Work

Inverted duplicate DNA sequences increase translocation rates through sequencing nanopores resulting in reduced base calling accuracy

Year: 2020

Type: article

Abstract: Inverted duplicated DNA sequences are a common feature of structural variants (SVs) and copy number variants (CNVs). Analysis of CNVs containing inverted duplicated DNA sequences using nanopore sequencing identified recurrent aberrant behavior characterized by low confidence, incorrect and missed base calls. Inverted duplicate DNA sequences in both yeast and human samples were observed to have systematic elevation in the electrical current detected at the nanopore, increased translocation rates and decreased sampling rates. The coincidence of inverted duplicated DNA sequences with dramatically reduced sequencing accuracy and an increased translocation rate suggests that secondary DNA structures may interfere with the dynamics of transit of the DNA through the nanopore.

Source: Nucleic Acids Research

DOI: 10.1093/nar/gkaa206

Authors: Pieter Spealman, Jaden Burrell, David Gresham

Institution: New York University

Language: English

Topic: Nanopore and Nanochannel Transport Studies

Subfield: Biomedical Engineering

Field: Engineering

Domain: Physical Sciences

Open Access status: gold

Estimated APC paid: $3,992

Funders: National Science Foundation, National Institutes of Health, National Institute of General Medical Sciences