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High-resolution detection of copy number alterations in single cells with HiScanner.

High-resolution detection of copy number alterations in single cells with HiScanner.

Authors :
Zhao Y
Luquette LJ
Veit AD
Wang X
Xi R
Viswanadham VV
Shao DD
Walsh CA
Yang HW
Johnson MD
Park PJ
Source :
BioRxiv : the preprint server for biology [bioRxiv] 2024 Apr 29. Date of Electronic Publication: 2024 Apr 29.
Publication Year :
2024

Abstract

Improvements in single-cell whole-genome sequencing (scWGS) assays have enabled detailed characterization of somatic copy number alterations (CNAs) at the single-cell level. Yet, current computational methods are mostly designed for detecting chromosome-scale changes in cancer samples with low sequencing coverage. Here, we introduce HiScanner (High-resolution Single-Cell Allelic copy Number callER), which combines read depth, B-allele frequency, and haplotype phasing to identify CNAs with high resolution. In simulated data, HiScanner consistently outperforms state-of-the-art methods across various CNA types and sizes. When applied to high-coverage scWGS data from human brain cells, HiScanner shows a superior ability to detect smaller CNAs, uncovering distinct CNA patterns between neurons and oligodendrocytes. For 179 cells we sequenced from longitudinal meningioma samples, integration of CNAs with point mutations revealed evolutionary trajectories of tumor cells. These findings show that HiScanner enables accurate characterization of frequency, clonality, and distribution of CNAs at the single-cell level in both non-neoplastic and neoplastic cells.

Details

Language :
English
ISSN :
2692-8205
Database :
MEDLINE
Journal :
BioRxiv : the preprint server for biology
Accession number :
38746445
Full Text :
https://doi.org/10.1101/2024.04.26.587806