Factors affecting the STR amplification success in poorly preserved bone samples

Investigative Genetics

Volumn 1, Issue 1, 2010, Pages

  Putkonen, Mikko T ^a   Palo, Jukka U ^a   Cano, Jose M ^a   Hedman, Minttu ^a   Sajantila, Antti ^a  

^a UNIVERSITY OF HELSINKI   (Finland)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ARTICLE; BONE TISSUE; CONTROLLED STUDY; DNA DEGRADATION; DNA EXTRACTION; DNA SYNTHESIS INHIBITION; DNA TEMPLATE; GENE AMPLIFICATION; GENOTYPE; HUMAN; HUMAN TISSUE; MAXIMUM LIKELIHOOD METHOD; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SHORT TANDEM REPEAT; TISSUE PRESERVATION; Y CHROMOSOME;

EID: 79953861177     PISSN: None     EISSN: 20412223     Source Type: Journal    
DOI: 10.1186/2041-2223-1-9     Document Type: Article

References (21)

1. Opel KL, Chung D, McCord BR. A study of PCR inhibition mechanisms using real time PCR. J Forensic Sci 2010, 55:25-33. 10.1111/j.1556-4029.2009.01245.x, 20015162.
2. Kontanis EJ, Reed FA. Evaluation of real-time PCR amplification efficiencies to detect PCR inhibitors. J Forensic Sci 2006, 51:795-804. 10.1111/j.1556-4029.2006.00182.x, 16882221.
3. Wilson IG. Inhibition and facilitation of nucleic acid amplification. Appl Environ Microbiol 1997, 63:3741-3751. 168683, 9327537.
4. Caragine T, Mikulasovich R, Tamariz J, Bajda E, Sebestyen J, Baum H, Prinz M. Validation of testing and interpretation protocols for low template DNA samples using AmpFlSTR® Identifiler®. Croat Med J 2009, 50:250-267. 10.3325/cmj.2009.50.250, 2702740, 19480021.
5. Julio JM, Chien Wei C, Robert EL, Dennis YW, Jennifer LB, Timothy PM, Lori KH. Development and validation of the development and validation of the AmpFlSTR® MiniFilerTM PCR amplification kit: A miniSTR multiplex for the analysis of degraded and/or PCR inhibited DNA. J Forensic Sci 2008, 53:838-852. 10.1111/j.1556-4029.2008.00760.x, 18540972.
6. Malmström H, Gilbert MTP, Thomas MG, Brandström M, Storå J, Molnar P, Andersen PK, Bendixen C, Holmlund G, Götherström A, Willerslev E. Ancient DNA reveals lack of continuity between Neolithic hunter-gatherers and contemporary Scandinavians. Curr Biol 2009, 19:1758-1762. 10.1016/j.cub.2009.09.017, 19781941.
7. Coble MD, Loreille OM, Wadhams MJ, Edson SM, Maynard K, Meyer CE, Niederstätter H, Berger C, Berger B, Falsetti AB, Gill P, Parson W, Finelli LN. Mystery solved: the identification of the two missing Romanov children using DNA analysis. PLoS ONE 2009, 4:e4838. 10.1371/journal.pone.0004838, 2652717, 19277206.
8. Parsons TJ, Huel R, Davoren J, Katzmarzyk C, Milos A, Selmanovic A, Smajlovic L, Coble MD, Rizvic A. Application of novel "mini-amplicon" STR multiplexes to high volume casework on degraded skeletal remains. Forensic Sci Int Genet 2007, 1:175-179. 10.1016/j.fsigen.2007.02.003, 19083751.
9. Palo JU, Hedman M, Söderholm N, Sajantila A. Repatriation and identification of Finnish World War II soldiers. Croat Med J 2007, 48:528-535. 2080560, 17696308.
10. Loreille OM, Diegoli TM, Irwin JA, Coble MD, Parsons TJ. High efficiency DNA extraction from bone by total demineralization. Forensic Sci Int Genet 2007, 1:191-195. 10.1016/j.fsigen.2007.02.006, 19083754.
11. Sambrook J, Fritsch EF, Maniatis T. Molecular Cloning. A Laboratory Manual 1989, New York: Cold Spring Harbor Laboratory Press, 2.
12. Niederstätter H, Köchl S, Grubwieser P, Pavlic M, Steinlechner M, Parson W. A modular real-time PCR concept for determining the quantity and quality of human nuclear and mitochondrial DNA. Forensic Sci Int Genet 2007, 1:29-34. 10.1016/j.fsigen.2006.10.007, 19083725.
13. Johnson PCD, Haydon DT. Maximum-likelihood estimation of allelic dropout and false allele error rates from microsatellite genotypes in the absence of reference data. Genetics 2007, 175:827-842. 10.1534/genetics.106.064618, 1800638, 17179070.
14. Rasmussen M, Li Y, Lindgreen S, Pedersen JS, Albrechtsen A, Moltke I, Metspalu M, Metspalu E, Kivisild T, Gupta R, Bertalan M, Nielsen K, Gilbert MT, Wang Y, Raghavan M, Campos PF, Kamp HM, Wilson AS, Gledhill A, Tridico S, Bunce M, Lorenzen ED, Binladen J, Guo X, Zhao J, Zhang X, Zhang H, Li Z, Chen M, Orlando L, Kristiansen K, Bak M, Tommerup N, Bendixen C, Pierre TL, Grønnow B, Meldgaard M, Andreasen C, Fedorova SA, Osipova LP, Higham TF, Ramsey CB, Hansen TV, Nielsen FC, Crawford MH, Brunak S, Sicheritz-Pontén T, Villems R, Nielsen R, Krogh A, Wang J, Willerslev E. Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature 463:757-762. 10.1038/nature08835, 20148029.
15. Sturk KA, Coble MD, Barritt SM, Irwin JA. Evaluation of modified Yfiler(TM) amplification strategy for compromised samples. Croat Med J 2009, 50:228-238. 10.3325/cmj.2009.50.228, 2702738, 19480019.
16. Schwarz C, Debruyne R, Kuch M, McNally E, Schwarcz H, Aubrey AD, Bada J, Poinar H. New insights from old bones: DNA preservation and degradation in permafrost preserved mammoth remains. Nucleic Acids Res 2009, 37:3215-3229. 10.1093/nar/gkp159, 2691819, 19321502.
17. Pääbo S. Ancient Dna - extraction, characterization, molecular-cloning, and enzymatic amplification. Proc Natl Acad Sci USA 1989, 86:1939-1943. 10.1073/pnas.86.6.1939, 286820, 2928314.
18. Hummel S, Schultes T, Bramanti B, Herrmann B. Ancient DNA profiling by megaplex amplications. Electrophoresis 1999, 20:1717-1721. 10.1002/(SICI)1522-2683(19990101)20:8<1717::AID-ELPS1717>3.0.CO;2-D, 10435437.
19. Wandeler P, Smith S, Morin PA, Pettifor RA, Funk SM. Patterns of nuclear DNA degeneration over time - a case study in historic teeth samples. Mol Ecol 2003, 12:1087-1093. 10.1046/j.1365-294X.2003.01807.x, 12753226.
20. Keyser-Tracqui C, Ludes B. Methods for the study of ancient DNA. Forensic DNA Typing Protocols 2005, 253-264.
21. Kolman CJ, Tuross N. Ancient DNA analysis of human populations. Am J Phys Anthropol 2000, 111:5-23. 10.1002/(SICI)1096-8644(200001)111:1<5::AID-AJPA2>3.0.CO;2-3, 10618586.