Heteroplasmic substitutions in the entire mitochondrial genomes of human colon cells detected by ultra-deep 454 sequencing

Katarzyna Skonieczna; Boris Malyarchuk; Arkadiusz Jawień; Andrzej Marszałek; Zbigniew Banaszkiewicz; Paweł Jarmocik; Marcelina Borcz; Piotr Bała; Tomasz Grzybowski

doi:10.1016/j.fsigen.2014.10.021

Heteroplasmic substitutions in the entire mitochondrial genomes of human colon cells detected by ultra-deep 454 sequencing

Forensic Sci Int Genet. 2015 Mar:15:16-20. doi: 10.1016/j.fsigen.2014.10.021. Epub 2014 Oct 31.

Authors

Katarzyna Skonieczna¹, Boris Malyarchuk², Arkadiusz Jawień³, Andrzej Marszałek⁴, Zbigniew Banaszkiewicz³, Paweł Jarmocik³, Marcelina Borcz⁵, Piotr Bała⁵, Tomasz Grzybowski⁶

Affiliations

¹ Department of Molecular and Forensic Genetics, Institute of Forensic Medicine, Ludwik Rydygier Collegium Medicum, Nicolaus Copernicus University, 9 Sklodowskiej-Curie Street, 85-094 Bydgoszcz, Poland.
² Institute of Biological Problems of the North, Far-East Branch of the Russian Academy of Sciences, 18 Portovaya Street, 685000 Magadan, Russia.
³ Department of Vascular Surgery and Angiology, Ludwik Rydygier Collegium Medicum, Nicolaus Copernicus University, 9 Sklodowskiej-Curie Street, 85-094 Bydgoszcz, Poland.
⁴ Department of Clinical Pathomorphology, Ludwik Rydygier Collegium Medicum, Nicolaus Copernicus University, 9 Sklodowskiej-Curie Street, 85-094 Bydgoszcz, Poland.
⁵ Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, 5a Pawinskiego Street, 02-106 Warsaw, Poland.
⁶ Department of Molecular and Forensic Genetics, Institute of Forensic Medicine, Ludwik Rydygier Collegium Medicum, Nicolaus Copernicus University, 9 Sklodowskiej-Curie Street, 85-094 Bydgoszcz, Poland. Electronic address: tgrzyb@cm.umk.pl.

PMID: 25465762
DOI: 10.1016/j.fsigen.2014.10.021

Abstract

Mitochondrial DNA (mtDNA) heteroplasmy has been widely described from clinical, evolutionary and analytical points of view. Historically, the majority of studies have been based on Sanger sequencing. However, next-generation sequencing technologies are now being used for heteroplasmy analysis. Ultra-deep sequencing approaches provide increased sensitivity for detecting minority variants. However, a phylogenetic a posteriori analysis revealed that most of the next-generation sequencing data published to date suffers from shortcomings. Because implementation of new technologies in clinical, population, or forensic studies requires proper verification, in this paper we present a direct comparison of ultra-deep 454 and Sanger sequencing for the detection of heteroplasmy in complete mitochondrial genomes of normal colon cells. The spectrum of heteroplasmic mutations is discussed against the background of mitochondrial DNA variability in human populations.

Keywords: 454 Sequencing; Haplogroup; Heteroplasmy; Low-level variants; Mitochondrial genome; Phylogeny.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Colon / cytology
Colon / metabolism*
DNA, Mitochondrial / genetics*
Genome, Mitochondrial*
High-Throughput Nucleotide Sequencing / methods*
Humans
Phylogeny

Substances

DNA, Mitochondrial