RT Journal Article
SR Electronic
T1 Ultraspecific somatic SNV and indel detection in single neurons using primary template-directed amplification
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.04.30.442032
DO 10.1101/2021.04.30.442032
A1 Lovelace J. Luquette
A1 Michael B. Miller
A1 Zinan Zhou
A1 Craig L. Bohrson
A1 Alon Galor
A1 Michael A. Lodato
A1 Charles Gawad
A1 Jay West
A1 Christopher A. Walsh
A1 Peter J. Park
YR 2021
UL http://biorxiv.org/content/early/2021/05/01/2021.04.30.442032.abstract
AB Primary template-directed amplification (PTA) is an improved amplification technique for single-cell DNA sequencing. We generated whole-genome analysis of 76 single neurons and developed SCAN2, a computational method to accurately identify both clonal and non-clonal somatic (i.e., limited to a single neuron) single nucleotide variants (SNVs) and small insertions and deletions (indels) using PTA data. Our analysis confirms an increase in non-clonal somatic mutation in single neurons with age, but revises estimates for the rate of this accumulation to be 15 SNVs per year. We also identify artifacts in other amplification methods. Most importantly, we show that somatic indels also increase by at least 2 indels per year per neuron and that indels may have a larger impact on gene function than somatic SNVs in human neurons.Competing Interest StatementThe authors declare the following competing interests: C. G. is Director and cofounder and J. W. is CEO and cofounder of Bioskryb, Inc., the manufacturer of PTA kits used in this study.