hi,
I am currently doing a project on gatric cancer, I specifically interested in those gastric cancers that have a MSI-H status. However I could not find any information regarding the MSI status in clinical_patient or clinical_sample files. I was wondering if any data regarding the MSI status would be available?
Thanks in advance,
Florenz
Created by Florenz Jan van Otterloo fjw-van-otterloo Dear Chelsea,
Thank you very much for your response!
I was exploring the file you linked in your previous answer and I have one question about the "msi_high" column. I see that the possible values for this column are the following:
- ">=30% of the markers exhibit instability"
- "2 or more of the 5 markers exhibit instability"
- "Other"
I understand what the first two values mean, but I am not sure about what "Other" means. Can you help me understand what does "Other" mean, please?
Thank you very much in advance!
Best,
Diego. @diegogl
Unfortunately we do not have MSIsensor numeric scores available in the data set. The available variables in the release can be browsed [here](https://www.synapse.org/Synapse:syn39433163).
Let me know if there is anything else I can help with. Hi Chelsea,
Thank you very much for your quick response! I am looking for data from the MSIsensor algorithm ([paper](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3967115/)). I see some MSI-PCR and MMR-IHC data in the file you kindly pointed me to. However, I cannot see these MSIsensor numeric scores. Can you point me to the column name in that file (that contains this information) or the place where I can find this data?
Thank you very much in advance.
Diego. @diegogl ,
Yes, you can find MSI data in the public CRC data release here: https://www.synapse.org/#!Synapse:syn39802567
The MSI data can be found in this file: pathology_report_level_dataset.csv
Best,
Chelsea Hi,
What about MSIsensor data? Is there any cancer type with MSIsensor scores available?
Thank you very much in advance.
Diego. @fjw-van-otterloo ,
Unfortunately I am not aware of any plans to add those reports for gastric cancers in the GENIE releases. I linked the CRC cohort since MSI status is commonly associated with CRC.
Let me know if there is anything else.
Best,
Chelsea Dear Chelsea,
Thank you for your response and the links. However the samples in the pathology report are all for colorectal cancer, as I am interested in gastric cancer I am still wondering if a similar report was available for those samples. I had a look at the GENIE BioPharma Collaborative BPC project, but could only find samples for NSCLC. Do you happen to know if there is any pathology report available for gastric cancer samples?
Thanks in advance,
Florenz Dear @fjw-van-otterloo,
Thank you for your interest in GENIE!
You should check out the **CRC data release** under the **GENIE BioPharma Collaborative BPC project**. The BPC project holds cancer specific releases that expand the clinical data elements from patients already enrolled in GENIE.
You can find the public CRC data release here: https://www.synapse.org/#!Synapse:syn39802567
The MSI status information can be found in this file: [pathology_report_level_dataset.csv](https://www.synapse.org/#!Synapse:syn39802586)
Let us know if you have any other questions!
Best,
Chelsea