Nanopore sequencing: An enrichment-free alternative to mitochondrial DNA sequencing

Roxanne R. Zascavage, Kelcie Thorson, John V. Planz

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Mitochondrial DNA sequence data are often utilized in disease studies, conservation genetics and forensic identification. The current approaches for sequencing the full mtGenome typically require several rounds of PCR enrichment during Sanger or MPS protocols followed by fairly tedious assembly and analysis. Here we describe an efficient approach to sequencing directly from genomic DNA samples without prior enrichment or extensive library preparation steps. A comparison is made between libraries sequenced directly from native DNA and the same samples sequenced from libraries generated with nine overlapping mtDNA amplicons on the Oxford Nanopore MinION™ device. The native and amplicon library preparation methods and alternative base calling strategies were assessed to establish error rates and identify trends of discordance between the two library preparation approaches. For the complete mtGenome, 16 569 nucleotides, an overall error rate of approximately 1.00% was observed. As expected with mtDNA, the majority of error was detected in homopolymeric regions. The use of a modified basecaller that corrects for ambiguous signal in homopolymeric stretches reduced the error rate for both library preparation methods to approximately 0.30%. Our study indicates that direct mtDNA sequencing from native DNA on the MinION™ device provides comparable results to those obtained from common mtDNA sequencing methods and is a reliable alternative to approaches using PCR-enriched libraries.

Original languageEnglish
Pages (from-to)272-280
Number of pages9
JournalElectrophoresis
Volume40
Issue number2
DOIs
StatePublished - 1 Jan 2019

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Nanopores
Mitochondrial DNA
DNA Sequence Analysis
Libraries
DNA
Forensic Genetics
Equipment and Supplies
Polymerase Chain Reaction
DNA sequences
Conservation
Nucleotides

Keywords

  • MinION
  • Nanopore
  • Sequencing
  • mtDNA

Cite this

Zascavage, Roxanne R. ; Thorson, Kelcie ; Planz, John V. / Nanopore sequencing : An enrichment-free alternative to mitochondrial DNA sequencing. In: Electrophoresis. 2019 ; Vol. 40, No. 2. pp. 272-280.
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Nanopore sequencing : An enrichment-free alternative to mitochondrial DNA sequencing. / Zascavage, Roxanne R.; Thorson, Kelcie; Planz, John V.

In: Electrophoresis, Vol. 40, No. 2, 01.01.2019, p. 272-280.

Research output: Contribution to journalArticle

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