lack of single-cell transcriptome data from the same patient

[ozuoano]

If there is a lack of single-cell transcriptome data from the same patient, can we use single-cell transcriptome data from multiple patients

with the same type of cancer for celltrek analysis?

[Puriney]

The caveat is that the transcriptome of cancer cells could be dominated by genomic aberrations. As seen in so many single-cell cancer cell UMAPs, cancer cells are clustered by patients. For the immune/stroma population, the risk is low.

But since CellTrek used the co-embedding strategy, there is a chance that it can remove the patient-specific effect. It is always to side-by-side check the co-embedding UMAP colored by 1) st/sc and 2) cell state/cell type. In this way, you would know if the single tumor cells find some matched spots on ST. Additionally, check the genes.