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.
Competing Interest Statement
SWS received research support from Cerevel Therapeutics. SWS is a member of the scientific advisory board of the Lewy Body Dementia Association and the Multiple System Atrophy Coalition. FJS receives research support from Genentech, Illumina, PacBio and Oxford Nanopore. All other authors declare no competing interests.
Footnotes
The manuscript has been revised to add links related to the bioinformatics tools used, the EGA accession number, and a supplementary file linking the results of the study with data in the EGA (Supplementary Table 4). We further analyzed the data to assess the accuracy of reported CNVs and added the finding results.