Sensitivity to copy number variation analysis in single cell genomics

Gene. 2022 Jan 15:808:145995. doi: 10.1016/j.gene.2021.145995. Epub 2021 Oct 7.

Abstract

While previous studies have given some guidance, the sensitivity of copy number calling in single-cell genomics is still not comprehensive. We studied the impact of sequencing depth and other factors on single-cell copy number analysis. Sequencing Data from 26 datasets were retrieved, and 2946 single cells passed the filter. Thirty-eight single cells were independently downscaled to evaluate copy number variation (CNV) detection sensitivity at different bin sizes. The sensitivity of whole genome amplification (WGA) approaches and cell types to CNV calling were evaluated using downsampling of 101 and 70 cells. Cluster analysis based on t-SNE was executed to evaluate CNV calling performance. Our results suggest 0.75× sequencing depth with moderate resolution (250 kb bin size) may be a practical guideline considering both sequencing cost and performance of copy number calling, which can be appropriately optimized based on amplification approach, cell type, and sample complexity.

Keywords: Copy number variation; Single cell sequencing; Tumor evolution; Variant calling; Whole genome amplification.

MeSH terms

  • Algorithms
  • DNA / genetics
  • DNA Copy Number Variations / genetics*
  • Genome, Human / genetics
  • Genomics / methods
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • Polymorphism, Single Nucleotide / genetics
  • Sequence Analysis, DNA / methods*
  • Single-Cell Analysis / methods

Substances

  • DNA