Research Paper Volume 12, Issue 8 pp 7603—7613
LUCS: a high-resolution nucleic acid sequencing tool for accurate long-read analysis of individual DNA molecules
- 1 Department of Biology, Laboratory of Aging and Infertility Research, Northeastern University, Boston, MA 02115, USA
- 2 On leave under a Student Exchange Program from the Institut für Pflanzengenetik, Leibniz Universität Hannover, Hannover D-30419, Germany
Received: April 6, 2020 Accepted: April 21, 2020 Published: April 28, 2020https://doi.org/10.18632/aging.103171
How to Cite
Copyright © 2020 Annis et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Nucleic acid sequence analyses are fundamental to all aspects of biological research, spanning aging, mitochondrial DNA (mtDNA) and cancer, as well as microbial and viral evolution. Over the past several years, significant improvements in DNA sequencing, including consensus sequence analysis, have proven invaluable for high-throughput studies. However, all current DNA sequencing platforms have limited utility for studies of complex mixtures or of individual long molecules, the latter of which is crucial to understanding evolution and consequences of single nucleotide variants and their combinations. Here we report a new technology termed LUCS (Long-molecule UMI-driven Consensus Sequencing), in which reads from third-generation sequencing are aggregated by unique molecular identifiers (UMIs) specific for each individual DNA molecule. This enables in-silico reconstruction of highly accurate consensus reads of each DNA molecule independent of other molecules in the sample. Additionally, use of two UMIs enables detection of artificial recombinants (chimeras). As proof of concept, we show that application of LUCS to assessment of mitochondrial genomes in complex mixtures from single cells was associated with an error rate of 1X10-4 errors/nucleotide. Thus, LUCS represents a major step forward in DNA sequencing that offers high-throughput capacity and high-accuracy reads in studies of long DNA templates and nucleotide variants in heterogenous samples.