Comparison of RegBounder to MCR and leave-1-out procedures applied to primary lung adenocarcinomas. The advantages of RegBounder over previous peak-finding procedures are illustrated for two well-described oncogene peaks identified in GISTIC analysis of 371 lung adenocarcinoma samples characterized on the Affymetrix 250K StyI SNP array (as published in ). (a) A well-described amplification peak is identified on chromosome 12p12.1 with MCR (red dotted lines) near to but not containing the known lung cancer oncogene KRAS. Because there are more than two apparent passenger events in this region, the leave-1-out peak (blue dotted lines) also does not contain KRAS. However, RegBounder (green dotted lines) produces a wider peak that captures KRAS. (b) An amplification peak on chromosome 5p15.33 contains hTERT, the catalytic subunit of the human telomerase holoenzyme, within the MCR (red dotted lines). In this case, RegBounder (green dotted lines) produces a narrower peak region than the corresponding leave-1-out peak (blue dotted lines), demonstrating the ability of RegBounder to achieve a greater balance between peak region size and accuracy. In both (a) and (b), the y-axis depicts the amplification G-score and the x-axis denotes position along the corresponding chromosome.
Mermel et al. Genome Biology 2011 12:R41 doi:10.1186/gb-2011-12-4-r41