Figure 1.

Schematic illustration of the Tumor Aberration Prediction Suite (TAPS) method for visualization of chromosomal aberrations in tumor samples. A scatter plot of the average Log-ratio and the allelic imbalance ratio of all segments in a sample reveals the aberrations present. (a) The example chromosome is segmented with respect to Log-ratio and allele frequency. (b) In the allele frequency pattern, the probes' distance from heterozygosity (equal signal from alleles A and B) is clustered on two means, representing heterozygous (d_het) and homozygous (d_hom) SNPs. The allelic imbalance ratio d_het/d_hom ranges from near zero with equal allelic copy numbers and low noise to near one with loss-of-heterozygosity (LOH), low normal cell contamination and low noise. (c) Schematic illustration of a Log-ratio/allelic imbalance ratio scatter plot. An example region in blue can be identified as cn2m0, that is, copy number 2 and minor copy number 0 (LOH). Each object in the scatter plot corresponds to a chromosomal segment. Segments are colored according to their chromosomal position (a) and segments on other chromosomes of the same sample are plotted in grey. The number of possible variants of allele-specific copy number increases with the total copy number. Lower copy numbers are more affected by noise and normal cell contamination, which reduce any allelic imbalance. Deletions and copy number neutral LOH may therefore show less allelic imbalance than high copy numbers that retain one or more copies of its minor allele. Note how variants with the same minor copy number tend to line up diagonally, facilitating the interpretation.