Figure 1

The whole-genome single-nucleotide polymorphism (SNP) array profile and genome alteration print (GAP). The whole-genome profile of genomic rearrangements in the BLC_B1_T45 sample measured by 300K Illumina SNP-array and corresponding GAP. (a) Allelic imbalances are represented by B-allele frequency (BAF). (b) Copy-number variation profile is represented by log R ratio (LRR), centered at zero. (c) The GAP of the sample is a combined sideview projection of segmented LRR and BAF. Each region of the genome is represented by two symmetric circles in the case of allelic imbalance and by one circle centered at BAF = 0.5 in the case of a balanced genotype. Attribution of copy numbers and genotypes corresponds to a near-diploid model of rearrangements. (d) "Reading" GAP pattern: the degree of stromal contamination, acquired and germline homozygosities, and subclones are indicated. (e) The best-fitting model GAP allows interpretation of the cluster structure and estimates contamination by normal DNA and contraction of the pattern on the LRR scale. Clusters are designated by the ratio of copy number to B (or major allele) counts.