Forensic implications of PCR inhibition - A review

Forensic Science International: Genetics

Volumn 6, Issue 3, 2012, Pages 297-305

  Alaeddini, Reza ^a  

^a LEGAL MEDICINE RESEARCH CENTER   (Iran)

Author keywords

Chaotropic agents; Forensic sciences; Humic compounds; Maillard reaction; PCR inhibition

Indexed keywords

DNA; MITOCHONDRIAL DNA; SILICON DIOXIDE;

CALORIMETRY; DILUTION; DNA BINDING; DNA DEGRADATION; DNA DETERMINATION; DNA EXTRACTION; DNA METABOLISM; DNA PURIFICATION; DNA STRAND BREAKAGE; DOT HYBRIDIZATION; ERROR; FORENSIC GENETICS; GEL ELECTROPHORESIS; GLYCATION; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; HUMIC SUBSTANCE; POLYMERASE CHAIN REACTION INHIBITION; PRIORITY JOURNAL; QUALITATIVE ANALYSIS; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; REVIEW; SURFACE CHARGE;

DNA; DNA CONTAMINATION; DNA FINGERPRINTING; DNA, MITOCHONDRIAL; DNA-DIRECTED DNA POLYMERASE; ENZYME INHIBITORS; FLUORESCENT DYES; GLYCOSYLATION; HUMANS; HUMIC SUBSTANCES; POLYMERASE CHAIN REACTION; SILICON DIOXIDE; SOIL;

EID: 84858446910     PISSN: 18724973     EISSN: 18780326     Source Type: Journal    
DOI: 10.1016/j.fsigen.2011.08.006     Document Type: Review

References (202)

1. Shepard E.M., and Herrera R.J. Iranian STR variation at the fringes of biogeographical demarcation Forensic Sci. Int. 158 2-3 2006 140 148
2. Alaeddini R., Walsh S.J., and Abbas A. Forensic implications of genetic analyses from degraded DNA - a review Forensic Sci. Int. Genet. 4 3 2010 148 157
3. Parsons T.J., and Weedn V.W. Chemical and ultrastructural aspects of decomposition Haglund W.D. Sorg M.H. Forensic Taphonomy: The Post-mortem Fate of Human Remains 1997 Robert B. Stern, CRC Press, Inc. 93 108
4. 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 (Pubitemid 26251366)
5. Longo M.C., Berninger M.S., and Hartley J.L. Use of uracil DNA glycosylase to control carry-over contamination in polymerase chain reactions Gene 93 1 1990 125 128 (Pubitemid 20353092)
6. Wilson I.G. Inhibition and facilitation of nucleic acid amplification Appl. Environ. Microbiol. 63 10 1997 3741 3751 (Pubitemid 27411322)
7. Holland M.M., Fisher D.L., Lee D.A., Bryson C.K., and Weedn V.W. Short tandem repeat loci: application to forensic and human remains identification EXS 67 1993 267 274
8. 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 (Pubitemid 37107410)
9. Sullivan K.M., Hopgood R., and Gill P. Identification of human remains by amplification and automated sequencing of mitochondrial DNA Int. J. Leg. Med. 105 2 1992 83 86
10. Powell H.A., Gooding C.M.C.M., Garrett S.D., Lund B.M., and McKee R.A. Proteinase inhibition of the detection of listeria monocytogenes in milk using the polymerase chain reaction Lett. Appl. Microbiol. 18 1994 59 61 (Pubitemid 24210480)
11. Saulnier P., and Andremont A. Detection of genes in feces by booster polymerase chain reaction J. Clin. Microbiol. 30 1992 2080 2083
12. Jacobsen C.S., and Rasmussen O.F. Development and application of a new method to extract bacterial DNA from soil based on separation of bacteria from soil with cation-exchange resin Appl. Environ. Microbiol. 58 1992 2458 2462
13. Simon M.C., Gray D.I., and Cook N. DNA extraction and PCR methods for the detection of listeria monocytogenes in cold-smoked salmon Appl. Environ. Microbiol. 62 1996 822 824 (Pubitemid 26071450)
14. Lienert K., and Fowler J.C.S. Analysis of mixed human/microbial DNA samples: a validation study of two PCR AMP-FLP typing methods BioTechniques 13 1992 276 281
15. Butler J.M. Forensic DNA Typing: Biology, Technology and Genetics of STR Markers 2nd ed. 2005 Elsevier Academic Press New York
16. Kontanis E.J., and Reed F.A. Evaluation of real-time PCR amplification efficiencies to detect PCR inhibitors J. Forensic Sci. 51 2006 795 804 (Pubitemid 44015185)
17. Larkin A., and Harbison S. An improved method for STR analysis of bloodstained denim Int. J. Leg. Med. 112 6 1999 388 390 (Pubitemid 29498150)
18. Eckhart L., Bach J., Ban J., and Tschachler E. Melanin binds reversibly to thermostable DNA polymerase and inhibits its activity Biochem. Biophys. Res. Commun. 271 3 2000 726 730 (Pubitemid 30444696)
19. Belec L., Authier J.R., Eliezer-Vanerot M.C., Piedouillet C., Ali Si Mohamed A.S., and Gherardi R.K. Myoglobin as a polymerase chain reaction (PCR) inhibitor: a limitation for PCR from skeletal muscle tissue avoided by the use of thermus thermophilus polymerase Muscle Nerve 21 8 1998 1064 1067 (Pubitemid 28287997)
20. Akane A., Matsubara K., Nakamura H., Takahashi S., and Kimura K. Identification of the heme compound copurified with deoxyribonucleic acid (DNA) from bloodstains, a major inhibitor of polymerase chain reaction (PCR) amplification J. Forensic Sci. 39 2 1994 362 372
21. Khan G., Kangro H.O., Coates P.J., and Heath R.B. Inhibitory effects of urine on the polymerase chain reaction for cytomegalovirus DNA J. Clin. Pathol. 44 5 1991 360 365
22. Monteiro L., Bonnemaison D., Vekris A., Petry K.G., Bonnet J., Vidal R., Cabrita J., and Megraud F. Complex polysaccharides as PCR inhibitors in feces: Helicobacter pylori model J. Clin. Microbiol. 35 4 1997 995 998 (Pubitemid 27146555)
23. Beckett S.M., Laughton S.J., Pozza L.D., McCowage G.B., Marshall G., Cohn R.J., Milne E., and Ashton L.J. Buccal swabs and treated cards: methodological considerations for molecular epidemiologic studies examining pediatric populations Am. J. Epidemiol. 167 10 2008 1260 1267 (Pubitemid 351670632)
24. Boddinghaus B., Wichelhaus T.A., Volker B., and Bittner T. Removal of PCR inhibitors by silica membranes: evaluating the amplicor mycobacterium tuberculosis kit J. Clin. Microbiol. 39 10 2001 3750 3752 (Pubitemid 32954538)
25. Karlsen F., Kalantari M., Chitemerere M., Johansson B., and Hagmar B. Modifications of human and viral deoxyribonucleic acid by formaldehyde fixation Lab. Invest. 71 4 1994 604 611 (Pubitemid 24338169)
26. Von Wurmb N., Meissner D., and Wegener R. Influence of cyanoacrylate on efficiency of forensic PCRs Forensic Sci. Int. 124 1 2001 11 16 (Pubitemid 33123354)
27. Chiou F.S., Pai C.Y., Hsu Y.P., Tsai C.W., and Yang C.H. Extraction of human DNA for PCR from chewed residues of betel quid using a novel "pvp/ctab" method J. Forensic Sci. 46 5 2001 1174 1179 (Pubitemid 33089430)
28. Fisher D.L., Holland M.M., Mitchell L., Sledzik P.S., Wilcox A.W., Wadhams M., and Weedn V.W. Extraction, evaluation, and amplification of DNA from decalcified and undecalcified united states civil war bone J. Forensic Sci. 38 1 1993 60 68 (Pubitemid 23064228)
29. Sorensen E., Hansen S.H., Eriksen B., and Morling N. Application of thiopropyl sepharose 6B for removal of PCR inhibitors from DNA extracts of a thigh bone recovered from the sea Int. J. Leg. Med. 117 4 2003 245 247 (Pubitemid 37039768)
30. Braid M.D., Daniels L.M., and Kitts C.L. Removal of PCR inhibitors from soil DNA by chemical flocculation J. Microbiol. Methods 52 3 2003 389 393 (Pubitemid 36078424)
31. Tsai Y.L., and Olson B.H. Rapid method for direct extraction of DNA from soil and sediments Appl. Environ. Microbiol. 57 4 1991 1070 1074
32. Bourke M.T., Scherczinger C.A., Ladd C., and Lee H.C. NaOH treatment to neutralize inhibitors of taq polymerase J. Forensic Sci. 44 5 1999 1046 1050 (Pubitemid 29420395)
33. Yoshii T., Tamura K., and Ishiyama I. presence of a PCR-inhibitor in hairs Nihon Hoigaku Zasshi 46 5 1992 313 316 (Pubitemid 23014991)
34. Watson R.J., and Blackwell B. Purification and characterization of a common soil component which inhibits the polymerase chain reaction Can. J. Microbiol. 46 7 2000 633 642 (Pubitemid 30625821)
35. Tebbe C.C., and Vahjen W. Interference of humic acids and DNA extracted directly from soil in detection and transformation of recombinant DNA from bacteria and a yeast Appl. Environ. Microbiol. 59 8 1993 2657 3665
36. Scholz M., Giddings I., and Pusch C.M. A polymerase chain reaction inhibitor of ancient hard and soft tissue DNA extracts is determined as human collagen type i Anal. Biochem. 259 2 1998 283 286 (Pubitemid 28265592)
37. Hanni C., Brousseau T., Laudet V., and Stehelin D. Isopropanol precipitation removes PCR inhibitors from ancient bone extracts Nucl. Acids Res. 23 5 1995 881 882
38. Al-Soud W.A., and Radstrom P. Effects of amplification facilitators on diagnostic PCR in the presence of blood,feces, and meat J. Clin. Microbiol. 38 12 2000 4463 4470 (Pubitemid 32244535)
39. Sutlovic D., Gamulin S., Definis-Gojanovic M., Gugic D., and Andjelinovic S. Interaction of humic acids with human DNA: proposed mechanisms and kinetics Electrophoresis 29 7 2008 1467 1472 (Pubitemid 351524358)
40. Preston C.M. Applications of NMR to soil organic matter analysis: history and prospects Soil Sci. 161 1996 144 166
41. Zhou J., Bruns M.A., and Tiedje J.M. DNA recovery from soils of diverse composition Appl. Environ. Microbiol. 62 2 1996 316 322 (Pubitemid 26047397)
42. Paabo S., Higuchi R.G., and Wilson A.C. Ancient DNA and the polymerase chain reaction, the emerging field of molecular archaeology J. Biol. Chem. 264 17 1989 9709 9712
43. Boom R., Sol C.J., Salimans M.M., Jansen C.L., Wertheim-van Dillen P.M., van der J., and Noordaa Rapid and simple method for purification of nucleic acids J. Clin. Microbiol. 28 3 1990 495 503 (Pubitemid 20078123)
44. Paabo S. Ancient DNA: extraction, characterization, molecular cloning, and enzymatic amplification Proc. Natl. Acad. Sci. U.S.A. 86 6 1989 1939 1943 (Pubitemid 19087044)
45. Primorac D. The role of DNA technology in identification of skeletal remains discovered in mass graves Forensic Sci. Int. 146S 2004 S163 S164
46. Pillai S.D., Josephson K.L., Bailey R.L., Gerba C.P., and Pepper I.L. Rapid method for processing soil samples for polymerase chain reaction amplification of specific gene sequences Environ. Microbiol. 57 1991 2383 2386
47. Wan W., and Yeow J.T. The effects of gold nanoparticles with different sizes on polymerase chain reaction efficiency Nanotechnology 20 32 2009 325702
48. Lantz P.G., Matsson M., Wadstrom T., and Radstrom P. Removal of PCR inhibitors from human fecal samples through the use of an aqueous two-phase system for sample preparation prior to PCR J. Microbiol. Methods 28 1997 159 167 (Pubitemid 27244800)
49. Alaeddini R., and Burgoyne L.A. Endogenous inhibition of DNA amplification from human skeletal remains The 18th International Symposium of the Forensic Sciences Fremantle (Perth), Australia 2006
50. Wurmb-Schwark N.V., Schwark T., Harbeck M., and Oehmichen M. A simple duplex-pcr to evaluate the DNA quality of anthropological and forensic samples prior short tandem repeat typing Leg. Med. 6 2004 80 88 (Pubitemid 38369039)
51. Paabo S. Molecular cloning of ancient egyptian mummy DNA Nature 314 6012 1985 644 645 (Pubitemid 15080846)
52. Hagelberg E., Bell L.S., Allen T., Boyde A., Jones S.J., and Clegg J.B. Analysis of ancient bone DNA: techniques and applications Philos. Trans. R. Soc. Lond. B Biol. Sci. 333 1268 1991 399 407
53. Imaizumi K., Noguchi K., Shiraishi T., Sekiguchi K., Senju H., Fujii K., Yoshida K., Kasai K., and Yoshino M. DNA typing of bone specimens-the potential use of the profiler test as a tool for bone identification Leg. Med. (Tokyo) 7 1 2005 31 41 (Pubitemid 39535765)
54. Huggett J.F., Novak T., Garson J.A., Green C., Morris-Jones S.D., Miller R.F., and Zumla A. Differential susceptibility of PCR reactions to inhibitors: an important and unrecognised phenomenon BMC Res. Notes 1 2008 70
55. Opel K.L., Chung D., and McCord B.R. A study of PCR inhibition mechanisms using real time PCR J. Forensic Sci. 55 1 2010 25 33
56. Katcher H.L., and Schwartz I. A distinctive property of tth DNA polymerase: enzymatic amplification in the presence of phenol BioTechniques 16 1994 84 92 (Pubitemid 2033212)
57. Rossen L., Norskov P.P., Holmstromet K., and Rasmussen O.F. Inhibition of PCR by components of food samples, microbial diagnostic assays and DNA-extraction solutions Int. J. Food Microbiol. 17 1992 37 45 (Pubitemid 23000398)
58. Al-Soud W.A., and Radstrom P. Capacity of nine thermostable DNA polymerases to mediate DNA amplification in the presence of PCR-inhibiting samples Appl. Environ. Microbiol. 64 10 1998 3748 3753 (Pubitemid 28462967)
59. Bickley J., Short J.K., McDowel D.G., and Parkes H.C. Polymerase chain reaction (PCR) detection of listeria monocytogenes in diluted milk and reversal of PCR inhibition caused by calcium ions Lett. Appl. Microbiol. 22 1996 152 158
60. Kim S., Labbe R.G., and Ryu S. Inhibitory effects of collagen on the PCR for detection of clostridium perfringens Appl. Environ. Microbiol. 66 3 2000 1213 1215 (Pubitemid 30130050)
61. Innis M.A., Myambo K.B., Gelfand D.H., and Brow M.A.D. DNA sequencing with thermus aquaticus DNA polymerase and direct sequencing of polymerase chain reaction-amplified DNA Proc. Natl. Acad. Sci. U.S.A. 85 1988 9436 9440 (Pubitemid 19027147)
62. Wiedbrauk D.L., Werner J.C.J.C., and Drevon A.M. Inhibition of PCR by aqueous and vitreous fluids J. Clin. Microbiol. 33 1995 2643 2646
63. Borkovsky O.K. Sources of organic matter in marine basins Mar. Geol. 3 1965 5 31
64. Rocha J.C., Rosa A.H., and Furlan M. An alternative methodologyfor the extraction of humic substances from organic soils J. Braz. Chem. Soc. 9 1 1998 51 56
65. Maillard L.C. Action des acides aminés sur les sucres: formation des mélanoidines par voie méthodique C. R. Hebd. Séances Acad. Sci. 154 1 1912 66 68
66. Bucala R., Model P., and Cerami A. Modification of dna by reducing sugars: a possible mechanism for nucleic acid aging and age-related dysfunction in gene expression Proc. Natl. Acad. Sci. U.S.A. 81 1984 105 109 (Pubitemid 14180836)
67. Abelson P.H., and Hare P.E. Reactions of amino acids with natural and artificial humics and kerogens Washington Yearbook, vol. 69 1971 Carnegie Inst. pp. 327-334
68. Parsons J.W. Isolation of humic substances from soils and sediments Frimmel F.H. Christman R.F. Humic Substances and Their Role in the Environment 1988 John Wiley and Sons Chichester 3 14
69. Zipper H., Buta C., Lammle K., Brunner H., Bernhagen J., and Vitzthum F. Mechanisms underlying the impact of humic acids on DNA quantification by SYBR Green I and consequences for the analysis of soils and aquatic sediments Nucl. Acids Res. 31 7 2003 e39
70. Steffan R.J., Goksoyr J., Bej A.K., and Atlas R.M. Recovery of dna from soils and sediments Appl. Environ. Microbiol. 54 12 1988 2908 2915
71. Dong D., Yan A., Liu H., Zhang X., and Xu Y. Removal of humic substances from soil DNA using aluminium sulfate J. Microbiol. Methods 66 2006 217 222 (Pubitemid 43903029)
72. Roose-Amsaleg E., Garnier-Sillam C.L., and Harry M. Extraction and purification of microbial dna from soil and sediment samples Appl. Soil Ecol. 18 2001 47 60 (Pubitemid 32774022)
73. Tsai Y.L., and Olson B.H. Detection of low numbers of bacterial cells in soils and sediments by polymerase chain reaction Appl. Environ. Microbiol. 58 2 1992 754 757
74. Muller-Wegener U. Interaction of humic substances with biota Frimmel F.H. Christman R.F. Humic Substances and Their Role in the Environment 1988 John Wiley and Sons, Inc. New York 179 192
75. Elfarissi F., and Pefferkorn E. Fragmentation of kaolinite aggregates induced by ion-exchange reactions within adsorbed humic acid layers J. Colloid Interface Sci. 221 1 2000 64 74 (Pubitemid 30046548)
76. Kallmeyer J., and Smith D.C. An improved electroelution method for separation of DNA from humic substances in marine sediment DNA extracts FEMS Microbiol. Ecol. 69 2009 125 131
77. Crecchio C., and Stotzky G. Binding of DNA on humic acids: effects on transformation of bacillus subtilis and resistance to DNase Soil Biol. Biochem. 30 8/9 1998 1061 1067 (Pubitemid 28329529)
78. Tsai Y.L., and Olsen B.H. Rapid method for separation of bacterial dna from humic substances in sediments for polymerase chain reaction Appl. Environ. Microbiol. 58 1992 2292 2295
79. Vettori C., Paffetti D., Pietramellara G., Stotzky G., and Gallori E. Amplification of bacterial DNA bound on clay minerals by the random amplified polymorphic DNA (RAPD) technique Ecology 20 1996 251 260 (Pubitemid 26273578)
80. 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
81. Hiramoto K., Kato T., and Kikugawa K. Generation of DNA-breaking activity in the maillard reaction of glucose-amino acid mixtures in a solid system Mutat. Res. 285 2 1993 191 198 (Pubitemid 23029568)
82. Hiramoto K., Kido K., and Kikugawa K. DNA breaking by Maillard products of glucose-amino acid mixtures formed in aqueous systems J. Agric. Food Chem. 42 1994 689 694
83. 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 (Pubitemid 28340782)
84. Young C., Burghoff R.L., Keim L.G., Minak-Bernero V., Lute J.R., and Hinton S.M. Poly1vinylpyrrolidone-agarose gel electrophoresis purification of polymerase chain reaction-amplifiable DNA from soils Appl. Environ. Microbiol. 59 1993 1972 1974 (Pubitemid 23171582)
85. Bucala R., Model P., Russel M., and Cerami A. Modification of DNA by glucose 6-phosphate induces DNA rearrangements in an escherichia coli plasmid Proc. Natl. Acad. Sci. U.S.A. 82 1985 8439 8442 (Pubitemid 16101094)
86. Ikan R. The Maillard Reaction: Consequences for the Chemical and Life Sciences 1st ed. 1996 John Wiley and Sons New York
87. Monnier V.M., and Cerami A. Detection of nonenzymatic browning products in the human lens Biochim. Biophys. Acta 760 1 1983 97 103 (Pubitemid 13013469)
88. Lee A.T., and Cerami A. In vitro and in vivo reactions of nucleic acids with reducing sugars Mutat. Res. 238 1990 185 191
89. Lee A.T., and Cerami A. The formation of reactive intermediate(s) of glucose 6-phosphate and lysine capable of rapidly reacting with dna Mutat. Res. 179 2 1987 151 158
90. 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 (Pubitemid 44400536)
91. 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 (Pubitemid 28340782)
92. Poinar H., Kuch M., McDonald G., Martin P., and Paabo S. Nuclear gene sequences from a late pleistocene sloth coprolite Curr. Biol. 12 2003 1150 1152 (Pubitemid 36815265)
93. Bachoon D.S., Otero E., and Hodson R.E. Effects of humic substances on fluorometric DNA quantification and DNA hybridization J. Microbiol. Methods 47 2001 73 82 (Pubitemid 32885609)
94. Rutledge R.G., and Cote C. Mathematics of quantitative kinetic PCR and the application of standard curves Nucl. Acids Res. 31 16 2003 e93
95. Guescini M., Sisti D., Rocchi M.B., Stocchi L., and Stocchi V. A new real-time PCR method to overcome significant quantitative inaccuracy due to slight amplification inhibition BMC Bioinformatics 9 2008 326
96. Ramakers C., Ruijter J.M., Deprez R.H., and Moorman A.F. Assumption-free analysis of quantitative real-time polymerase chain reaction (PCR) data Neurosci. Lett. 339 1 2003 62 66 (Pubitemid 36263221)
97. Stahlberg A., Aman P., Ridell B., Mostad P., and Kubista M. Quantitative real-time PCR method for detection of b-lymphocyte monoclonality by comparison of κ and λ immunoglobulin light chain expression Clin. Chem. 49 1 2003 51 59 (Pubitemid 36078553)
98. Sambrook J., and Russell D.W. Molecular Cloning, A Laboratory Manual 3rd ed. 2001 CSHL Press pages 5.55-5.59
99. Saiki R.K., Walsh P.S., Levenson C.H., and Erlich H.A. Genetic analysis of amplified DNA with immobilized sequence-specific oligonucleotide probes Proc. Natl. Acad. Sci. USA 86 1989 6230 6234 (Pubitemid 19210628)
100. Katz E.D., and Dong M.W. Rapid analysis and purification of polymerase chain reaction products by high-performance liquid chromatography BioTechniques 8 1990 546 555 (Pubitemid 20153763)
101. Mantero G., Zonaro A., Albertini A., Bertolo P., and Primi D. Dna enzyme immunoassay: general method for detecting products of polymerase chain reaction Clin. Chem. 37 1991 5422 5429
102. Imaizumi K., Miyasaka S., and Yoshino M. Quantitative analysis of amplifiable DNA in tissues exposed to various environments using competitive PCR assays Sci. Justice 44 4 2004 199 208 (Pubitemid 39388298)
103. 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
104. Swango K.L., Hudlow W.R., Timken M.D., and Buoncristiani M.R. Developmental validation of a multiplex qPCR assay for assessing the quantity and quality of nuclear DNA in forensic samples Forensic Sci. Int. 170 16 2007 35 45 (Pubitemid 46994792)
105. Green R.L., Roinestad I.C., Boland C., and Hennessy L.K. Developmental validation of the quantifiler real-time PCR kits for the quantification of human nuclear DNA samples J. Forensic Sci. 50 4 2005 809 825 (Pubitemid 40917796)
106. King C.E., Debruyne R., Kuch M., Schwarz C., and Poinar H.N. A quantitative approach to detect and overcome PCR inhibition in ancient DNA extracts BioTechniques 47 5 2009 941 949
107. Alonso A., Andelinovic S., Martin P., Sutlovic D., Erceg I., Huffine E., de Simon L.F., Albarran C., Definis-Gojanovic M., Fernandez-Rodriguez A., Garcia P., Drmic I., Rezic B., Kuret S., Sancho M., and Primorac D. DNA typing from skeletal remains: evaluation of multiplex and megaplex STR systems on DNA isolated from bone and teeth samples Croat. Med. J. 42 3 2001 260 266 (Pubitemid 32606988)
108. Oikarinen S., Tauriainen S., Viskari H., Simell O., Knip M., Virtanen S., and Hyoty H. PCR inhibition in stool samples in relation to age of infants J. Clin. Virol. 44 3 2009 211 214
109. Ruano G., Pagliaro E.M., Schwartz T.R., Lamy K., Messina D., Gaensslen R.E., and Lee H.C. Heat-soaked PCR: an efficient method for DNA amplification with applications to forensic analysis BioTechniques 13 2 1992 266 274
110. Kermekchiev M.B., Tzekov A., and Barnes W.M. Cold-sensitive mutants of taq DNA polymerase provide a hot start for PCR BioTechniques 31 21 2003 6139 6147 (Pubitemid 37442341)
111. Eilert K.D., and Foran D.R. Polymerase resistance to polymerase chain reaction inhibitors in bone J. Forensic Sci. 54 2009 1001 1007
112. Viltrop T., Krjutskov K., Palta P., and Metspalu A. Comparison of dna extraction methods for multiplex polymerase chain reaction Anal. Biochem. 398 2 2010 260 262
113. Evison M.P., Smillie D.M., and Chamberlain A.T. Extraction of single-copy nuclear DNA from forensic specimens with a variety of postmortem histories J. Forensic Sci. 42 6 1997 1032 1038 (Pubitemid 27495823)
114. Van Vollenhoven P., Heyns C.F., de Beer P.M., Whitaker P., Van Helden P.D., and Victor T. Polymerase chain reaction in the diagnosis of urinary tract tuberculosis Urol. Res. 24 1996 107 111 (Pubitemid 26141826)
115. Verkooyen R.P., Luijendijk A., Huisman W.M., Goessens W.H., Kluytmans J.A., van Rijsoort-Vos J.H., and Verbrugh H.A. Detection of PCR inhibitors in cervical specimens by using the AMPLICOR chlamydia trachomatis assay J. Clin. Microbiol 34 1996 3072 3074 (Pubitemid 26389360)
116. Lantz P.G., Tjerneld F., Borch E., Hahn-Hagerdal B., and Radstrom P. Enhanced sensitivity in PCR detection of listeria monocytogenes in soft cheese through use of an aqueous two-phase system as a sample preparation method Appl. Environ. Microbiol. 60 1994 3416 3418 (Pubitemid 24272375)
117. Lindqvist R., Norling B.B., and Lambertz S.T. A rapid sample preparation method for detection of food pathogens based on buoyant density centrifugation Appl. Microbiol. 24 1997 306 310 (Pubitemid 27163334)
118. Wernars K., Delfgou E., Soentoro P.S., and Notermans S. Successful approach for detection of low numbers of enterotoxigenic escherichia coli in minced meat by using the polymerase chain reaction Appl. Environ. Microbiol. 57 1991 1914 1919
119. DiMichele L.J., and Lewis M.J. Rapid, species-specific detection of lactic acid bacteria from beer using the polymerase chain reaction J. Am. Brew. Chem. Soc. 51 1993 63 66
120. Thornton C.G., and Passen S. Inhibition of PCR amplification by phytic acid, and treatment of bovine fecal specimens with phytase to reduce inhibition J. Microbiol. Methods 59 2004 43 52 (Pubitemid 39119912)
121. Fluit A.C., Terensma R., Visser M.J.C., Aarsman C.J.M., Poppelier M.J.J.G., Keller B.H.I., Klapwijk P., and Verhoef J. Detection of listeria monocytogenes in cheese with the magnetic immuno-polymerase chain reaction assay Appl. Environ. Microbiol. 59 1993 1289 1293 (Pubitemid 23141131)
122. Jacobsen C.S. Microscale detection of specific bacterial DNA in soil with a magnetic capture-hybridization and PCR amplification assay Appl. Environ. Microbiol. 61 9 1995 3347 3352
123. Yankson K.K., and Steck T.R. Strategy for extracting dna from clay soil and detecting a specific target sequence via selective enrichment and real-time (quantitative) PCR amplification Appl. Environ. Microbiol. 75 18 2009 6017 6021
124. Chandler D.P., Schreckhise R.W., Smith J.L., and Bolton H. Jr. Electroelution to remove humic compounds from soil DNA and RNA extracts J. Microbiol. Methods 28 1997 11 19 (Pubitemid 27112747)
125. Gabriel M.N., Calloway C.D., Reynolds R.L., and Primorac D. Identification of human remains by immobilized sequence-specific oligonucleotide probe analysis of mtDNA hypervariable regions I and II Croat. Med. J. 44 3 2003 293 298 (Pubitemid 36828145)
126. Hedges J.I. Polymerization of humic substances in natural environments Frimmel F.H. Christman R.F. Humic Substances and Their Role in the Environment 1988 John Wiley and Sons Chichester, UK 45 58
127. Berthelet M., Whyte L.G., and Greer C.W. Rapid, direct extraction of DNA from soils for PCR analysis using polyvinylpolypyrrolidone spin columns FEMS Microbiol. Lett. 138 1991 17 22 (Pubitemid 26183242)
128. Trevors J.T., Lee H., and Cook S. Direct extraction of DNA from soil Microb. Releases 1 1992 111 115
129. Sutlovic D., Gojanovic M.D., and Andelinovic S. Rapid extraction of human DNA containing humic acid Croat. Chem. Acta 80 1 2007 117 120
130. Hoff-Olsen P., Mevag B., Staalstroem E., Hovde B., Egeland T., and Olaison B. Extraction of DNA from decomposed human tissue, an evaluation of five extraction methods for short tandem repeat typing Forensic Sci. Int. 105 1999 171 183 (Pubitemid 29502182)
131. Jung J.M., Comey C.T., Baer D.B., and Budowle B. Extraction strategy for obtaining DNA from bloodstains for PCR amplification and typing of the HLA-DQ alpha gene Int. J. Leg. Med. 104 3 1991 145 148
132. Moreira D. Efficient removal of PCR inhibitors using agarose-embedded DNA preparations Nucl. Acids Res. 26 13 1998 3309 3310 (Pubitemid 28288935)
133. Harry M., Gambier B., Bourezgui Y., and Garnier-Sillam E. Evaluation of purification procedures for dna extracted from organic rich samples: interference with humic substances Analysis 27 1999 439 442
134. Hou W., Lian B., and Rothenberg S. Two electrophoreses in different pH buffers to purify forest soil DNA contaminated with humic substances Afr. J. Biotechnol. 9 16 2010 2401 2407
135. LaMontagne M.G., Michel F.C. Jr., Holden P.A., and Reddy C.A. Evaluation of extraction and purification methods for obtaining PCR-amplifiable DNA from compost for microbial community analysis J. Microbiol. Methods 49 2002 255 264 (Pubitemid 34183472)
136. Rogan P.K., and Salvo J.J. Molecular genetics of pre-columbian south american mummies Mol. Evol. 122 1990 223 234
137. Jackson C.R., Harper J.P., Willoughby D., Roden E.E., and Churchill P.F. A simple, efficient method for the separation of humic substances and DNA from environmental samples Appl. Environ. Microbiol. 63 12 1997 4993 4995 (Pubitemid 27524249)
138. Shutler G.G., Gagnon P., Verret G., Kalyn H., Korkosh S., Johnston E., and Halverson J. Removal of a PCR inhibitor and resolution of DNA STR types in mixed human-canine stains from a five year old case J. Forensic Sci. 44 3 1999 623 626 (Pubitemid 29230764)
139. Liu W., Marsh T.L., Cheng H., and Forney L.J. Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA Appl. Environ. Microbiol. 63 1997 4516 4522 (Pubitemid 27485783)
140. Boivin-Jahns V., Ruimy R., Bianchi A., Daumas S., and Christen R. Bacterial diversity in deep-subsurface clay environment Appl. Environ. Microbiol. 62 1996 3405 3412
141. Zheng H.Z., Pang D.W., Lu Z.X., Zhang Z.L., and Xie Z.X. Combing DNA on CTAB-coated surfaces Biophys. Chem. 112 1 2004 27 33
142. Saano A., Tas E., Pippola S., Lindstrom K., and Van Elsas J.D. Extraction and analysis of microbial dna from soil Van Elsas J.D. Trevors J.T. Nucleic Acids in the Environment: Methods and Applications 1995 Springer-Verlag Heidelberg, Germany 49 67
143. Liu Q., Li J., Tao W., Zhu Y., and Yao S. Comparative study on the interaction of DNA with three different kinds of surfactants and the formation of multilayer films Bioelectrochemistry 70 2 2007 301 307 (Pubitemid 46507946)
144. Porteous L.A., and Armstrong J.L. Recovery of bulk DNA from soil by a rapid, small-scale extraction method Curr. Microbiol. 22 1991 345 348
145. Leff L.G., Dana J.R., McArthur J.V., and Shimkets L.J. Comparison of methods of DNA extraction from stream sediments Appl. Environ. Microbiol. 61 1995 1141 1143
146. Ogram A., Sayler G.S., and Barkay T. The extraction and purification of microbial DNA from sediments J. Microbiol. Methods 7 2-3 1987 57 66
147. Hilger A.B., and Myrold D.D. Method for extraction of frankia DNA from soil Agriculture, Ecosystems and Environment 34 1-4 1991 107 113
148. Porteous L.A., and Armstrong J.L. A simple mini-method to extract dna directly from soil for use with polymerase chain reaction amplification Curr. Microbiol. 27 2 1993 115 118 (Pubitemid 23206305)
149. Borneman J., Skroch P.W., O'Sullivan K.M., Palus J.A., Rumjanek N.G., Jansen J.L., Nienhuis J., and Triplett E.W. Molecular microbial diversity of an agricultural soil in wisconsin Appl. Environ. Microbiol. 62 6 1996 1935 1943 (Pubitemid 26168984)
150. Picard C., Ponsonnet C., Paget E., Nesme X., and Simonet P. Detection and enumeration of bacteria in soil by direct dna extraction and polymerase chain reaction Appl. Environ. Microbiol. 58 9 1992 2717 2722
151. Shen W.H., and Hohn B. DMSO improves PCR amplification of DNA with complex secondary structure Trends Genet. 8 7 1992 44 47
152. Sidhu M.K., Liao M.J., and Rashidbaigi A. Dimethyl sulfoxide improves RNA amplification BioTechniques 21 1 1996 44 47 (Pubitemid 26250432)
153. Higashi K., Terui Y., Inomata E., Katagiri D., Nomura Y., Someya T., Nishimura K., Kashiwagi K., Kawai G., and Igarashi K. Selective structural change of bulged-out region of double-stranded RNA containing bulged nucleotides by spermidine Biochem. Biophys. Res. Commun. 370 4 2008 572 577
154. Kikuchi A., Sawamura T., Kawase N., Kitajima Y., Yoshida T., Daimaru O., Nakakita T., and Itoh S. Utility of spermidine in PCR amplification of stool samples Biochem. Genet. 48 5-6 2010 428 432
155. Walsh P.S., Metzger D.A., and Higuchi R. Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material Biotechniques 10 4 1991 506 513
156. Juniper S.K., Cambon M-A., Lesongeur F., and Barbier G. Extraction and purification of DNA from organic rich subsurface sediments (ODP Leg 169S) Mar. Geol. 174 2001 241 247 (Pubitemid 32442654)
157. Lalueza-Fox C. Analysis of ancient mitochondrial dna from extinct aborigines from tierra del fuego-patagonia Anc. Biomol. 1 1996 43 54
158. Ye J., Ji A., Parra E.J., Zheng X., Jiang C., Zhao X., Hu L., and Tu Z. A simple and efficient method for extracting DNA from old and burned bone J. Forensic Sci. 49 4 2004 754 759 (Pubitemid 38924209)
159. Taberlet P., Griffin S., Goossens B., Questiau S., Manceau V., Escaravage N., Waits L.P., and Bouvet J. Reliable genotyping of samples with very low DNA quantities using PCR Nucl. Acids Res. 24 16 1996 3189 3194 (Pubitemid 26278559)
160. Poinar H.N. The top 10 list: criteria of authenticity for DNA from ancient and forensic samples Prog. Forensics Genet. 9 2003 575 579
161. Sarkar S., Kapelner G., and Sommer S.S. Formamide can dramatically improve the specificity of PCR Nucl. Acids Res. 18 1990 6465
162. Wu J.R., and Yeh Y.C. Requirement of a functional gene 32 product of bacteriophage T4 in UV J. Virol. 12 1973 758 765
163. Kreader C.A. Relief of amplification inhibition in PCR with bovine serum albumin or T4 gene 32 protein Appl. Environ. Microbiol. 62 1996 1102 1106 (Pubitemid 26071491)
164. Curry S., Mandelkow H., Brick P., and Franks N. Crystal structure of human serum albumin complexed with fatty acid Nat. Struct. Biol. 5 1998 827 835
165. Frackman S., Kobs G., Simpson D., and Storts D. Betaine and DMSO: enhancing agents for PCR Promega Notes 27 1998
166. Santoro M.M., Liu Y., Khan S.M., Hou L.X., and Bolen D.W. Increased thermal stability of proteins in the presence of naturally occurring osmolytes Biochemistry 31 1992 5278 5283
167. Rees W.A., Yager T.D., Korte J., and Von Hippel P.H. Betaine can eliminate the base pair composition dependence of DNA melting Biochemistry 32 1993 137 144 (Pubitemid 23033330)
168. Edwards C.J., MacHugh D.E., Dobney K.M., Martin L., Russell N., Horwitz L.K., McIntosh S.K., MacDonald K.C., Helmer D., Tresset A., Vigne J.D., and Bradley D.G. Ancient DNA analysis of 101 cattle remains: limits and prospects J. Archaeol. Sci. 31 2004 695 710
169. Kermekchiev M.B., Kirilova L.I., Vail E.E., and Barnes W.M. Mutants of Taq DNA polymerase resistant to PCR inhibitors allow DNA amplification from whole blood and crude soil samples Nucl. Acids Res. 37 2009 e40
170. Matheson C.D., Gurney C., Esau N., and Lehto R. Assessing PCR inhibition from humic substances Open Enzyme Inhib. J. 3 2010 38 45
171. Hedman J., Nordgaard A., Rasmusson B., Ansell R., and Radstrom P. Improved forensic DNA analysis through the use of alternative DNA polymerases and statistical modeling of DNA profiles BioTechniques 47 5 2009 951 958
172. Hedman J., Nordgaard A., Dufva C., Rasmusson B., Ansell R., and Radstrom P. Synergy between DNA polymerases increases polymerase chain reaction inhibitor tolerance in forensic DNA analysis Anal. Biochem. 405 2 2010 192 200
173. Pavlov A., Pavlova N., Kozyavkin S., and Slesarev A. Recent developments in the optimization of thermostable DNA polymerases for efficient applications Trends Biotechnol. 22 5 2004 253 260 (Pubitemid 38515743)
174. 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
175. 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
176. Nelson K., and Melton T. Forensic mitochondrial dna analysis of 116 casework skeletal samples J. Forensic Sci. 52 3 2007 557 561 (Pubitemid 46642907)
177. 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 (Pubitemid 41248176)
178. 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 (Pubitemid 30368601)
179. Lutz S., Weisser H.J., Heizmann J., and Pollak S. mtDNA as a tool for identification of human remains, identification using mtDNA Int. J. Leg. Med. 109 4 1996 205 209
180. 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 (Pubitemid 23152892)
181. 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. Leg. Med. 112 2 1999 98 100 (Pubitemid 29138375)
182. 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 (Pubitemid 27341624)
183. Ginther C., Issel-Tarver L., and King M.C. Identifying individuals by sequencing mitochondrial DNA from teeth Nat. Genet. 2 2 1992 135 138
184. 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 (Pubitemid 36378380)
185. 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 (Pubitemid 32606996)
186. Butler J.M., and Levin B.C. Forensic applications of mitochondrial DNA Trends Biotechnol. 16 4 1998 158 162 (Pubitemid 28172664)
187. Lee H.Y., Park M.J., Kim N.Y., Sim J.E., Yang W.I., and Shin K.J. Simple and highly effective dna extraction methods from old skeletal remains using silica columns Forensic Sci. Int. Genet. 4 5 2010 275 280
188. Vanek D., Saskova L., and Koch H. Kinship and y-chromosome analysis of 7th century human remains: novel dna extraction and typing procedure for ancient material Croat. Med. J. 50 3 2009 286 295
189. Davoren J., Vanek D., Konjhodzic R., Crews J., Huffine E., and Parsons T.J. Highly effective DNA extraction method for nuclear short tandem repeat testing of skeletal remains from mass graves Croat. Med. J. 48 4 2007 478 485 (Pubitemid 47330048)
190. Rohland N., and Hofreiter M. Comparison and optimization of ancient dna extraction BioTechniques 42 2007 343 352
191. Nagy M., Otremba P., Kruger C., Bergner-Greiner S., Anders P., Henske B., Prinz M., and Roewer L. Optimization and validation of a fully automated silica-coated magnetic beads purification technology in forensics Forensic Sci. Int. 152 1 2005 13 22 (Pubitemid 40804495)
192. Hanselle T., Otte M., Schnibbe T., Smythe E., and Krieg-Schneider F. Isolation of genomic dna from buccal swabs for forensic analysis, using fully automated silica-membrane purification technology Leg. Med. (Tokyo) 5 Suppl 1 2003 S145 S149
193. V.V. Padhye, C. York, A. Burkiewiez, Nucleic acid purification on silica gel and glass mixture. United States patent US 5,658,548, Promega Corporation, August 1997.
194. Yang D.Y., Eng B., Waye J.S., Dudar J.C., and Saunders S.R. Technical note: improved dna extraction from ancient bones using silica-based spin columns Am. J. Phys. Anthropol. 105 1998 539 543 (Pubitemid 28183584)
195. Lindahl T. The croonian lecture, 1996: endogenous damage to DNA Philos. Trans. R. Soc. Lond. B Biol. Sci. 351 1347 1996 1529 1538 (Pubitemid 27012695)
196. Pashley R.M., and Kitchener J.A. Surface forces in adsorbed multilayer of water on quartz J. Colloid Interface Sci. 71 1979 491 500
197. Parida S.K., Dash S., Patel S., and Mishra B.K. Adsorption of organic molecules on silica surface Adv. Colloid Interface Sci. 121 2006 77 110 (Pubitemid 44278748)
198. Melzak K.A., Sherwood C.S., Turner R.F.B., and Haynes C.A. Driving forces for DNA adsorption to silica in perchlorate solutions J. Colloid Interface Sci. 181 1996 635 644 (Pubitemid 26252010)
199. Hoss M., and Paabo S. DNA extraction from Pleistocene bones by a silica based purification method Nucl. Acids Res. 21 1993 3913 3914 (Pubitemid 23254529)
200. Montpetit S.A., Fitch I.T., and O'Donnell P.T. A simple automated instrument for DNA extraction in forensic casework J. Forensic Sci. 50 3 2005 343 352
201. Poeckh T., Lopez S., Fuller A.O., Solomon M.J., and Larson R.G. Adsorption and elution characteristics of nucleic acids on silica surfaces and their use in designing a miniaturized purification unit Anal. Biochem. 373 2 2008 253 262
202. Kovatsi L., Nikou D., Triantaphyllou S., Njau S.N., Voutsaki S., and Kouidou S. DNA repair enables sex identification in genetic material from human teeth Hippokratia 13 3 2009 165 168