scONE-seq: A single-cell multi-omics method enables simultaneous dissection of phenotype and genotype heterogeneity from frozen tumors

Single-cell multi-omics can provide a unique perspective on tumor cellular heterogeneity. Most previous single -cell whole-genome RNA sequencing (scWGS-RNA-seq) methods demonstrate utility with intact cells from fresh samples. Among them, many are not applicable to frozen samples that cannot produce intact single-cell sus-pensions. We have developed scONE-seq, a versatile scWGS-RNA-seq method that amplifies single-cell DNA and RNA without separating them from each other and hence is compatible with frozen biobanked samples. We benchmarked scONE-seq against existing methods using fresh and frozen samples to demonstrate its performance in various aspects. We identified a unique transcriptionally normal-like tumor clone by analyzing a 2-year frozen astrocytoma sample, demonstrating that performing single-cell multi-omics interrogation on biobanked tissue by scONE-seq could enable previously unidentified discoveries in tumor biology.

Automated summary

Single-cell multi-omics provides a unique perspective on tumor cellular heterogeneity. We developed scONE-seq, a versatile method for single-cell whole-genome RNA sequencing that is compatible with frozen biobanked samples. By comparing with existing methods, we demonstrated the performance of scONE-seq in various aspects and identified a unique transcriptionally normal-like tumor clone in a frozen astrocytoma sample, suggesting the potential of scONE-seq in uncovering previously unidentified discoveries in tumor biology.