Signal intensity ratios (cyanine-5/cyanione-3) are calculated after hybridization and image scanning and reveal the copy number differences between the test and reference genomes. (B) Test and reference DNA samples are sequenced independently to identify CNVs using next-generation sequencing. The sequenced reads are mapped to the reference genome by sequence alignment. The number of mapped reads in each sliding window is counted. The mapped reads ratios (test mapped reads count/reference mapped reads count) reflect the copy number differences between the test and reference genomes.