New Method Enables Single-Cell Allele-Specific Copy Number Estimation

Changes in chromatin accessibility and genetic alterations, including copy number aberrations (CNA), play pivotal roles in cancer development and progression. To address this need, Wu and colleagues developed an approach, dubbed Alleloscope, to integrate allele-specific copy number information with chromatin accessibility data from single-cell DNA sequencing (scDNA-seq) and transposase-accessible chromatin sequencing (scATAC-seq) analyses, respectively. In breast, colorectal, and gastrointestinal tumor samples and cancer cell lines, Alleloscope segmented genomes into regions of homogeneous population-average allele-specific copy number before performing haplotype phasing. For each cell and region, Alleloscope calculated the copy number of the major parental haplotype divided by the total copy number, as well as the total copy fold change compared with normal diploid cells. The accuracy of Alleloscope was validated with linked-read whole-genome sequencing analyses. Compared with CHISEL, the only other method for allele-specific copy number analysis using scDNA-seq data, Alleloscope had higher sensitivity and specificity and uncovered genetic alterations that would have otherwise gone undetected in bulk or single-cell analyses of total copy number, including alterations such as copy neutral loss-of-heterozygosity events and multiallelic CNAs. Alleloscope was used to analyze scATAC-seq data from basal cell carcinoma samples, assigning cells into subpopulations defined by ATAC-seq peak signals that were overlayed with subpopulations defined by CNA events and thus enabling integration of assessment of chromatin accessibility with allele-specific changes in copy number. In a gastric cancer cell line, Alleloscope analysis of scDNA-seq and scATAC-seq facilitated reconstruction of the tumor phylogeny of various subclones and corresponding CNA events. Adjustment for CNA refined the number of differentially accessible peaks (DAP), removing peaks whose change in signal were due to underlying changes in copy numbers while enabling identification of new DAPs that were previously obscured by CNA. In summary, this work presents a novel method to detect and integrate allele-specific copy number changes with chromatin remodeling.

Wu CY, Lau BT, Kim HS, Sathe A, Grimes SM, Ji HP, et al. Integrative single-cell analysis of allele-specific copy number alterations and chromatin accessibility in cancer. Nat Biotechnol 2021 May 20 [Epub ahead of print].

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