Highly Effective DNA Extraction Method for Nuclear Short Tandem Repeat Testing of Skeletal Remains from Mass Graves

Overview

Journal Croat Med J

Specialty General Medicine

Date 2007 Aug 19

PMID 17696302

Citations 18

Authors

Jon Davoren

Daniel Vanek

Rijad Konjhodzic

John Crews

Edwin Huffine

Thomas J Parsons

Affiliations

Soon will be listed here.

Abstract

Aim: To quantitatively compare a silica extraction method with a commonly used phenol/chloroform extraction method for DNA analysis of specimens exhumed from mass graves.

Methods: DNA was extracted from twenty randomly chosen femur samples, using the International Commission on Missing Persons (ICMP) silica method, based on Qiagen Blood Maxi Kit, and compared with the DNA extracted by the standard phenol/chloroform-based method. The efficacy of extraction methods was compared by real time polymerase chain reaction (PCR) to measure DNA quantity and the presence of inhibitors and by amplification with the PowerPlex 16 (PP16) multiplex nuclear short tandem repeat (STR) kit.

Results: DNA quantification results showed that the silica-based method extracted on average 1.94 ng of DNA per gram of bone (range 0.25-9.58 ng/g), compared with only 0.68 ng/g by the organic method extracted (range 0.0016-4.4880 ng/g). Inhibition tests showed that there were on average significantly lower levels of PCR inhibitors in DNA isolated by the organic method. When amplified with PP16, all samples extracted by silica-based method produced 16 full loci profiles, while only 75% of the DNA extracts obtained by organic technique amplified 16 loci profiles.

Conclusions: The silica-based extraction method showed better results in nuclear STR typing from degraded bone samples than a commonly used phenol/chloroform method.

Citing Articles

Comparative evaluation of various DNA extraction methods and analysis of DNA degradation levels in commercially marketed Chestnut rose juices and beverages.

Ren Y, Ma Y, Li Y, Song Y, Zhao W, Huang X BMC Biotechnol. 2025; 25(1):9.

PMID: 39838339 PMC: 11748555. DOI: 10.1186/s12896-024-00933-7.

Identification of skeletal remains in Croatia and Bosnia and Herzegovina, including the homeland war - a 30-year review.

Primorac D, Andelinovic S, Definis-Gojanovic M, Skaro V, Projic P, coklo M Croat Med J. 2024; 65(3):239-248.

PMID: 38868970 PMC: 11157258.

Y-STR analysis of highly degraded DNA from skeletal remains over 70 years old.

Zhang J, Li X, Li L, Chen A, Zhang S Forensic Sci Res. 2024; 9(2):owae020.

PMID: 38617445 PMC: 11014468. DOI: 10.1093/fsr/owae020.

A novel approach for rapid cell assessment to estimate DNA recovery from human bone tissue.

Le T, Muratovic D, Handt O, Henry J, Linacre A Forensic Sci Med Pathol. 2021; 17(4):649-659.

PMID: 34633584 DOI: 10.1007/s12024-021-00428-3.

Thermal Effects on DNA Degradation in Blood and Seminal Stains: Forensic View.

Abdel Hady R, Thabet H, Ebrahem N, Yassa H Acad Forensic Pathol. 2021; 11(1):7-23.

PMID: 34040682 PMC: 8129487. DOI: 10.1177/1925362121998547.

References

Alonso A, Martin P, Albarran C, Garcia P, de Simon L, Jesus Iturralde M . Challenges of DNA profiling in mass disaster investigations. Croat Med J. 2005; 46(4):540-8. View

Huffine E, CREWS J, Kennedy B, Bomberger K, Zinbo A . Mass identification of persons missing from the break-up of the former Yugoslavia: structure, function, and role of the International Commission on Missing Persons. Croat Med J. 2001; 42(3):271-5. View

Whitaker J, Clayton T, Urquhart A, Millican E, Downes T, Kimpton C . Short tandem repeat typing of bodies from a mass disaster: high success rate and characteristic amplification patterns in highly degraded samples. Biotechniques. 1995; 18(4):670-7. View

Schmerer W, Hummel S, Herrmann B . Optimized DNA extraction to improve reproducibility of short tandem repeat genotyping with highly degraded DNA as target. Electrophoresis. 1999; 20(8):1712-6. DOI: 10.1002/(SICI)1522-2683(19990101)20:8<1712::AID-ELPS1712>3.0.CO;2-6. View

Alonso A, Andelinovic S, MARTIN P, Sutlovic D, Erceg I, Huffine E . DNA typing from skeletal remains: evaluation of multiplex and megaplex STR systems on DNA isolated from bone and teeth samples. Croat Med J. 2001; 42(3):260-6. View

Salamon M, Tuross N, Arensburg B, Weiner S . Relatively well preserved DNA is present in the crystal aggregates of fossil bones. Proc Natl Acad Sci U S A. 2005; 102(39):13783-8. PMC: 1236542. DOI: 10.1073/pnas.0503718102. View

Kochl S, Niederstatter H, Parson W . DNA extraction and quantitation of forensic samples using the phenol-chloroform method and real-time PCR. Methods Mol Biol. 2004; 297:13-30. DOI: 10.1385/1-59259-867-6:013. View

Holland M, Cave C, Holland C, Bille T . Development of a quality, high throughput DNA analysis procedure for skeletal samples to assist with the identification of victims from the World Trade Center attacks. Croat Med J. 2003; 44(3):264-72. View

Parsons T, Huel R, Davoren J, Katzmarzyk C, Milos A, Selmanovic A . Application of novel "mini-amplicon" STR multiplexes to high volume casework on degraded skeletal remains. Forensic Sci Int Genet. 2008; 1(2):175-9. DOI: 10.1016/j.fsigen.2007.02.003. View

10.

Prado V, Castro A, Oliveira C, Souza K, Pena S . Extraction of DNA from human skeletal remains: practical applications in forensic sciences. Genet Anal. 1997; 14(2):41-4. DOI: 10.1016/s1050-3862(97)00004-1. View

11.

Clayton T, Whitaker J, Maguire C . Identification of bodies from the scene of a mass disaster using DNA amplification of short tandem repeat (STR) loci. Forensic Sci Int. 1995; 76(1):7-15. DOI: 10.1016/0379-0738(95)01787-9. View

12.

Milos A, Selmanovic A, Smajlovic L, Huel R, Katzmarzyk C, Rizvic A . Success rates of nuclear short tandem repeat typing from different skeletal elements. Croat Med J. 2007; 48(4):486-93. PMC: 2080564. View

13.

Edson S, Ross J, Coble M, Parsons T, Barritt S . Naming the Dead - Confronting the Realities of Rapid Identification of Degraded Skeletal Remains. Forensic Sci Rev. 2015; 16(1):63-90. View

14.

Rohland N, Hofreiter M . Comparison and optimization of ancient DNA extraction. Biotechniques. 2007; 42(3):343-52. DOI: 10.2144/000112383. View

15.

Loreille O, Diegoli T, Irwin J, Coble M, Parsons T . High efficiency DNA extraction from bone by total demineralization. Forensic Sci Int Genet. 2008; 1(2):191-5. DOI: 10.1016/j.fsigen.2007.02.006. View

16.

Biesecker L, Bailey-Wilson J, Ballantyne J, Baum H, Bieber F, Brenner C . Epidemiology. DNA identifications after the 9/11 World Trade Center attack. Science. 2005; 310(5751):1122-3. DOI: 10.1126/science.1116608. View

17.

Hoss M, Paabo S . DNA extraction from Pleistocene bones by a silica-based purification method. Nucleic Acids Res. 1993; 21(16):3913-4. PMC: 309938. DOI: 10.1093/nar/21.16.3913. View

18.

Whitaker J, Cotton E, Gill P . A comparison of the characteristics of profiles produced with the AMPFlSTR SGM Plus multiplex system for both standard and low copy number (LCN) STR DNA analysis. Forensic Sci Int. 2001; 123(2-3):215-23. DOI: 10.1016/s0379-0738(01)00557-6. View

19.

Budimlija Z, Prinz M, Zelson-Mundorff A, Wiersema J, Bartelink E, MacKinnon G . World Trade Center human identification project: experiences with individual body identification cases. Croat Med J. 2003; 44(3):259-63. View