Mitochondrial DNA in Fornescis: Principles, Applications, and Limitations

Authors

  • Mohammed Mahdi Al–Zubaidi Department of Molecular genetics and DNA fingerprinting, Forensic DNA Research and Training Center, Al-Nahrain University, Jadiriya, Baghdad, Iraq
  • Asia Abdul Lateef Mahdi Forensic DNA Center for Research and Training , Al-Nahrain University, Jadriya, Baghdad, Iraq
  • Reem Husam Al-Tabra Forensic DNA Center for Research and Training , Al-Nahrain University, Jadriya, Baghdad, Iraq
  • Halah Khalid Ibrahim Al-Sammaraie Forensic DNA Center for Research and Training , Al-Nahrain University, Jadriya, Baghdad, Iraq
  • Ban Ameen Abd el_Jabbar Forensic DNA Center for Research and Training , Al-Nahrain University, Jadriya, Baghdad, Iraq
  • Asmaa A. Jawad Al-Nahrain University
  • Sura Nabil Hameed Forensic DNA Center for Research and Training , Al-Nahrain University, Jadriya, Baghdad, Iraq

DOI:

https://doi.org/10.22401/b44vjp57

Keywords:

STR , MtDMA , Forensic science , VNTR Fingerprinting

Abstract

Forensic science involves the scientific analysis and interpretation of evidence that is used in legal proceedings to establish guilt or innocence. The use of mitochondrial DNA (mtDNA) in forensics is crucial as it has several advantages over other types of DNA. For instance, mtDNA is more resistant to degradation than nuclear DNA, making it suitable for analysis even in small or degraded samples. Additionally, mtDNA is maternally inherited, and this makes it useful in tracing an individual's maternal lineage or identifying relationships between individuals across multiple generations. Another advantage of mtDNA analysis is its reliability and accuracy since it is less prone to errors or contamination. This is because mtDNA is found in the mitochondria, which are separate from the cell nucleus and are less likely to be affected by extraneous DNA or contamination. Overall, the use of mtDNA in forensic science has significantly improved the accuracy and reliability of criminal investigations, making it a vital tool in the criminal justice system. In mitochondrial DNA (mtDNA) analysis, the two regions of the mtDNA genome that are typically analyzed are hypervariable regions 1 and 2 (HV1 and HV2). HV1 and HV2 are non-coding regions of the mtDNA genome, meaning that they do not contain information for the production of proteins. Instead, they contain a high degree of variation in their nucleotide sequences, which makes them useful for identifying individuals and their maternal lineages. The interpretation of mtDNA analysis results from HV1 and HV2 involves comparing the nucleotide sequences obtained from the evidence sample to a reference database of mtDNA sequences. This comparison is done to identify any matches or differences between the sample and the reference sequences. If there are no differences or only a few, the sample is considered to be a match to the reference sequence. The more differences there are between the sample and the reference sequences, the less likely it is that the sample and reference sequences came from the same individual or maternal lineage.The interpretation of mtDNA analysis results from HV1 and HV2 can be used to provide information about the identity and maternal lineage of an individual. For example, if an evidence sample matches a reference sequence from a known maternal relative, this can be used to support the identification of the individual.

References

Morgan, R.M.; "Forensic science. The importance of identity in theory and practice”. Forensic Sci. Int. Synergy,1: 239-242, 2019.

Budowle, B.; Baechtel, F.S.; "Modifications to improve the effectiveness of restriction fragment length polymorphism typing. Applied and theoretical electrophoresis". J. Electrophor., 1(4): 181-187 ,1990 .

Gill, P.; Jeffreys, A.J.; Werrett, D.J.; “Forensic application of DNA fingerprints”. Nature, 318(6046): 577-579, 1985.

Jeffreys, A.J.; Wilson, V.; Thein, S.L.; "Hypervariable ‘minisatellite’regions in human DNA". Nature, 314(6006): 67-73 ,1985 .

Budowle, B.; Van-Daal, A.; “Forensically relevant SNP classes. Bio techniques, 44(5): 603-610, 2008.

Comey, C.T.; Budowle, B.; “Validation studies on the analysis of the HLA DQα locus using the polymerase chain reaction”. J. Forensic Sci., 36(6): 1633-1648, 1991.

Holland, M.M.; Fisher, D.L.; Mitchell, L.G.; Rodriquez, W.C.; Canik, J.J.; Merril, C.R.; Weedn, V.W.; “Mitochondrial DNA sequence analysis of human skeletal remains: identification of remains from the Vietnam War” J. Forensic Sci., 38(3): 542-553, 1993.

Nwawuba, S.U.; Mohammed, K. A.; Adams ,T. B.; Omusi, P.I.; Ayevbuomwan, D.E.; Hopgood, R.; “Forensic DNA Profiling: Autosomal Short Tandem Repeat as a Prominent Marker in Crime Investigation”. Malays J Med Sci, 27(4): 22-35, 2020.

Budowle, B.,; Allard, M.W.; Wilson, M.R.; Chakraborty, R.; " Forensics and mitochondrial DNA: applications, debates, and foundations”. Annu Rev Genomics Hum Genet, 4(1): 119-141, 2003 .

Rolalindp, M.; Brianj, S.; Peter, J.H.; Andda, V.; el al.; “Testing migration patterns and estimating founding populationsize in Polynesia by using human mtDNA sequences”. PNAS Nexus 95: 9047-9052, 1998.

Underhill, P.A.; Kivisild, T.; “Use of Y chromosome and mitochondrial DNA population structure in tracing human migrations”. Ann. Rev. Genet., 41: 539-564, 2007.

Cann, R.L.; Stoneking, M.; Wilson, A.C.; “Mitochondrial DNA and human evolution”. Nature, 325(6099): 31-36, 1987.

Kayser, M.; “Forensic use of Y-chromosome DNA: a general overview”. Hum. Genet., 136(5): 621-635, 2017.

Goodwin, W.; Linacre, A.; Vanezis, P.; "The use of mitochondrial DNA and short tandem repeat typing in the identification of air crash victims", Forensic Sci. Int. Genet., 20(8): 1707-1711, 1999.

Mohammadi, A.; Ramezani, M.; “DNA markers evaluation to preparing a genetic database for identification in crimes and incidents”. Int. J. Med. Rev., 5(2):50–54, 2018.

Logan, D.C.; "The mitochondrial compartment". J. Exp. Bot., 57(6): 1225-1243, 2006.

Malyarchuk, B.; Rogozin, I.B.; "Mutagenesis by transient misalignment in the human mitochondrial DNA control region”. Ann. Hum. Genet 68: 324– 339, 2004.

Okamoto, K.; Shaw, J.; "Mitochondrial Morphology and Dynamics in Yeast and Multicellular Eukaryotes". Annu. Rev., 39: 503–536, 2005.

Taanman J.W.; "The mitochondrial genome: structure, transcription, translation and replication". Biochim. Biophys. Acta ,1410: 103-123, 1999.

Gyllensten , U.B.; Whiarton, A. J.; Wilson , A.C.; "Paternalinheritance of mitochondrial ONA in mice". Nature. 352: 255-257, 1991.

Bermisheva, M.A.; Viktorova, T.V.; Khusnutdinova, E.K.; "Polymorphism of human mitochondrial DNA". Russ. J. Genet, 39(8): 849-859, 2003.

Richards, M.; CorteReal, H.; Forster, P.; Macaulay, V.; Wilkinson Herbots, H.; Demaine, A.; et al.; "Paleolithic and neolithic lineages in the European mitochondrial gene pool". Am. J. Hum. Genet., 59(1): 185-203, 1996.

Anderson S.; Bankier A.; Barrell B.; de-Bruijn M.; Coulson A.; Drouin J.; Eperon I.; "Sequence and organization of the human mitochondrial genome". Nature, 290(5806): 457-465, 1981.

Butler, J.M.; Hill, C.R.; "Biology and genetics of new autosomal STR loci useful for forensic DNA analysis". Forensic Sci. Rev.24(1): 15-26, 2012.

Wallace D.C.; Shoffner, J.M.; Watts, R.L.; Juncos, J.L.; Torroni, A.; "Mitochondrial oxidative phosphorylation defects in Parkinson’s disease". Ann. Neurol,32: 113-114, 1992.

Zeviani, M.; Bertagnolio, B.; Uziel, G.; "Neurological presentations of mitochondrial diseases". J. Inh. Metab. Dis.,19: 504-520, 1996.

Stoneking, M.; “Hyperviable sites in the mtDNA control region are mutational hotspots”. Am. J. Hum. Genet., 67(4): 1029-1032, 2000 .

Pakendorf B.; Stoneking M.; "Mitochondrial DNA and human evolution". Am. J. Hum. Genet. 6: 165-183, 2005.

Howell, N.; Elson, J.L..; Howell, C.; Turnbull, D.M.; "Relative rates of evolution in the coding and control regions of African mtDNAs". Mol. Biol. Evol.24: 2213-2221,2007 .

Piercy, R.; Sullivan, K.M..; Benson, N.; Gill, P.; "The application of mitochondrial DNA typing to the study of white Caucasian genetic identification". Int. J. Legal Med,106: 85-90, 1993.

Andrews, R.M.; Kubacka Chinnery PF.; Lightowlers, R.N.; Turnbull, D.M.; et al.; "Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA". Nat. Genet, 23: 147-153, 1999.

Bandelt, H.J.; Parson, W.; "Consistent treatment of length variants in the human mtDNA control region: a reappraisal". Int. J. Legal Med., 122: 11-21, 2008 .

Lee, H.Y.; Chung, U.; Yoo, J.E.; Park, M.J.; and Shin, K.J.; " Quantitative and qualitative profiling of mtdna". Electrophoresis, 25(1): 28-34, 2004.

Lutz-Bonengel, S.; Sanger, T.; Pollak, S.; Szibor, K.; "Different methods to determine length heteroplasmy within the mitochondrial control region". Int. J. Legal Med., 118(5): 274-281, 2004.

Bini, C.; Pappalardo, G.; “mtDNA HVI length heteroplasmic profile in different tissues of maternally related members”. Forensic Sci. Int., 152(1): 35-38 ,2005.

Malik, S.; Sudoyo, H.; Pramoonjago, P.; Suryadi, H.; Sukarna, T.; Njunting, M.; et al.; “Nuclear mitochondrial interplay in the modulation of the homopolymeric tract length heteroplasmy in the control (D-loop) region of the mitochondrial DNA”. Hum Genet., 110(5): 402-411, 2002.

Cann, R.L.; Brown, W.M.; Wilson, A.C.; “Polymorphic sites and the mechanism of evolution in human mitochondrial DNA”. J. Mol. Evol. 106: 479-499, 1984.

Giles, R.E.; Blanc, H.; Cann, H.M.; Wallace, D.C.; “Maternal inheritance of human mitochondrial DNA”. PNAS. 77: 6715-6719, 1980.

Zuckerman, S.H.; Solus, J.F.; Gillespie, F.P.; Eisenstadt, J.M.; "Retention of both parental mitochondrial DNA species in mouse-Chinese hamster somatic cell hybrids". Somatic Cell Mol. Genet.,10: 85-92,1984.

Brown, W.M.; George, M.; Wilson, A.C.; "Rapid evolution of animal mitochondrial DNA". PNAS,76: 1967-1971,1979.

Alan, J. R.; Mark, S.; “Peopling of Sahul: mtDNA Variation in Aboriginal Australian and Papua New Guinean Populations". Am. J. Hum. Genet., 65(3): 808-828, 1999.

Wilson, A.C.; Cann, R.L.; Carr, S.M.; George, M.; Gyllensten, U.B.; Helm-Bychowski, K.M.; Higuchi, R.G.; Palumbi, S.R.; "Mitochondrial DNA and two perspectives on evolutionary genetics". PNAS Nexus, 26: 375-400, 1985.

Wallace, D.C.; "Mitochondrial DNA variation in human evolution and disease". Gene., 238: 211–230,1999.

Krings, M.; "Neandertal DNA sequences and the origin of modern humans". Cell, 90:19–30, 1997.

Holland, M.M.; Parsons, T.J; "Mitochondrial DNA Sequence Analysis-Validation and Use for Forensic Casework". Forensic Sci. Rev., 11(1), 21-50, 1999.

Gill, P.; et al.; " Identification of the remains of the Romano family by DNA analysis". Nat. Genet., 6,130–135,1994.

Ivanov, P.L.; Wadhams, M.J.; Roby, R.K.; Holland, M.M.; Weedn, V.W.; Parsons, T.J.; "Mitochondrial DNA sequence heteroplasmy in the Grand Duke of Russia Georgij Romanov establishes the authenticity of the remains of Tsar Nicholas II". Nat. Genet., 12(4): 417-420, 1996.

Coble, M.D.; Loreille, O.M.; Wadhams, M.J.; Edson, S.M.; Maynard, K., Meyer; C.E., Finelli, L.N.; “Mystery solved: the identification of the two missing Romanov children using DNA analysis”. Plo. Son., 4(3): e4838, 2009.

Gill, P.; et al.; "Establishing the identity of Anna Anderson Manahan". Nat. Genet., 9: 9–10, 1995.

Rai A "Richard III -- the final act , Br. Dent. J., 214: 415-417, 2013.

Gill P.; Ivanov P.L.; Kimpton C.; Piercy R,; Benson N.; "Identification of the remains of the Romanov family by DNA analysis". Nat. Genet., 6: 130-135, 1994.

Butler, J.M.; Levin, B.C.; "Forensic applications of mitochondrial DNA". Trends Biotechnol., 16(4), 158-162, 1998.

Sultana, G.N.N.; Sultan, M.Z.; "Mitochondrial DNA and methods for forensic identification". J. Forensic. Sci. Crim., Inv., 9(1), 2018.

Parsons, T.J.; et al.; “A high observed substitution rate in the human mitochondrial DNA control region”. Nat. Genet., 15: 363–368, 1997.

Budowle, B.; "Forensics and mitochondrial DNA: Applications, debates, and foundations". Annu. Rev. Genom. Hum. Genet., 4: 119–141, 2003.

Sanger, F.; "DNA sequencing with chain-terminating inhibitors". Proceedings of the National Academy of Sciences of the United States of America, PNAS .74: 5463–5467, 1977.

Wilson, M.R.; et al.; “Validation of mitochondrial DNA sequencing for forensic casework analysis". Int. J. Leg. Med., 108, 68–74, 1995.

Lee R.E.; Gaensslen Eds., Forensic Sci. Int. (pp. 76–97). Chicago: Year Book Medical Publishers.

Stewart, J.E.; et al.; “Length variation in HV2 of the human mitochondrial DNA control region”. JFS, 46, 862–870, 2001.

Mikkelsen, M.; et al.; “Application of full mitochondrial genome sequencing using 454 GS FLX pyrosequencing”. Forensic Sci. Int. Genet., 2: 518–519, 2009.

SWGDAM "Guidelines for mitochondrial DNA (mtDNA) nucleotide sequence interpretation. Forensic Sci. Int, 5(2), 2003.

Wilson, M.R.; et al.; "Recommendations for consistent treatment of length variants in the human mitochon- drial DNA control region"., Forensic Sci. Int., 129: 35–42, 2002.

Parson, W.; Bandelt, H.-J.; "Extended guidelines for mtDNA typing of population data in forensic science". Forensic Sci. Int. Genet, 1: 13–19, 2007.

Olivio, P.D.; M.J. Van de Walle, P.J.; Laipis, W. W.H.; "Nucleotide sequence evidence for rapid genotypic shifts in the bovine mitochondrial DNA D-loop". Nature, 306: 400-402, 1983.

Budowle B.; DiZinno J.A.; Wilson M.R.; "Interpretation guidelines for mito- chondrial DNA sequencing". Presented at Int. Symp. Hum. Identif., 10th, Madison, Wis, 1999.

Stewart, J.E.; Fisher, C.L,.; Aagaard, P.J.; Wilson, M.R., Isenberg, A.R.; "Length variation in HV2 of the human mitochon- drial DNA control region". J. Forensic Sci., 46: 862–70, 2001.

Bendall, K.E.; Sykes, B.C.; “Length hetero-plasmy in the first hypervariable segment of the human mtDNA control region”. J. Hum. Genet., 57: 248–256, 1995.

Sullivan, K.M.; et al.; “A single difference in mtDNA control region sequence observed between hair shaft and reference samples from a single donor: Proceedings of the seventh international symposium on human identification ISHI 1996. Madison, Wisconsin". Promega Corporation., 126–130, 1997.

Wilson, M.R.; "A family exhibiting heteroplasmy in the human mitochondrial DNA control region reveals both somatic mosaicism and pronounced segregation of mitotypes". Hum. Genet., 100: 167–171, 1997.

Sekiguchi, K..; “Inter- and intragenerational transmission of a human mitochondrial DNA heteroplasmy among 13 maternally-related individuals and differences between and within tissues in two family members". Mitochondrion, 2: 401–414, 2003.

Stoneking, M.; "Hypervariable sites in the mtDNA control region are mutational hotspots". Am. J. Hum. Genet., 67: 1029–1032, 2000.

Tully, L.A.; et al.; “A sensitive denaturing gradient-gel electrophoresis assay reveals a high frequency of het- eroplasmy in hypervariable region 1 of the human mtDNA control region”. Am. J. Hum. Genet., 67: 432–443, 2000.

Calloway, C.D.; "The frequency of heteroplasmy in the HVII region of mtDNA differs across tissue types and increases with age". Am. J. Hum. Genet., 66: 1384–1397, 2000.

Lagerström-Fermér, M.; "Heteroplasmy of the human mtDNA control region remains constant during life". Am. J. Hum. Genet., 68: 1299–1301, 2001.

Budowle B.; Adams D.E.; Comey C.C.; Merril C.R.; "Mitochondrial DNA: a possible genetic material suitable for forensic analysis". Forensic Sci. Int., 278: 76–97, 1990.

Monnat R.J.; Loeb, L.A.; “Nucleotide sequence preservation of human mito- chondrial DNA”. Proc. Natl. Acad. Sci. USA 82: 2895–99, 1985.

Monnat, R.J.; Reay, D.T.; "Nucleotide sequence identity of mitochondrial DNA from different human tissues". Gene 43: 205–11, 1986.

Gill, P.; Ivanov, P.L.; Kimpton, C.; Piercy, R., Benson, N.; "Identification of the remains of the Romanov family by DNA analysis". Nat. Genet. 6: 130–35, 1994.

Ivanov, P.L..; Wadhams, M.J.; Roby, R.K..; Holland, M.M., Weedn, V.W.; Parsons, T.J.; "Mitochondrial DNA sequence het- eroplasmy in the Grand Duke of Russia Georgij Romanov establishes the authen- ticity of the remains of Tsar Nicholas II". Nat. Genet. 12: 417–20, 1996.

Ingman, M.H.; Kaessmann, S.; Pääbo, U.; Gyllesten, G.; “Mitochondrial genome variation and the origin of modern humans”. Nature, 408(6813): 708-713, 2000.

Pesole, G.C.; Gissi, A.; De-Chirico. A.; Saccone, C.; "Nucleotide substitution rate of mammalian mitochondrial genomes". J. Mol. Evol., 48(4): 429-434, 1999.

Wallace, D.C.; Lott, M.T.; Brown, M.D.; Huoponen, K.; Toroni, A.; "Human gene mapping 1995: A compendium. John Hopkins University Press". Baltimore, 1995.

Torroni, A.; K. Huoponen, P.; Francalacci, M.; Petrozzi, L.; Morelli, R.; “Classification of European mtDNAs from an analysis of three European populations”. Genetics, 144(4): 1835-1850, 1996.

Quintana-Murci, L.O.; Semino, H.J.; Bandelt, G.; Passarino, K.M.; et al.; “Genetic evidence of an early exit of Homo sapiens sapiens from Africa through eastern Africa”. Nature genetics, Nat.Genet., 23(4): 437-441, 1999.

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2024-06-15

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Mitochondrial DNA in Fornescis: Principles, Applications, and Limitations. ANJS 2024, 27 (2), 50-62. https://doi.org/10.22401/b44vjp57.

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