Accurate SNV detection in single cells by transposon-based whole-genome amplification of complementary strands

Single-nucleotide variants (SNVs), pertinent to aging and disease, occur sporadically in the human genome, hence necessitating single-cell measurements. However, detection of single-cell SNVs suffers from false positives (FPs) due to intracellular single-stranded DNA damage and the process of whole-...

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Bibliographic Details
Published in:Proceedings of the National Academy of Sciences - PNAS 2021-02, Vol.118 (8), p.1-8
Main Authors: Xing, Dong, Tan, Longzhi, Chang, Chi-Han, Li, Heng, Xie, X. Sunney
Format: Article
Language:English
Subjects:
Biological Sciences
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Summary:Single-nucleotide variants (SNVs), pertinent to aging and disease, occur sporadically in the human genome, hence necessitating single-cell measurements. However, detection of single-cell SNVs suffers from false positives (FPs) due to intracellular single-stranded DNA damage and the process of whole-genome amplification (WGA). Here, we report a single-cell WGA method termed multiplexed end-tagging amplification of complementary strands (META-CS), which eliminates nearly all FPs by virtue of DNA complementarity, and achieved the highest accuracy thus far. We validated META-CS by sequencing kindred cells and human sperm, and applied it to other human tissues. Investigation of mature single human neurons revealed increasing SNVs with age and potentially unrepaired strand-specific oxidative guanine damage. We determined SNV frequencies along the genome in differentiated single human blood cells, and identified cell type-dependent mutational patterns for major types of lymphocytes.
ISSN:0027-8424
1091-6490
DOI:10.1073/pnas.2013106118