A Protocol for mtGenome Analysis on Large Sample Numbers

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-throug...

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Main Authors:	Igor G. Hamoy, André M. Ribeiro-Dos-Santos, Luiz Alvarez, Silvanira Barbosa, Artur Silva, Sidney Santos, Leonor Gusmão, ândrea Ribeiro-Dos-Santos
Format:	Article
Language:	English
Published:	SAGE Publishing 2014-01-01
Series:	Bioinformatics and Biology Insights
Online Access:	https://doi.org/10.4137/BBI.S14623

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spelling	doaj-56b9d37dd464418ea2992f40074865712020-11-25T02:34:09ZengSAGE PublishingBioinformatics and Biology Insights1177-93222014-01-01810.4137/BBI.S14623A Protocol for mtGenome Analysis on Large Sample NumbersIgor G. Hamoy0André M. Ribeiro-Dos-Santos1Luiz Alvarez2Silvanira Barbosa3Artur Silva4Sidney Santos5Leonor Gusmão6ândrea Ribeiro-Dos-Santos7Authors with equal contribution.Authors with equal contribution.Institute of Molecular Pathology and Immunology of the University of Porto, Universidade do Porto. Porto, Portugal.Instituto de Ciěncias Biológicas, Universidade Federal do Pará, Belém, PA, Brazil.Instituto de Ciěncias Biológicas, Universidade Federal do Pará, Belém, PA, Brazil.Núcleo de Pesquisa em Oncologia, Universidade Federal do Pará, Belém, PA, Brazil.Institute of Molecular Pathology and Immunology of the University of Porto, Universidade do Porto. Porto, Portugal.Núcleo de Pesquisa em Oncologia, Universidade Federal do Pará, Belém, PA, Brazil.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.https://doi.org/10.4137/BBI.S14623
collection	DOAJ
language	English
format	Article
sources	DOAJ
author	Igor G. Hamoy André M. Ribeiro-Dos-Santos Luiz Alvarez Silvanira Barbosa Artur Silva Sidney Santos Leonor Gusmão ândrea Ribeiro-Dos-Santos
spellingShingle	Igor G. Hamoy André M. Ribeiro-Dos-Santos Luiz Alvarez Silvanira Barbosa Artur Silva Sidney Santos Leonor Gusmão ândrea Ribeiro-Dos-Santos A Protocol for mtGenome Analysis on Large Sample Numbers Bioinformatics and Biology Insights
author_facet	Igor G. Hamoy André M. Ribeiro-Dos-Santos Luiz Alvarez Silvanira Barbosa Artur Silva Sidney Santos Leonor Gusmão ândrea Ribeiro-Dos-Santos
author_sort	Igor G. Hamoy
title	A Protocol for mtGenome Analysis on Large Sample Numbers
title_short	A Protocol for mtGenome Analysis on Large Sample Numbers
title_full	A Protocol for mtGenome Analysis on Large Sample Numbers
title_fullStr	A Protocol for mtGenome Analysis on Large Sample Numbers
title_full_unstemmed	A Protocol for mtGenome Analysis on Large Sample Numbers
title_sort	protocol for mtgenome analysis on large sample numbers
publisher	SAGE Publishing
series	Bioinformatics and Biology Insights
issn	1177-9322
publishDate	2014-01-01
description	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.
url	https://doi.org/10.4137/BBI.S14623
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A Protocol for mtGenome Analysis on Large Sample Numbers

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