Hello everyone,
I would like to find a database available on Internet to select a population of GBM patients who display the EGFR V3 mutation. An in this cohort of patients, I would like also to study the expression of specific genes (the level of expression more precisely).
Thanks in advance for your advice :)
Thanks Sarah,
But I tried with EGFRV3 gene but I cannot find any answer in term of glioblastoma…
Cbioportal only recognizes the EGFR receptor family by ERBB notation. Did you try searching ERBB3:MUT ? It appears that there is one case from the TCGA database (TCGA-02-0083)
yes, even writing EGFRVIII it works but for this name it recognizes nothing in GBM patients. As 25 to 30% of GBM patients display this deletion I thought I could find more cases EGFRVIII in this database… But it seems its quite poor for this alteration
It is not clear to me why this would be an important issue. The nuclear gene defects in GBM have little to do with the origin or the progression of the disease.
This is because EGFRvIII is not a simple mutation but an intragenic rearrangement within the EGFR gene (not ERBB3 Sarah, which is a different gene) resulting in a multiexon deletion (http://www.pnas.org/content/89/10/4309.abstract). It is likely the standard TCGA and cBio pipelines are not picking it up because the deletion is too large for a mutation but too small for a whole-gene deletion.
I have checked the copy number data as well and GISTIC2 seems to be picking up the EGFR amplification but not the intragenic deletion. This might be complicated by the fact that once EGFR is detected as amplified by these pipelines, the associated intragenic deletion is not detected, as the amplification 'overrides' the truncation. It might be necessary for you to download the raw data and analyse the sequencing reads from the EGFR gene manually. To access raw TCGA data you need to have approval from the NIH. But once you have that, since you are interested in single-gene analysis, it might not take too long to write a script to detect the deletion.
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