Precise identification of cancer cells from allelic imbalances in single cell transcriptomes
Mi K. Trinh, Clarissa N. Pacyna, Gerda Kildisiute, Christine Thevanesan, Alice Piapi, Kirsty Ambridge, Nathaniel D. Anderson, Eleonora Khabirova, Elena Prigmore, Karin Straathof, Sam Behjati, Matthew D. Young
Abstract
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.
Topics & Concepts
BiologyCancer cellCancerAlleleGenotypeTranscriptomeIdentification (biology)Computational biologyGeneticsCellCancer researchGeneGene expressionBotanyCancer Genomics and DiagnosticsSingle-cell and spatial transcriptomicsRNA modifications and cancer