Evaluation of DNA Extraction Methods Developed for Forensic and Ancient DNA Applications Using Bone Samples of Different Age
The efficient extraction of DNA from challenging samples, such as bones, is critical for the success of downstream genotyping analysis in molecular genetic disciplines. Even though the ancient DNA community has developed several protocols targeting small DNA fragments that are typically present in d...
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MDPI AG
2021-01-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/12/2/146 |
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| author | Catarina Xavier Mayra Eduardoff Barbara Bertoglio Christina Amory Cordula Berger Andrea Casas-Vargas Johannes Pallua Walther Parson |
| author_facet | Catarina Xavier Mayra Eduardoff Barbara Bertoglio Christina Amory Cordula Berger Andrea Casas-Vargas Johannes Pallua Walther Parson |
| author_sort | Catarina Xavier |
| collection | DOAJ |
| description | The efficient extraction of DNA from challenging samples, such as bones, is critical for the success of downstream genotyping analysis in molecular genetic disciplines. Even though the ancient DNA community has developed several protocols targeting small DNA fragments that are typically present in decomposed or old specimens, only recently forensic geneticists have started to adopt those protocols. Here, we compare an ancient DNA extraction protocol (Dabney) with a bone extraction method (Loreille) typically used in forensics. Real-time quantitative PCR and forensically representative typing methods including fragment size analysis and sequencing were used to assess protocol performance. We used four bone samples of different age in replicates to study the effects of both extraction methods. Our results confirm Loreille’s overall increased gain of DNA when enough tissue is available and Dabney’s improved efficiency for retrieving shorter DNA fragments that is beneficial when highly degraded DNA is present. The results suggest that the choice of extraction method needs to be based on available sample, degradation state, and targeted genotyping method. We modified the Dabney protocol by pooling parallel lysates prior to purification to study gain and performance in single tube typing assays and found that up to six parallel lysates lead to an almost linear gain of extracted DNA. These data are promising for further forensic investigations as the adapted Dabney protocol combines increased sensitivity for degraded DNA with necessary total DNA amount for forensic applications. |
| first_indexed | 2024-03-09T03:57:43Z |
| format | Article |
| id | doaj.art-9eb3577adea6419b888430be235ec19f |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-09T03:57:43Z |
| publishDate | 2021-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-9eb3577adea6419b888430be235ec19f2023-12-03T14:17:35ZengMDPI AGGenes2073-44252021-01-0112214610.3390/genes12020146Evaluation of DNA Extraction Methods Developed for Forensic and Ancient DNA Applications Using Bone Samples of Different AgeCatarina Xavier0Mayra Eduardoff1Barbara Bertoglio2Christina Amory3Cordula Berger4Andrea Casas-Vargas5Johannes Pallua6Walther Parson7Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, AustriaInstitute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, AustriaDepartment of Public Health, Experimental and Forensic Medicine, Section of Legal Medicine and Forensic Sciences, University of Pavia, 27100 Pavia, ItalyInstitute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, AustriaInstitute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, AustriaGrupo de Genética de Poblaciones e Identificación, Instituto de Genética, Universidad Nacional de Colombia, 11001 Bogotá, ColombiaInstitute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, AustriaInstitute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, AustriaThe efficient extraction of DNA from challenging samples, such as bones, is critical for the success of downstream genotyping analysis in molecular genetic disciplines. Even though the ancient DNA community has developed several protocols targeting small DNA fragments that are typically present in decomposed or old specimens, only recently forensic geneticists have started to adopt those protocols. Here, we compare an ancient DNA extraction protocol (Dabney) with a bone extraction method (Loreille) typically used in forensics. Real-time quantitative PCR and forensically representative typing methods including fragment size analysis and sequencing were used to assess protocol performance. We used four bone samples of different age in replicates to study the effects of both extraction methods. Our results confirm Loreille’s overall increased gain of DNA when enough tissue is available and Dabney’s improved efficiency for retrieving shorter DNA fragments that is beneficial when highly degraded DNA is present. The results suggest that the choice of extraction method needs to be based on available sample, degradation state, and targeted genotyping method. We modified the Dabney protocol by pooling parallel lysates prior to purification to study gain and performance in single tube typing assays and found that up to six parallel lysates lead to an almost linear gain of extracted DNA. These data are promising for further forensic investigations as the adapted Dabney protocol combines increased sensitivity for degraded DNA with necessary total DNA amount for forensic applications.https://www.mdpi.com/2073-4425/12/2/146bone DNA extractionDNA quantificationIon S5 sequencingmtDNA sequencingVISAGE Basic ToolMiSeq FGx |
| spellingShingle | Catarina Xavier Mayra Eduardoff Barbara Bertoglio Christina Amory Cordula Berger Andrea Casas-Vargas Johannes Pallua Walther Parson Evaluation of DNA Extraction Methods Developed for Forensic and Ancient DNA Applications Using Bone Samples of Different Age Genes bone DNA extraction DNA quantification Ion S5 sequencing mtDNA sequencing VISAGE Basic Tool MiSeq FGx |
| title | Evaluation of DNA Extraction Methods Developed for Forensic and Ancient DNA Applications Using Bone Samples of Different Age |
| title_full | Evaluation of DNA Extraction Methods Developed for Forensic and Ancient DNA Applications Using Bone Samples of Different Age |
| title_fullStr | Evaluation of DNA Extraction Methods Developed for Forensic and Ancient DNA Applications Using Bone Samples of Different Age |
| title_full_unstemmed | Evaluation of DNA Extraction Methods Developed for Forensic and Ancient DNA Applications Using Bone Samples of Different Age |
| title_short | Evaluation of DNA Extraction Methods Developed for Forensic and Ancient DNA Applications Using Bone Samples of Different Age |
| title_sort | evaluation of dna extraction methods developed for forensic and ancient dna applications using bone samples of different age |
| topic | bone DNA extraction DNA quantification Ion S5 sequencing mtDNA sequencing VISAGE Basic Tool MiSeq FGx |
| url | https://www.mdpi.com/2073-4425/12/2/146 |
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