biostudies-literatureTrinh MKWellcome Trust884https://www.ebi.ac.uk/biostudies/studies/S-EPMC9452529biostudies-literatureUnknown5(1)A fundamental step of tumour single cell mRNA analysis is separating cancer and non-cancer cells. We show that the common approach to separation, using shifts in average expression, can lead to erroneous biological conclusions. By contrast, allelic imbalances representing copy number changes directly detect the cancer genotype and accurately separate cancer from non-cancer cells. Our findings provide a definitive approach to identifying cancer cells from single cell mRNA sequencing data.Communications biologyPrecise identification of cancer cells from allelic imbalances in single cell transcriptomes.PMC9452529223135/Z/21/Z206194108413/A/15/DAmbridge KPrigmore EThevanesan CPacyna CNStraathof KBehjati SPiapi AKhabirova ETrinh MKAnderson NDKildisiute GYoung MDfalsePrecise identification of cancer cells from allelic imbalances in single cell transcriptomes.A fundamental step of tumour single cell mRNA analysis is separating cancer and non-cancer cells. We show that the common approach to separation, using shifts in average expression, can lead to erroneous biological conclusions. By contrast, allelic imbalances representing copy number changes directly detect the cancer genotype and accurately separate cancer from non-cancer cells. Our findings provide a definitive approach to identifying cancer cells from single cell mRNA sequencing data.2022-01-01T00:00:00Z2022 Sep2025-04-18T22:42:31.564Z2025-04-07T10:30:13.173ZS-EPMC94525293607110310.1038/s42003-022-03808-9