deleted gene not in GISTIC peak

Question

[neuro3030]

Hi,

After running GISTIC, I see one of the output file all_lesions.conf_xx lists the significantly altered peaks, which then correspond to likely altered genes (listed in a different file).

However, when reviewing gene-level copy number information in the file thresholded.by_genes, I see some genes that are recurrently altered do not intersect with the significant peaks.

For instance, the gene EGFR shows hemizygous deletion (coded as -1) in 90% of my samples, yet this is not within a significantly deleted peak region.

Any ideas why this might be? thanks

[Kevin Blighe]

Well, at least the 90% figure corroborates with the expected deletion frequency of this gene in, I assume, lung cancer samples that you've got. Does it not list any segment of EGFR as deleted? Did you look in the del_genes.conf_XX.txt file?