ATTC offers a service for cell line authentication based on short tandem repeat profiling (https://www.atcc.org/Services/Testing_Services/Cell_Authentication_Testing_Service.aspx).  In the lab, we often use patterns of SNVs derived from analysis of whole exome sequencing to ensure our cell lines are what we think they are, but this gets rather expensive if you have many cell lines to analyze.

-Benjamin Vincent 

Hi Benjamin, thank-you for your reply! 

When you say expensive, do you mean both in terms of financial & person hours?  I can't imagine it being more costly to do in-house QC than outsourcing, unless it is very time intensive. 

Ideally I want to set up a regular testing schedule for all cell lines we work with.  At the moment we are still a new lab, so total is currently less than 10, though over time I imagine that will grow substantially. 

Any advice is greatly appreciated.

-Sélène Tyndale-

Whole exome for us is expensive mostly in terms of financial cost (roughly $920 per sample).  If you are willing to develop a targeted exome capture based assay, you can do this for MUCH cheaper.  The only reason we don't is that we work with cancer cell lines with some degree of genetic instability and we are also looking for evidence of genetic change over time (as well as ongoing validation).

Thank-you.  I am developing protocols with leukemia (cancer) cell lines, while IRBs are being approved to get samples from leukemia patients.  Our sequencing panel includes ATAC-seq, mRNA-seq, & promoter capture HiC-seq. 

I am curious if any of the sequencing data we are already generating could be used in place of exomes to develop in house cell line QC protocols.  Any ideas?

Thank-you,

Sélène

Yes I think so, presuming you have unique variants in each line that are traceable (i.e. expressed variants for RNA-seq data) - However your mileage may vary :)  We have done variant calling from mRNA seq data using UNCqeR (https://www.ncbi.nlm.nih.gov/pubmed/26076459)

-Benjamin