Figure 1

Example cancer SNP data. (Top panel) SNP data showing the distribution of Log R Ratio (LRR) and B allele frequencies (BAF) values across chromosome 1 for a cancer cell line (HCC1395) and its matched normal (HCC1395BL). The normal sample is characterized by a typical diploid pattern of zero mean LRR (copy number 2) and BAF values distributed around 0, 0.5 and 1 (genotypes AA, AB and BB) with occasional aberrations due to copy germline number variants (CNV). The cancer cell line consists of complex patterns of LRR and BAF values due to a variety of copy number alterations and loss-of-heterozygosity events. (Bottom panel) SNP data is shown for a single copy deletion and duplication on chromosome 21 for various normal-cancer cell line dilutions. In the presence of normal DNA contamination, the LRR signals for the deletion and duplication are diminished in magnitude and the distribution of the BAF values reflects the aggregated effect of mixed normal and cancer genotypes at each SNP. Note - the Log R Ratio values are smoothed and thinned for illustrative purposes.