I believe this is more of a broad question; and I am resorting to here because I found very limited (and not specific) information on the topic. Briefly, I am planning on performing DNA sequencing in mesenchymal stem cells (MSC) extracted from cord blood, with the following in mind:
1. Are those cells a good source (in terms of quantity and quality) for germline SNP's investigation?
2. If so, do the discovered variants truly reflect the presence of a germline variant?
What is known about mesenchymal stem cells is that they can be quite heterogeneous and harvest site-dependent. Specifically, for cord blood-derived MSC the heterogeneous composition was shown to undergo dynamic clonal selection in culture, with an initial massive reduction in diversity and a selection of single clones over time, starting in the early passages (Selich et al., 2016).
So, the most concerning questions I have for now are:
1. Is it a reasonable approach to use these MSC's for germline variant investigation? (considering that (a) the MSC's have been expanded for 1-2 passages prior to sequencing; and (b) it is a panel sequencing rather than WES or WGS)?**
2. What would you opt as your analysis pipeline, GATK best practices?
3. What else should I be considering in this experimental setting?
Any help is much appreciated. And of course, article references are also very welcomed. Maybe this is a topic with a lot of discussion within the research field, and I might be missing it. I don't know.
Thanks a lot!