Fig. 1.

Amplified regions within a chromosome. The figure displays an example of amplification status of calls across a chromosome as observed in real data. Recurrent stretches (or regions) of amplification are denoted by lines that span across many of the samples, highlighted by the translucent rectangle, with the driver SNP located at the midpoint, as indicated by the dotted line. Non-recurrent (or sample-specific) amplified regions are represented as stray stretches. During the evaluation experiments that simulate such data, four parameters are defined and tested: (i) the mean length of recurrently amplified regions in base pairs, (ii) the number of recurrently amplified regions across the genome, (iii) the mean length of non-recurrently (or sample specific) amplified regions in base pairs, and (iv) the number of non-recurrently (or sample specific) amplified regions per sample.