Resolving single-cell copy number profiling for large datasets

Abstract

The advances of single-cell DNA sequencing (scDNA-seq) enable us to characterize the genetic heterogeneity of cancer cells. However, the high noise and low coverage of scDNA-seq impede the estimation of copy number variations (CNVs). In addition, existing tools suffer from intensive execution time and often fail on large datasets. Here, we propose SeCNV, a novel method that leverages structural entropy, to profile the copy numbers. SeCNV adopts a local Gaussian kernel to construct a matrix, depth congruent map, capturing the similarities between any two bins along the genome. Then SeCNV partitions the genome into segments by minimizing the structural entropy from the depth congruent map. With the partition, SeCNV estimates the copy numbers within each segment for cells. We simulate nine datasets with various breakpoint distributions and amplitudes of noise to benchmark SeCNV. SeCNV achieves a robust performance, i.e., the F1-scores are higher than 0.95 for breakpoint detections, significantly outperforming state-of-the-art methods. SeCNV successfully processes large datasets (>50,000 cells) within four minutes while other tools failed to finish within the time limit, i.e., 120 hours. We apply SeCNV to single-nucleus sequencing (SNS) datasets from two breast cancer patients and acoustic cell tagmentation (ACT) sequencing datasets from eight breast cancer patients. SeCNV successfully reproduces the distinct subclones and infers tumor heterogeneity. SeCNV is available at https://github.com/deepomicslab/SeCNV.