Additional file 7.

Supplementary Figure S4: GeneGISTIC versus standard GISTIC. (a) GeneGISTIC helps identify genes subject to non-overlapping deletion, such as NF1. The left panel shows the 12 samples with focal deletions affecting NF1, many of which do not overlap. As a result, the standard GISTIC marker score (blue line, right panel) has multiple local maxima over NF1. By contrast, the GeneGISTIC score counts all of these deletions as contributing to the NF1 score, resulting in a score for NF1 (red line, right panel) that is significantly greater than that assigned to any of the individual markers covering NF1. (b) GeneGISTIC does not score deletions occurring outside of genes. The left panel shows a region of focal deletion occurring just outside the PCHD9 gene on chromosome 13. These deletions result in a peak in the markers deletion score (blue line, right panel) that is not detected by GeneGISTIC.

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Mermel et al. Genome Biology 2011 12:R41   doi:10.1186/gb-2011-12-4-r41