Evaluation of the precision ID mtDNA whole genome panel on two massively parallel sequencing systems

August Eric Woerner, Angela Dawn Ambers, Frank R. Wendt, Jonathan L. King, Rodrigo Soares Moura-Neto, Rosane Silva, Bruce Budowle

Research output: Contribution to journalArticle

8 Citations (Scopus)

Abstract

Sequencing whole mitochondrial genomes by capillary electrophoresis is a costly and time/labor-intensive endeavor. Many of the previous Sanger sequencing-based approaches generated amplicons that were several kilobases in length; lengths that are likely not amenable for most forensic applications. However, with the advent of massively parallel sequencing (MPS) short-amplicon multiplexes covering the entire mitochondrial genome can be sequenced relatively easily and rapidly. Recently, the Precision ID mtDNA Whole Genome Panel (Thermo Fisher Scientific by Applied Biosystems™) has been introduced. This panel is composed of 162 amplicons (in two multiplexes) that are considerably smaller in length (∼163bp) and thus are more amenable to analyzing challenged samples. This panel was evaluated on both the Ion S5™ System (Thermo Fisher Scientific) and the MiSeq™ FGx Desktop Sequencer (Illumina). A script was developed to extract phased haplotypes associated with these amplicons. Levels of read-depth were compared across sequencing pools and between sequencing technologies and haplotype concordances were assessed. Given modest thresholds on read depth, the haplotypes identified by either technology were consistent. Nuclear mitochondrial sequences (Numts) were also inferred, and the effect of different mapping strategies commonly used to filter out Numts were contrasted. Some Numts are co-amplified with this amplification kit, and while the choice of reference sequence can mitigate some of these effects, some data from the mitochondrial genome were lost in the process in this study. This study demonstrates that the Ion and MiSeq platforms provide consistent haplotype estimation of the whole mitochondrial genome, thus providing further support for the reliability and validity of the Precision ID mtDNA Whole Genome Panel.

Original languageEnglish
Pages (from-to)213-224
Number of pages12
JournalForensic Science International: Genetics
Volume36
DOIs
StatePublished - 1 Sep 2018

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High-Throughput Nucleotide Sequencing
Mitochondrial Genome
Mitochondrial DNA
Haplotypes
Genome
Ions
Technology
Capillary Electrophoresis
Reproducibility of Results

Keywords

  • Haplotype assessment
  • Ion S5
  • Massively parallel sequencing
  • MiSeq
  • Numts
  • Precision ID whole genome panel
  • Whole mitochondrial genome
  • mtDNA

Cite this

Woerner, August Eric ; Ambers, Angela Dawn ; Wendt, Frank R. ; King, Jonathan L. ; Moura-Neto, Rodrigo Soares ; Silva, Rosane ; Budowle, Bruce. / Evaluation of the precision ID mtDNA whole genome panel on two massively parallel sequencing systems. In: Forensic Science International: Genetics. 2018 ; Vol. 36. pp. 213-224.
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Evaluation of the precision ID mtDNA whole genome panel on two massively parallel sequencing systems. / Woerner, August Eric; Ambers, Angela Dawn; Wendt, Frank R.; King, Jonathan L.; Moura-Neto, Rodrigo Soares; Silva, Rosane; Budowle, Bruce.

In: Forensic Science International: Genetics, Vol. 36, 01.09.2018, p. 213-224.

Research output: Contribution to journalArticle

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AU - Silva, Rosane

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