Figure 3

Chromosome 2 in a bladder tumour sample. In this chromosome, we can distinguish two events: an unbalanced amplification coloured in orange (only one allele is duplicated) and a heterozygous deletion of the q-arm coloured in blue. A. For each SNP heterozygous in the germline DNA, the normalized intensities (as defined in Methods equation 4) of each allele are plotted. The colours represent the estimated state of the SNP: black for state 0 (germline state), blue for state 1 (heterozygous deletion: loss of one allele), green for state 2 (homozygous deletion: loss of both alleles), purple for state 3 (uniparental di/polysomy: loss of one allele and multiplication of the other one), orange for state 4 (unbalanced amplification: multiplication of one allele) and red for state 5 (balanced amplification: multiplication of the two alleles). B. Shown is the region of LOH. C. For each SNP homozygous in the germline DNA, the normalized intensities (as defined in Methods equation 4) of each allele are plotted. The absent allele is coloured in grey. D. Shown is the estimated sequence of hidden states. The colours indicate the posterior probabilities of the states: blue > 0.99, green > 0.95, orange > 0.9 and red < 0.9.