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

Ester Kalef-Ezra; Zeliha Gozde Turan; Diego Perez-Rodriguez; Ida Bomann; Sairam Behera; Caoimhe Morley; Sonja W Scholz; Zane Jaunmuktane; Jonas Demeulemeester; Fritz J Sedlazeck; Christos Proukakis

doi:10.1101/2023.08.07.552289

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

bioRxiv [Preprint]. 2023 Nov 21:2023.08.07.552289. doi: 10.1101/2023.08.07.552289.

Authors

Ester Kalef-Ezra^{1

2}, Zeliha Gozde Turan^{1

2}, Diego Perez-Rodriguez¹, Ida Bomann¹, Sairam Behera³, Caoimhe Morley¹, Sonja W Scholz^{4

5}, Zane Jaunmuktane^{1

2

6}, Jonas Demeulemeester^{2

7

8

9}, Fritz J Sedlazeck^{2

3

10

11}, Christos Proukakis^{1

2}

Affiliations

¹ Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK.
² Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815.
³ Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston TX 77030, USA.
⁴ Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA.
⁵ Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA.
⁶ Queen Square Brain Bank for Neurological disorders, UCL Queen Square Institute of Neurology, London, UK.
⁷ Department of Oncology, KU Leuven, Leuven, Belgium.
⁸ Cancer Genomics Laboratory, The Francis Crick Institute, London, UK.
⁹ VIB Center for Cancer Biology, Leuven, Belgium.
¹⁰ Department of Molecular and Human Genetics, Baylor College of Medicine, TX, USA.
¹¹ Department of Computer Science, Rice University, 6100 Main Street, Houston, TX, USA.

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.

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Abstract

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