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Updated: Dec 24, 2025

Sequencing of mRNA from Whole Blood using Nanopore Sequencing
Published on: June 3, 2019
Inverted duplicate DNA sequences increase translocation rates through sequencing nanopores resulting in reduced base
Pieter Spealman1, Jaden Burrell1, David Gresham1
1Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA.
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.
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