Mitochondrial DNA in forensic analyses
Abstract
This review article presents mitochondrial DNA (mtDNA) analyses in forensic genetics. Typing of nuclear DNA in old and poorly preserved biological samples is often unsuccessful and instead of nuclear DNA, mtDNA polymorphisms can be used for human identification. MtDNA is due to multy copy nature and circular conformation less prone to degradation and retain longer time. The most polymorphic control region is regularly used in forensic casework and mtDNA heteroplasmy must be considered in the identification cases and analyses of biological traces. The poorly preserved biological samples are mainly old skeletal remains - bones and teeth, old nails, feces, urine and hair shafts. The latter are micro traces, often found by criminalists at crime scenes. We will describe each type of biological material in more detail. In addition to morphological structure, we will pay special attention to the environmental impacts on the preservation of DNA in each type of biological material, optimization of extraction methods for effective isolation and optimal sampling. Due to low amounts of DNA, these samples are exposed to DNA contamination with persons involved in sampling procedures and genetic testing. To prevent and track potential contamination, different measures are used and they will be described. MtDNA analyses are often used in forensics to solve different cases and some applications of mtDNA in Slovenia and worldwide will be discussed.
Downloads
References
Zupanič Pajnič I, Šterlinko H, Bala ic J, Komel R. Parentage testing with 14 STR loci and population data for 5 STRs in the Slovenian population. Int J Legal Med. 2001;114(3):178–80. https://doi.org/10.1007/s004140000179 PMID:11296891
Zupanič Pajnič I, Balažic J, Komel R. Sequence polymorphism of the mitochondrial DNA control region in the Slovenian population. Int J Legal Med. 2004 Feb;118(1):1–4. https://doi.org/10.1007/s00414-003-0394-3 PMID:14534795
Fisher DL, Holland MM, Mitchell L, Sledzik PS, Wilcox AW, Wadhams M, et al. Extraction, evaluation, and amplification of DNA from decalcified and undecalcified United States Civil War bone. J Forensic Sci. 1993 Jan;38(1):60–8. https://doi.org/10.1520/JFS13376J PMID:8426158
Coble MD, Vallone PM, Just RS, Diegoli TM, Smith BC, Parsons TJ. Effective strategies for forensic analysis in the mitochondrial DNA coding region. Int J Legal Med. 2006 Jan;120(1):27–32. https://doi.org/10.1007/s00414-005-0044-z PMID:16261373
Zupanič Pajnič I. Identifikacija oseb iz starih in slabo ohranjenih bioloških materialov s polimorfizmi mitohondrijske DNA [PhD Thesis]. Ljubljana: I. Zupanič Pajnič; 2007.
Obal M. Uporaba različnih skeletnih elementov za genetsko identifikacijo žrtev druge svetovne vojne [Master ҆s Thesis]. Ljubljana: M. Obal; 2018.
Anderson S, Bankier AT, Barrell BG, de Bruijn MH, Coulson AR, Drouin J, et al. Sequence and organization of the human mitochondrial genome. Nature. 1981 Apr;290(5806):457–65. https://doi.org/10.1038/290457a0 PMID:7219534
Vogel F, Motulsky AG. Human genetics - problems and approaches, Springer-Verlag, Berlin, 1997: p. 83–87, 114–127, 145–193, 495–582, 593–594, 602–604, 610–621, 705–711. https://doi.org/10.1007/978-3-540-37654-5
Bendall KE, Macaulay VA, Sykes BC. Variable levels of a heteroplasmic point mutation in individual hair roots. Am J Hum Genet. 1997 Dec;61(6):1303–8. https://doi.org/10.1086/301636 PMID:9399894
Howell N, Kubacka I, Mackey DA. How rapidly does the human mitochondrial genome evolve? Am J Hum Genet. 1996 Sep;59(3):501–9. PMID:8751850
Holland MM, Fisher DL, Mitchell LG, Rodriquez WC, Canik JJ, Merril CR, et al. Mitochondrial DNA sequence analysis of human skeletal remains: identification of remains from the Vietnam War. J Forensic Sci. 1993 May;38(3):542–53. https://doi.org/10.1520/JFS13439J PMID:8515208
Hopwood AJ, Mannucci A, Sullivan KM. DNA typing from human faeces. Int J Legal Med. 1996;108(5):237–43. https://doi.org/10.1007/BF01369817 PMID:8721422
Tully G, Bär W, Brinkmann B, Carracedo A, Gill P, Morling N, et al. Considerations by the European DNA profiling (EDNAP) group on the working practices, nomenclature and interpretation of mitochondrial DNA profiles. Forensic Sci Int. 2001 Dec;124(1):83–91. https://doi.org/10.1016/S0379-0738(01)00573-4 PMID:11741765
Sullivan KM, Hopgood R, Gill P. Identification of human remains by amplification and automated sequencing of mitochondrial DNA. Int J Legal Med. 1992;105(2):83–6. https://doi.org/10.1007/BF02340829 PMID:1520642
Piercy R, Sullivan KM, Benson N, Gill P. The application of mitochondrial DNA typing to the study of white Caucasian genetic identification. Int J Legal Med. 1993;106(2):85–90. https://doi.org/10.1007/BF01225046 PMID:8217870
Lutz S, Wittig H, Weisser HJ, Heizmann J, Junge A, Dimo-Simonin N, et al. Is it possible to differentiate mtDNA by means of HVIII in samples that cannot be distinguished by sequencing the HVI and HVII regions? Forensic Sci Int. 2000 Sep;113(1-3):97–101. https://doi.org/10.1016/S0379-0738(00)00222-X PMID:10978608
Cann RL, Stoneking M, Wilson AC. Mitochondrial DNA and human evolution. Nature. 1987 Jan;325(6099):31–6. https://doi.org/10.1038/325031a0 PMID:3025745
Lorente JA, Entrala C, Alvarez JC, Lorente M, Arce B, Heinrich B, et al. Social benefits of non-criminal genetic databases: missing persons and human remains identification. Int J Legal Med. 2002 Jun;116(3):187–90. https://doi.org/10.1007/s004140100255 PMID:12111326
Bär W, Brinkmann B, Budowle B, Carracedo A, Gill P, Holland M, et al. DNA commission of the International society for forensic genetics: guidelines for mitochondrial DNA typing. Int J Legal Med. 2000;113(4):193–6. https://doi.org/10.1007/s004140000149 PMID:10929233
Allen M, Engström AS, Meyers S, Handt O, Saldeen T, von Haeseler A, et al. Mitochondrial DNA sequencing of shed hairs and saliva on robbery caps: sensitivity and matching probabilities. J Forensic Sci. 1998 May;43(3):453–64. https://doi.org/10.1520/JFS16169J PMID:9608683
Parson W, Brandstätter A, Alonso A, Brandt N, Brinkmann B, Carracedo A, et al. The EDNAP mitochondrial DNA population database (EMPOP) collaborative exercises: organisation, results and perspectives. Forensic Sci Int. 2004 Jan;139(2-3):215–26. https://doi.org/10.1016/j.forsciint.2003.11.008 PMID:15040920
Linch CA, Whiting DA, Holland MM. Human hair histogenesis for the mitochondrial DNA forensic scientist. J Forensic Sci. 2001 Jul;46(4):844–53. https://doi.org/10.1520/JFS15056J PMID:11451065
Wilson MR, Polanskey D, Replogle J, DiZinno JA, Budowle B. A family exhibiting heteroplasmy in the human mitochondrial DNA control region reveals both somatic mosaicism and pronounced segregation of mitotypes. Hum Genet. 1997 Aug;100(2):167–71. https://doi.org/10.1007/s004390050485 PMID:9254844
Tully G, Barritt SM, Bender K, Brignon E, Capelli C, Dimo-Simonin N, et al. Results of a collaborative study of the EDNAP group regarding mitochondrial DNA heteroplasmy and segregation in hair shafts. Forensic Sci Int. 2004 Feb;140(1):1–11. https://doi.org/10.1016/S0379-0738(03)00181-6 PMID:15013160
Calloway CD, Reynolds RL, Herrin GL Jr, Anderson WW. The frequency of heteroplasmy in the HVII region of mtDNA differs across tissue types and increases with age. Am J Hum Genet. 2000 Apr;66(4):1384–97. https://doi.org/10.1086/302844 PMID:10739761
Gill P, Ivanov PL, Kimpton C, Piercy R, Benson N, Tully G, et al. Identification of the remains of the Romanov family by DNA analysis. Nat Genet. 1994 Feb;6(2):130–5. https://doi.org/10.1038/ng0294-130 PMID:8162066
Ivanov PL, Wadhams MJ, Roby RK, Holland MM, Weedn VW, Parsons TJ. Mitochondrial DNA sequence heteroplasmy in the Grand Duke of Russia Georgij Romanov establishes the authenticity of the remains of Tsar Nicholas II. Nat Genet. 1996 Apr;12(4):417–20. https://doi.org/10.1038/ng0496-417 PMID:8630496
Parsons TJ, Muniec DS, Sullivan K, Woodyatt N, Alliston-Greiner R, Wilson MR, et al. A high observed substitution rate in the human mitochondrial DNA control region. Nat Genet. 1997 Apr;15(4):363–8. https://doi.org/10.1038/ng0497-363 PMID:9090380
Bendall KE, Macaulay VA, Baker JR, Sykes BC. Heteroplasmic point mutations in the human mtDNA control region. Am J Hum Genet. 1996 Dec;59(6):1276–87. PMID:8940273
Campos PF, Craig OE, Turner-Walker G, Peacock E, Willerslev E, Gilbert MT. DNA in ancient bone - where is it located and how should we extract it? Ann Anat. 2012 Jan;194(1):7–16. https://doi.org/10.1016/j.aanat.2011.07.003 PMID:21855309
Allen C, Harper V. Laboratory Manual for Anatomy and Physiology. 4th ed. Hoboken (NJ): Wiley; 2011. p. 96–8.
Kemp BM, Smith DG. Use of bleach to eliminate contaminating DNA from the surface of bones and teeth. Forensic Sci Int. 2005 Nov;154(1):53–61. https://doi.org/10.1016/j.forsciint.2004.11.017 PMID:16182949
Hochmeister MN, Budowle B, Borer UV, Eggmann U, Comey CT, Dirnhofer R. Typing of deoxyribonucleic acid (DNA) extracted from compact bone from human remains. J Forensic Sci. 1991 Nov;36(6):1649–61. https://doi.org/10.1520/JFS13189J PMID:1685164
Hagelberg E, Sykes B, Hedges R. Ancient bone DNA amplified. Nature. 1989 Nov;342(6249):485. https://doi.org/10.1038/342485a0 PMID:2586623
Miloš A, Selmanović A, Smajlović L, Huel RL, Katzmarzyk C, Rizvić A, et al. Success rates of nuclear short tandem repeat typing from different skeletal elements. Croat Med J. 2007 Aug;48(4):486–93. PMID:17696303
Hansen HB, Damgaard PB, Margaryan A, Stenderup J, Lynnerup N, Willerslev E, et al. Comparing Ancient DNA Preservation in Petrous Bone and Tooth Cementum. PLoS One. 2017 Jan;12(1):e0170940. https://doi.org/10.1371/journal.pone.0170940 PMID:28129388
Siriboonpiputtana T, Rinthachai T, Shotivaranon J, Peonim V, Rerkamnuaychoke B. Forensic genetic analysis of bone remain samples. Forensic Sci Int. 2018 Mar;284:167–75. https://doi.org/10.1016/j.forsciint.2017.12.045 PMID:29408726
Mundorff A, Davoren JM. Examination of DNA yield rates for different skeletal elements at increasing post mortem intervals. Forensic Sci Int Genet. 2014 Jan;8(1):55–63. https://doi.org/10.1016/j.fsigen.2013.08.001 PMID:24315589
Andronowski JM, Mundorff AZ, Pratt IV, Davoren JM, Cooper DM. 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 May;28:211–8. https://doi.org/10.1016/j.fsigen.2017.03.002 PMID:28315820
Alvarez García A, Muñoz I, Pestoni C, Lareu MV, Rodríguez-Calvo MS, Carracedo A. Effect of environmental factors on PCR-DNA analysis from dental pulp. Int J Legal Med. 1996r;109(3):125–9. https://doi.org/10.1007/BF01369671 PMID:8956985
Rubio L, Martinez LJ, Martinez E, Martin de las Heras S. Study of short- and long-term storage of teeth and its influence on DNA. J Forensic Sci. 2009 Nov;54(6):1411–3. https://doi.org/10.1111/j.1556-4029.2009.01159.x PMID:19804532
Higgins D, Austin JJ. Teeth as a source of DNA for forensic identification of human remains: a review. Sci Justice. 2013 Dec;53(4):433–41. https://doi.org/10.1016/j.scijus.2013.06.001 PMID:24188345
Mansour H, Krebs O, Sperhake JP, Augustin C, Koehne T, Amling M, et al. Cementum as a source of DNA in challenging forensic cases. J Forensic Leg Med. 2018 Feb;54:76–81. https://doi.org/10.1016/j.jflm.2017.12.015 PMID:29328966
Smith BC, Fisher DL, Weedn VW, Warnock GR, Holland MM. A systematic approach to the sampling of dental DNA. J Forensic Sci. 1993 Sep;38(5):1194–209. https://doi.org/10.1520/JFS13524J PMID:8228888
Higgins D, Kaidonis J, Austin J, Townsend G, James H, Hughes T. Dentine and cementum as sources of nuclear DNA for use in human identification. Aust J Forensic Sci. 2011;43(4):287–95. https://doi.org/10.1080/00450618.2011.583278.
Petrovič D, Zorc M. Histologija, Univerza v Ljubljani Medicinska fakulteta Inštitut za histologijo in embriologijo, Ljubljana, 2005. p. 35–42, 115–23, 166–68.
Gilbert MT, Janaway RC, Tobin DJ, Cooper A, Wilson AS. Histological correlates of post mortem mitochondrial DNA damage in degraded hair. Forensic Sci Int. 2006 Jan;156(2-3):201–7. https://doi.org/10.1016/j.forsciint.2005.02.019 PMID:15922527
Schlenker A, Grimble K, Azim A, Owen R, Hartman D. Toenails as an alternative source material for the extraction of DNA from decomposed human remains. Forensic Sci Int. 2016 Jan;258:1–10. https://doi.org/10.1016/j.forsciint.2015.10.025 PMID:26610200
Cline RE, Laurent NM, Foran DR. The fingernails of Mary Sullivan: developing reliable methods for selectively isolating endogenous and exogenous DNA from evidence. J Forensic Sci. 2003 Mar;48(2):328–33. https://doi.org/10.1520/JFS2002107 PMID:12664990
Hellmann A, Rohleder U, Schmitter H, Wittig M. STR typing of human telogen hairs—a new approach. Int J Legal Med. 2001;114(4-5):269–73. https://doi.org/10.1007/s004140000175 PMID:11355409
Gallimore JM, McElhoe JA, Holland MM. Assessing heteroplasmic variant drift in the mtDNA control region of human hairs using an MPS approach. Forensic Sci Int Genet. 2018 Jan;32:7–17. https://doi.org/10.1016/j.fsigen.2017.09.013 PMID:29024924
Linch CA, Smith SL, Prahlow JA. Evaluation of the human hair root for DNA typing subsequent to microscopic comparison. J Forensic Sci. 1998 Mar;43(2):305–14. https://doi.org/10.1520/JFS16137J PMID:9544538
Graffy EA, Foran DR. A simplified method for mitochondrial DNA extraction from head hair shafts. J Forensic Sci. 2005 Sep;50(5):1119–22. https://doi.org/10.1520/JFS2005126 PMID:16225218
Baker LE, McCormick WF, Matteson KJ. A silica-based mitochondrial DNA extraction method applied to forensic hair shafts and teeth. J Forensic Sci. 2001 Jan;46(1):126–30. https://doi.org/10.1520/JFS14923J PMID:11210897
McNevin D, Wilson-Wilde L, Robertson J, Kyd J, Lennard C. Short tandem repeat (STR) genotyping of keratinised hair. Part 2. An optimised genomic DNA extraction procedure reveals donor dependence of STR profiles. Forensic Sci Int. 2005 Oct;153(2-3):247–59. https://doi.org/10.1016/j.forsciint.2005.05.005 PMID:15998572
Johnson DJ, Martin LR, Roberts KA. STR-typing of human DNA from human fecal matter using the QIAGEN QIAamp stool mini kit. J Forensic Sci. 2005 Jul;50(4):802–8. https://doi.org/10.1520/JFS2004428 PMID:16078481
Roy R. Analysis of human fecal material for autosomal and Y chromosome STRs. J Forensic Sci. 2003 Sep;48(5):1035–40. https://doi.org/10.1520/JFS2002348 PMID:14535665
Vandenberg N, van Oorschot RA. Extraction of human nuclear DNA from feces samples using the QIAamp DNA Stool Mini Kit. J Forensic Sci. 2002 Sep;47(5):993–5. https://doi.org/10.1520/JFS15502J PMID:12353586
Sípoli Marques MA, Pinto Damasceno LM, Gualberto Pereira HM, Caldeira CM, Pereira Dias BF, de Giacomo Vargens D, et al. DNA typing: an accessory evidence in doping control. J Forensic Sci. 2005 May;50(3):587–92. PMID:15932091
Tsongalis GJ, Anamani DE, Wu AH. Identification of urine specimen donors by the PM+DQA1 amplification and typing kit. J Forensic Sci. 1996 Nov;41(6):1031–4. https://doi.org/10.1520/JFS14043J PMID:8914292
Linfert DR, Wu AH, Tsongalis GJ. The effect of pathologic substances and adulterants on the DNA typing of urine. J Forensic Sci. 1998 Sep;43(5):1041–5. https://doi.org/10.1520/JFS14354J PMID:9729822
Milde A, Haas-Rochholz H, Kaatsch HJ. Improved DNA typing of human urine by adding EDTA. Int J Legal Med. 1999;112(3):209–10. https://doi.org/10.1007/s004140050237 PMID:10335891
Tsuchimochi T, Iwasa M, Maeno Y, Koyama H, Inoue H, Isobe I, et al. Chelating resin-based extraction of DNA from dental pulp and sex determination from incinerated teeth with Y-chromosomal alphoid repeat and short tandem repeats. Am J Forensic Med Pathol. 2002 Sep;23(3):268–71. https://doi.org/10.1097/00000433-200209000-00013 PMID:12198355
Rohland N, Hofreiter M. Ancient DNA extraction from bones and teeth. Nat Protoc. 2007;2(7):1756–62. https://doi.org/10.1038/nprot.2007.247 PMID:17641642
Parson W, Gusmão L, Hares DR, Irwin JA, Mayr WR, Morling N, et al. DNA Commission of the International Society for Forensic Genetics: revised and extended guidelines for mitochondrial DNA typing. Forensic Sci Int Genet. 2014;13:134–42. https://doi.org/10.1016/j.fsigen.2014.07.010 PMID:25117402
Zupanič Pajnič I. Extraction of DNA from Human Skeletal Material. In: Goodwin W: Forensic DNA Typing Protocols. Methods in Molecular Biology. Humana Press, New York, NY, 2016;1420:89-108.
Jehaes E, Decorte R, Peneau A, Petrie JH, Boiry PA, Gilissen A, et al. Mitochondrial DNA analysis on remains of a putative son of Louis XVI, King of France and Marie-Antoinette. Eur J Hum Genet. 1998 Jul-Aug;6(4):383–95. https://doi.org/10.1038/sj.ejhg.5200227 PMID:9781047
Anslinger K, Weichhold G, Keil W, Bayer B, Eisenmenger W. Identification of the skeletal remains of Martin Bormann by mtDNA analysis. Int J Legal Med. 2001;114(3):194–6. https://doi.org/10.1007/s004140000176 PMID:11296895
Parson W, Brandstätter A, Niederstätter H, Grubwieser P, Scheithauer R. Unravelling the mystery of Nanga Parbat. Int J Legal Med. 2007 Jul;121(4):309–10. https://doi.org/10.1007/s00414-006-0098-6 PMID:16673142
Lleonart R, Riego E, Saínz de la Peña MV, Bacallao K, Amaro F, Santiesteban M, et al. Forensic identification of skeletal remains from members of Ernesto Che Guevara’s guerrillas in Bolivia based on DNA typing. Int J Legal Med. 2000;113(2):98–101. https://doi.org/10.1007/PL00007716 PMID:10741484
Mukaida M, Kimura H, Takada Y, Masuda T, Nakata Y. The personal identification of many samples recovered from under the sea. Forensic Sci Int. 2000 Sep;113(1-3):79–85. https://doi.org/10.1016/S0379-0738(00)00219-X PMID:10978605
Handt O, Richards M, Trommsdorff M, Kilger C, Simanainen J, Georgiev O, et al. Molecular genetic analyses of the Tyrolean Ice Man. Science. 1994 Jun;264(5166):1775–8. https://doi.org/10.1126/science.8209259 PMID:8209259
Krings M, Stone A, Schmitz RW, Krainitzki H, Stoneking M, Pääbo S. Neandertal DNA sequences and the origin of modern humans. Cell. 1997 Jul;90(1):19–30. https://doi.org/10.1016/S0092-8674(00)80310-4 PMID:9230299
Andelinović S, Sutlović D, Erceg Ivkosić I, Škaro V, Ivkosić A, Paić F, et al. Twelve-year experience in identification of skeletal remains from mass graves. Croat Med J. 2005 Aug;46(4):530–9. PMID:16100755
Parsons TJ, Huel RM, Bajunović Z, Rizvić A. Large scale DNA identification: the ICMP experience. Forensic Sci Int Genet. 2019 Jan;38:236–44. https://doi.org/10.1016/j.fsigen.2018.11.008 PMID:30469017
Zupanič Pajnič I, Gornjak Pogorelc B, Balažic J. Molecular genetic identification of skeletal remains from the Second World War Konfin I mass grave in Slovenia. Int J Legal Med. 2010 Jul;124(4):307–17. https://doi.org/10.1007/s00414-010-0431-y PMID:20217112
Zupanič Pajnič I. Molecular genetic identification of the Slovene home guard victims [in Slovenian]. Zdrav Vestn. 2008;77(11):745–50.
Zupanič Pajnič I, Petaros A, Balažic J, Geršak K. Searching for the mother missed since the Second World War. J Forensic Leg Med. 2016 Nov;44:138–42. https://doi.org/10.1016/j.jflm.2016.10.015 PMID:27810583
Strobl C, Eduardoff M, Bus MM, Allen M, Parson W. Evaluation of the precision ID whole MtDNA genome panel for forensic analyses. Forensic Sci Int Genet. 2018 Jul;35:21–5. https://doi.org/10.1016/j.fsigen.2018.03.013 PMID:29626805
Sturk-Andreaggi K, Peck MA, Boysen C, Dekker P, McMahon TP, Marshall CK. AQME: A forensic mitochondrial DNA analysis tool for next-generation sequencing data. Forensic Sci Int Genet. 2017 Nov;31:189–97. https://doi.org/10.1016/j.fsigen.2017.09.010 PMID:29080494
Copyright (c) 2019 Slovenian Medical Journal
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.
The Author transfers to the Publisher (Zdravniški vestnik/Slovenian Medical Journal) all economic copyrights following form Article 22 of the Slovene Copyright and Related Rights Act (ZASP), including the right of reproduction, the right of distribution, the rental right, the right of public performance, the right of public transmission, the right of public communication by means of phonograms and videograms, the right of public presentation, the right of broadcasting, the right of rebroadcasting, the right of secondary broadcasting, the right of communication to the public, the right of transformation, the right of audiovisual adaptation and all other rights of the author according to ZASP.
The aforementioned rights are transferred non-exclusively, for an unlimited number of editions, for the term of the statutory
The Author can make use of his work himself or transfer subjective rights to others only after 3 months from date of first publishing in the journal Zdravniški vestnik/Slovenian Medical Journal.
The Publisher (Zdravniški vestnik/Slovenian Medical Journal) has the right to transfer the rights, acquired parties without explicit consent of the Author.
The Author consents that the Article be published under the Creative Commons BY-NC 4.0 (attribution-non-commercial) or comparable licence.