Fig. 1

Description of the copy number classification schema. The copy number classification schema consists of 48 mutually exclusive channels, divided by heterozygosity status, segment size, and total copy number (TCN). a In the heterozygous state, both alleles are retained and either one or both alleles can be amplified. This amplification can be focal (top panel) or it can encompass a chromosome or even the whole genome (bottom panel). The heterozygous category is further subdivided based on TCN (TCN = 1, TCN = 2, TCN = 3 or 4, TCN = 5 to 8, and TCN >= 9). b In a state of loss of heterozygosity (LOH), one of the alleles is lost. The remaining allele can then be duplicated (i.e., copy neutral LOH), and undergo more amplification resulting in higher total copy number states. The LOH category is further subdivided based on TCN (TCN = 1, TCN = 2, TCN = 3 or 4, TCN = 5 to 8, and TCN >= 9). The heterozygous and LOH categories are further divided on the basis of the size of the segment: 0 – 100 kb, 100 kb – 1 Mb, 1 Mb – 10 Mb, 10 Mb – 40 Mb, > 40 Mb. High-level LOH or heterozygous amplifications (e.g., TCN = 5 to 8 or TCN >= 9) can be carried on extrachromosomal DNA (depicted as red circles) as well as on linear chromosomes. c Homozygous deletions result in the loss of both alleles, and are divided on the basis of the size of the deleted segment: 0 – 100 kb, 100 kb – 1 Mb, and > 1 Mb