Question re: cell line data

[Chen, Hui-Zi]

Dear cBioportal Group,

 

I am hoping you can help reconcile some data for me.

 

I have been trying to find small cell lung cancer cell lines with inactivating KMT2C mutations.

 

I have accessed 2 datasets: CCLE (Broad, 2019) and CCLE (Broad, Nat Rev cancer 2025). I presume there’s a high degree of overlap in the samples that are analyzed between the two datasets.

 

From the first Broad 2019 dataset, the following 2 cell lines showed non-sense mutations in KMT2C: COLO-668 and DMS454

 

However, I am unable to find KMT2C mutations in these two cell lines from the 2025 dataset (have crossed referenced with DepMap as well).

 

Are you able to help clarify which dataset is correct with regards to the KMT2C mutations, as this will be important for the experiments that we are planning ahead for.

 

Thanks so much for your assistance!

Huizi Chen

 

Huizi Chen, MD PhD

Assistant Professor

Division of Hematology & Oncology

Department of Medicine

Medical College of Wisconsin

Milwaukee, WI 53226

 

[Curation Team]

Hi Huizi Chen, 

Thanks for reaching out. Because the DepMap portal is dynamic, we rely on the data files provided from the specific release for the datasets in cBioPortal. We generally recommend using the most recent dataset when possible.

The DepMap mutation calling and annotation pipeline underwent several updates over the years and in the 2025 release, several changes were introduced including:

• Minimum read depth threshold increased (2 -> 5): variants with lower read support that were previously reported may now be filtered out due to insufficient coverage.
• Variant annotation updates (VEP v110 -> v113): updated population allele frequency information and annotation logic may change variant interpretation, potentially leading to variants being reclassified or filtered.

Both above could explain why the KMT2C nonsense mutations observed in COLO-668 and DMS454 in the 2019 dataset are no longer present. For more details, all the omic pipeline updates for each of the releases can be found in the release announcements.

Please let us know if you have any other questions about the dataset.

Best,

Rima