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-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.

Automated summary

A single-cell WGA method called META-CS has been developed to eliminate false positives in single-cell SNV detection, achieving the highest accuracy in measurements so far. Validation studies on kindred cells, human sperm, and other human tissues have confirmed the effectiveness of META-CS, revealing an increase in SNVs in mature single human neurons with age and cell type-dependent SNV frequencies and mutational patterns in single human blood cells.