Improvement of short tandem repeat analysis of samples highly contaminated by humic acid

Journal of Forensic and Legal Medicine

Volumn 20, Issue 7, 2013, Pages 922-928

  Seo, Seung Bum ^a,b   Jin, Hong Xuan ^a   Lee, Hye Young ^a   Ge, Jianye ^b   King, Jonathan L ^b   Lyoo, Sung Hee ^a   Shin, Dong Hoon ^a   Lee, Soong Deok ^a  

^a Seoul National University   (South Korea)

^b UNIVERSITY OF NORTH TEXAS   (United States)

Author keywords

DNA recovery; Forensic DNA typing; Humic acid; Inhibitor; Short tandem repeat

Indexed keywords

DNA POLYMERASE; HUMIC ACID; TAQ POLYMERASE;

ANALYTICAL EQUIPMENT; ARTICLE; DNA EXTRACTION; DNA FINGERPRINTING; DNA ISOLATION; DNA PURIFICATION; POLYMERASE CHAIN REACTION; SHORT TANDEM REPEAT;

DNA RECOVERY; FORENSIC DNA TYPING; HUMIC ACID; INHIBITOR; SHORT TANDEM REPEAT;

DNA; DNA CONTAMINATION; DNA FINGERPRINTING; HUMANS; HUMIC SUBSTANCES; MICROSATELLITE REPEATS; POLYMERASE CHAIN REACTION;

EID: 84883360783     PISSN: 1752928X     EISSN: 18787487     Source Type: Journal    
DOI: 10.1016/j.jflm.2013.08.001     Document Type: Article

References (35)

1. R. Lleonart, E. Riego, M.V. Saínz de la Peña, K. Bacallao, F. Amaro, and M. Santiesteban Forensic identification of skeletal remains from members of Ernesto Che Guevara's guerrillas in Bolivia based on DNA typing Int J Legal Med 113 2000 98 101 (Pubitemid 30123538)
2. S. Hummel, T. Schultes, B. Bramanti, and B. Herrmann Ancient DNA profiling by megaplex amplications Electrophoresis 20 1999 1717 1721 (Pubitemid 29320463)
3. N. Di Nunno, S.S. Saponetti, V. Scattarella, P. Emanuel, S.L. Baldassarra, and G. Volpe DNA extraction: an anthropologic aspect of bone remains from sixth- to seventh-century ad bone remains Am J Forensic Med Pathol 28 2007 333 341 (Pubitemid 350190877)
4. Y.L. Tsai, and B.H. Olson Rapid method for separation of bacterial DNA from humic substances in sediments for polymerase chain reaction Appl Environ Microbiol 58 1992 2292 2295
5. S.B. Seo, H.Y. Lee, A.H. Zhang, H.Y. Kim, D.H. Shin, and S.D. Lee Effects of humic acid on DNA quantification with Quantifiler® Human DNA Quantification kit and short tandem repeat amplification efficiency Int J Legal Med 126 2012 961 968
6. H. Zipper, C. Buta, K. Lämmle, H. Brunner, J. Bernhagen, and F. Vitzthum Mechanisms underlying the impact of humic acids on DNA quantification by SYBR Green I and consequences for the analysis of soils and aquatic sediments Nucleic Acids Res 31 2003 e39
7. C.A. Kreader Relief of amplification inhibition in PCR with bovine serum albumin or T4 gene 32 protein Appl Environ Microbiol 62 1996 1102 1106 (Pubitemid 26071491)
8. C.D. Matheson, C. Gurney, N. Esau, and R. Lehto Assessing PCR inhibition from humic substances Open Enzym Inhib J 3 2010 38 45
9. D. Sutlovic, S. Gamulin, M. Definis-Gojanovic, D. Gugic, and S. Andjelinovic Interaction of humic acids with human DNA: proposed mechanisms and kinetics Electrophoresis 29 2008 1467 1472 (Pubitemid 351524358)
10. K.L. Opel, D. Chung, and B.R. McCord A study of PCR inhibition mechanisms using real time PCR J Forensic Sci 55 2010 25 33
11. M.D. Braid, L.M. Daniels, and C.L. Kitts Removal of PCR inhibitors from soil DNA by chemical flocculation J Microbiol Methods 52 2003 389 393 (Pubitemid 36078424)
12. M.G. Brevnov, H.S. Pawar, J. Mundt, L.M. Calandro, M.R. Furtado, and J.G. Shewale Developmental validation of the PrepFiler Forensic DNA Extraction Kit for extraction of genomic DNA from biological samples J Forensic Sci 54 2009 599 607
13. S.B. Seo, A. Zhang, H.Y. Kim, J.A. Yi, H.Y. Lee, and D.H. Shin Technical note: efficiency of total demineralization and ion-exchange column for DNA extraction from bone Am J Phys Anthropol 141 2010 158 162
14. H.Y. Lee, M.J. Park, N.Y. Kim, J.E. Sim, W.I. Yang, and K.J. Shin Simple and highly effective DNA extraction methods from old skeletal remains using silica columns Forensic Sci Int Genet 4 2010 275 280
15. C.P. Davis, J.L. King, B. Budowle, A.J. Eisenberg, and M.A. Turnbough Extraction platform evaluations: a comparison of AutoMate Express™, EZ1® Advanced XL, and Maxwell® 16 Bench-top DNA extraction systems Leg Med 14 2012 36 39
16. F.X. Ricaut, C. Keyser-Tracqui, E. Crubézy, and B. Ludes STR-genotyping from human medieval tooth and bone samples Forensic Sci Int 151 2005 31 35 (Pubitemid 40797657)
17. C.C. Tebbe, and W. Vahjen 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 1993 2657 2665 (Pubitemid 23223011)
18. European Biotech Network. I-genomic Soil DNA Extraction Mini kit. Available from: http://euro-bio-net.net/network/index.php?option=com- content&view=article&id=195:i-genomic-soil-dna-extraction-mini- kit&catid=66:dna-a-rna-&Itemid=361 [cited 29.04.13].
19. QIAGEN Companies QIAamp® stool handbook 2010 QIAGEN Companies Hilden, Germany
20. E.J. Lee, N.Y. Kim, I.K. Hwang, K.L. Lee, M.S. Yang, and Y.S. Kim STR-genotyping of bone and teeth samples using QIAamp DNA Stool Mini kit Korean J Forensic Sci 9 2008 46 51
21. I.G. Wilson Inhibition and facilitation of nucleic acid amplification Appl Environ Microbiol 63 1997 3741 3751 (Pubitemid 27411322)
22. D. Sutlović, M. Definis Gojanović, S. Andelinović, D. Gugić, and D. Primorac Taq polymerase reverses inhibition of quantitative real time polymerase chain reaction by humic acid Croat Med J 46 2005 556 562 (Pubitemid 41248179)
23. K.D. Eilert, and D.R. Foran Polymerase resistance to polymerase chain reaction inhibitors in bone J Forensic Sci 54 2009 1001 1007
24. O. Henegariu, N.A. Heerema, S.R. Dlouhy, G.H. Vance, and P.H. Vogt Multiplex PCR: critical parameters and step-by-step protocol Biotechniques 23 1997 504 511 (Pubitemid 27398202)
25. QIAGEN Companies QIAquick® spin handbook 2008 QIAGEN Companies Hilden, Germany
26. QIAGEN Companies QIAamp® DNA Investigator handbook 2007 QIAGEN Companies Hilden, Germany
27. Applied Biosystems PrepFiler™ Forensic DNA Extraction kit user's manual 2008 Applied Biosystems Foster City, CA
28. Applied Biosystems AmpFlSTR® Identifiler® PCR amplification kit user's manual 2006 Applied Biosystems Foster City, CA
29. Applied Biosystems Quantifiler™ human DNA quantification kit user's manual 2006 Applied Biosystems Foster City, CA
30. J. Bessetti An introduction to PCR inhibitors vol. 10 2007 Promega Corporation 9 10
31. Takara Bio Inc TaKaRa Ex Taq™ Hot Start Version 2007 Takara Bio Inc Shiga, Japan
32. Applied Biosystems AmpliTaq® Gold DNA polymerase handbook 2007 Applied Biosystems Foster City, CA
33. D.H. Buckley, and T.M. Schmidt The structure of microbial communities in soil and the lasting impact of cultivation Microb Ecol 42 2001 11 21 (Pubitemid 32731567)
34. Z. Zhang, M.B. Kermekchiev, and W.M. Barnes Direct DNA amplification from crude clinical samples using a PCR enhancer cocktail and novel mutants of Taq J Mol Diagn 12 2010 152 161
35. W.D. Loomis Overcoming problems of phenolics and quinones in the isolation of plant enzymes and organelles Methods Enzymol 31 1974 528 544