Single-Cell, Genome-wide Sequencing Identifies Clonal Somatic Copy-Number Variation in the Human Brain

Xuyu Cai,Gilad D Evrony,Hillel S Lehmann,Princess C Elhosary,Bhaven K Mehta,Annapurna Poduri,Christopher A Walsh

doi:10.1016/j.celrep.2014.07.043

Abstract

SUMMARYDe novo copy-number variants (CNVs) can cause neuropsychiatric disease, but the degree to which they occur somatically, and during development, is unknown. Single-cell whole-genome sequencing (WGS) in >200 single cells, including >160 neurons from three normal and two pathological human brains, sensitively identified germline trisomy of chromosome 18 but found most (≥95%) neurons in normal brain tissue to be euploid. Analysis of a patient with hemimegalencephaly (HMG) due to a somatic CNV of chromosome 1q found unexpected tetrasomy 1q in ~20% of neurons, suggesting that CNVs in a minority of cells can cause widespread brain dysfunction. Single-cell analysis identified large (>1 Mb) clonal CNVs in lymphoblasts and in single neurons from normal human brain tissue, suggesting that some CNVs occur during neurogenesis. Many neurons contained one or more large candidate private CNVs, including one at chromosome 15q13.2-13.3, a site of duplication in neuropsychiatric conditions. Large private and clonal somatic CNVs occur in normal and diseased human brains.

Highlights

Several recent studies have implicated somatic mutations in a range of diseases, including neurodevelopmental disorders (Biesecker and Spinner, 2013; Jamuar et al, 2014; Poduri et al, 2013; Veltman and Brunner, 2012), with the manifestations of somatic disorders determined by the mutation, its prevalence in the tissue, and the time point during development when the mutation occurred (Poduri et al, 2013)
Since all current single-cell studies rely on genome amplification, which introduces biases and artifacts, we performed copy-number variants (CNVs) analysis of single human neurons using two different methods: multiple displacement amplification (MDA)-based single-cell whole-genome amplification (Evrony et al, 2012; Wang et al, 2012; Xu et al, 2012) and a PCRbased method known as GenomePlex, marketed by Sigma (Van der Aa et al, 2013; Voet et al, 2013; Yin et al, 2013)
We show that clonal somatic CNVs exist both in normal brain and in HMG

Summary

Introduction

Several recent studies have implicated somatic mutations in a range of diseases, including neurodevelopmental disorders (Biesecker and Spinner, 2013; Jamuar et al, 2014; Poduri et al, 2013; Veltman and Brunner, 2012), with the manifestations of somatic disorders determined by the mutation, its prevalence in the tissue, and the time point during development when the mutation occurred (Poduri et al, 2013). Advances in single-cell genomics allow direct assessment of single neuronal genomes from postmortem human brains, enabling systematic characterization of somatic aneuploidies and subchromosomal CNVs (Evrony et al, 2012; Gole et al, 2013; McConnell et al, 2013). Our analysis of single neuronal genomes from normal and diseased human brains with both MDA and GenomePlex shows, consistent with recent reports, that somatic aneuploidy is rare but somatic CNVs are not rare (Gole et al, 2013; McConnell et al, 2013). We show that clonal somatic CNVs exist both in normal brain and in HMG

Results

Discussion

Conclusion