DemoTape: Computational demultiplexing of targeted single-cell sequencing data
Abstract
Background Single-cell sequencing can provide novel insights into the understanding and treatment of diseases. In cancer, for example, intratumor heterogeneity is a major cause of treatment resistance and relapse. Although technological progress has substantially increased the throughput of sequenced cells, single-cell sequencing remains cost and labor-intensive. Multiplexing, i.e., the pooling and subsequent joint preparation and sequencing of samples, followed by a demultiplexing step, is a common practice to reduce expenses and confounding batch effects, especially in single-cell RNA sequencing.
Results Here, we introduce demoTape, a computational demultiplexing method for targeted single-cell DNA sequencing (scDNA-seq) data based on a distance metric between individual cells at single-nucleotide polymorphisms loci. To validate demoTape, we sequence three B-cell lymphoma patients separately and multiplexed on the Tapestri platform. We find similar genotypes, clones, and evolutionary histories in all three samples when comparing the individual with the demultiplexed samples. Using the three individually sequenced samples, we simulate multiplexed ground truth data and show that demoTape outperforms state-of-the-art demultiplexing methods designed for RNA sequencing data. Additionally, we demonstrate through downsampling that the inferred clonal composition remained largely stable for samples with fewer cells despite the inevitable loss in resolution of low-frequency clones.
Conclusions Multiplexing and subsequent genotype-based demultiplexing of scDNA-seq will reduce costs and workload, eventually allowing the sequencing of more samples. This will open new possibilities and accelerate the investigation of biological questions where cellular heterogeneity on the genomic level plays a crucial role. Show more
Permanent link
https://doi.org/10.3929/ethz-b-000717303Publication status
publishedExternal links
Journal / series
bioRxivPublisher
Cold Spring Harbor LaboratorySubject
Targeted single-cell DNA sequencing; Single-cell DNA panel sequencing; Genotype-based demultiplexing; Distance-based demultiplexing; Tapestri platform; Intratumor heterogeneityOrganisational unit
09711 - Moor, Andreas / Moor, Andreas
Funding
766030 - Computational ONcology TRaining Alliance (EC)
609883 - Mechanisms of Evasive Resistance in Liver Cancer (EC)
Related publications and datasets
Is supplemented by: https://github.com/cbg-ethz/demoTape
More
Show all metadata
ETH Bibliography
yes
Altmetrics