Paper

Extraction of DNA from Skeletonized Postcranial Remains: A Discussion of Protocols and Testing Modalities^† ^‡

Corresponding Author

Suni M. Edson M.S.

[email protected]

Armed Forces DNA Identification Laboratory, Armed Forces Medical Examiner System, 115 Purple Heart Drive, Dover AFB, DE, 19902

College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia

Corresponding author: Suni M. Edson, M.S. E-mail: [email protected]Search for more papers by this author

Suni M. Edson M.S.,

Corresponding Author

Suni M. Edson M.S.

[email protected]

Armed Forces DNA Identification Laboratory, Armed Forces Medical Examiner System, 115 Purple Heart Drive, Dover AFB, DE, 19902

College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia

Corresponding author: Suni M. Edson, M.S. E-mail: [email protected]Search for more papers by this author

First published: 29 March 2019

https://doi.org/10.1111/1556-4029.14050

Citations: 17

^†

Presented in part at the 69th Annual Scientific Meeting of the American Academy of Forensic Sciences, February 13–18, 2017, in New Orleans, LA.

^‡

The opinions or assertions presented are the private views of the author and should not be construed as official or as reflecting the views of the Department of Defense, the Defense Health Agency, the Armed Forces Medical Examiner System, or the Defense POW/MIA Accounting Agency.

Share a link

Email
Wechat
Bluesky

Abstract

This paper provides a retrospective of the DNA analysis performed by the Armed Forces Medical Examiner–Armed Forces DNA Identification Laboratory between 1990 and 2018. Over 13,000 postcranial osseous materials, comprised of wartime losses from World War II, the Korean War, and South-East Asia, were examined by the following: mitochondrial DNA sequencing, a modified AmpFlSTR® Yfiler™, AmpFlSTR® MiniFiler™, PowerPlex® Fusion, or NGS. Four different DNA extraction protocols were used: incomplete demineralization coupled with an organic purification; complete demineralization with an organic purification; complete demineralization with an inorganic purification using QIAquick PCR Purification Kit; and a protocol designed specifically for use with next-generation sequencing. In general, complete demineralization coupled with an organic purification was the optimal extraction protocol for sequencing of mitochondrial DNA, regardless of the osseous element tested. For STR testing, demineralization paired with an inorganic purification provided optimum results, regardless of kit used or osseous element tested.

References

1Mundorff A, Davoren JM. Examination of DNA yield rates for different skeletal elements at increasing post mortem intervals. Forensic Sci Int Genet 2014; 8(1): 55–63.
10.1016/j.fsigen.2013.08.001
CAS PubMed Web of Science® Google Scholar
2Andronowski JM, Mundorff AZ, Pratt IV, Davoren JM, Cooper DML. Evaluating differential nuclear DNA yield rates and osteocyte numbers among human bone tissue types: a synchrotron radiation micro-CT approach. Forensic Sci Int Genet 2017; 28: 211–8.
10.1016/j.fsigen.2017.03.002
CAS PubMed Web of Science® Google Scholar
3Barta JL, Monroe C, Crockford SJ, Kemp BM. Mitochondrial DNA preservation across 3000-year-old northern fur seal ribs is not related to bone density: implications for forensic investigations. Forensic Sci Int 2014; 239: 11–8.
10.1016/j.forsciint.2014.02.029
CAS PubMed Web of Science® Google Scholar
4Hines DZC, Vennemeyer M, Amory S, Huel RLM, Hanson I, Katzmarzyk C, et al. Prioritized sampling of bone and teeth for DNA analysis in commingled remains. In: BJ Adams, JE Byrd, editors. Commingled human remains: methods in recovery, analysis, and identification. Cambridge, MA: Elsevier Inc, 2014; 275–305.
10.1016/B978-0-12-405889-7.00013-7
Google Scholar
5Edson SM, Ross JP, Coble MD, Parsons TJ, Barritt SM. Naming the dead: confronting the realities of the rapid identification of degraded skeletal remains. Forensic Sci Rev 2004; 16(1): 63–90.
CAS PubMed Google Scholar
6Edson SM, Christensen AF, Barritt SM, Meehan A, Leney MD, Finelli LN. Sampling of the cranium for mitochondrial DNA analysis of human skeletal remains. Forensic Sci Int Genet Suppl Series 2009; 2(1): 269–70.
10.1016/j.fsigss.2009.09.029
Google Scholar
7Kulstein G, Hadrys T, Wiegand P. As solid as a rock – comparison of CE- and MPS-based analyses of the petrosal bone as a source of DNA for forensic identification of challenging cranial bones. Int J Legal Med 2018; 132(1): 13–24.
10.1007/s00414-017-1653-z
PubMed Web of Science® Google Scholar
8Leney M. Sampling skeletal remains for ancient DNA (aDNA): a measure of success. Hist Archeol 2006; 40(3): 31–49.
10.1007/BF03376731
Web of Science® Google Scholar
9Mundorff AZ, Bartelink EJ, Mar-Cash E. DNA Preservation in skeletal elements from the World Trade Center Disaster: recommendations for mass fatality management. J Forensic Sci 2009; 54(4): 739–45.
10.1111/j.1556-4029.2009.01045.x
CAS PubMed Web of Science® Google Scholar
10Edson SM, McMahon TP. Extraction of DNA from skeletal remains. In: W Goodwin, editor. Forensic DNA typing protocols, methods in molecular biology. vol. 1420. New York, NY: Humana Press, 2016; 69–87.
10.1007/978-1-4939-3597-0_6
Google Scholar
11Gabriel M, Huffine E, Ryan J, Holland M, Parsons T. Improved mtDNA sequence analysis of forensic remains using a “mini-primer set” amplification strategy. J Forensic Sci 2001; 46(2): 247–53.
10.1520/JFS14957J
CAS PubMed Web of Science® Google Scholar
12Sturk KA, Coble MD, Barritt SM, Irwin JA. Evaluation of modified Yfiler™ amplification strategy for compromised samples. Croat Med J 2009; 50: 228–38.
10.3325/cmj.2009.50.228
CAS PubMed Web of Science® Google Scholar
13Irwin JA, Edson SM, Loreille O, Just RS, Barritt SM, Lee DA, et al. DNA identification of “Earthquake McGoon” 50 years postmortem. J Forensic Sci 2007; 52(5): 1115–8.
10.1111/j.1556-4029.2007.00506.x
CAS PubMed Web of Science® Google Scholar
14Marshall C, Sturk-Andreaggi K, Daniels-Higginbotham J, Oliver RS, Barritt-Ross SM, McMahon TP. Performance evaluation of a mitogenome capture and Illumina sequencing protocol using non-probative, case-type skeletal samples: implications for the use of a positive control in a next-generation sequencing procedure. Forensic Sci Int Genet 2017; 31: 198–206.
10.1016/j.fsigen.2017.09.001
CAS PubMed Web of Science® Google Scholar
15Anderson S, Bankier AT, Barrell GB, de Bruijn MH, Coulson AR, Drouin J, et al. Sequence and organization of the human mitochondrial genome. Nature 1981; 290: 457–65.
10.1038/290457a0
CAS PubMed Web of Science® Google Scholar
16Andrews RM, Kubacaka I, Chinnery PF, Lightowlers RN, Turnbull DM, Howell N. Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nat Genet 1999; 23(2): 147.
10.1038/13779
CAS PubMed Web of Science® Google Scholar
17Edson SM, Sturk-Andreaggi K, Christensen AF, Barritt-Ross SM. The use of mitochondrial 12S rRNA gene sequencing in a human identification laboratory for species determination of compromised skeletal remains. In: RD Bradley, HH Genoways, DJ Schmidly, LC Bradley, editors. From field to laboratory: a memorial volume in honor of Robert J. Baker. Lubbock, TX: Special Publications of Museum of Texas Tech University, In press. Number 71.
Google Scholar
18Antinick TC, Foran DR. Intra- and inter-element variability in mitochondrial and nuclear DNA from fresh and environmentally exposed skeletal remains. J Forensic Sci 2019; 64(1): 88–97.
10.1111/1556-4029.13843
CAS PubMed Web of Science® Google Scholar
19Amory S, Huel R, Bilić A, Loreille O, Parsons TJ. Automatable full demineralization DNA extraction procedure from degraded skeletal remains. Forensic Sci Int Genet 2012; 6(3): 398–406.
10.1016/j.fsigen.2011.08.004
CAS PubMed Web of Science® Google Scholar
20Hong S-B, Kim Y, Park J-H. High-efficiency automated DNA extraction method for degraded old skeletal samples. Forensic Sci Int Genet Suppl Ser 2017; 6: e365–7.
10.1016/j.fsigss.2017.09.108
Web of Science® Google Scholar
21Edson SM. DNA typing from skeletal remains: a study of inhibitors using mass spectrometry. Forensic Sci Int Genet Suppl Ser 2017; 6: e337–9.
10.1016/j.fsigss.2017.09.119
Web of Science® Google Scholar
22Seutin G, White BN, Boag PT. Preservation of avian blood and tissue samples for DNA analyses. Can J Zool 1991; 69(1): 82–90.
10.1139/z91-013
CAS Web of Science® Google Scholar
23Lee HW, Kim NY, Park MJ, Sim JE, Yang WI, Shin K-J. DNA typing for the identification of old skeletal remains from Korean War victims. J Forensic Sci 2010; 55: 1422–9.
10.1111/j.1556-4029.2010.01411.x
CAS PubMed Web of Science® Google Scholar
24Loreille OM, Diegoli TM, Irwin JA, Coble MD, Parsons TJ. High efficiency DNA extraction from bone by total demineralization. Forensic Sci Int Genet 2007; 1(2): 191–5.
10.1016/j.fsigen.2007.02.006
PubMed Web of Science® Google Scholar
25Loreille OM, Parr RL, McGregor KA, Fitzpatrick CM, Lyon C, Yang DY, et al. Integrated DNA and fingerprint analyses in the identification of 60-year-old mummified human remains discovered on an Alaskan glacier. J Forensic Sci 2010; 55: 813–8.
10.1111/j.1556-4029.2010.01356.x
CAS PubMed Web of Science® Google Scholar

Citing Literature

Volume64, Issue5

September 2019

Pages 1312-1323

Extraction of DNA from Skeletonized Postcranial Remains: A Discussion of Protocols and Testing Modalities^† ^‡

Abstract

References

Citing Literature

References

Information

About Wiley Online Library

Help & Support

Opportunities

Connect with Wiley

Extraction of DNA from Skeletonized Postcranial Remains: A Discussion of Protocols and Testing Modalities† ‡

Abstract

References

Citing Literature

References

Related

Information

Extraction of DNA from Skeletonized Postcranial Remains: A Discussion of Protocols and Testing Modalities^† ^‡