When I use B cells as a reference to identify cancer cells, why some genes on chromosome 6 missing appear all tested cells

broadinstitute / infercnv

Inferring CNV from Single-Cell RNA-Seq

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When I use B cells as a reference to identify cancer cells, why some genes on chromosome 6 missing appear all tested cells #560

Open yanwuanxin opened 1 year ago

GeorgescuC commented 1 year ago

Hi @yanwuanxin ,

Since this is chromosome 6, what you are seeing is most likely the cluster of MHC genes that is on that chromosome. It is a known occurence when looking at immune cells with infercnv.

Regards, Christophe.