OncotreeCode CMLBCRABL1 does not include all cell lines with BCR-ABL fusion

Issues and Bugs
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1

Hi,

I’ve been working with lymphoid and myeloid cell lines recently and noticed that the majority of CML cell lines are referenced by their OncotreeCode of CML, whilst a few others are referenced by CMLBCRABL1. I had a look on Cellosaurus for these CML cell lines and found the vast majority of these cell lines also contain the BCR-ABL fusion. I’m a bit confused why these cell lines have been classified separately to the other CMLBCRABL1 cell lines, and if there is a reason why I should indeed be keeping these separated for downstream analyses?
If not, is this a bug in how the OncotreeCodes have been mapped to respective cell lines? Is their documentation anywhere on how you map the OncotreeCodes to cell lines?

e.g. JK-1 (ACH-000241) is classified as CML by OncotreeCode but also contains BCR-ABL1 fusion according to Cellosaurus (https://www.cellosaurus.org/CVCL_2079 & see ref Genomic amplification of BCR/ABL1 and a region downstream of ABL1 in chronic myeloid leukaemia: a FISH mapping study of CML patients and cell lines - PMC).

Thanks,
Ben

2

Hi Ben,

Thank you for your observation. We have updated the appropriate lines to have the Oncotree codes reflect the BCR-ABL fusion and be consistent with the Cellosaurus NCIt designation, which will be available in the next release. With our more granular coding, we are reviewing past designations to ensure they are updated.

Thanks,
Samantha

3

No worries, happy to help. Thanks for the quick response.