Forensic Science International: Genetics
Volume 4, Issue 3 , Pages 148-157 , April 2010

Forensic implications of genetic analyses from degraded DNA—A review

  • Reza Alaeddini

      Affiliations

    • School of Chemical and Biomolecular Engineering, University of Sydney, Sydney, Australia
    • ,
  • Simon J. Walsh

      Affiliations

    • Forensic and Data Centres, Australian Federal Police, Canberra, Australia
    • Corresponding Author InformationCorresponding author. Fax: +61 2 6223 3270.
    • ,
  • Ali Abbas

      Affiliations

    • School of Chemical and Biomolecular Engineering, University of Sydney, Sydney, Australia

Received 28 August 2008 ,Revised 30 August 2009 ,Accepted 11 September 2009.

References 

  1. Lindahl T. The croonian lecture, 1996: endogenous damage to DNA. Philos. Trans. R. Soc. Lond. B: Biol. Sci. 1996;351(1347):1529–1538
  2. A.A. Vass, Beyond the grave understanding human decomposition, 2001.
  3. Jennings RB, Ganote CE, Reimer KA. Ischemic tissue injury. Am. J. Pathol. 1975;81(1):179–198
  4. Ilse G, Kovacs K, Ryan N, Horvath E, Ilse D. Autolytic changes in the rat adenohypophysis. A histologic, immunocytologic and electron microscopic study. Exp. Pathol. (Jena). 1979;17(4):185–195
  5. Zeiss CJ. The apoptosis–necrosis continuum: insights from genetically altered mice. Vet. Pathol. 2003;40(5):481–495
  6. Shimizu S, Eguchi Y, Kosaka H, Kamiike W, Matsuda H, Tsujimoto Y. Prevention of hypoxia-induced cell death by bcl-2 and bcl-xl. Nature. 1995;374(6525):811–813
  7. Collan Y, Salmenpera M. Electron microscopy of postmortem autolysis of rat muscle tissue. Acta Neuropathol. 1976;35(3):219–233
  8. Dive C, Gregory CD, Phipps DJ, Evans DL, Milner AE, Wyllie AH. Analysis and discrimination of necrosis and apoptosis (programmed cell-death) by multiparameter flow-cytometry. Biochim. Biophys. Acta. 1992;1133(3):275–285
  9. Krysko DV, Vanden Berghe T, D’Herde K, Vandenabeele P. Apoptosis and necrosis: detection, discrimination and phagocytosis. Methods. 2008;44(3):205–221
  10. Gill-King H. Chemical and ultrastructural aspects of decomposition. In:  Haglund MH,  Sorg WD editor. Forensic Taphonomy: The Postmortem Fate of Human Remains. Robert B. Stern, CRC press, Inc.; 1997;p. 93–108
  11. Tomita Y, Nihira M, Ohno Y, Sato S. Ultrastructural changes during in situ early postmortem autolysis in kidney, pancreas, liver, heart and skeletal muscle of rats. Leg. Med. (Tokyo). 2004;6(1):25–31
  12. Nicotera P, Leist M. Energy supply and the shape of death in neurons and lymphoid cells. Cell Death Differ. 1997;4(6):435–442
  13. Tsujimoto Y. Apoptosis and necrosis: intracellular atp level as a determinant for cell death modes. Cell Death Differ. 1997;4(6):429–434
  14. Trump BF, Berezesky IK. Calcium-mediated cell injury and cell death. FASEB J. 1995;9(2):219–228
  15. Reimer KA, Lowe JE, Jennings RB. Effect of the calcium antagonist verapamil on necrosis following temporary coronary artery occlusion in dogs. Circulation. 1977;55(4):581–587
  16. Hajnoczky G, Davies E, Madesh M. Calcium signaling and apoptosis. Biochem. Biophys. Res. Commun. 2003;304(3):445–454
  17. Kroemer G, Galluzzi L, Brenner C. Mitochondrial membrane permeabilization in cell death. Physiol. Rev. 2007;87(1):99–163
  18. Jambrina E, Alonso R, Alcalde M, del Carmen Rodriguez M, Serrano A, Martinez AC, et al. Calcium influx through receptor-operated channel induces mitochondria-triggered paraptotic cell death. J. Biol. Chem. 2003;278(16):14134–14145
  19. De Duve C, Wattiaux R. Functions of lysosomes. Annu. Rev. Physiol. 1966;28:435–492
  20. Lindahl T. Instability and decay of the primary structure of DNA. Nature. 1993;362(6422):709–715
  21. Hofreiter M, Jaenicke V, Serre D, Haeseler Av A, Paabo S. DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA. Nucleic Acids Res. 2001;29(23):4793–4799
  22. Yuyama K, Yamamoto H, Nishizaki I, Kato T, Sora I, Ya-mamoto T. Caspase-independent cell death by low concentrations of nitric oxide in pc12 cells: involvement of cytochrome c oxidase inhibition and the production of reactive oxygen species in mitochondria. J. Neurosci. Res. 2003;73(3):351–363
  23. Donovan M, Cotter TG. Caspase-independent photoreceptor apoptosis in vivo and differential expression of apoptotic protease activating factor-1 and caspase-3 during retinal development. Cell Death Differ. 2002;9(11):1220–1231
  24. Counis MF, Torriglia A. Acid DNAses and their interest among apoptotic endonucleases. Biochimie. 2006;88(12):1851–1858
  25. Chien KR, Abrams J, Serroni A, Martin JT, Far-ber JL. Accelerated phospholipid degradation and associated membrane dysfunction in irreversible, ischemic liver cell injury. J. Biol. Chem. 1978;253(13):4809–4817
  26. Ayala-Torres S, Chen Y, Svoboda T, Rosenblatt J, Van B, Houten . Analysis of gene-specific DNA damage and repair using quantitative polymerase chain reaction. Methods. 2000;22(2):135–147
  27. Hofreiter M, Serre D, Poinar HN, Kuch M, Paabo S. Ancient DNA. Nat. Rev. Genet. 2001;2(5):353–359
  28. Filipski J, Leblanc J, Youdale T, Sikorska M, Walker PR. Periodicity of DNA folding in higher order chromatin structures. EMBO J. 1990;9(4):1319–1327
  29. Martelli AM, Bareggi R, Bortul R, Grill V, Narducci P, Zweyer M. The nuclear matrix and apoptosis. Histochem. Cell. Biol. 1997;108(1):1–10
  30. Brown DG, Sun XM, Cohen GM. Dexamethasone-induced apoptosis involves cleavage of DNA to large fragments prior to inter-nucleosomal fragmentation. J. Biol. Chem. 1993;268(5):3037–3039
  31. Anzai N, Kawabata H, Hirama T, Masutani H, Ueda Y, Yoshida Y, et al. Types of nuclear endonuclease activity capable of inducing internucleosomal DNA fragmentation are completely different between human cd34+ cells and their granulocytic descendants. Blood. 1995;86(3):917–923
  32. Huang HS, Matevossian A, Jiang Y, Akbarian S. Chromatin immunoprecipitation in postmortem brain. J. Neurosci. Methods. 2006;156(1–2):284–292
  33. Huang P, Ballal K, Plunkett W. Biochemical characterization of the protein activity responsible for high molecular weight DNA fragmentation during drug-induced apoptosis. Cancer Res. 1997;57(16):3407–3414
  34. Walker PR, Pandey S, Sikorska M. Degradation of chromatin in apoptotic cells. Cell Death Differ. 1995;2(2):97–104
  35. Sun XM, Cohen GM. Mg(2+)-dependent cleavage of DNA into kilobase pair fragments is responsible for the initial degradation of DNA in apoptosis. J. Biol. Chem. 1994;269(21):14857–14860
  36. Nakamura M, Sakaki Y, Watanabe N, Takagi Y. Purification and characterization of the Ca2+ plus Mg2+-dependent endodeoxyri-bonuclease from calf thymus chromatin. J. Biochem. 1981;89(1):143–152
  37. Barry MA, Eastman A. Identification of deoxyribonuclease ii as an endonuclease involved in apoptosiss. Arch Biochem. Biophys. 1993;300(1):440–450
  38. Simpson G, Roomes D, Reeves B. Successful treatment of empyema thoracis with human recombinant deoxyribonuclease. Thorax. 2003;58(4):365–366
  39. Giannakis C, Forbes IJ, Zalewski PD. Ca2+/Mg2+-dependent nuclease: tissue distribution, relationship to inter-nucleosomal DNA fragmentation and inhibition by Zn2+. Biochem. Biophys. Res. Commun. 1991;181(2):915–920
  40. Gavrieli Y, Sherman Y, Ben-Sasson SA. Identification of programmed cell death in situ via specific labeling of nuclear DNA fragmentation. J. Cell. Biol. 1992;119(3):493–501
  41. Shiokawa D, Tanuma S. Characterization of human DNAse i family endonucleases and activation of DNAse gamma during apoptosis. Biochemistry. 2001;40(1):143–152
  42. Sunaga S, Yoshimori A, Shiokawa D, Tanuma S. Structure basis for the inhibitory mechanism of a novel DNAse gamma-specific inhibitor, dr396. Bioorg. Med. Chem. 2006;14(12):4217–4226
  43. Baranovskii AG, Buneva VN, Nevinsky GA. Human deoxyribonucleases. Biochemistry (Mosc). 2004;69(6):587–601
  44. Mukae N, Enari M, Sakahira H, Fukuda Y, Inazawa J, Toh H, et al. Molecular cloning and characterization of human caspase-activated DNAse. Proc. Natl. Acad. Sci. U.S.A. 1998;95(16):9123–9128
  45. Lieberman J, Fan Z. Nuclear war: the granzyme a-bomb. Curr. Opin. Immunol. 2003;15(5):553–559
  46. Widlak P, Li LY, Wang X, Garrard WT. Action of recombinant human apoptotic endonuclease g on naked DNA and chromatin substrates: cooperation with exonuclease and DNAse i. J. Biol. Chem. 2001;276(51):48404–48409
  47. Cymerman IA, Chung I, Beckmann BM, Bujnicki JM, Meiss G. Exog, a novel paralog of endonuclease g in higher eukaryotes. Nucleic Acids Res. 2008;36(4):1369–1379
  48. Antheunisse J. DNA decomposition by soil microorganisms. Antonie Van Leeuwenhoek. 1971;37(2):258–259
  49. Antheunisse J. Decomposition of nucleic acids and some of their degradation products by microorganisms. Antonie Van Leeuwenhoek. 1972;38(3):311–327
  50. Nedwell DB. The input and mineralization of organic carbon in anaerobic sediments. In:  Marshal KC editors. In Advances in Microbial Ecology, vol. 7. New York and London: Plenum Press; 1984;p. 93–131
  51. Eglinton G, Logan GA. Molecular preservation. Philos. Trans. R. Soc. Lond. B: Biol. Sci. 1991;333(1268):315–327
  52. Gotherstrom A, Collins MJ, Angerbjrn A, Lidn K. Bone preservation and DNA amplification. Archaeometry. 2002;44(3):395–404
  53. Paabo S, Poinar H, Serre D, Jaenicke-Despres V, Hebler J, Roh-land N, et al. Genetic analyses from ancient DNA. Annu. Rev. Genet. 2004;38:645–679
  54. Serpersu EH, Shortle D, Mildvan AS. Kinetic and magnetic resonance studies of active-site mutants of staphylococcal nuclease: factors contributing to catalysis. Biochemistry. 1987;26(5):1289–1300
  55. Crine P, Verly WG. A study of DNA spontaneous degradation. Biochim. Biophys. Acta. 1976;442(1):50–57
  56. Tamm C, Shapiro HS, Lipshitz R, Chargaff E. Distribution density of nucleotides within a desoxyribonucleic acid chain. J. Biol. Chem. 1953;203(2):673–688
  57. Donald Mr Mc BP, Kaufmann . The degradation by ribonuclease of substrates other than ribonucleic acid. J. Histochem. Cytochem. 1954;2(5):387–394
  58. Lindahl T, Andersson A. Rate of chain breakage at apurinic sites in double-stranded deoxyribonucleic acid. Biochemistry. 1972;11(19):3618–3623
  59. Lindahl T, Nyberg B. Rate of depurination of native deoxyribonucleic acid. Biochemistry. 1972;11(19):3610–3618
  60. Geigl EM. On the circumstances surrounding the preservation and analysis of very old DNA. Archaeometry. 2002;44:337–342
  61. Paabo S. Ancient DNA: extraction, characterization, molecular cloning, and enzymatic amplification. Proc. Natl. Acad. Sci. U.S.A. 1989;86(6):1939–1943
  62. Sancar A, Lindsey-Boltz LA, Unsal-Kacmaz K, Linn S. Molecular mechanisms of mammalian DNA repair and the DNA damage checkpoints. Annu. Rev. Biochem. 2004;73:39–85
  63. Freese E, Cashel M. Crosslinking of deoxyribonucleic acid by exposure to low ph. Biochim. Biophys. Acta. 1964;91:67–77
  64. Goffin C, Verly WG. Interstrand DNA crosslinks due to ap (apurinic/apyrimidinic) sites. FEBS Lett. 1983;161(1):140–144
  65. Dutta U, Cohenford MA, Dain JA. Nonenzymatic glycation of DNA nucleosides with reducing sugars. Anal. Biochem. 2005;345(2):171–180
  66. Seidel W, Pischetsrieder M. DNA-glycation leads to depurination by the loss of n2-carboxyethylguanine in vitro. Cell. Mol. Biol. (Noisy-le-grand). 1998;44(7):1165–1170
  67. Teoule R, Cadet J. In:  Bertinchamps AJ,  Hutterman J,  Kohnlein W,  Teoule R editor. Effects of Ionizing Radiation on DNA. Berlin: Springer; 1978;p. 171–203
  68. Hoss M, Jaruga P, Zastawny TH, Dizdaroglu M, Paabo S. DNA damage and DNA sequence retrieval from ancient tissues. Nucleic Acids Res. 1996;24(7):1304–1307
  69. Hall A, Ballantyne J. Characterization of uvc-induced DNA damage in bloodstains: forensic implications. Anal. Bioanal. Chem. 2004;380(1):72–83
  70. Butler JM. Forensic DNA Typing: Biology, Technology, and Genetics of STR Markers. 2nd ed.. New York: Elsevier Academic Press; 2005;
  71. Sobrino B, Brion M, Carracedo A. SNPs in forensic genetics: a review on SNP typing methodologies. Forensic Sci. Int. 2005;154(2–3):181–194
  72. Fattorini P, Ciofuli R, Cossutta F, Giulianini P, Edomi P, Furlanut M, et al. Fidelity of polymerase chain reaction-direct sequencing analysis of damaged forensic samples. Electrophoresis. 1999;20(17):3349–3357
  73. Sparkes R, Kimpton C, Gilbard S, Carne P, Andersen J, Ol-droyd N, et al. The validation of a 7-locus multiplex STR test for use in forensic casework. (ii). Artefacts, casework studies and success rates. Int. J. Legal Med. 1996;109(4):195–204
  74. Alonso A, Martin P, Albarran C, Garcia P, Primorac D, Garcia O, et al. Specific quantification of human genomes from low copy number DNA samples in forensic and ancient DNA studies. Croat. Med. J. 2003;44(3):273–280
  75. Krenke BE, Tereba A, Anderson SJ, Buel E, Culhane S, Finis CJ, et al. Validation of a 16-locus fluorescent multiplex system. J. Forensic Sci. 2002;47(4):773–785
  76. Irwin JA, Leney MD, Loreille O, Barritt SM, 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):1322–1327
  77. Takahashi M, Kato Y, Mukoyama H, Kanaya H, Kamiyama S. Evaluation of five polymorphic microsatellite markers for typing DNA from decomposed human tissues-correlation between the size of the alleles and that of the template DNA. Forensic Sci. Int. 1997;90(1–2):1–9
  78. Chung DT, Drabek J, Opel KL, Butler JM, McCord BR. A study on the effects of degradation and template concentration on the amplification efficiency of the STR miniplex primer sets. J. Forensic Sci. 2004;49(4):733–740
  79. Butler JM, Shen Y, McCord BR. The development of reduced size STR amplicons as tools for analysis of degraded DNA. J. Forensic Sci. 2003;48(5):1054–1064
  80. Butler JM, Levin BC. Forensic applications of mitochondrial DNA. Trends Biotechnol. 1998;16(4):158–162
  81. J.M. Butler, C.H. Becker, Improved analysis of DNA short tandem repeats with time-of-flight mass spectrometry, Technical Report, National Institute of Justice, 2001.
  82. Schmalzing D, Koutny L, Adourian A, Belgrader P, Matsudaira P, Ehrlich D. DNA typing in thirty seconds with a microfabricated device. Proc. Natl. Acad. Sci. U.S.A. 1997;94(19):10273–10278
  83. Gill P. An assessment of the utility of single nucleotide polymorphisms (SNPs) for forensic purposes. Int. J. Legal Med. 2001;114(4–5):204–210
  84. Onori N, Onofri V, Alessandrini F, Buscemi L, Pesaresi M, Turchi C, et al. Post-mortem DNA damage: a comparative study of STRs and SNPs typing efficiency in simulated forensic samples. In: In International Congress Series, volume 1288. 2006;p. 510–512
  85. Bogenhagen D, Clayton DA. The number of mitochondrial deoxyribonucleic acid genomes in mouse l and human hela cells. quantitative isolation of mitochondrial deoxyribonucleic acid. J. Biol. Chem. 1974;249(24):7991–7995
  86. Robin ED, Wong R. Mitochondrial DNA molecules and virtual number of mitochondria per cell in mammalian cells. J. Cell. Physiol. 1988;136(3):507–513
  87. Andelinovic S, Sutlovic D, Erceg Ivkosic I, Skaro V, Ivkosic A, Paic F, et al. Twelve-year experience in identification of skeletal remains from mass graves. Croat. Med. J. 2005;46(4):530–539
  88. 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):83–86
  89. Gabriel MN, Calloway CD, Reynolds RL, Primorac D. Identification of human remains by immobilized sequence-specific oligonu-cleotide probe analysis of mtDNA hypervariable regions i and ii. Croat. Med. J. 2003;44(3):293–298
  90. Seo Y, Uchiyama T, Shimizu K, Takahama K. Identification of remains by sequencing of mitochondrial DNA control region. Am. J. Forensic Med. Pathol. 2000;21(2):138–143
  91. Lutz S, Weisser HJ, Heizmann J, Pollak S. mtDNA as a tool for identification of human remains. identification using mtDNA. Int. J. Legal Med. 1996;109(4):205–209
  92. 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):542–553
  93. Mornstad H, Pfeiffer H, Yoon C, Teivens A. Demonstration and semi-quantification of mtDNA from human dentine and its relation to age. Int. J. Legal Med. 1999;112(2):98–100
  94. Yamada Y, Ohira H, Iwase H, Takatori T, Nagao M, Ohtani S. Sequencing mitochondrial DNA from a tooth and application to forensic odontology. J. Forensic Odontostomatol. 1997;15(1):13–16
  95. Ginther C, Issel-Tarver L, King MC. Identifying individuals by sequencing mitochondrial DNA from teeth. Nat. Genet. 1992;2(2):135–138
  96. 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;48(2):328–333
  97. Melton T, Nelson K. Forensic mitochondrial DNA analysis: two years of commercial casework experience in the united states. Croat. Med. J. 2001;42(3):298–303
  98. Arezi B, Xing W, Sorge JA, Hogrefe HH. Amplification efficiency of thermostable DNA polymerases. Anal. Biochem. 2003;321(2):226–235
  99. Utsuno H, Minaguchi K. Influence of template DNA degradation on the genotyping of SNPs and STR polymorphisms from forensic materials by PCR. Bull. Tokyo Dent. Coll. 2004;45(1):33–46
  100. Poinar HN. The top 10 list: criteria of authenticity for DNA from ancient and forensic samples. Prog. Forensics Genet. 2003;9:575–579
  101. Gill P. Application of low copy number DNA profiling. Croat. Med. J. 2001;42(3):229–232
  102. Taberlet P, Griffin S, Goossens B, Questiau S, Manceau V, Es-caravage N, et al. Reliable genotyping of samples with very low DNA quantities using PCR. Nucleic Acids Res. 1996;24(16):3189–3194
  103. B. Budowle, D. Hobson, J. Smerick, J. Smith, Low copy number: consideration and caution, In Twelfth International Symposium on Human Identification, 2001. Available on: http://www.promega.com.
  104. Strom CM, Rechitsky S. Use of nested PCR to identify charred human remains and minute amounts of blood. J. Forensic Sci. 1998;43(3):696–700
  105. Hanson EK, Ballantyne J. Whole genome amplification strategy for forensic genetic analysis using single or few cell equivalents of genomic DNA. Anal. Biochem. 2005;346(2):246–257
  106. Smith PJ, Ballantyne J. Simplified low-copy-number DNA analysis by post-PCR purification. J. Forensic Sci. 2007;52(4):820–829
  107. Di Bernardo G, Del Gaudio S, Cammarota M, Gaiderisi U, Cas-cino A, Cipollaro M. Enzymatic repair of selected cross-linked ho-moduplex molecules enhances nuclear gene rescue from pompeii and herculaneum remains. Nucleic Acids Res. 2002;30(4):e16
  108. Budowle BA, Eisenberg J, van Daal A. Validity of low copy number typing and applications to forensic science. Croat. Med. J. 2009;50(3):207–217
  109. Handt O, Krings M, Ward RH, Paabo S. The retrieval of ancient human DNA sequences. Am. J. Hum. Genet. 1996;59(2):368–376
  110. Heid CA, Stevens J, Livak KJ, Williams PM. Real time quantitative PCR. Genome Res. 1996;6(10):986–994
  111. Walsh PS, Erlich HA, Higuchi R. Preferential PCR amplification of alleles: mechanisms and solutions. PCR Methods Appl. 1992;1(4):241–250
  112. 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;18(4):670–677
  113. Wiegand P, Kleiber M. Less is more-length reduction of STR amplicons using redesigned primers. Int. J. Legal Med. 2001;114(4–5):285–287
  114. Dixon LA, Dobbins AE, Pulker HK, Butler JM, Val-lone 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
  115. Yoshida K, Sekiguchi K, Kasai K, Sato H, Seta S, Sens-abaugh GF. Evaluation of new primers for csf1po. Int. J. Legal Med. 1997;110(1):36–38
  116. Saiki RK, Gelfand DH, Stoffel S, Scharf SJ, Higuchi R, Horn GT, et al. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science. 1988;239(4839):487–491
  117. Keohavong P, Thilly WG. Fidelity of DNA polymerases in DNA amplification. Proc. Natl. Acad. Sci. U.S.A. 1989;86(23):9253–9257
  118. Eckert KA, Kunkel TA. DNA polymerase fidelity and the polymerase chain reaction. PCR Methods Appl. 1991;1(1):17–24
  119. Gilbert MT, Binladen J, Miller W, Wiuf C, Willerslev E, Poinar H, et al. Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis. Nucleic Acids Res. 2007;35(1):1–10
  120. Hoff-Olsen P, Jacobsen S, Mevag B, Olaisen B. Microsatellite stability in human post-mortem tissues. Forensic Sci. Int. 2001;119(3):273–278
  121. Hansen A, Willerslev E, Wiuf C, Mourier T, Arctander P. Statistical evidence for miscoding lesions in ancient DNA templates. Mol. Biol. Evol. 2001;18(2):262–265
  122. Willerslev E, Hansen AJ, Christensen B, Steffensen JP, Arctander P. Diversity of holocene life forms in fossil glacier ice. Proc. Natl. Acad. Sci. U.S.A. 1999;96(14):8017–8021
  123. Cooper A, Lalueza-Fox C, Anderson S, Rambaut A, Austin J, Ward R. Complete mitochondrial genome sequences of two extinct moas clarify ratite evolution. Nature. 2001;409(6821):704–707
  124. Pusch CM, Nicholson GJ, Bachmann L, Scholz M. Degenerate oligonucleotide-primed preamplification of ancient DNA allows the retrieval of authentic DNA sequences. Anal. Biochem. 2000;279(1):118–122
  125. Zhang L, Cui X, Schmitt K, Hubert R, Navidi W, Arnheim N. Whole genome amplification from a single cell: implications for genetic analysis. Proc. Natl. Acad. Sci. U.S.A. 1992;89(13):5847–5851
  126. Satoh K, Takahashi K, Itoh Y, Kobayashi R. Typing of DNA using the primer extension preamplification (pep) method-studies of reliability of typing and detection limits. Nihon Hoigaku Zasshi. 1998;52(3):184–190
  127. Lawlor DA, Dickel CD, Hauswirth WW, Parham P. Ancient hla genes from 7,500-year-old archaeological remains. Nature. 1991;349(6312):785–788
  128. Handt O, Richards M, Trommsdorff M, Kilger C, Simanainen J, Georgiev O, et al. Molecular genetic analyses of the tyrolean ice man. Science. 1994;264(5166):1775–1778
  129. Wilson IG. Inhibition and facilitation of nucleic acid amplification. Appl. Environ. Microbiol. 1997;63(10):3741–3751
  130. Pusch CM, Giddings I, Scholz M. Repair of degraded duplex DNA from prehistoric samples using Escherichia coli DNA polymerase i and t4 DNA ligase. Nucleic Acids Res. 1998;26(3):857–859
  131. Dean FB, Hosono S, Fang L, Wu X, Faruqi AF, Bray-Ward P, et al. Comprehensive human genome amplification using multiple displacement amplification. Proc. Natl. Acad. Sci. U.S.A. 2002;99(8):5261–5266
  132. Vasan S, Zhang X, Kapurniotu A, Bernhagen J, Teichberg S, Basgen J, et al. An agent cleaving glucose-derived protein crosslinks in vitro and in vivo. Nature. 1996;382(6588):275–278
  133. Poinar HN, Hofreiter M, Spaulding WG, Martin PS, Stankiewicz BA, Bland H, et al. Molecular coproscopy: dung and diet of the extinct ground sloth nothrotheriops shastensis. Science. 1998;281(5375):402–406
  134. Kemp BM, Monroe C, Smith DG. Repeat silica extraction: a simple technique for the removal of PCR inhibitors from DNA extracts. J. Archaeol. Sci. 2006;33(12):1680–1689
  135. J.L. Bada, X.S. Wang, H. Hamilton, Preservation of key biomolecules in the fossil record: current knowledge and future challenges, Philos. Trans. R. Soc. Lond. B: Biol. Sci. 354 (1379) (1999) 7787.
  136. Willerslev E, Hansen AJ, Poinar HN. Isolation of nucleic acids and cultures from fossil ice and permafrost. Trends Ecol. Evol. 2004;19(3):141–147
  137. Willerslev E, Cooper A. Ancient DNA. Proc. Biol. Sci. 2005;272(1558):3–16
  138. Tabatabai MA. Soil enzymes. In:  Miller RH,  Keeney DR editor. Methods of Soil Analysis. 2nd ed.. Madison, WI: American Society of Agronomy Soil Science Society of America; 1982;p. 903–947
  139. Ludes B, Pfitzinger H, Mangin P. DNA fingerprinting from tissues after variable postmortem periods. J. Forensic Sci. 1993;38(3):686–690
  140. Parsons TJ, Weedn VW. Chemical and ultrastructural aspects of decomposition. In:  Haglund WD,  Sorg MH editor. Forensic Taphonomy: The Post-mortem Fate of Human Remains. Robert B. Stern, CRC press, Inc.; 1997;p. 93–108
  141. van Bergen PF, Bland HA, Horton MC, Evershed RP. Chemical and morphological changes in archaeological seeds and fruits during preservation by desiccation. Geochim. Cosmochim. Acta. 1997;61:1919–1930
  142. Poinar HN, Stankiewicz BA. Protein preservation and DNA retrieval from ancient tissues. Proc. Natl. Acad. Sci. U.S.A. 1999;96(15):8426–8431
  143. Romanowski G, Lorenz MG, Wackernagel W. Adsorption of plasmid DNA to mineral surfaces and protection against DNAse i. Appl. Environ. Microbiol. 1991;57(4):1057–1061
  144. Rydberg B. The rate of strand separation in alkali of DNA of irradiated mammalian cells. Radiat. Res. 1975;61(2):274–287
  145. Kanter PM, Schwartz HS. A fluorescence enhancement assay for cellular DNA damage. Mol. Pharmacol. 1982;22(1):145–151
  146. Kohn KW, Erickson LC, Ewig RA, Friedman CA. Fractionation of DNA from mammalian cells by alkaline elution. Biochemistry. 1976;15(21):4629–4637
  147. Batel R, Jaksic Z, Bihari N, Hamer B, Fafandel M, Chauvin C, et al. A microplate assay for DNA damage determination (fast micromethod). Anal. Biochem. 1999;270(2):195–200
  148. Jaksic Z, Batel R. DNA integrity determination in marine invertebrates by fast micromethod. Aquat. Toxicol. 2003;65(4):361–376
  149. Dhawan A, Bajpayee M, Parmar D. Comet assay: a reliable tool for the assessment of DNA damage in different models. Cell Biol. Toxicol. 2009;25(1):5–32
  150. Kalinowski DP, Illenye S, Van Houten B. Analysis of DNA damage and repair in murine leukemia l1210 cells using a quantitative polymerase chain reaction assay. Nucleic Acids Res. 1992;20(13):3485–3494
  151. Swango KL, Timken MD, Chong MD, Buoncristiani MR. A quantitative PCR assay for the assessment of DNA degradation in forensic samples. Forensic Sci. Int. 2006;158(1):14–26
  152. Dobbs LJ, Madigan MN, Carter AB, Earls L. Use of fta gene guard filter paper for the storage and transportation of tumor cells for molecular testing. Arch. Pathol. Lab. Med. 2002;126(1):56–63
  153. Alonso A, Martin P, Albarran C, Garcia P, Garcia O, de Simon LF, et al. Real-time PCR designs to estimate nuclear and mitochondrial DNA copy number in forensic and ancient DNA studies. Forensic Sci. Int. 2004;139(2–3):141–149
  154. Johnson LA, Ferris JA. Analysis of postmortem DNA degradation by single-cell gel electrophoresis. Forensic Sci. Int. 2002;126(1):43–47
  155. Zhen JL, Zhang XD, Niu QS. Relationship between the postmortem interval and nuclear DNA changes of heart muscular cells in mice. Fa Yi Xue Za Zhi. 2006;22(3):173–176

PII: S1872-4973(09)00148-3

doi: 10.1016/j.fsigen.2009.09.007

Forensic Science International: Genetics
Volume 4, Issue 3 , Pages 148-157 , April 2010

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