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

Pieter Spealman, Jaden Burrell, David Gresham

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)4940-4945
Number of pages6
JournalNucleic acids research
Volume48
Issue number9
DOIs
StatePublished - May 21 2020

ASJC Scopus subject areas

  • Genetics

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