title: A Protocol for mtGenome Analysis on Large Sample Numbers.
abstract: The mitochondrial genome is widely studied in a variety of fields, such as population, forensic, and human and medical genetics. Most studies have been limited to a small portion of the sequence that, although highly diverse, does not describe the total variability. The arrival of modern high-throughput sequencing technologies has made it possible to investigate larger sequences in a shorter amount of time as well as in a more affordable fashion. This work aims to describe a protocol for sequencing and analyzing the complete mitochondrial genome with the Ion PGM™ platform. To evaluate the protocol, the mitochondrial genome was sequenced to approximately 210 Mbp, with high-quality sequences distributed between 12 samples that had an average coverage of 1023× per sample. Several variant callers were compared to improve the protocol outcome. The results suggest that it is possible to run up to 120 samples per run without any loss of any significant quality. Therefore, this protocol is an efficient and accurate tool for full mitochondrial genome analysis.
authors.affiliation: Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil. ; Universidade Federal Rural da Amazônia, Campus de Capanema, PA, Brazil.
authors.forename: Igor G
authors.initials: IG
authors.lastname: Hamoy
authors.affiliation: Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil.
authors.forename: André M
authors.initials: AM
authors.lastname: Ribeiro-Dos-Santos
authors.affiliation: Institute of Molecular Pathology and Immunology of the University of Porto, Universidade do Porto. Porto, Portugal.
authors.forename: Luiz
authors.initials: L
authors.lastname: Alvarez
authors.affiliation: Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil.
authors.forename: Silvanira
authors.initials: S
authors.lastname: Barbosa
authors.affiliation: Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil.
authors.forename: Artur
authors.initials: A
authors.lastname: Silva
authors.affiliation: Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil. ; Núcleo de Pesquisa em Oncologia, Universidade Federal do Pará, Belém, PA, Brazil.
authors.forename: Sidney
authors.initials: S
authors.lastname: Santos
authors.affiliation: Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil. ; Institute of Molecular Pathology and Immunology of the University of Porto, Universidade do Porto. Porto, Portugal.
authors.forename: Leonor
authors.initials: L
authors.lastname: Gusmão
authors.affiliation: Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil. ; Núcleo de Pesquisa em Oncologia, Universidade Federal do Pará, Belém, PA, Brazil.
authors.forename: Andrea
authors.initials: A
authors.lastname: Ribeiro-Dos-Santos
keywords: analysis protocol; mitochondrial DNA; next-generation sequencing; polymorphism; population genetics