Single-cell genome sequencing of human neurons identifies somatic point mutation and indel enrichment in regulatory elements

TY - JOUR

T1 - Single-cell genome sequencing of human neurons identifies somatic point mutation and indel enrichment in regulatory elements

AU - Luquette, Lovelace J

AU - Miller, Michael B

AU - Zhou, Zinan

AU - Bohrson, Craig L

AU - Zhao, Yifan

AU - Jin, Hu

AU - Gulhan, Doga

AU - Ganz, Javier

AU - Bizzotto, Sara

AU - Kirkham, Samantha

AU - Hochepied, Tino

AU - Libert, Claude

AU - Galor, Alon

AU - Kim, Junho

AU - Lodato, Michael A

AU - Garaycoechea, Juan I

AU - Gawad, Charles

AU - West, Jay

AU - Walsh, Christopher A

AU - Park, Peter J

N1 - © 2022. The Author(s), under exclusive licence to Springer Nature America, Inc.

PY - 2022/10

Y1 - 2022/10

N2 - Accurate somatic mutation detection from single-cell DNA sequencing is challenging due to amplification-related artifacts. To reduce this artifact burden, an improved amplification technique, primary template-directed amplification (PTA), was recently introduced. We analyzed whole-genome sequencing data from 52 PTA-amplified single neurons using SCAN2, a new genotyper we developed to leverage mutation signatures and allele balance in identifying somatic single-nucleotide variants (SNVs) and small insertions and deletions (indels) in PTA data. Our analysis confirms an increase in nonclonal somatic mutation in single neurons with age, but revises the estimated rate of this accumulation to 16 SNVs per year. We also identify artifacts in other amplification methods. Most importantly, we show that somatic indels increase by at least three per year per neuron and are enriched in functional regions of the genome such as enhancers and promoters. Our data suggest that indels in gene-regulatory elements have a considerable effect on genome integrity in human neurons.

AB - Accurate somatic mutation detection from single-cell DNA sequencing is challenging due to amplification-related artifacts. To reduce this artifact burden, an improved amplification technique, primary template-directed amplification (PTA), was recently introduced. We analyzed whole-genome sequencing data from 52 PTA-amplified single neurons using SCAN2, a new genotyper we developed to leverage mutation signatures and allele balance in identifying somatic single-nucleotide variants (SNVs) and small insertions and deletions (indels) in PTA data. Our analysis confirms an increase in nonclonal somatic mutation in single neurons with age, but revises the estimated rate of this accumulation to 16 SNVs per year. We also identify artifacts in other amplification methods. Most importantly, we show that somatic indels increase by at least three per year per neuron and are enriched in functional regions of the genome such as enhancers and promoters. Our data suggest that indels in gene-regulatory elements have a considerable effect on genome integrity in human neurons.

KW - Genome, Human/genetics

KW - High-Throughput Nucleotide Sequencing/methods

KW - Humans

KW - INDEL Mutation/genetics

KW - Neurons

KW - Nucleotides

KW - Point Mutation

KW - Polymorphism, Single Nucleotide/genetics

KW - Single-Cell Analysis

U2 - 10.1038/s41588-022-01180-2

DO - 10.1038/s41588-022-01180-2

M3 - Article

C2 - 36163278

SN - 1061-4036

VL - 54

SP - 1564

EP - 1571

JO - Nature Genetics

JF - Nature Genetics

IS - 10

ER -