Single-cell somatic copy number variants in brain using different amplification methods and reference genomes

Abstract

The presence of somatic mutations, including copy number variants (CNVs), in the brain is well recognized. Comprehensive study requires single-cell whole genome amplification, with several methods available, prior to sequencing. We compared PicoPLEX with two recent adaptations of multiple displacement amplification (MDA): primary template-directed amplification (PTA) and droplet MDA, across 93 human brain cortical nuclei. We demonstrated different properties for each, with PTA providing the broadest amplification, PicoPLEX the most even, and distinct chimeric profiles. Furthermore, we performed CNV calling on two brains with multiple system atrophy and one control brain using different reference genomes. We found that 38% of brain cells have at least one Mb-scale CNV, with some supported by bulk sequencing or single-cells from other brain regions. Our study highlights the importance of selecting whole genome amplification method and reference genome for CNV calling, while supporting the existence of somatic CNVs in healthy and diseased human brain.

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

“…15 Knouse et al reported a significantly lower frequency (2.2%; 95% CI 0.3%–7.9%) for large CNAs in human brain cells 35 . More recently, Kalef-Ezra et al applied PTA to human brain cells and found 33.8% to have at least one megabase-scale CNA 36 . These discrepancies highlight the need for further research into the prevalence of CNAs in the human brain.…”