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A backup of official sequenza repos
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The issue of cellularity in adjacent and tumor tissues #1

Open shenhaizhongdechanrao opened 1 month ago

shenhaizhongdechanrao commented 1 month ago

Hi, I used Sequenza to obtain the cellularity of adjacent and tumor tissues, using normal BAM files from white blood cells. I have a question: why is the cellularity of adjacent tissues higher than that of the tumor tissues? Can you explain this?

LiuCanidk commented 2 days ago

I guess the cellularity estimated by sequenza was an index reflecting the degree of CNV compared to the reference sample (here is your white blood cells). So the cellularity is not the true cellularity. I guess the higher cellularity value as you see, represented higher CNV mutation burden in the adjacent tissue than that of the tumor tissues.

We may hypothesize that tumor tissues should have higher CNV profiles. As far as I know, however, not all maligant cells can be identified using CNV profiles. One of the example I knew was the gastric cancer, and its neutrophil cells can be identified as having big CNVs using inferCNV with scRNA-seq data. So, I guess your result is unusual but an interesting observation.

Hope it helps