Evaluation of mitogenome sequence concordance, heteroplasmy detection, and haplogrouping in a worldwide lineage study using the Precision ID mtDNA Whole Genome Panel

Christina Strobl, Jennifer Churchill Cihlar, Robert Lagacé, Sharon Wootton, Chantal Roth, Nicole Huber, Lisa Schnaller, Bettina Zimmermann, Gabriela Huber, Seah Lay Hong, Rodrigo Moura-Neto, Rosane Silva, Farida Alshamali, Luis Souto, K. Anslinger, Balazs Egyed, Renata Jankova-Ajanovska, Andrea Casas-Vargas, Wiliam Usaquén, D. SilvaClaudia Barletta-Carrillo, Dean Herman Tineo, Carlos Vullo, Reinhard Würzner, Catarina Xavier, Leonor Gusmão, Harald Niederstätter, Martin Bodner, B. Budowle, Walther Parson

Research output: Contribution to journalArticle

Abstract

The emergence of Massively Parallel Sequencing technologies enabled the analysis of full mitochondrial (mt)DNA sequences from forensically relevant samples that have, so far, only been typed in the control region or its hypervariable segments. In this study, we evaluated the performance of a commercially available multiplex-PCR-based assay, the Precision ID mtDNA Whole Genome Panel (Thermo Fisher Scientific), for the amplification and sequencing of the entire mitochondrial genome (mitogenome) from even degraded forensic specimens. For this purpose, more than 500 samples from 24 different populations were selected to cover the vast majority of established superhaplogroups. These are known to harbor different signature sequence motifs corresponding to their phylogenetic background that could have an effect on primer binding and, thus, could limit a broad application of this molecular genetic tool. The selected samples derived from various forensically relevant tissue sources and were DNA extracted using different methods. We evaluated sequence concordance and heteroplasmy detection and compared the findings to conventional Sanger sequencing as well as an orthogonal MPS platform. We discuss advantages and limitations of this approach with respect to forensic genetic workflow and analytical requirements.

Original languageEnglish
Pages (from-to)244-251
Number of pages8
JournalForensic Science International: Genetics
Volume42
DOIs
StatePublished - Sep 2019

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Mitochondrial Genome
Mitochondrial DNA
Forensic Genetics
Genome
High-Throughput Nucleotide Sequencing
Workflow
Multiplex Polymerase Chain Reaction
Molecular Biology
Technology
DNA
Population

Keywords

  • Forensic genetics
  • Haplogroups
  • Massively parallel sequencing
  • Mitochondrial genome
  • MtDNA
  • Phylogeny

Cite this

Strobl, Christina ; Churchill Cihlar, Jennifer ; Lagacé, Robert ; Wootton, Sharon ; Roth, Chantal ; Huber, Nicole ; Schnaller, Lisa ; Zimmermann, Bettina ; Huber, Gabriela ; Lay Hong, Seah ; Moura-Neto, Rodrigo ; Silva, Rosane ; Alshamali, Farida ; Souto, Luis ; Anslinger, K. ; Egyed, Balazs ; Jankova-Ajanovska, Renata ; Casas-Vargas, Andrea ; Usaquén, Wiliam ; Silva, D. ; Barletta-Carrillo, Claudia ; Tineo, Dean Herman ; Vullo, Carlos ; Würzner, Reinhard ; Xavier, Catarina ; Gusmão, Leonor ; Niederstätter, Harald ; Bodner, Martin ; Budowle, B. ; Parson, Walther. / Evaluation of mitogenome sequence concordance, heteroplasmy detection, and haplogrouping in a worldwide lineage study using the Precision ID mtDNA Whole Genome Panel. In: Forensic Science International: Genetics. 2019 ; Vol. 42. pp. 244-251.
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abstract = "The emergence of Massively Parallel Sequencing technologies enabled the analysis of full mitochondrial (mt)DNA sequences from forensically relevant samples that have, so far, only been typed in the control region or its hypervariable segments. In this study, we evaluated the performance of a commercially available multiplex-PCR-based assay, the Precision ID mtDNA Whole Genome Panel (Thermo Fisher Scientific), for the amplification and sequencing of the entire mitochondrial genome (mitogenome) from even degraded forensic specimens. For this purpose, more than 500 samples from 24 different populations were selected to cover the vast majority of established superhaplogroups. These are known to harbor different signature sequence motifs corresponding to their phylogenetic background that could have an effect on primer binding and, thus, could limit a broad application of this molecular genetic tool. The selected samples derived from various forensically relevant tissue sources and were DNA extracted using different methods. We evaluated sequence concordance and heteroplasmy detection and compared the findings to conventional Sanger sequencing as well as an orthogonal MPS platform. We discuss advantages and limitations of this approach with respect to forensic genetic workflow and analytical requirements.",
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author = "Christina Strobl and {Churchill Cihlar}, Jennifer and Robert Lagac{\'e} and Sharon Wootton and Chantal Roth and Nicole Huber and Lisa Schnaller and Bettina Zimmermann and Gabriela Huber and {Lay Hong}, Seah and Rodrigo Moura-Neto and Rosane Silva and Farida Alshamali and Luis Souto and K. Anslinger and Balazs Egyed and Renata Jankova-Ajanovska and Andrea Casas-Vargas and Wiliam Usaqu{\'e}n and D. Silva and Claudia Barletta-Carrillo and Tineo, {Dean Herman} and Carlos Vullo and Reinhard W{\"u}rzner and Catarina Xavier and Leonor Gusm{\~a}o and Harald Niederst{\"a}tter and Martin Bodner and B. Budowle and Walther Parson",
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Strobl, C, Churchill Cihlar, J, Lagacé, R, Wootton, S, Roth, C, Huber, N, Schnaller, L, Zimmermann, B, Huber, G, Lay Hong, S, Moura-Neto, R, Silva, R, Alshamali, F, Souto, L, Anslinger, K, Egyed, B, Jankova-Ajanovska, R, Casas-Vargas, A, Usaquén, W, Silva, D, Barletta-Carrillo, C, Tineo, DH, Vullo, C, Würzner, R, Xavier, C, Gusmão, L, Niederstätter, H, Bodner, M, Budowle, B & Parson, W 2019, 'Evaluation of mitogenome sequence concordance, heteroplasmy detection, and haplogrouping in a worldwide lineage study using the Precision ID mtDNA Whole Genome Panel', Forensic Science International: Genetics, vol. 42, pp. 244-251. https://doi.org/10.1016/j.fsigen.2019.07.013

Evaluation of mitogenome sequence concordance, heteroplasmy detection, and haplogrouping in a worldwide lineage study using the Precision ID mtDNA Whole Genome Panel. / Strobl, Christina; Churchill Cihlar, Jennifer; Lagacé, Robert; Wootton, Sharon; Roth, Chantal; Huber, Nicole; Schnaller, Lisa; Zimmermann, Bettina; Huber, Gabriela; Lay Hong, Seah; Moura-Neto, Rodrigo; Silva, Rosane; Alshamali, Farida; Souto, Luis; Anslinger, K.; Egyed, Balazs; Jankova-Ajanovska, Renata; Casas-Vargas, Andrea; Usaquén, Wiliam; Silva, D.; Barletta-Carrillo, Claudia; Tineo, Dean Herman; Vullo, Carlos; Würzner, Reinhard; Xavier, Catarina; Gusmão, Leonor; Niederstätter, Harald; Bodner, Martin; Budowle, B.; Parson, Walther.

In: Forensic Science International: Genetics, Vol. 42, 09.2019, p. 244-251.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Evaluation of mitogenome sequence concordance, heteroplasmy detection, and haplogrouping in a worldwide lineage study using the Precision ID mtDNA Whole Genome Panel

AU - Strobl, Christina

AU - Churchill Cihlar, Jennifer

AU - Lagacé, Robert

AU - Wootton, Sharon

AU - Roth, Chantal

AU - Huber, Nicole

AU - Schnaller, Lisa

AU - Zimmermann, Bettina

AU - Huber, Gabriela

AU - Lay Hong, Seah

AU - Moura-Neto, Rodrigo

AU - Silva, Rosane

AU - Alshamali, Farida

AU - Souto, Luis

AU - Anslinger, K.

AU - Egyed, Balazs

AU - Jankova-Ajanovska, Renata

AU - Casas-Vargas, Andrea

AU - Usaquén, Wiliam

AU - Silva, D.

AU - Barletta-Carrillo, Claudia

AU - Tineo, Dean Herman

AU - Vullo, Carlos

AU - Würzner, Reinhard

AU - Xavier, Catarina

AU - Gusmão, Leonor

AU - Niederstätter, Harald

AU - Bodner, Martin

AU - Budowle, B.

AU - Parson, Walther

PY - 2019/9

Y1 - 2019/9

N2 - The emergence of Massively Parallel Sequencing technologies enabled the analysis of full mitochondrial (mt)DNA sequences from forensically relevant samples that have, so far, only been typed in the control region or its hypervariable segments. In this study, we evaluated the performance of a commercially available multiplex-PCR-based assay, the Precision ID mtDNA Whole Genome Panel (Thermo Fisher Scientific), for the amplification and sequencing of the entire mitochondrial genome (mitogenome) from even degraded forensic specimens. For this purpose, more than 500 samples from 24 different populations were selected to cover the vast majority of established superhaplogroups. These are known to harbor different signature sequence motifs corresponding to their phylogenetic background that could have an effect on primer binding and, thus, could limit a broad application of this molecular genetic tool. The selected samples derived from various forensically relevant tissue sources and were DNA extracted using different methods. We evaluated sequence concordance and heteroplasmy detection and compared the findings to conventional Sanger sequencing as well as an orthogonal MPS platform. We discuss advantages and limitations of this approach with respect to forensic genetic workflow and analytical requirements.

AB - The emergence of Massively Parallel Sequencing technologies enabled the analysis of full mitochondrial (mt)DNA sequences from forensically relevant samples that have, so far, only been typed in the control region or its hypervariable segments. In this study, we evaluated the performance of a commercially available multiplex-PCR-based assay, the Precision ID mtDNA Whole Genome Panel (Thermo Fisher Scientific), for the amplification and sequencing of the entire mitochondrial genome (mitogenome) from even degraded forensic specimens. For this purpose, more than 500 samples from 24 different populations were selected to cover the vast majority of established superhaplogroups. These are known to harbor different signature sequence motifs corresponding to their phylogenetic background that could have an effect on primer binding and, thus, could limit a broad application of this molecular genetic tool. The selected samples derived from various forensically relevant tissue sources and were DNA extracted using different methods. We evaluated sequence concordance and heteroplasmy detection and compared the findings to conventional Sanger sequencing as well as an orthogonal MPS platform. We discuss advantages and limitations of this approach with respect to forensic genetic workflow and analytical requirements.

KW - Forensic genetics

KW - Haplogroups

KW - Massively parallel sequencing

KW - Mitochondrial genome

KW - MtDNA

KW - Phylogeny

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