Forensic implications of genetic analyses from degraded DNA-A review

Forensic Science International: Genetics

Volumn 4, Issue 3, 2010, Pages 148-157

  Alaeddini, Reza ^a   Walsh, Simon J ^b   Abbas, Ali ^a  

^a UNIVERSITY OF SYDNEY   (Australia)

^b Forensic and Data Centres   (Australia)

Author keywords

Cell death; Deoxyribonuclease; DNA degradation; Forensics; PCR

Indexed keywords

ANALYTIC METHOD; DECOMPOSITION; DNA DEGRADATION; DNA DETERMINATION; DNA SEQUENCE; DNA TEMPLATE; FORENSIC GENETICS; GENETIC ANALYSIS; HUMAN; OUTCOME ASSESSMENT; PRIORITY JOURNAL; REVIEW;

CELL DEATH; DNA; DNA DAMAGE; DNA DEGRADATION, NECROTIC; DNA FINGERPRINTING; DNA FRAGMENTATION; HUMANS; OXIDATIVE STRESS; POLYMERASE CHAIN REACTION; POSTMORTEM CHANGES;

EID: 77649340438     PISSN: 18724973     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.fsigen.2009.09.007     Document Type: Review

References (155)

1. Lindahl T. The croonian lecture, 1996: endogenous damage to DNA. Philos. Trans. R. Soc. Lond. B: Biol. Sci. 351 1347 (1996) 1529-1538
2. A.A. Vass, Beyond the grave understanding human decomposition, 2001.
3. Jennings R.B., Ganote C.E., and Reimer K.A. Ischemic tissue injury. Am. J. Pathol. 81 1 (1975) 179-198
4. Ilse G., Kovacs K., Ryan N., Horvath E., and Ilse D. Autolytic changes in the rat adenohypophysis. A histologic, immunocytologic and electron microscopic study. Exp. Pathol. (Jena) 17 4 (1979) 185-195
5. Zeiss C.J. The apoptosis-necrosis continuum: insights from genetically altered mice. Vet. Pathol. 40 5 (2003) 481-495
6. Shimizu S., Eguchi Y., Kosaka H., Kamiike W., Matsuda H., and Tsujimoto Y. Prevention of hypoxia-induced cell death by bcl-2 and bcl-xl. Nature 374 6525 (1995) 811-813
7. Collan Y., and Salmenpera M. Electron microscopy of postmortem autolysis of rat muscle tissue. Acta Neuropathol. 35 3 (1976) 219-233
8. Dive C., Gregory C.D., Phipps D.J., Evans D.L., Milner A.E., and Wyllie A.H. Analysis and discrimination of necrosis and apoptosis (programmed cell-death) by multiparameter flow-cytometry. Biochim. Biophys. Acta 1133 3 (1992) 275-285
9. Krysko D.V., Vanden Berghe T., D'Herde K., and Vandenabeele P. Apoptosis and necrosis: detection, discrimination and phagocytosis. Methods 44 3 (2008) 205-221
10. Gill-King H. Chemical and ultrastructural aspects of decomposition. In: Haglund M.H., and Sorg W.D. (Eds). Forensic Taphonomy: The Postmortem Fate of Human Remains (1997), Robert B. Stern, CRC press, Inc. 93-108
11. Tomita Y., Nihira M., Ohno Y., and Sato S. Ultrastructural changes during in situ early postmortem autolysis in kidney, pancreas, liver, heart and skeletal muscle of rats. Leg. Med. (Tokyo) 6 1 (2004) 25-31
12. Nicotera P., and Leist M. Energy supply and the shape of death in neurons and lymphoid cells. Cell Death Differ. 4 6 (1997) 435-442
13. Tsujimoto Y. Apoptosis and necrosis: intracellular atp level as a determinant for cell death modes. Cell Death Differ. 4 6 (1997) 429-434
14. Trump B.F., and Berezesky I.K. Calcium-mediated cell injury and cell death. FASEB J. 9 2 (1995) 219-228
15. Reimer K.A., Lowe J.E., and Jennings R.B. Effect of the calcium antagonist verapamil on necrosis following temporary coronary artery occlusion in dogs. Circulation 55 4 (1977) 581-587
16. Hajnoczky G., Davies E., and Madesh M. Calcium signaling and apoptosis. Biochem. Biophys. Res. Commun. 304 3 (2003) 445-454
17. Kroemer G., Galluzzi L., and Brenner C. Mitochondrial membrane permeabilization in cell death. Physiol. Rev. 87 1 (2007) 99-163
18. Jambrina E., Alonso R., Alcalde M., del Carmen Rodriguez M., Serrano A., Martinez A.C., Garcia-Sancho J., and Izquierdo M. Calcium influx through receptor-operated channel induces mitochondria-triggered paraptotic cell death. J. Biol. Chem. 278 16 (2003) 14134-14145
19. De Duve C., and Wattiaux R. Functions of lysosomes. Annu. Rev. Physiol. 28 (1966) 435-492
20. Lindahl T. Instability and decay of the primary structure of DNA. Nature 362 6422 (1993) 709-715
21. Hofreiter M., Jaenicke V., Serre D., Haeseler Av A., and Paabo S. DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA. Nucleic Acids Res. 29 23 (2001) 4793-4799
22. Yuyama K., Yamamoto H., Nishizaki I., Kato T., Sora I., and 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. 73 3 (2003) 351-363
23. Donovan M., and Cotter T.G. Caspase-independent photoreceptor apoptosis in vivo and differential expression of apoptotic protease activating factor-1 and caspase-3 during retinal development. Cell Death Differ. 9 11 (2002) 1220-1231
24. Counis M.F., and Torriglia A. Acid DNAses and their interest among apoptotic endonucleases. Biochimie 88 12 (2006) 1851-1858
25. Chien K.R., Abrams J., Serroni A., Martin J.T., and Far-ber J.L. Accelerated phospholipid degradation and associated membrane dysfunction in irreversible, ischemic liver cell injury. J. Biol. Chem. 253 13 (1978) 4809-4817
26. Ayala-Torres S., Chen Y., Svoboda T., Rosenblatt J., Van B., and Houten. Analysis of gene-specific DNA damage and repair using quantitative polymerase chain reaction. Methods 22 2 (2000) 135-147
27. Hofreiter M., Serre D., Poinar H.N., Kuch M., and Paabo S. Ancient DNA. Nat. Rev. Genet. 2 5 (2001) 353-359
28. Filipski J., Leblanc J., Youdale T., Sikorska M., and Walker P.R. Periodicity of DNA folding in higher order chromatin structures. EMBO J. 9 4 (1990) 1319-1327
29. Martelli A.M., Bareggi R., Bortul R., Grill V., Narducci P., and Zweyer M. The nuclear matrix and apoptosis. Histochem. Cell. Biol. 108 1 (1997) 1-10
30. Brown D.G., Sun X.M., and Cohen G.M. Dexamethasone-induced apoptosis involves cleavage of DNA to large fragments prior to inter-nucleosomal fragmentation. J. Biol. Chem. 268 5 (1993) 3037-3039
31. Anzai N., Kawabata H., Hirama T., Masutani H., Ueda Y., Yoshida Y., and Okuma M. Types of nuclear endonuclease activity capable of inducing internucleosomal DNA fragmentation are completely different between human cd34+ cells and their granulocytic descendants. Blood 86 3 (1995) 917-923
32. Huang H.S., Matevossian A., Jiang Y., and Akbarian S. Chromatin immunoprecipitation in postmortem brain. J. Neurosci. Methods 156 1-2 (2006) 284-292
33. Huang P., Ballal K., and Plunkett W. Biochemical characterization of the protein activity responsible for high molecular weight DNA fragmentation during drug-induced apoptosis. Cancer Res. 57 16 (1997) 3407-3414
34. Walker P.R., Pandey S., and Sikorska M. Degradation of chromatin in apoptotic cells. Cell Death Differ. 2 2 (1995) 97-104
35. Sun X.M., and Cohen G.M. Mg(2+)-dependent cleavage of DNA into kilobase pair fragments is responsible for the initial degradation of DNA in apoptosis. J. Biol. Chem. 269 21 (1994) 14857-14860
36. 2+-dependent endodeoxyri-bonuclease from calf thymus chromatin. J. Biochem. 89 1 (1981) 143-152
37. Barry M.A., and Eastman A. Identification of deoxyribonuclease ii as an endonuclease involved in apoptosiss. Arch Biochem. Biophys. 300 1 (1993) 440-450
38. Simpson G., Roomes D., and Reeves B. Successful treatment of empyema thoracis with human recombinant deoxyribonuclease. Thorax 58 4 (2003) 365-366
39. 2+. Biochem. Biophys. Res. Commun. 181 2 (1991) 915-920
40. Gavrieli Y., Sherman Y., and Ben-Sasson S.A. Identification of programmed cell death in situ via specific labeling of nuclear DNA fragmentation. J. Cell. Biol. 119 3 (1992) 493-501
41. Shiokawa D., and Tanuma S. Characterization of human DNAse i family endonucleases and activation of DNAse gamma during apoptosis. Biochemistry 40 1 (2001) 143-152
42. Sunaga S., Yoshimori A., Shiokawa D., and Tanuma S. Structure basis for the inhibitory mechanism of a novel DNAse gamma-specific inhibitor, dr396. Bioorg. Med. Chem. 14 12 (2006) 4217-4226
43. Baranovskii A.G., Buneva V.N., and Nevinsky G.A. Human deoxyribonucleases. Biochemistry (Mosc) 69 6 (2004) 587-601
44. Mukae N., Enari M., Sakahira H., Fukuda Y., Inazawa J., Toh H., and Nagata S. Molecular cloning and characterization of human caspase-activated DNAse. Proc. Natl. Acad. Sci. U.S.A. 95 16 (1998) 9123-9128
45. Lieberman J., and Fan Z. Nuclear war: the granzyme a-bomb. Curr. Opin. Immunol. 15 5 (2003) 553-559
46. Widlak P., Li L.Y., Wang X., and Garrard W.T. Action of recombinant human apoptotic endonuclease g on naked DNA and chromatin substrates: cooperation with exonuclease and DNAse i. J. Biol. Chem. 276 51 (2001) 48404-48409
47. Cymerman I.A., Chung I., Beckmann B.M., Bujnicki J.M., and Meiss G. Exog, a novel paralog of endonuclease g in higher eukaryotes. Nucleic Acids Res. 36 4 (2008) 1369-1379
48. Antheunisse J. DNA decomposition by soil microorganisms. Antonie Van Leeuwenhoek 37 2 (1971) 258-259
49. Antheunisse J. Decomposition of nucleic acids and some of their degradation products by microorganisms. Antonie Van Leeuwenhoek 38 3 (1972) 311-327
50. Nedwell D.B. The input and mineralization of organic carbon in anaerobic sediments. In: Marshal K.C. (Ed). In Advances in Microbial Ecology, vol. 7 (1984), Plenum Press, New York and London 93-131
51. Eglinton G., and Logan G.A. Molecular preservation. Philos. Trans. R. Soc. Lond. B: Biol. Sci. 333 1268 (1991) 315-327
52. Gotherstrom A., Collins M.J., Angerbjrn A., and Lidn K. Bone preservation and DNA amplification. Archaeometry 44 3 (2002) 395-404
53. Paabo S., Poinar H., Serre D., Jaenicke-Despres V., Hebler J., Roh-land N., Kuch M., Krause J., Vigilant L., and Hofreiter M. Genetic analyses from ancient DNA. Annu. Rev. Genet. 38 (2004) 645-679
54. Serpersu E.H., Shortle D., and Mildvan A.S. Kinetic and magnetic resonance studies of active-site mutants of staphylococcal nuclease: factors contributing to catalysis. Biochemistry 26 5 (1987) 1289-1300
55. Crine P., and Verly W.G. A study of DNA spontaneous degradation. Biochim. Biophys. Acta 442 1 (1976) 50-57
56. Tamm C., Shapiro H.S., Lipshitz R., and Chargaff E. Distribution density of nucleotides within a desoxyribonucleic acid chain. J. Biol. Chem. 203 2 (1953) 673-688
57. Donald Mr Mc B.P., and Kaufmann. The degradation by ribonuclease of substrates other than ribonucleic acid. J. Histochem. Cytochem. 2 5 (1954) 387-394
58. Lindahl T., and Andersson A. Rate of chain breakage at apurinic sites in double-stranded deoxyribonucleic acid. Biochemistry 11 19 (1972) 3618-3623
59. Lindahl T., and Nyberg B. Rate of depurination of native deoxyribonucleic acid. Biochemistry 11 19 (1972) 3610-3618
60. Geigl E.M. On the circumstances surrounding the preservation and analysis of very old DNA. Archaeometry 44 (2002) 337-342
61. Paabo S. Ancient DNA: extraction, characterization, molecular cloning, and enzymatic amplification. Proc. Natl. Acad. Sci. U.S.A. 86 6 (1989) 1939-1943
62. Sancar A., Lindsey-Boltz L.A., Unsal-Kacmaz K., and Linn S. Molecular mechanisms of mammalian DNA repair and the DNA damage checkpoints. Annu. Rev. Biochem. 73 (2004) 39-85
63. Freese E., and Cashel M. Crosslinking of deoxyribonucleic acid by exposure to low ph. Biochim. Biophys. Acta 91 (1964) 67-77
64. Goffin C., and Verly W.G. Interstrand DNA crosslinks due to ap (apurinic/apyrimidinic) sites. FEBS Lett. 161 1 (1983) 140-144
65. Dutta U., Cohenford M.A., and Dain J.A. Nonenzymatic glycation of DNA nucleosides with reducing sugars. Anal. Biochem. 345 2 (2005) 171-180
66. Seidel W., and Pischetsrieder M. DNA-glycation leads to depurination by the loss of n2-carboxyethylguanine in vitro. Cell. Mol. Biol. (Noisy-le-grand) 44 7 (1998) 1165-1170
67. Teoule R., and Cadet J. In: Bertinchamps A.J., Hutterman J., Kohnlein W., and Teoule R. (Eds). Effects of Ionizing Radiation on DNA (1978), Springer, Berlin 171-203
68. Hoss M., Jaruga P., Zastawny T.H., Dizdaroglu M., and Paabo S. DNA damage and DNA sequence retrieval from ancient tissues. Nucleic Acids Res. 24 7 (1996) 1304-1307
69. Hall A., and Ballantyne J. Characterization of uvc-induced DNA damage in bloodstains: forensic implications. Anal. Bioanal. Chem. 380 1 (2004) 72-83
70. Butler J.M. Forensic DNA Typing: Biology, Technology, and Genetics of STR Markers. 2nd ed. (2005), Elsevier Academic Press, New York
71. Sobrino B., Brion M., and Carracedo A. SNPs in forensic genetics: a review on SNP typing methodologies. Forensic Sci. Int. 154 2-3 (2005) 181-194
72. Fattorini P., Ciofuli R., Cossutta F., Giulianini P., Edomi P., Furlanut M., and Previdere C. Fidelity of polymerase chain reaction-direct sequencing analysis of damaged forensic samples. Electrophoresis 20 17 (1999) 3349-3357
73. Sparkes R., Kimpton C., Gilbard S., Carne P., Andersen J., Ol-droyd N., Thomas D., Urquhart A., and Gill P. 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. 109 4 (1996) 195-204
74. Alonso A., Martin P., Albarran C., Garcia P., Primorac D., Garcia O., Fernandez de Simon L., Garcia-Hirschfeld J., Sancho M., and Fernandez-Piqueras J. Specific quantification of human genomes from low copy number DNA samples in forensic and ancient DNA studies. Croat. Med. J. 44 3 (2003) 273-280
75. Krenke B.E., Tereba A., Anderson S.J., Buel E., Culhane S., Finis C.J., Tomsey C.S., Zachetti J.M., Masibay A., Rabbach D.R., Amiott E.A., and Sprecher C.J. Validation of a 16-locus fluorescent multiplex system. J. Forensic Sci. 47 4 (2002) 773-785
76. Irwin J.A., Leney M.D., Loreille O., Barritt S.M., Christensen A.F., Holland T.D., Smith B.C., and Parsons T.J. Application of low copy number STR typing to the identification of aged, degraded skeletal remains. J. Forensic Sci. 52 6 (2007) 1322-1327
77. Takahashi M., Kato Y., Mukoyama H., Kanaya H., and 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. 90 1-2 (1997) 1-9
78. Chung D.T., Drabek J., Opel K.L., Butler J.M., and McCord B.R. A study on the effects of degradation and template concentration on the amplification efficiency of the STR miniplex primer sets. J. Forensic Sci. 49 4 (2004) 733-740
79. Butler J.M., Shen Y., and McCord B.R. The development of reduced size STR amplicons as tools for analysis of degraded DNA. J. Forensic Sci. 48 5 (2003) 1054-1064
80. Butler J.M., and Levin B.C. Forensic applications of mitochondrial DNA. Trends Biotechnol. 16 4 (1998) 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., and Ehrlich D. DNA typing in thirty seconds with a microfabricated device. Proc. Natl. Acad. Sci. U.S.A. 94 19 (1997) 10273-10278
83. Gill P. An assessment of the utility of single nucleotide polymorphisms (SNPs) for forensic purposes. Int. J. Legal Med. 114 4-5 (2001) 204-210
84. Onori N., Onofri V., Alessandrini F., Buscemi L., Pesaresi M., Turchi C., and Tagliabracci A. Post-mortem DNA damage: a comparative study of STRs and SNPs typing efficiency in simulated forensic samples. In International Congress Series, volume 1288 (2006) 510-512
85. Bogenhagen D., and Clayton D.A. The number of mitochondrial deoxyribonucleic acid genomes in mouse l and human hela cells. quantitative isolation of mitochondrial deoxyribonucleic acid. J. Biol. Chem. 249 24 (1974) 7991-7995
86. Robin E.D., and Wong R. Mitochondrial DNA molecules and virtual number of mitochondria per cell in mammalian cells. J. Cell. Physiol. 136 3 (1988) 507-513
87. Andelinovic S., Sutlovic D., Erceg Ivkosic I., Skaro V., Ivkosic A., Paic F., Rezic B., Definis-Gojanovic M., and Primorac D. Twelve-year experience in identification of skeletal remains from mass graves. Croat. Med. J. 46 4 (2005) 530-539
88. Sullivan K.M., Hopgood R., and Gill P. Identification of human remains by amplification and automated sequencing of mitochondrial DNA. Int. J. Legal Med. 105 2 (1992) 83-86
89. Gabriel M.N., Calloway C.D., Reynolds R.L., and Primorac D. Identification of human remains by immobilized sequence-specific oligonu-cleotide probe analysis of mtDNA hypervariable regions i and ii. Croat. Med. J. 44 3 (2003) 293-298
90. Seo Y., Uchiyama T., Shimizu K., and Takahama K. Identification of remains by sequencing of mitochondrial DNA control region. Am. J. Forensic Med. Pathol. 21 2 (2000) 138-143
91. Lutz S., Weisser H.J., Heizmann J., and Pollak S. mtDNA as a tool for identification of human remains. identification using mtDNA. Int. J. Legal Med. 109 4 (1996) 205-209
92. Holland M.M., Fisher D.L., Mitchell L.G., Rodriquez W.C., Canik J.J., Merril C.R., and Weedn V.W. Mitochondrial DNA sequence analysis of human skeletal remains: identification of remains from the vietnam war. J. Forensic Sci. 38 3 (1993) 542-553
93. Mornstad H., Pfeiffer H., Yoon C., and Teivens A. Demonstration and semi-quantification of mtDNA from human dentine and its relation to age. Int. J. Legal Med. 112 2 (1999) 98-100
94. Yamada Y., Ohira H., Iwase H., Takatori T., Nagao M., and Ohtani S. Sequencing mitochondrial DNA from a tooth and application to forensic odontology. J. Forensic Odontostomatol. 15 1 (1997) 13-16
95. Ginther C., Issel-Tarver L., and King M.C. Identifying individuals by sequencing mitochondrial DNA from teeth. Nat. Genet. 2 2 (1992) 135-138
96. Cline R.E., Laurent N.M., and Foran D.R. The fingernails of mary sullivan: developing reliable methods for selectively isolating endogenous and exogenous DNA from evidence. J. Forensic Sci. 48 2 (2003) 328-333
97. Melton T., and Nelson K. Forensic mitochondrial DNA analysis: two years of commercial casework experience in the united states. Croat. Med. J. 42 3 (2001) 298-303
98. Arezi B., Xing W., Sorge J.A., and Hogrefe H.H. Amplification efficiency of thermostable DNA polymerases. Anal. Biochem. 321 2 (2003) 226-235
99. Utsuno H., and Minaguchi K. Influence of template DNA degradation on the genotyping of SNPs and STR polymorphisms from forensic materials by PCR. Bull. Tokyo Dent. Coll. 45 1 (2004) 33-46
100. Poinar H.N. The top 10 list: criteria of authenticity for DNA from ancient and forensic samples. Prog. Forensics Genet. 9 (2003) 575-579
101. Gill P. Application of low copy number DNA profiling. Croat. Med. J. 42 3 (2001) 229-232
102. Taberlet P., Griffin S., Goossens B., Questiau S., Manceau V., Es-caravage N., Waits L.P., and Bouvet J. Reliable genotyping of samples with very low DNA quantities using PCR. Nucleic Acids Res. 24 16 (1996) 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 C.M., and Rechitsky S. Use of nested PCR to identify charred human remains and minute amounts of blood. J. Forensic Sci. 43 3 (1998) 696-700
105. Hanson E.K., and Ballantyne J. Whole genome amplification strategy for forensic genetic analysis using single or few cell equivalents of genomic DNA. Anal. Biochem. 346 2 (2005) 246-257
106. Smith P.J., and Ballantyne J. Simplified low-copy-number DNA analysis by post-PCR purification. J. Forensic Sci. 52 4 (2007) 820-829
107. Di Bernardo G., Del Gaudio S., Cammarota M., Gaiderisi U., Cas-cino A., and Cipollaro M. Enzymatic repair of selected cross-linked ho-moduplex molecules enhances nuclear gene rescue from pompeii and herculaneum remains. Nucleic Acids Res. 30 4 (2002) e16
108. Budowle B.A., Eisenberg J., and van Daal A. Validity of low copy number typing and applications to forensic science. Croat. Med. J. 50 3 (2009) 207-217
109. Handt O., Krings M., Ward R.H., and Paabo S. The retrieval of ancient human DNA sequences. Am. J. Hum. Genet. 59 2 (1996) 368-376
110. Heid C.A., Stevens J., Livak K.J., and Williams P.M. Real time quantitative PCR. Genome Res. 6 10 (1996) 986-994
111. Walsh P.S., Erlich H.A., and Higuchi R. Preferential PCR amplification of alleles: mechanisms and solutions. PCR Methods Appl. 1 4 (1992) 241-250
112. Whitaker J.P., Clayton T.M., Urquhart A.J., Millican E.S., Downes T.J., Kimpton C.P., and Gill P. Short tandem repeat typing of bodies from a mass disaster: high success rate and characteristic amplification patterns in highly degraded samples. Biotechniques 18 4 (1995) 670-677
113. Wiegand P., and Kleiber M. Less is more-length reduction of STR amplicons using redesigned primers. Int. J. Legal Med. 114 4-5 (2001) 285-287
114. Dixon L.A., Dobbins A.E., Pulker H.K., Butler J.M., Val-lone P.M., Coble M.D., Parson W., Berger B., Grubwieser P., Mo-gensen H.S., Morling N., Nielsen K., Sanchez J.J., Petkovski E., Car-racedo A., Sanchez-Diz P., Ramos-Luis E., Brion M., Irwin J.A., Just R.S., Loreille O., Parsons T.J., Syndercombe-Court D., Schmit-ter H., Stradmann-Bellinghausen B., Bender K., and Gill P. Analysis of artificially degraded DNA using STRs and SNPs-results of a collaborative european (eDNAp) exercise. Forensic Sci. Int. 164 1 (2006) 33-44
115. Yoshida K., Sekiguchi K., Kasai K., Sato H., Seta S., and Sens-abaugh G.F. Evaluation of new primers for csf1po. Int. J. Legal Med. 110 1 (1997) 36-38
116. Saiki R.K., Gelfand D.H., Stoffel S., Scharf S.J., Higuchi R., Horn G.T., Mullis K.B., and Erlich H.A. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239 4839 (1988) 487-491
117. Keohavong P., and Thilly W.G. Fidelity of DNA polymerases in DNA amplification. Proc. Natl. Acad. Sci. U.S.A. 86 23 (1989) 9253-9257
118. Eckert K.A., and Kunkel T.A. DNA polymerase fidelity and the polymerase chain reaction. PCR Methods Appl. 1 1 (1991) 17-24
119. Gilbert M.T., Binladen J., Miller W., Wiuf C., Willerslev E., Poinar H., Carlson J.E., Leebens-Mack J.H., and Schuster S.C. Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis. Nucleic Acids Res. 35 1 (2007) 1-10
120. Hoff-Olsen P., Jacobsen S., Mevag B., and Olaisen B. Microsatellite stability in human post-mortem tissues. Forensic Sci. Int. 119 3 (2001) 273-278
121. Hansen A., Willerslev E., Wiuf C., Mourier T., and Arctander P. Statistical evidence for miscoding lesions in ancient DNA templates. Mol. Biol. Evol. 18 2 (2001) 262-265
122. Willerslev E., Hansen A.J., Christensen B., Steffensen J.P., and Arctander P. Diversity of holocene life forms in fossil glacier ice. Proc. Natl. Acad. Sci. U.S.A. 96 14 (1999) 8017-8021
123. Cooper A., Lalueza-Fox C., Anderson S., Rambaut A., Austin J., and Ward R. Complete mitochondrial genome sequences of two extinct moas clarify ratite evolution. Nature 409 6821 (2001) 704-707
124. Pusch C.M., Nicholson G.J., Bachmann L., and Scholz M. Degenerate oligonucleotide-primed preamplification of ancient DNA allows the retrieval of authentic DNA sequences. Anal. Biochem. 279 1 (2000) 118-122
125. Zhang L., Cui X., Schmitt K., Hubert R., Navidi W., and Arnheim N. Whole genome amplification from a single cell: implications for genetic analysis. Proc. Natl. Acad. Sci. U.S.A. 89 13 (1992) 5847-5851
126. Satoh K., Takahashi K., Itoh Y., and Kobayashi R. Typing of DNA using the primer extension preamplification (pep) method-studies of reliability of typing and detection limits. Nihon Hoigaku Zasshi 52 3 (1998) 184-190
127. Lawlor D.A., Dickel C.D., Hauswirth W.W., and Parham P. Ancient hla genes from 7,500-year-old archaeological remains. Nature 349 6312 (1991) 785-788
128. Handt O., Richards M., Trommsdorff M., Kilger C., Simanainen J., Georgiev O., Bauer K., Stone A., Hedges R., and Schaffner W. Molecular genetic analyses of the tyrolean ice man. Science 264 5166 (1994) 1775-1778
129. Wilson I.G. Inhibition and facilitation of nucleic acid amplification. Appl. Environ. Microbiol. 63 10 (1997) 3741-3751
130. Pusch C.M., Giddings I., and Scholz M. Repair of degraded duplex DNA from prehistoric samples using Escherichia coli DNA polymerase i and t4 DNA ligase. Nucleic Acids Res. 26 3 (1998) 857-859
131. Dean F.B., Hosono S., Fang L., Wu X., Faruqi A.F., Bray-Ward P., Sun Z., Zong Q., Du Y., Du J., Driscoll M., Song W., Kingsmore S.F., Egholm M., and Lasken R.S. Comprehensive human genome amplification using multiple displacement amplification. Proc. Natl. Acad. Sci. U.S.A. 99 8 (2002) 5261-5266
132. Vasan S., Zhang X., Kapurniotu A., Bernhagen J., Teichberg S., Basgen J., Wagle D., Shih D., Terlecky I., Bucala R., Cerami A., Egan J., and Ulrich P. An agent cleaving glucose-derived protein crosslinks in vitro and in vivo. Nature 382 6588 (1996) 275-278
133. Poinar H.N., Hofreiter M., Spaulding W.G., Martin P.S., Stankiewicz B.A., Bland H., Evershed R.P., Possnert G., and Paabo S. Molecular coproscopy: dung and diet of the extinct ground sloth nothrotheriops shastensis. Science 281 5375 (1998) 402-406
134. Kemp B.M., Monroe C., and Smith D.G. Repeat silica extraction: a simple technique for the removal of PCR inhibitors from DNA extracts. J. Archaeol. Sci. 33 12 (2006) 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 A.J., and Poinar H.N. Isolation of nucleic acids and cultures from fossil ice and permafrost. Trends Ecol. Evol. 19 3 (2004) 141-147
137. Willerslev E., and Cooper A. Ancient DNA. Proc. Biol. Sci. 272 1558 (2005) 3-16
138. Tabatabai M.A. Soil enzymes. In: Miller R.H., and Keeney D.R. (Eds). Methods of Soil Analysis. 2nd ed. (1982), American Society of Agronomy Soil Science Society of America, Madison, WI 903-947
139. Ludes B., Pfitzinger H., and Mangin P. DNA fingerprinting from tissues after variable postmortem periods. J. Forensic Sci. 38 3 (1993) 686-690
140. Parsons T.J., and Weedn V.W. Chemical and ultrastructural aspects of decomposition. In: Haglund W.D., and Sorg M.H. (Eds). Forensic Taphonomy: The Post-mortem Fate of Human Remains (1997), Robert B. Stern, CRC press, Inc. 93-108
141. van Bergen P.F., Bland H.A., Horton M.C., and Evershed R.P. Chemical and morphological changes in archaeological seeds and fruits during preservation by desiccation. Geochim. Cosmochim. Acta 61 (1997) 1919-1930
142. Poinar H.N., and Stankiewicz B.A. Protein preservation and DNA retrieval from ancient tissues. Proc. Natl. Acad. Sci. U.S.A. 96 15 (1999) 8426-8431
143. Romanowski G., Lorenz M.G., and Wackernagel W. Adsorption of plasmid DNA to mineral surfaces and protection against DNAse i. Appl. Environ. Microbiol. 57 4 (1991) 1057-1061
144. Rydberg B. The rate of strand separation in alkali of DNA of irradiated mammalian cells. Radiat. Res. 61 2 (1975) 274-287
145. Kanter P.M., and Schwartz H.S. A fluorescence enhancement assay for cellular DNA damage. Mol. Pharmacol. 22 1 (1982) 145-151
146. Kohn K.W., Erickson L.C., Ewig R.A., and Friedman C.A. Fractionation of DNA from mammalian cells by alkaline elution. Biochemistry 15 21 (1976) 4629-4637
147. Batel R., Jaksic Z., Bihari N., Hamer B., Fafandel M., Chauvin C., Schroder H.C., Muller W.E., and Zahn R.K. A microplate assay for DNA damage determination (fast micromethod). Anal. Biochem. 270 2 (1999) 195-200
148. Jaksic Z., and Batel R. DNA integrity determination in marine invertebrates by fast micromethod. Aquat. Toxicol. 65 4 (2003) 361-376
149. Dhawan A., Bajpayee M., and Parmar D. Comet assay: a reliable tool for the assessment of DNA damage in different models. Cell Biol. Toxicol. 25 1 (2009) 5-32
150. Kalinowski D.P., Illenye S., and Van Houten B. Analysis of DNA damage and repair in murine leukemia l1210 cells using a quantitative polymerase chain reaction assay. Nucleic Acids Res. 20 13 (1992) 3485-3494
151. Swango K.L., Timken M.D., Chong M.D., and Buoncristiani M.R. A quantitative PCR assay for the assessment of DNA degradation in forensic samples. Forensic Sci. Int. 158 1 (2006) 14-26
152. Dobbs L.J., Madigan M.N., Carter A.B., and Earls L. Use of fta gene guard filter paper for the storage and transportation of tumor cells for molecular testing. Arch. Pathol. Lab. Med. 126 1 (2002) 56-63
153. Alonso A., Martin P., Albarran C., Garcia P., Garcia O., de Simon L.F., Garcia-Hirschfeld J., Sancho M., de La Rua C., and Fernandez-Piqueras J. Real-time PCR designs to estimate nuclear and mitochondrial DNA copy number in forensic and ancient DNA studies. Forensic Sci. Int. 139 2-3 (2004) 141-149
154. Johnson L.A., and Ferris J.A. Analysis of postmortem DNA degradation by single-cell gel electrophoresis. Forensic Sci. Int. 126 1 (2002) 43-47
155. Zhen J.L., Zhang X.D., and Niu Q.S. Relationship between the postmortem interval and nuclear DNA changes of heart muscular cells in mice. Fa Yi Xue Za Zhi 22 3 (2006) 173-176