I have thawed primary tumor cells and performed FACS. They were EpCAM positive cells. Then, I expanded them as organoids in 3D and did another FACS analysis. Again, they were EpCAM positive. I also sent organoids to pathology for IHC. Results showed they expressed EpCAM, EGFR, and panCK. But to my surprise, the Ampli LowPass sequencing results showed they had a balanced profile like normal cells. How could that be explained? Any help (comments, papers, ...) is appreciated. Thank you.
I think this is the paper about the Ampli LowPass sequencing technique. Although, I didn't read it thoroughly but from the abstract and result section titles, it appears that this technique is designed for detecting CNVs. Since it is low pass (i.e. low coverage), it may not detect substitutions and small indels accurately.
Your cells may have mutations but not big chromosomal rearrangements. It is not necessary for tumour cells to have such chromosomal aberrations. In fact a simple overexpression of an oncogene or a point mutation causing reduced/loss of activity of a tumor supressor (for e.g. p53) is enough for tumorigenesis.