Detection of genome-wide low-frequency mutations with Paired-End and Complementary Consensus Sequencing (PECC-Seq) revealed end-repair-derived artifacts as residual errors release_rpzhk2hxtjfyrpkyqycuqtnqqm [as of editgroup_36lxy5vss5faledt577cggiazi]

by Xinyue You, Suresh Thiruppathi, Weiying Liu, Yiyi Cao, Mikihiko Naito, Chie Furihata, Masamitsu Honma, Yang Luan, Takayoshi Suzuki

Published in Archives of Toxicology by Springer Science and Business Media LLC.

2020  

Abstract

To improve the accuracy and the cost-efficiency of next-generation sequencing in ultralow-frequency mutation detection, we developed the Paired-End and Complementary Consensus Sequencing (PECC-Seq), a PCR-free duplex consensus sequencing approach. PECC-Seq employed shear points as endogenous barcodes to identify consensus sequences from the overlap in the shortened, complementary DNA strand-derived paired-end reads for sequencing error correction. With the high accuracy of PECC-Seq, we identified the characteristic base substitution errors introduced by the end-repair process of mechanical fragmentation-based library preparations, which were prominent at the terminal 7 bp of the library fragments in the 5'-NpCpA-3' and 5'-NpCpT-3' trinucleotide context. As demonstrated at the human genome scale (TK6 cells), after removing these potential end-repair artifacts from the terminal 7 bp, PECC-Seq could reduce the sequencing error frequency to mid-10-7 with a relatively low sequencing depth. For TA base pairs, the background error rate could be suppressed to mid-10-8. In mutagen-treated (6 μg/mL methyl methanesulfonate or 12 μg/mL N-nitroso-N-ethylurea) TK6, increases in mutagen treatment-related mutant frequencies could be detected, indicating the potential of PECC-Seq in detecting genome-wide ultra-rare mutations. In addition, our finding on the patterns of end-repair artifacts may provide new insights into further reducing technical errors not only for PECC-Seq, but also for other next-generation sequencing techniques.
In text/plain format

Archived Content

There are no accessible files associated with this release. You could check other releases for this work for an accessible version.

Type  article-journal
Stage   published
Date   2020-07-31
Language   en ?
Container Metadata
Not in DOAJ
In Keepers Registry
ISSN-L:  0340-5761
Work Entity
access all versions, variants, and formats of this works (eg, pre-prints)
Catalog Record
Revision: 63982b9d-053d-4446-9e17-291b03f29e8f
API URL: JSON