使用不同扩增方法和参考基因组检测大脑中的单细胞体细胞拷贝数变异。

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

机构信息

Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK.

Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.

出版信息

Commun Biol. 2024 Oct 9;7(1):1288. doi: 10.1038/s42003-024-06940-w.

DOI:10.1038/s42003-024-06940-w

PMID:39384904

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11464624/

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. Here we compare 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 demonstrate different properties for each, with PTA providing the broadest amplification, PicoPLEX the most even, and distinct chimeric profiles. Furthermore, we perform CNV calling on two brains with multiple system atrophy and one control brain using different reference genomes. We find that 20.6% 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.

摘要

体细胞突变（包括拷贝数变异）在大脑中普遍存在。在测序之前，需要采用单细胞全基因组扩增方法，目前已有多种方法可供选择。在此，我们将 PicoPLEX 与两种最近的多重置换扩增（MDA）方法——初级模板定向扩增（PTA）和液滴 MDA——在 93 个人脑皮质核中进行了比较。我们证明了每种方法都有不同的特点，PTA 提供了最广泛的扩增，PicoPLEX 提供了最均匀的扩增，而不同的嵌合体谱。此外，我们使用不同的参考基因组，对两个多系统萎缩大脑和一个对照大脑进行了拷贝数变异（CNV）调用。我们发现，20.6%的脑细胞至少有一个 Mb 级别的 CNV，其中一些得到了批量测序或其他大脑区域的单细胞的支持。我们的研究强调了为 CNV 调用选择全基因组扩增方法和参考基因组的重要性，同时支持了健康和患病人类大脑中存在体细胞 CNV 的观点。