The Use of Mitochondrial DNA Single Nucleotide Polymorphisms to Assist in the Resolution of Three Challenging Forensic Cases
Rebecca S. Just M.F.S.
Armed Forces DNA Identification Laboratory, Armed Forces Institute of Pathology, AFIP Annex, 1413 Research Blvd., Rockville, MD 20850.
Search for more papers by this authorMark D. Leney Ph.D.
Joint POW/MIA Accounting Command—Central Identification Laboratory, 310 Worchester Ave. Bldg. 45, Hickam AFB, HI 96853.
Present address: Massachusetts Biologic Laboratories, University of Massachusetts Medical School, Jamaica Plain, MA 02310.
Scientific Advisor, The National League of Families of American Prisoners and Missing in Southeast Asia, 1005 Glebe Road, Suite 170, Arlington, VA 22201.
Search for more papers by this authorSuzanne M. Barritt M.S.
Armed Forces DNA Identification Laboratory, Armed Forces Institute of Pathology, AFIP Annex, 1413 Research Blvd., Rockville, MD 20850.
Search for more papers by this authorChristopher W. Los M.S.F.S.
Armed Forces DNA Identification Laboratory, Armed Forces Institute of Pathology, AFIP Annex, 1413 Research Blvd., Rockville, MD 20850.
Search for more papers by this authorBrion C. Smith D.D.S.
Armed Forces DNA Identification Laboratory, Armed Forces Institute of Pathology, AFIP Annex, 1413 Research Blvd., Rockville, MD 20850.
Search for more papers by this authorThomas D. Holland Ph.D.
Joint POW/MIA Accounting Command—Central Identification Laboratory, 310 Worchester Ave. Bldg. 45, Hickam AFB, HI 96853.
Search for more papers by this authorThomas J. Parsons Ph.D.
Armed Forces DNA Identification Laboratory, Armed Forces Institute of Pathology, AFIP Annex, 1413 Research Blvd., Rockville, MD 20850.
International Commission on Missing Persons, Alipasina 45 A, 71000 Sarajevo, Bosnia.
Search for more papers by this authorRebecca S. Just M.F.S.
Armed Forces DNA Identification Laboratory, Armed Forces Institute of Pathology, AFIP Annex, 1413 Research Blvd., Rockville, MD 20850.
Search for more papers by this authorMark D. Leney Ph.D.
Joint POW/MIA Accounting Command—Central Identification Laboratory, 310 Worchester Ave. Bldg. 45, Hickam AFB, HI 96853.
Present address: Massachusetts Biologic Laboratories, University of Massachusetts Medical School, Jamaica Plain, MA 02310.
Scientific Advisor, The National League of Families of American Prisoners and Missing in Southeast Asia, 1005 Glebe Road, Suite 170, Arlington, VA 22201.
Search for more papers by this authorSuzanne M. Barritt M.S.
Armed Forces DNA Identification Laboratory, Armed Forces Institute of Pathology, AFIP Annex, 1413 Research Blvd., Rockville, MD 20850.
Search for more papers by this authorChristopher W. Los M.S.F.S.
Armed Forces DNA Identification Laboratory, Armed Forces Institute of Pathology, AFIP Annex, 1413 Research Blvd., Rockville, MD 20850.
Search for more papers by this authorBrion C. Smith D.D.S.
Armed Forces DNA Identification Laboratory, Armed Forces Institute of Pathology, AFIP Annex, 1413 Research Blvd., Rockville, MD 20850.
Search for more papers by this authorThomas D. Holland Ph.D.
Joint POW/MIA Accounting Command—Central Identification Laboratory, 310 Worchester Ave. Bldg. 45, Hickam AFB, HI 96853.
Search for more papers by this authorThomas J. Parsons Ph.D.
Armed Forces DNA Identification Laboratory, Armed Forces Institute of Pathology, AFIP Annex, 1413 Research Blvd., Rockville, MD 20850.
International Commission on Missing Persons, Alipasina 45 A, 71000 Sarajevo, Bosnia.
Search for more papers by this authorPresent address: Massachusetts Biologic Laboratories, University of Massachusetts Medical School, Jamaica Plain, MA 02310.
Scientific Advisor, The National League of Families of American Prisoners and Missing in Southeast Asia, 1005 Glebe Road, Suite 170, Arlington, VA 22201.
Abstract
Abstract: Mitochondrial DNA (mtDNA) single nucleotide polymorphisms (SNPs) in an 11-plex assay were typed in three missing person cases involving highly degraded human remains. Unlike the traditional forensic approach to analyzing mtDNA which focuses on sequencing portions of the noncoding Control Region, this assay targets discriminatory SNPs that reside principally in the coding region. In two of the cases, the SNP typing successfully excluded one of two reference families that could not be excluded on the basis of mtDNA hypervariable region sequencing alone, and resulted in the final resolution of both decades-old cases. In a third case, SNP typing confirmed the sorting and reassociation of multiple commingled skeletal elements. The application of a specific mtDNA SNP assay in these cases demonstrates its utility in distinguishing samples when the most common Caucasian hypervariable region type is encountered in forensic casework.
References
- 1 Holland MM, Cave CA, Holland CA, Parsons TJ. 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.
- 2 Davoren J, Vanek D, Konjhodzić R, Huffine E, Parsons TJ. A highly effective DNA extraction method for nuclear STR testing of skeletal remains from mass graves. Croat Med J 2007; 48: 478–85.
- 3 Loreille O, Diegoli T, Irwin J, Coble M, Parsons T. High efficiency DNA extraction from bone by total demineralization. Forensic Sci Int Genet 2007; 1(2): 191–5.
- 4 Miloš A, Selamanović A, Smajlović L, Huel R, Katzmarzyk C, Rizvić A, et al. Success rates of nuclear STR typing from different skeletal elements. Croat Med J 2007; 48: 486–93.
- 5 Parsons TJ, Huel R, Davoren J, Katzmarzyk C, Miloš A, Selmanović A, et al. Application of novel “mini-amplicon” STR multiplexes to high volume casework on degraded skeletal remains. Forensic Sci Int Genet 2007; 1: 175–9.
- 6 Irwin JA, Leney MD, Barritt SM, Loreille O, Christensen AF, Holland TD, et al. Application of low copy number STR typing to the identification of aged, degraded skeletal remains. J Forensic Sci 2007; 52(6): 1322–7.
- 7 Whitaker JP, Clayton TM, Urquhart AJ, Millican ES, Downes TJ, Kimpton CP, et al. Short tandem repeat typing of bodies from a mass disaster: high success rate and characteristic amplification patterns in highly degraded samples. BioTechniques 1995; 184(4): 670–7.
- 8 Dixon LA, Dobbins AE, Pulker H, Butler JM, Vallone PM, Coble MD, et al. Analysis of artificially degraded DNA using STRs and SNPs—results of a collaborative European (EDNAP) exercise. Forensic Sci Int 2006; 164(1): 33–44.
- 9 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; 38(3): 542–53.
- 10 Butler JM, Levin BC. Forensic applications of mitochondrial DNA. Trends Biotechnol 1998; 16: 158–62.
- 11 Holland MM, Parsons TJ. Mitochondrial DNA sequence analysis—validation and use for forensic casework. Forensic Sci Rev 1999; 11: 21–50.
- 12 Carracedo A, Bar W, Lincoln P, Mayr W, Morling N, Olaisen B, et al. DNA Commission of the International Society for Forensic Genetics: guidelines for mitochondrial DNA typing. Forensic Sci Int 2000; 110: 79–85.
- 13 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; 113: 97–101.
- 14 Edson SM, Ross JP, Coble MD, Parsons TJ, Barritt SM. Naming the dead—confronting the realities of rapid identification of degraded skeletal remains. Forensic Sci Rev 2004; 16(1): 64–89.
- 15 Parsons TJ, Coble MD. Increasing the forensic discrimination of mitochondrial DNA testing through analysis of the entire mitochondrial genome. Croat Med J 2001; 42: 304–9.
- 16 Lutz-Bonengel S, Schmidt U, Schmidt T, Pollak S. Sequence polymorphisms within the human mitochondrial genes MTATP6, MTATP8, and MTND4. Int J Legal Med 2003; 117: 133–42.
- 17 Coble MD, Just RS, O’Callaghan JE, Letmanyi IH, Peterson CT, Irwin JA, et al. Single nucleotide polymorphisms over the entire mtDNA genome that increase the power of forensic testing in Caucasians. Int J Legal Med 2004; 118: 137–46.
- 18 Just RS, Irwin JA, O’Callaghan JE, Saunier JL, Coble MD, Vallone PM, et al. Toward increased utility of mtDNA in forensic identifications. Forensic Sci Int 2004; 146S: 147–9.
- 19 Andreasson H, Asp A, Alderborn A, Gyllensten Y, Allen M. Mitochondrial sequence analysis for forensic identification using pyrosequencing technology. BioTechniques 2002; 32: 124–33.
- 20 Quintáns B, Álvarez-Iglesias V, Salas A, Phillips C, Lareu MV, Carracedo A. Typing of mitochondrial DNA coding region SNPs of forensic and anthropological interest using SNaPshot minisequencing. Forensic Sci Int 2004; 140(2–3): 251–7.
- 21 Vallone PM, Just RS, Coble MD, Butler GM, Parsons TJ. A multiplex allele specific primer extension assay for forensically informative SNPs distributed throughout the mitochondrial genome. Intl J Legal Med 2004; 118: 147–57.
- 22 Divne AM, Allen M. A DNA microarray system for forensic SNP analysis. Forensic Sci Int 2005; 154(2–3): 111–21.
- 23 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; 120: 27–32.
- 24 Hall TA, Budowle B, Jiang Y, Blyn L, Eshoo M, Sannes-Lowery KA, et al. Base composition analysis of human mitochondrial DNA using electrospray ionization mass spectrometry: a novel tool for the identification and differentiation of humans. Anal Biochem 2005; 344(1): 53–69.
- 25 Sigurdsson S, Hedman M, Sistonen P, Sajantila A, Syvänen AC. A microarray system for genotyping 150 single nucleotide polymorphisms in the coding region of human mitochondrial DNA. Genomics 2006; 87(4): 534–42.
- 26 Bär W, Brinkman 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: 193–6.
- 27 SWGDAM. Guidelines for mitochondrial DNA (mtDNA) nucleotide sequence interpretation. Forensic Sci Commun 2003; 5(2).
- 28 Torroni A, Achilli A, Macauley V, Richards M, Bandelt H-J. Harvesting the fruit of the human mtDNA tree. Trends Genet 2006; 22(6): 339–45.
- 29 Achilli A, Rengo C, Magri C, Battaglia C, Olivieri A, Scozzari R, et al. The molecular dissection of mtDNA haplogroup H confirms that the Franco-Catabrian glacial refuge was a major source for the European gene pool. Am J Hum Genet 2004; 75: 910–8.
- 30 Richards M, Macaulay V, Hickey E, Vega E, Sykes B, Guida V, et al. Tracing European founder lineages in the Near Eastern mtDNA pool. Am J Hum Genet 2000; 67: 1251–76.
- 31 Malyarchuk BA, Grzybowski T, Derenko MV, Czarny J, Crobnič K, Miścicka-Śliwka D. Mitochondrial DNA variability in Poles and Russians. Annal Hum Genet 2003; 67: 412–25.
- 32 Nilsson M, Andréasson-Jansson H, Ingman M, Allen M. Evaluation of mitochondrial DNA coding region assays for increased discrimination in forensic analysis. Forensic Sci Int Gene 2008; 2(1): 1–8.