Request for Detailed Genetic Information on Common Human Cell Lines in DepMap

Q&A
1

Hello DepMap team and community members,

I am currently working on a project that requires information on the genetic background of commonly used human cell lines, such as HEK293, Jurkat, K562, and others. While I appreciate the wealth of data provided by the DepMap project, I am specifically interested in obtaining more detailed information about key oncogenes (e.g., P53, KRAS) and their mutational status, as well as other relevant genetic characteristics, like homozygosity, ploidy, and so on.

From the latest DepMap release, I could not locate the following details:

Mutations in key oncogenes and tumor suppressor genes, along with their zygosity (homozygous or heterozygous).
Ploidy of the cell line and any associated chromosomal aberrations.
Other relevant genetic alterations that might influence the behavior of the cell line or its response to experimental treatments.
Any additional metadata or annotations that would aid in the interpretation of the genetic data, such as growth characteristics or known functional consequences of the mutations.

I understand that the scope of the DepMap project is vast and the information I am seeking might be available somewhere within the data or associated resources. Therefore, I would be grateful if someone could guide me on how to access these specific details within DepMap or point me to any additional resources that could help.

Also, if there are any plans to include such information in future DepMap releases or if there are ongoing collaborations with other projects that could provide this level of detail, I would love to hear about those as well.

Thank you in advance for your assistance!

Best regards,
Matvei

2

Hi Matvei,

Apologies for the late reply. In order to systematically extract the information you described here, in addition to interacting with the portal visualization tools, I would recommend checking out the file downloads page, especially the following files:

Mutations in key oncogenes and tumor suppressor genes: OmicsSomaticMutations.csv
Ploidy (plus whole genome doubling status, loss of heterozygosity, chromosomal instability, MSI, etc.): currently a beta feature that have not been released publicly yet, but we are planning to in the near future
Other relevant genetic alterations: there are several datasets can be potentially relevant. For example, OmicsCNGene.csv contains copy number alterations. OmicsFusionFiltered.csv contains gene fusions.
Metadata: Model.csv and/or ModelCondition.csv

Hope this answers your questions!
Simone