Figure 5.

Genome alteration print (GAP) for Affymetrix single-nucleotide polymorphism (SNP) GeneChip SNP 6.0 array. BLC_B1_T45 tumor sample measured on two SNP-array platforms, analyzed by using GAP, and superimposed by color code: (a) GAP for Affymetrix; and (b) GAP for Illumina. Copy numbers obtained from the Illumina GAP were coded by colors indicated at the bottom of the Figure. Concordance between Affymetrix and Illumina patterns is illustrated by the relevant Illumina-derived color gradation on Affymetrix GAP. Germline homozygous regions are boxed. The main cluster patterns are indicated by hexagonal frames. The differences in relative cluster sizes are due to different distributions of SNPs measured along the genome in Illumina and Affymetrix chips.