Bioinformatics Tools for NGS-Based Identification of Single Nucleotide Variants and Large-Scale Rearrangements in Mitochondrial DNA
The unique features of mitochondrial DNA (mtDNA), including its circular and multicopy nature, the possible coexistence of wild-type and mutant molecules (i.e., heteroplasmy) and the presence of nuclear mitochondrial DNA segments (NUMTs), make the diagnosis of mtDNA diseases particularly challenging...
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MDPI AG
2025-02-01
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| Online Access: | https://www.mdpi.com/2673-6284/14/1/9 |
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| author | Marco Barresi Giulia Dal Santo Rossella Izzo Andrea Zauli Eleonora Lamantea Leonardo Caporali Daniele Ghezzi Andrea Legati |
| author_facet | Marco Barresi Giulia Dal Santo Rossella Izzo Andrea Zauli Eleonora Lamantea Leonardo Caporali Daniele Ghezzi Andrea Legati |
| author_sort | Marco Barresi |
| collection | DOAJ |
| description | The unique features of mitochondrial DNA (mtDNA), including its circular and multicopy nature, the possible coexistence of wild-type and mutant molecules (i.e., heteroplasmy) and the presence of nuclear mitochondrial DNA segments (NUMTs), make the diagnosis of mtDNA diseases particularly challenging. The extensive deployment of next-generation sequencing (NGS) technologies has significantly advanced the diagnosis of mtDNA-related diseases. However, the vast amounts and diverse types of sequencing data complicate the interpretation of these variants. From sequence alignment to variant calling, NGS-based mtDNA sequencing requires specialized bioinformatics tools, adapted for the mitochondrial genome. This study presents the use of new bioinformatics approaches, optimized for short- and long-read sequencing data, to enhance the accuracy of mtDNA analysis in diagnostics. Two recent and emerging free bioinformatics tools, Mitopore and MitoSAlt, were evaluated on patients previously diagnosed with single nucleotide variants or large-scale deletions. Analyses were performed in Linux-based environments and web servers implemented in Python, Perl, Java, and R. The results indicated that each tool demonstrated high sensitivity and specific accuracy in identifying and quantifying various types of pathogenic variants. The study suggests that the integrated and parallel use of these tools offers a significant advantage over traditional methods in interpreting mtDNA genetic variants, reducing the computational demands, and provides an accurate diagnostic solution. |
| format | Article |
| id | doaj-art-0b0a80a87fc6454faa6f1be7413ce044 |
| institution | DOAJ |
| issn | 2673-6284 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | BioTech |
| spelling | doaj-art-0b0a80a87fc6454faa6f1be7413ce0442025-08-20T02:42:46ZengMDPI AGBioTech2673-62842025-02-01141910.3390/biotech14010009Bioinformatics Tools for NGS-Based Identification of Single Nucleotide Variants and Large-Scale Rearrangements in Mitochondrial DNAMarco Barresi0Giulia Dal Santo1Rossella Izzo2Andrea Zauli3Eleonora Lamantea4Leonardo Caporali5Daniele Ghezzi6Andrea Legati7Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20126 Milan, ItalyUnit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20126 Milan, ItalyUnit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20126 Milan, ItalyUnit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20126 Milan, ItalyUnit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20126 Milan, ItalyLaboratory of Neurogenetics, IRCCS Institute of Neurological Sciences, 40139 Bologna, ItalyUnit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20126 Milan, ItalyUnit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20126 Milan, ItalyThe unique features of mitochondrial DNA (mtDNA), including its circular and multicopy nature, the possible coexistence of wild-type and mutant molecules (i.e., heteroplasmy) and the presence of nuclear mitochondrial DNA segments (NUMTs), make the diagnosis of mtDNA diseases particularly challenging. The extensive deployment of next-generation sequencing (NGS) technologies has significantly advanced the diagnosis of mtDNA-related diseases. However, the vast amounts and diverse types of sequencing data complicate the interpretation of these variants. From sequence alignment to variant calling, NGS-based mtDNA sequencing requires specialized bioinformatics tools, adapted for the mitochondrial genome. This study presents the use of new bioinformatics approaches, optimized for short- and long-read sequencing data, to enhance the accuracy of mtDNA analysis in diagnostics. Two recent and emerging free bioinformatics tools, Mitopore and MitoSAlt, were evaluated on patients previously diagnosed with single nucleotide variants or large-scale deletions. Analyses were performed in Linux-based environments and web servers implemented in Python, Perl, Java, and R. The results indicated that each tool demonstrated high sensitivity and specific accuracy in identifying and quantifying various types of pathogenic variants. The study suggests that the integrated and parallel use of these tools offers a significant advantage over traditional methods in interpreting mtDNA genetic variants, reducing the computational demands, and provides an accurate diagnostic solution.https://www.mdpi.com/2673-6284/14/1/9bioinformaticsmtDNAmitochondrial DNANGS |
| spellingShingle | Marco Barresi Giulia Dal Santo Rossella Izzo Andrea Zauli Eleonora Lamantea Leonardo Caporali Daniele Ghezzi Andrea Legati Bioinformatics Tools for NGS-Based Identification of Single Nucleotide Variants and Large-Scale Rearrangements in Mitochondrial DNA BioTech bioinformatics mtDNA mitochondrial DNA NGS |
| title | Bioinformatics Tools for NGS-Based Identification of Single Nucleotide Variants and Large-Scale Rearrangements in Mitochondrial DNA |
| title_full | Bioinformatics Tools for NGS-Based Identification of Single Nucleotide Variants and Large-Scale Rearrangements in Mitochondrial DNA |
| title_fullStr | Bioinformatics Tools for NGS-Based Identification of Single Nucleotide Variants and Large-Scale Rearrangements in Mitochondrial DNA |
| title_full_unstemmed | Bioinformatics Tools for NGS-Based Identification of Single Nucleotide Variants and Large-Scale Rearrangements in Mitochondrial DNA |
| title_short | Bioinformatics Tools for NGS-Based Identification of Single Nucleotide Variants and Large-Scale Rearrangements in Mitochondrial DNA |
| title_sort | bioinformatics tools for ngs based identification of single nucleotide variants and large scale rearrangements in mitochondrial dna |
| topic | bioinformatics mtDNA mitochondrial DNA NGS |
| url | https://www.mdpi.com/2673-6284/14/1/9 |
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