PHFinder: assisted detection of point heteroplasmy in Sanger sequencing chromatograms
Heteroplasmy is the presence of two or more organellar genomes (mitochondrial or plastid DNA) in an organism, tissue, cell or organelle. Heteroplasmy can be detected by visual inspection of Sanger sequencing chromatograms, where it appears as multiple peaks of fluorescence at a single nucleotide pos...
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PeerJ Inc.
2023-09-01
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| Online Access: | https://peerj.com/articles/16028.pdf |
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| author | Marcos Suárez Menéndez Vania E. Rivera-León Jooke Robbins Martine Berube Per J. Palsbøll |
| author_facet | Marcos Suárez Menéndez Vania E. Rivera-León Jooke Robbins Martine Berube Per J. Palsbøll |
| author_sort | Marcos Suárez Menéndez |
| collection | DOAJ |
| description | Heteroplasmy is the presence of two or more organellar genomes (mitochondrial or plastid DNA) in an organism, tissue, cell or organelle. Heteroplasmy can be detected by visual inspection of Sanger sequencing chromatograms, where it appears as multiple peaks of fluorescence at a single nucleotide position. Visual inspection of chromatograms is both consuming and highly subjective, as heteroplasmy is difficult to differentiate from background noise. Few software solutions are available to automate the detection of point heteroplasmies, and those that are available are typically proprietary, lack customization or are unsuitable for automated heteroplasmy assessment in large datasets. Here, we present PHFinder, a Python-based, open-source tool to assist in the detection of point heteroplasmies in large numbers of Sanger chromatograms. PHFinder automatically identifies point heteroplasmies directly from the chromatogram trace data. The program was tested with Sanger sequencing data from 100 humpback whales (Megaptera novaeangliae) tissue samples with known heteroplasmies. PHFinder detected most (90%) of the known heteroplasmies thereby greatly reducing the amount of visual inspection required. PHFinder is flexible and enables explicit specification of key parameters to infer double peaks (i.e., heteroplasmies). |
| first_indexed | 2024-03-09T05:06:16Z |
| format | Article |
| id | doaj.art-b230a1d24d2248cd92230267e386a58b |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T05:06:16Z |
| publishDate | 2023-09-01 |
| publisher | PeerJ Inc. |
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| spelling | doaj.art-b230a1d24d2248cd92230267e386a58b2023-12-03T12:54:26ZengPeerJ Inc.PeerJ2167-83592023-09-0111e1602810.7717/peerj.16028PHFinder: assisted detection of point heteroplasmy in Sanger sequencing chromatogramsMarcos Suárez Menéndez0Vania E. Rivera-León1Jooke Robbins2Martine Berube3Per J. Palsbøll4Marine Evolution and Conservation, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The NetherlandsMarine Evolution and Conservation, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The NetherlandsCenter for Coastal Studies, Provincetown, MA, United States of AmericaMarine Evolution and Conservation, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The NetherlandsMarine Evolution and Conservation, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The NetherlandsHeteroplasmy is the presence of two or more organellar genomes (mitochondrial or plastid DNA) in an organism, tissue, cell or organelle. Heteroplasmy can be detected by visual inspection of Sanger sequencing chromatograms, where it appears as multiple peaks of fluorescence at a single nucleotide position. Visual inspection of chromatograms is both consuming and highly subjective, as heteroplasmy is difficult to differentiate from background noise. Few software solutions are available to automate the detection of point heteroplasmies, and those that are available are typically proprietary, lack customization or are unsuitable for automated heteroplasmy assessment in large datasets. Here, we present PHFinder, a Python-based, open-source tool to assist in the detection of point heteroplasmies in large numbers of Sanger chromatograms. PHFinder automatically identifies point heteroplasmies directly from the chromatogram trace data. The program was tested with Sanger sequencing data from 100 humpback whales (Megaptera novaeangliae) tissue samples with known heteroplasmies. PHFinder detected most (90%) of the known heteroplasmies thereby greatly reducing the amount of visual inspection required. PHFinder is flexible and enables explicit specification of key parameters to infer double peaks (i.e., heteroplasmies).https://peerj.com/articles/16028.pdfChromatogramsDetectionHeteroplasmySangerSoftwareAB1 |
| spellingShingle | Marcos Suárez Menéndez Vania E. Rivera-León Jooke Robbins Martine Berube Per J. Palsbøll PHFinder: assisted detection of point heteroplasmy in Sanger sequencing chromatograms PeerJ Chromatograms Detection Heteroplasmy Sanger Software AB1 |
| title | PHFinder: assisted detection of point heteroplasmy in Sanger sequencing chromatograms |
| title_full | PHFinder: assisted detection of point heteroplasmy in Sanger sequencing chromatograms |
| title_fullStr | PHFinder: assisted detection of point heteroplasmy in Sanger sequencing chromatograms |
| title_full_unstemmed | PHFinder: assisted detection of point heteroplasmy in Sanger sequencing chromatograms |
| title_short | PHFinder: assisted detection of point heteroplasmy in Sanger sequencing chromatograms |
| title_sort | phfinder assisted detection of point heteroplasmy in sanger sequencing chromatograms |
| topic | Chromatograms Detection Heteroplasmy Sanger Software AB1 |
| url | https://peerj.com/articles/16028.pdf |
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