Too many genes in specific chromosomal regions - GISTIC results

Question

[rin]

Hi all

I have performed a GISTIC2.0 analysis in my samples, but after analyzing the results I found something that seemed a little off. In the results, there are some regions that are annotated to contain thousands of genes, e.g. 17q21.31 has 1018 genes according with the results. In the meanwhile, OMIM and http://atlasgeneticsoncology.org/ are showing far fewer genes for the same region. Has someone experienced the same?

Thank you. R

Answer 1

[Kevin Blighe]

That should not be surprising. OMIM and Atlas of Genetics and Cytogenetics in Oncology and Haematology are disease specific respositories that will only list genes relating to disease, whatever they may be. On the other hand, and depending on how you annotated your GISTIC 2.0 intervals, all genes (whether non-coding or coding, or associated to disease or not) will be listed.

Kevin