Good afternoon,
Using the clinical patient, clinical sample, and structural variant data, how can I:
1) identify a list of patients that have been **tested** for RET-fusion positive non-small cell lung cancer
AND
2) identify the number of patients that in fact **have** RET-fusion positive non-small cell lung cancer
Thanks in advance for your help!
Created by David Merola davemerola @davemerola,
Apologies for the delay in response.
> Identify a list of patients that have been tested for RET-fusion positive non-small cell lung cancer
You can select for patients that have the following criteria:
1. Panel has RET covered in BED region and has includeInPanel = True (using the genomic_information.txt file)
2. Panel has SV alteration_types (from assay_information file)
3. Patient was assayed by a panel with the above criteria (using the clinical sample file)
4. Patient indicated to have NSCLC (using the clinical sample file)
> identify the number of patients that in fact have RET-fusion positive non-small cell lung cancer
You can select for patients that have samples with the following criteria in the structural variant file (data_sv.txt):
1. EVENT_INFO like '%RET%'
2. CANCER_TYPE = 'Non-Small Cell Lung Cancer';
You can also filter using [cBioPortal](https://genie.cbioportal.org/) by following the process:
1. Select "NSCLC" under Cancer Type
2. Select "RET" under Structural Variant Genes
Let me know if this helps! Dear @davemerola,
Thank you for your interest in the GENIE dataset. We will provide an answer as soon as we can!
Best,
Chelsea