Fig. 1: Overview of allele-specific copy number estimation of single-cells with Alleloscope.

1. The algorithm operates on raw read count matrices for reference allele (Ref) and alternative allele (Alt) computed from single-cell DNA or ATAC sequencing. 2. First, we obtain a segmentation of the genome based on sample-matched whole genome or whole exome sequencing data using FALCON⁵. If scDNA-seq is available, cells can be pooled to derive a pseudo-bulk. 3. We first define ${\widehat{\theta }}_{ir}$ as the major haplotype proportion for cell i for region r derived from the segmentation. Then for each region r, Alleloscope simultaneously phase SNPs (${\widehat{I}}_j$) and estimate cell major haplotype proportion (${\widehat{\theta }}_{ir}$) by expectation maximization (EM) algorithm. In the E-step, information is pooled across cells to estimate the phasing of each SNP. In the M-step, information is pooled across all SNPs in the region are pooled to estimate the major haplotype proportion ${\widehat{\theta }}_{ir}$ for each cell. The toy example shows a scenario with two cells for a region containing 5 SNPs, with cell 2 carrying an amplification of the major haplotype (in pink). For each cell and each SNP, alleles that are observed in a sequenced read are bolded in black (we assume that only one read is observed, reflecting the sparsity of the data). The true phase (I_j) of the SNPs and the true major haplotype proportion (θ_ir) are shown. 4. After ${\widehat{\theta }}_{ir}$ are estimated for each region $r,{\widehat{\theta }}_{ir}$’s are pooled across all regions to identify candidate normal cells and candidate normal regions for computing a normalized coverage ${\widehat{\rho }}_{ir}$ for region r in cell i. Matched normal can be specified if available. 5. Alleloscope assigns integer allele-specific copy numbers to each cell for each region based on the (${\widehat{\rho }}_{ir},{\widehat{\theta }}_{ir}$) pairs.