Alexej Abyzov1, Flora M Vaccarino2, Abhiram Natu2 and Milovan Suvakov1*
1Mayo clinic
2Yale University
suvakov.milovan [at] mayo.edu
Abstract
Somatic mosaicism encompasses a wide spectrum of genomic alterations, yet the landscape of copy number variation in individual cells remains poorly characterized due to amplification biases in traditional single-cell genomics. Here, we present our results on detecting mosaic copy number variations (CNVs) utilizing Primary Template-directed Amplification (PTA) to sequence single genomes across different normal human tissues. By achieving bulk-like uniform genome coverage, PTA enables the detection of copy number changes ranging from massive megabase-scale alterations to highly focal events at single-cell resolution. In this presentation, we detail the broader landscape of overall mosaic CNVs, capturing frequent sub-chromosomal copy-number changes and whole-chromosome aneuploidies, such as the loss of chromosome Y. We further highlight the capacity of PTA to reconstruct a striking example of a complex, multi-break rearrangement between several chromosomes in a single cell. Using orthogonal evidence from both sequencing depth and discordant read fragments, we capture a complex mutational event entirely invisible to bulk sequencing. Furthermore, we demonstrate that it is possible to accurately identify locus-restricted deletions within the T-cell receptor (TCR) loci. These stepwise focal copy-number losses faithfully reflect canonical somatic V(D)J immune rearrangements, validating our ability to detect biologically expected alterations. Together, these results demonstrate that single-cell PTA provides an expansive view of somatic mosaicism, uncovering extensive copy number diversity and localized genomic changes in normal tissues.
Keywords: mosaicism, single-cell, PTA, CNV, CNVpytor