Figure 1

Estimating ploidy number in NB tumors with complex genomic profiles. Allele specific intensities, calculated using the AsCNAR algorithm, makes it possible to estimate the copy number for each chromosome in complex tumors. Arrows indicate differences seen only on the allele specific level that would have been overlooked or misjudged using other methods, for example 1+1 vs. 2+0 or 2+1 vs. 3+0. Several examples of near CN-LOH is also shown; chromosomes 3, 4, 10, 11, 12 and 19 all show an allelic distribution of 2+0 in NB01 which has an overall ploidy of ~2,3n, and chromosome 3 in NB02 has an allelic distribution of 2+0 in an otherwise near triploid tumor (overall ploidy ~2,8n). The multi-colored line shows the total copy number for the different chromosomes and the red and green lines show the strongest and weakest allele intensity respectively. Total copy number is written above each chromosome and allele specific copy numbers are written underneath the allele intensity plot as: red/green.