A Comparison and Integration of MiSeq and MinION Platforms for Sequencing Single Source and Mixed Mitochondrial Genomes

Michael R Lindberg; Sarah E Schmedes; F Curtis Hewitt; Jamie L Haas; Krista L Ternus; Dana R Kadavy; Bruce Budowle

doi:10.1371/journal.pone.0167600

A Comparison and Integration of MiSeq and MinION Platforms for Sequencing Single Source and Mixed Mitochondrial Genomes

PLoS One. 2016 Dec 9;11(12):e0167600. doi: 10.1371/journal.pone.0167600. eCollection 2016.

Authors

Michael R Lindberg¹, Sarah E Schmedes², F Curtis Hewitt¹, Jamie L Haas¹, Krista L Ternus¹, Dana R Kadavy¹, Bruce Budowle^{2

3}

Affiliations

¹ Signature Science, LLC, Austin, Texas, United States of America.
² Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, Fort Worth, Texas, United States of America.
³ Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia.

Abstract

Single source and multiple donor (mixed) samples of human mitochondrial DNA were analyzed and compared using the MinION and the MiSeq platforms. A generalized variant detection strategy was employed to provide a cursory framework for evaluating the reliability and accuracy of mitochondrial sequences produced by the MinION. The feasibility of long-read phasing was investigated to establish its efficacy in quantitatively distinguishing and deconvolving individuals in a mixture. Finally, a proof-of-concept was demonstrated by integrating both platforms in a hybrid assembly that leverages solely mixture data to accurately reconstruct full mitochondrial genomes.

Publication types

Comparative Study

MeSH terms

DNA, Mitochondrial / genetics*
Gene Frequency
Genome, Mitochondrial*
High-Throughput Nucleotide Sequencing / instrumentation*
Humans
Polymorphism, Single Nucleotide
Sequence Analysis, DNA / instrumentation*

Substances

DNA, Mitochondrial

Grants and funding

We note that the funder (Signature Science) provided support in the form of salaries for authors [ML, JH, CH, KT, and DK)], but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the ‘author contributions’ section.