Figure 9

Visualization of individual copy number measurements without matched normal samples. (a-c) Copy number measurements for tumor 48 in genome order from chromosome 1 on the left to chromosome 22 and X on the right. Data are segregated by higher and lower copy number estimates and by homozygosity or heterozygosity. Blue and orange data points are the higher allele copy measurement while green and red data points are the lower copy number measurements. Blue and red data points are homozygous alleles while orange and green are heterozygous alleles. (a) The entire genome. (b) Chromosome 1 through the first 100 Mbp of chromosome 5. (c) Chromosome 1 and the first 50 Mbp of chromosome 2, showing key features of ACN data: an amplification is seen near position 5e7; an extra copy of 1q is seen between ~1.5e8 and 2.5e8; a deletion of 1 copy is seen on the p arm of chromosome 2 between ~2.5e8 and 3e8 (observed in (b) as a complete loss of one copy of chromosome 2). (d) A small section of chromosome 5 from tumor 44. One chromosome is at copy number 0.5 across this region, which indicates a loss of that chromosome. The black arrow shows a region at total copy number 2, which likely includes reduplication of the lost chromosome in the tumor. The red arrow shows a region where both alleles are at copy number 0.5, suggesting a complete deletion. The green arrow shows copy number 1 for the yellow alleles