A Customized Human Mitochondrial DNA Database (hMITO DB v1.0) for Rapid Sequence Analysis, Haplotyping and Geo-Mapping
The field of mitochondrial genomics has advanced rapidly and has revolutionized disciplines such as molecular anthropology, population genetics, and medical genetics/oncogenetics. However, mtDNA next-generation sequencing (NGS) analysis for matrilineal haplotyping and phylogeographic inference remai...
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-08-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/24/17/13505 |
| _version_ | 1797582386044600320 |
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| author | Jane Shen-Gunther Rutger S. Gunther Hong Cai Yufeng Wang |
| author_facet | Jane Shen-Gunther Rutger S. Gunther Hong Cai Yufeng Wang |
| author_sort | Jane Shen-Gunther |
| collection | DOAJ |
| description | The field of mitochondrial genomics has advanced rapidly and has revolutionized disciplines such as molecular anthropology, population genetics, and medical genetics/oncogenetics. However, mtDNA next-generation sequencing (NGS) analysis for matrilineal haplotyping and phylogeographic inference remains hindered by the lack of a consolidated mitogenome database and an efficient bioinformatics pipeline. To address this, we developed a customized human mitogenome database (hMITO DB) embedded in a CLC Genomics workflow for read mapping, variant analysis, haplotyping, and geo-mapping. The database was constructed from 4286 mitogenomes. The macro-haplogroup (A to Z) distribution and representative phylogenetic tree were found to be consistent with published literature. The hMITO DB automated workflow was tested using mtDNA-NGS sequences derived from Pap smears and cervical cancer cell lines. The auto-generated read mapping, variants track, and table of haplotypes and geo-origins were completed in 15 min for 47 samples. The mtDNA workflow proved to be a rapid, efficient, and accurate means of sequence analysis for translational mitogenomics. |
| first_indexed | 2024-03-10T23:20:27Z |
| format | Article |
| id | doaj.art-6603129f41bb4dafba8f0d868f16ad6f |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T23:20:27Z |
| publishDate | 2023-08-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-6603129f41bb4dafba8f0d868f16ad6f2023-11-19T08:18:18ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-08-0124171350510.3390/ijms241713505A Customized Human Mitochondrial DNA Database (hMITO DB v1.0) for Rapid Sequence Analysis, Haplotyping and Geo-MappingJane Shen-Gunther0Rutger S. Gunther1Hong Cai2Yufeng Wang3Gynecologic Oncology & Clinical Investigation, Department of Clinical Investigation, Brooke Army Medical Center, Fort Sam Houston, San Antonio, TX 78234, USANuclear Medicine & Molecular Imaging, Department of Radiology, Brooke Army Medical Center, Fort Sam Houston, San Antonio, TX 78234, USADepartment of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX 78249, USADepartment of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX 78249, USAThe field of mitochondrial genomics has advanced rapidly and has revolutionized disciplines such as molecular anthropology, population genetics, and medical genetics/oncogenetics. However, mtDNA next-generation sequencing (NGS) analysis for matrilineal haplotyping and phylogeographic inference remains hindered by the lack of a consolidated mitogenome database and an efficient bioinformatics pipeline. To address this, we developed a customized human mitogenome database (hMITO DB) embedded in a CLC Genomics workflow for read mapping, variant analysis, haplotyping, and geo-mapping. The database was constructed from 4286 mitogenomes. The macro-haplogroup (A to Z) distribution and representative phylogenetic tree were found to be consistent with published literature. The hMITO DB automated workflow was tested using mtDNA-NGS sequences derived from Pap smears and cervical cancer cell lines. The auto-generated read mapping, variants track, and table of haplotypes and geo-origins were completed in 15 min for 47 samples. The mtDNA workflow proved to be a rapid, efficient, and accurate means of sequence analysis for translational mitogenomics.https://www.mdpi.com/1422-0067/24/17/13505bioinformaticshypervariable regionmitochondrial DNAmitochondrial genomicsmitochondrial haplogroupmolecular anthropology |
| spellingShingle | Jane Shen-Gunther Rutger S. Gunther Hong Cai Yufeng Wang A Customized Human Mitochondrial DNA Database (hMITO DB v1.0) for Rapid Sequence Analysis, Haplotyping and Geo-Mapping International Journal of Molecular Sciences bioinformatics hypervariable region mitochondrial DNA mitochondrial genomics mitochondrial haplogroup molecular anthropology |
| title | A Customized Human Mitochondrial DNA Database (hMITO DB v1.0) for Rapid Sequence Analysis, Haplotyping and Geo-Mapping |
| title_full | A Customized Human Mitochondrial DNA Database (hMITO DB v1.0) for Rapid Sequence Analysis, Haplotyping and Geo-Mapping |
| title_fullStr | A Customized Human Mitochondrial DNA Database (hMITO DB v1.0) for Rapid Sequence Analysis, Haplotyping and Geo-Mapping |
| title_full_unstemmed | A Customized Human Mitochondrial DNA Database (hMITO DB v1.0) for Rapid Sequence Analysis, Haplotyping and Geo-Mapping |
| title_short | A Customized Human Mitochondrial DNA Database (hMITO DB v1.0) for Rapid Sequence Analysis, Haplotyping and Geo-Mapping |
| title_sort | customized human mitochondrial dna database hmito db v1 0 for rapid sequence analysis haplotyping and geo mapping |
| topic | bioinformatics hypervariable region mitochondrial DNA mitochondrial genomics mitochondrial haplogroup molecular anthropology |
| url | https://www.mdpi.com/1422-0067/24/17/13505 |
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