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Andreeva TV, Malyarchuk AB, Soshkina AD, Dudko NA, Plotnikova MY, Rogaev EI. Methodologies for Ancient DNA Extraction from Bones for Genomic Analysis: Approaches and Guidelines. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422090034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Mckinnon M, Higgins D. Comparison of bone demineralisation procedures for DNA recovery from burned remains. Forensic Sci Int Genet 2020; 51:102448. [PMID: 33373911 DOI: 10.1016/j.fsigen.2020.102448] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 11/09/2020] [Accepted: 12/01/2020] [Indexed: 11/26/2022]
Abstract
Recovering DNA from modern incinerated bones can be challenging and may require alteration of routine DNA extraction protocols. It has been postulated that incinerated bones share some similarities with ancient bones, including fragmented DNA, surface contamination and highly mineralised structure, all of which can inhibit the successful recovery of genetic material. For this reason, ancient DNA extraction protocols are often used for incinerated modern samples; however, their effectiveness is still somewhat unclear. Much of this uncertainty exists around the demineralisation step of extraction, specifically the length of incubation and retention or removal of supernatant. As obtaining human samples for forensic research can be challenging, porcine models (Sus scrofa domesticus) are often used as substitutes. This study developed real time PCR assays for porcine nuclear DNA in order to investigate the effects of modified demineralisation protocols on DNA yield from femurs exposed to either short (60 min) or prolonged (120 min) burning. Gradient PCR results indicated 56 °C was the ideal amplification temperature for targeted amplicons, with melt curve analysis showing short and long amplicons corresponded to 80.3 °C and 83 °C peaks respectively. Results of altered extraction protocol showed a trend towards higher DNA yields from longer demineralisation periods however this was not significant. By comparison, retaining supernatant post-demineralisation resulted in significantly greater DNA yields compared to discarding it (P < 0.009). Although DNA content yield decreased with burn duration, the demineralisation treatment variations appeared to have the same effect for all burn lengths. These results suggest that for incinerated modern bone retaining the supernatant following demineralisation can dramatically increase DNA yield.
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Affiliation(s)
- Meghan Mckinnon
- Discipline of Anatomy and Pathology, Adelaide Medical School, The University of Adelaide, Adelaide, Australia.
| | - Denice Higgins
- Forensic Odontology Unit, Adelaide Dental School, The University of Adelaide, Adelaide, Australia
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McCord BR, Gauthier Q, Cho S, Roig MN, Gibson-Daw GC, Young B, Taglia F, Zapico SC, Mariot RF, Lee SB, Duncan G. Forensic DNA Analysis. Anal Chem 2019; 91:673-688. [PMID: 30485738 DOI: 10.1021/acs.analchem.8b05318] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Bruce R McCord
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Quentin Gauthier
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Sohee Cho
- Department of Forensic Medicine , Seoul National University , Seoul , 08826 , South Korea
| | - Meghan N Roig
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Georgiana C Gibson-Daw
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Brian Young
- Niche Vision, Inc. , Akron , Ohio 44311 , United States
| | - Fabiana Taglia
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Sara C Zapico
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Roberta Fogliatto Mariot
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Steven B Lee
- Forensic Science Program, Justice Studies Department , San Jose State University , San Jose , California 95192 , United States
| | - George Duncan
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
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Corrêa HSD, Pedro FLM, Volpato LER, Pereira TM, Siebert Filho G, Borges ÁH. Forensic DNA typing from teeth using demineralized root tips. Forensic Sci Int 2017; 280:164-168. [DOI: 10.1016/j.forsciint.2017.10.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 08/28/2017] [Accepted: 10/04/2017] [Indexed: 10/18/2022]
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Nielsen EE, Morgan JAT, Maher SL, Edson J, Gauthier M, Pepperell J, Holmes BJ, Bennett MB, Ovenden JR. Extracting DNA from 'jaws': high yield and quality from archived tiger shark (Galeocerdo cuvier) skeletal material. Mol Ecol Resour 2016; 17:431-442. [PMID: 27508520 DOI: 10.1111/1755-0998.12580] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 06/10/2016] [Accepted: 06/23/2016] [Indexed: 11/30/2022]
Abstract
Archived specimens are highly valuable sources of DNA for retrospective genetic/genomic analysis. However, often limited effort has been made to evaluate and optimize extraction methods, which may be crucial for downstream applications. Here, we assessed and optimized the usefulness of abundant archived skeletal material from sharks as a source of DNA for temporal genomic studies. Six different methods for DNA extraction, encompassing two different commercial kits and three different protocols, were applied to material, so-called bio-swarf, from contemporary and archived jaws and vertebrae of tiger sharks (Galeocerdo cuvier). Protocols were compared for DNA yield and quality using a qPCR approach. For jaw swarf, all methods provided relatively high DNA yield and quality, while large differences in yield between protocols were observed for vertebrae. Similar results were obtained from samples of white shark (Carcharodon carcharias). Application of the optimized methods to 38 museum and private angler trophy specimens dating back to 1912 yielded sufficient DNA for downstream genomic analysis for 68% of the samples. No clear relationships between age of samples, DNA quality and quantity were observed, likely reflecting different preparation and storage methods for the trophies. Trial sequencing of DNA capture genomic libraries using 20 000 baits revealed that a significant proportion of captured sequences were derived from tiger sharks. This study demonstrates that archived shark jaws and vertebrae are potential high-yield sources of DNA for genomic-scale analysis. It also highlights that even for similar tissue types, a careful evaluation of extraction protocols can vastly improve DNA yield.
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Affiliation(s)
- E E Nielsen
- National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, 8600, Silkeborg, Denmark.,School of Biomedical Sciences, The University of Queensland, St Lucia, Brisbane, Qld., 4072, Australia
| | - J A T Morgan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Brisbane, Qld., 4072, Australia
| | - S L Maher
- School of Biomedical Sciences, The University of Queensland, St Lucia, Brisbane, Qld., 4072, Australia
| | - J Edson
- Queensland Brain Institute, The University of Queensland, St Lucia, Brisbane, Qld., 4072, Australia
| | - M Gauthier
- QFAB Bioinformatics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Qld., 4072, Australia
| | - J Pepperell
- Pepperell Research and Consulting Pty Ltd, Noosaville, Qld., 4566, Australia
| | - B J Holmes
- School of Biomedical Sciences, The University of Queensland, St Lucia, Brisbane, Qld., 4072, Australia
| | - M B Bennett
- School of Biomedical Sciences, The University of Queensland, St Lucia, Brisbane, Qld., 4072, Australia
| | - J R Ovenden
- School of Biomedical Sciences, The University of Queensland, St Lucia, Brisbane, Qld., 4072, Australia
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