A new method of separating cancer cells from non-cancer cells has been developed by researchers at the Wellcome Sanger Institute, in a boost for those working to better understand cancer biology using single-cell mRNA sequencing.
The study, published in Communications Biology, improves on existing methods to identify which cells in a sample are cancerous and provides crucial data on the microenvironment of tumours. The software is openly available for researchers around the world to apply to their own data, advancing the effectiveness of single-cell sequencing to understand cancer.
In this study, researchers at the Wellcome Sanger Institute performed whole genome sequencing and single-cell mRNA sequencing on samples collected by Great Ormond Street Hospital (GOSH). By locating imbalances of alleles in these data, which indicate copy number changes in the genome, the team was able to identify cancer cells more reliably than with previous methods. This approach will primarily be useful for validating new cancer cell types and better understanding the microenvironment of tumour tissue.
Currently, the best method of separating cancer and non-cancer cells is to measure the average gene expression of cells in the sample, with higher or lower expression used to distinguish cancer cells from healthy cells. But this method can lead to false conclusions.
“Being able to know how the transcriptome is different in cells with aberrant genomes, such as those found in cancers, is valuable knowledge and will expand the questions that we can answer using single-cell sequencing.” said Dr Matt Young, Wellcome Sanger Institute.