Integrative single-cell analysis of allele-specific copy number alterations and chromatin accessibility in cancer
- 20 May 2021
- journal article
- research article
- Published by Springer Science and Business Media LLC in Nature Biotechnology
- Vol. 39 (10), 1259-1269
- https://doi.org/10.1038/s41587-021-00911-w
Abstract
Cancer progression is driven by both somatic copy number aberrations (CNAs) and chromatin remodeling, yet little is known about the interplay between these two classes of events in shaping the clonal diversity of cancers. We present Alleloscope, a method for allele-specific copy number estimation that can be applied to single-cell DNA- and/or transposase-accessible chromatin-sequencing (scDNA-seq, ATAC-seq) data, enabling combined analysis of allele-specific copy number and chromatin accessibility. On scDNA-seq data from gastric, colorectal and breast cancer samples, with validation using matched linked-read sequencing, Alleloscope finds pervasive occurrence of highly complex, multiallelic CNAs, in which cells that carry varying allelic configurations adding to the same total copy number coevolve within a tumor. On scATAC-seq from two basal cell carcinoma samples and a gastric cancer cell line, Alleloscope detected multiallelic copy number events and copy-neutral loss-of-heterozygosity, enabling dissection of the contributions of chromosomal instability and chromatin remodeling to tumor evolution.Keywords
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Funding Information
- U.S. Department of Health & Human Services | National Institutes of Health (1U2CCA233285-01, P01HG00205ESH, P01HG00205ESH, P01HG00205ESH, P01HG00205ESH, P01HG00205ESH, 5R01-HG006137-07)
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