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Full mtDNA genome sequencing of Brazilian admixed populations: A forensic-focused evaluation of a MPS application as an alternative to Sanger sequencing methods.
Forensic Sci Int Genet. 2019 09; 42:154-164.FS

Abstract

The use of Massive Parallel Sequencing (MPS) techniques have been proposed by the forensic community as an alternative to Sanger sequencing methods in routine forensic casework analysis regarding mitochondrial DNA (mtDNA). Interesting features of MPS include high throughput, ability to simultaneously genotype a significant number of samples by barcoding techniques, processing automation, reduced time and costs, among others. Advantages include the capability of generating full mtDNA genome sequences versus usual techniques, usually limited to hypervariable or control regions exclusively. In this work, 96 reference single-source samples from three different Brazilian cities were subjected to full mtDNA genome sequencing by MPS techniques using an early-access version of Precision ID mtDNA Whole Genome Panel on an Ion Torrent PGM platform (Thermo Fisher Scientific, Waltham, MA, USA). Complete, high-quality sequences were obtained and sequencing performance was evaluated via four different metrics. As a subset of evaluated samples have been previously submitted for Sanger sequencing of the control region, a comparative analysis of both methods' results was conducted in order to compare technique adequacy within a forensic context. Even though this study is one of the first to report full mtDNA genome sequences for Brazilian admixed populations, the observed haplotypes exhibit a predominance of Native American and African maternal lineages in the studied sample set, reproducing results described in the literature for control regions only. Interpopulation analysis among Brazilian and 26 worldwide populations was also carried out. The results indicate that MPS-generated full mtDNA genome sequences may have great utility in forensic real casework applications, with a pronounced gain of genetic information and discrimination power provided by coding region evaluation and the enhanced capacity of heteroplasmies determination. Database construction and other relevant factors concerning implementation of such techniques in Brazilian forensic laboratories are also discussed.

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Publisher Full Text (DOI)

Authors+Show Affiliations

Avila E
Setor Técnico-Científico, Superintendência Regional do Rio Grande do Sul, Polícia Federal, Porto Alegre, Brazil; Escola de Ciências, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil; Instituto Nacional de Ciência e Tecnologia INCT Ciências Forenses, Porto Alegre, Brazil. Electronic address: e.avila@edu.pucrs.br.
Graebin P
Escola de Ciências, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil.
Chemale G
Setor Técnico-Científico, Superintendência Regional do Rio Grande do Sul, Polícia Federal, Porto Alegre, Brazil.
Freitas J
Instituto Nacional de Criminalística, Polícia Federal, Brasília, DF, Brazil.
Kahmann A
Instituto de Matemática, Estatística e Física, Universidade Federal de Rio Grande, Rio Grande, Brazil.
Alho CS
Escola de Ciências, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil; Instituto Nacional de Ciência e Tecnologia INCT Ciências Forenses, Porto Alegre, Brazil.

MeSH

BrazilDNA, MitochondrialGenetics, PopulationGenome, MitochondrialHaplotypesHigh-Throughput Nucleotide SequencingHumansPolymerase Chain ReactionSequence Analysis, DNA

Pub Type(s)

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

Language

eng

PubMed ID

31325893

Citation

Avila, E, et al. "Full mtDNA Genome Sequencing of Brazilian Admixed Populations: a Forensic-focused Evaluation of a MPS Application as an Alternative to Sanger Sequencing Methods." Forensic Science International. Genetics, vol. 42, 2019, pp. 154-164.
Avila E, Graebin P, Chemale G, et al. Full mtDNA genome sequencing of Brazilian admixed populations: A forensic-focused evaluation of a MPS application as an alternative to Sanger sequencing methods. Forensic Sci Int Genet. 2019;42:154-164.
Avila, E., Graebin, P., Chemale, G., Freitas, J., Kahmann, A., & Alho, C. S. (2019). Full mtDNA genome sequencing of Brazilian admixed populations: A forensic-focused evaluation of a MPS application as an alternative to Sanger sequencing methods. Forensic Science International. Genetics, 42, 154-164. https://doi.org/10.1016/j.fsigen.2019.07.004
Avila E, et al. Full mtDNA Genome Sequencing of Brazilian Admixed Populations: a Forensic-focused Evaluation of a MPS Application as an Alternative to Sanger Sequencing Methods. Forensic Sci Int Genet. 2019;42:154-164. PubMed PMID: 31325893.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Full mtDNA genome sequencing of Brazilian admixed populations: A forensic-focused evaluation of a MPS application as an alternative to Sanger sequencing methods. AU - Avila,E, AU - Graebin,P, AU - Chemale,G, AU - Freitas,J, AU - Kahmann,A, AU - Alho,C S, Y1 - 2019/07/09/ PY - 2019/03/29/received PY - 2019/07/03/revised PY - 2019/07/08/accepted PY - 2019/7/22/pubmed PY - 2019/12/20/medline PY - 2019/7/21/entrez KW - Brazil KW - Forensic KW - Massive parallel sequencing KW - Mitochondrial full genome KW - Mitochondrial haplotypes KW - Next generation sequencing KW - mtDNA SP - 154 EP - 164 JF - Forensic science international. Genetics JO - Forensic Sci Int Genet VL - 42 N2 - The use of Massive Parallel Sequencing (MPS) techniques have been proposed by the forensic community as an alternative to Sanger sequencing methods in routine forensic casework analysis regarding mitochondrial DNA (mtDNA). Interesting features of MPS include high throughput, ability to simultaneously genotype a significant number of samples by barcoding techniques, processing automation, reduced time and costs, among others. Advantages include the capability of generating full mtDNA genome sequences versus usual techniques, usually limited to hypervariable or control regions exclusively. In this work, 96 reference single-source samples from three different Brazilian cities were subjected to full mtDNA genome sequencing by MPS techniques using an early-access version of Precision ID mtDNA Whole Genome Panel on an Ion Torrent PGM platform (Thermo Fisher Scientific, Waltham, MA, USA). Complete, high-quality sequences were obtained and sequencing performance was evaluated via four different metrics. As a subset of evaluated samples have been previously submitted for Sanger sequencing of the control region, a comparative analysis of both methods' results was conducted in order to compare technique adequacy within a forensic context. Even though this study is one of the first to report full mtDNA genome sequences for Brazilian admixed populations, the observed haplotypes exhibit a predominance of Native American and African maternal lineages in the studied sample set, reproducing results described in the literature for control regions only. Interpopulation analysis among Brazilian and 26 worldwide populations was also carried out. The results indicate that MPS-generated full mtDNA genome sequences may have great utility in forensic real casework applications, with a pronounced gain of genetic information and discrimination power provided by coding region evaluation and the enhanced capacity of heteroplasmies determination. Database construction and other relevant factors concerning implementation of such techniques in Brazilian forensic laboratories are also discussed. SN - 1878-0326 UR - https://www.unboundmedicine.com/medline/citation/31325893/Full_mtDNA_genome_sequencing_of_Brazilian_admixed_populations:_A_forensic_focused_evaluation_of_a_MPS_application_as_an_alternative_to_Sanger_sequencing_methods_ DB - PRIME DP - Unbound Medicine ER -