A Customized Human Mitochondrial DNA Database (hMITO DB v1.0) for Rapid Sequence Analysis, Haplotyping and Geo-Mapping

dc.contributor.authorShen-Gunther, Jane
dc.contributor.authorGunther, Rutger S.
dc.contributor.authorCai, Hong
dc.contributor.authorWang, Yufeng
dc.date.accessioned2023-09-08T12:44:57Z
dc.date.available2023-09-08T12:44:57Z
dc.date.issued2023-08-31
dc.date.updated2023-09-08T12:44:59Z
dc.description.abstractThe 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.
dc.description.departmentMolecular Microbiology and Immunology
dc.identifierdoi: 10.3390/ijms241713505
dc.identifier.citationInternational Journal of Molecular Sciences 24 (17): 13505 (2023)
dc.identifier.urihttps://hdl.handle.net/20.500.12588/2034
dc.rightsAttribution 4.0 United States
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.subjectbioinformatics
dc.subjecthypervariable region
dc.subjectmitochondrial DNA
dc.subjectmitochondrial genomics
dc.subjectmitochondrial haplogroup
dc.subjectmolecular anthropology
dc.subjectnext generation sequencing
dc.subjectoncogenetics
dc.subjectphylogeography
dc.titleA Customized Human Mitochondrial DNA Database (hMITO DB v1.0) for Rapid Sequence Analysis, Haplotyping and Geo-Mapping
dc.typeArticle

Files

Original bundle

Now showing 1 - 1 of 1
Loading...
Thumbnail Image
Name:
ijms-24-13505.pdf
Size:
6.45 MB
Format:
Adobe Portable Document Format

License bundle

Now showing 1 - 1 of 1
No Thumbnail Available
Name:
license.txt
Size:
1.86 KB
Format:
Item-specific license agreed upon to submission
Description: