Hello all,
I am working with GENIE v10. The clinical sample data has a "Sample.Type" column that specifies if the tumor was primary, not collected, etc. I filtered on R as follows:
GENIE.samples <- read.delim("GENIE Release 10/data_clinical_sample.txt", stringsAsFactors = F)
GENIE.samples <- GENIE.samples[GENIE.samples$Cancer.Type == "Glioma" & GENIE.samples$Cancer.Type.Detailed != "Ependymoma", ]
You'll see that all of the remaining samples are gliomas. Most of them are labeled as metastatic but are really local recurrences. Excluding the mislabeled cases, there are still 100+ metastatic gliomas. If gliomas can't metastasize, why are there any metastatic cases at all? Granted, they make up less than 0.05% of total gliomas in GENIE. Why
Are glioma metastases rare, or are they biologically impossible?
I parsed the GENIE v10 data guide and found that one contributing institution (VICC) prioritized “Rare tumors and metastatic tumors... for sequencing.” Nonetheless, most of the "truly" metastatic glioma cases are from MSK-IMPACT468.
You can find the data release on synapse.org: https://www.synapse.org/#!Synapse:syn7222066/wiki/410924
Look for a file named "data_clinical_sample_10.0.txt"
Thank you for your insight!
