Evaluation of modified Yfiler™ amplification strategy for compromised samples

Croatian Medical Journal

Volumn 50, Issue 3, 2009, Pages 228-238

  Sturk, Kimberly A ^a   Coble, Michael D ^a   Barritt, Suzanne M ^a   Irwin, Jodi A ^a  

^a Armed Forces DNA Identification Laboratory   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; ARTICLE; CASE REPORT; DNA EXTRACTION; GENE AMPLIFICATION; GENE IDENTIFICATION; HUMAN; INCIDENCE; POLYMERASE CHAIN REACTION; SHORT TANDEM REPEAT; Y CHROMOSOME; FORENSIC GENETICS; GENETICS; METHODOLOGY;

DNA; MICROSATELLITE DNA;

ALLELES; CHROMOSOMES, HUMAN, Y; DNA; FORENSIC GENETICS; HUMANS; MICROSATELLITE REPEATS; POLYMERASE CHAIN REACTION;

EID: 70149108266     PISSN: 03539504     EISSN: 13328166     Source Type: Journal    
DOI: 10.3325/cmj.2009.50.228     Document Type: Article

References (39)

1. Coble MD, Just RS, O'Callaghan JE, Letmanyi IH, Peterson CT, Irwin JA, et al. Single nucleotide polymorphisms over the entire mtDNA genome that increase the power of forensic testing in Caucasians. Int J Legal Med. 2004; 118: 137-46. Medline:14760490 doi:10.1007/s00414-004-0427-6 (Pubitemid 40895606)
2. Parsons TJ, Coble MD. Increasing the forensic discrimination of mitochondrial DNA testing through analysis of the entire mitochondrial DNA genome. Croat Med J. 2001; 42: 304-9. Medline:11387644
3. Just RS, Diegoli TM, Saunier JL, Irwin JA, Parsons TJ. Complete mitochondrial genome sequences for 265 African American and U. S. "hispanic" individuals. Forensic Sci Int; Genet. 2008; 2: e45-8. Medline:19083815 doi:10.1016/j.fsigen. 2007.12.001
4. Irwin JA, Edson SM, Loreille O, Just RS, Barritt SM, Lee DA, et al. DNA identification of "Earthquake McGoon" 50 years postmortem. J Forensic Sci. 2007; 52: 1115-8. Medline:17645740 doi:10.1111/j.1556-4029.2007.00506.x (Pubitemid 47339067)
5. 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: 1322-7. Medline:17944905 doi:10.1111/j.1556-4029.2007.00506.x (Pubitemid 47339067)
6. Findlay I, Taylor A, Quirke P, Frazier R, Urquhart A. DNA fingerprinting from single cells. Nature. 1997; 389: 555-6. Medline:9335493 doi:10.1038/39225 (Pubitemid 27446163)
7. van Oorschot RA, Jones MK. DNA fingerprints from fingerprints. Nature. 1997; 387: 767. Medline:9194555 doi:10.1038/42838
8. Gill P, Whitaker J, Flaxman C, Brown N, Buckleton J. An investigation of the rigor of interpretation rules for STRs derived from less than 100 pg of DNA. Forensic Sci Int. 2000; 112: 17-40. Medline:10882828 doi:10.1016/S0379-0738 (00) 00158-4
9. Gill P. Application of low copy number DNA profiling. Croat Med J. 2001; 42: 229-32. Medline:11387628
10. Whitaker J P, Cotton EA, Gill P. A comparison of the characteristics of profiles produced with the AMPFlSTR SGM Plus multiplex system for both standard and low copy number (LCN) STR DNA analysis. Forensic Sci Int. 2001; 123: 215-23. Medline:11728750 doi:10.1016/S0379-0738 (01) 00557-6
11. Prinz M, Schifner L, Sebestyen JA, Bajda E, Tamariz J, Schaler RC, et al. Maximization of STR DNA typing success for touched objects. Progress in Forensic Genetics. International Congress Series, Volume 1288, Progress in Forensic Genetics 11 Proceedings of the 21st International ISFG Congress held in Ponta Delgada, the Azores, Portugal 13-16 September 2005. Amsterdam: Elsevier; 2006. p. 651-3.
12. Lindahl T. Instability and decay of the primary structure of DNA. Nature. 1993; 362: 709-15. Medline:8469282 doi:10.1038/362709a0 (Pubitemid 23125973)
13. Richards M, Smalley K, Sykes B, Hedges R. Archaeology and genetics: analysing DNA from skeletal remains. World Archaeol. 1993; 25: 18-28. Medline:16471022
14. Tuross N. The biochemistry of ancient DNA in bone. Experientia. 1994; 50: 530. Medline:7517371 doi:10.1007/BF01921721 (Pubitemid 24212378)
15. Bickley J, Short JK, McDowell DG, Parkes HC. Polymerase chain reaction (PCR) detection of Listeria monocytogenes in diluted milk and reversal of PCR inhibition caused by calcium ions. Lett Appl Microbiol. 1996; 22: 153-8. Medline:8936376 doi:10.1111/j.1472-765X.1996.tb01131.x
16. Taberlet P, Griffin S, Goossens B, Questiau S, Manceau V, Escaravage N, et al. Reliable genotyping of samples with very low DNA quantities using PCR. Nucleic Acids Res. 1996; 24: 3189-94. Medline:8774899 doi:10.1093/nar/24.16.3189
17. Schultes T, Hummel S, Herrmann B. Recognizing and overcoming inconsistencies in microsatellite typing of ancient DNA samples. Ancient Biomolecules. 1997; 1: 227-33.
18. Schmerer WM, Hummel S, Herrmann B. Reproducibility of aDNA typing. Anthropol Anz. 1997; 55: 199-206. Medline:9341087
19. Gerstenberger J, Hummel S, Schultes T, Hack B, Herrmann B. Reconstruction of a historical genealogy by means of STR analysis and Y-haplotyping of ancient DNA. Eur J Hum Genet. 1999; 7: 469-77. Medline:10352937 doi:10.1038/sj.ejhg. 5200322 (Pubitemid 29261332)
20. Hofreiter M, Serre D, Poinar HN, Kuch M, Paabo S. Ancient DNA. Reviews. 2001; 2: 353-9.
21. Hansen AJ, Mitchell DL, Wiuf C, Paniker L, Brand TB, Binladen J, et al. Crosslinks rather than strand breaks determine access to ancient DNA sequences from frozen sediments. Genetics. 2006; 173: 1175-9. Medline:16582426 doi:10.1534/genetics.106.057349 (Pubitemid 43945929)
22. Scholz M, Giddings I, Pusch CM. A polymerase chain reaction inhibitor of ancient hard and soft tissue DNA extracts is determined as human collagen type I. Anal Biochem. 1998; 259: 283-6. Medline:9618211 doi:10.1006/abio.1998.2676 (Pubitemid 28265592)
23. 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: 191-5. Medline:19083754 doi:10.1016/j.fsigen. 2007.02.006
24. ™ PCR amplification kit: a male specific, single amplification 17 Y-STR multiplex system. J Forensic Sci. 2006; 51: 64-75. Medline:16423225 doi:10.1111/j.1556- 4029.2005.00016.x
25. ™ PCR amplification kit user's manual. Foster City (CA): Applied Biosystems; 2006.
26. Willerslev E, Cooper A. Ancient DNA. Proc Biol Sci. 2005; 272: 3-16. Medline:15875564 doi:10.1098/rspb.2004.2813
27. Paabo S, Poinar H, Serre D, Jaenicke-Despres V, Hebler J, Rohland N, et al. Genetic analyses from ancient DNA. Annu Rev Genet. 2004; 38: 645-79. Medline:15568989 doi:10.1146/annurev. genet.37.110801.143214
28. Dixon LA, Dobbins AE, Pulker HK, Butler JM, Vallone 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: 33-44. Medline:16343834 doi:10.1016/j.forsciint.2005.11.011 (Pubitemid 44692068)
29. Edson SM, Ross JP, Coble MD, Parsons TJ, Barritt SM. Naming the dead - confronting the realities of rapid identification of degraded skeletal remains. Forensic Science review. 2004; 16: 63-90.
30. ™ results. J Forensic Sci. 2009; 54: 103-7. Medline:19018932 doi:10.1111/j.1556- 4029.2008.00914.x
31. Fatolitis L, Ballantyne J. The US Y-STR database. Profiles in DNA. 2008; 11: 13-4.
32. Willuweit S, Roewer L. International Forensic Y Chromosome User Group. Y chromosome haplotype reference database (YHRD): update. Forensic Sci Int; Genet. 2007; 1: 83-7. Medline:19083734 doi:10.1016/j.fsigen. 2007.01.017
33. Decker AE, Kline MC, Redman JW, Reid TM, Butler JM. Analysis of mutations in father-son pairs with 17 Y-STR loci. Forensic Sci Int; Genet. 2008; 2: e31-5. Medline:19083812 doi:10.1016/j.fsigen. 2007.08.016
34. redd AJ, Agellon AB, Kearney VA, Contreras VA, Karafet T, Park H, et al. Forensic value of 14 novel STRs on the human Y chromosome. Forensic Sci Int. 2002; 130: 97-111. Medline:12477629 doi:10.1016/S0379-0738 (02) 00347-X
35. Schoske R, Vallone PM, Ruitberg CM, Butler JM. Multiplex PCR design strategy used for the simultaneous amplification of 10 Y chromosome short tandem repeat (STR) loci. Anal Bioanal Chem. 2003; 375: 333-43. Medline:12589496
36. Gabriel MN, Huffine EF, Ryan JH, Holland MM, Parsons TJ. Improved MtDNA sequence analysis of forensic remains using a "miniprimer set" amplification strategy. J Forensic Sci. 2001; 46: 247-53. Medline:11305426
37. 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: 733-40. Medline:15317187 doi:10.1520/JFS2003269
38. Coble MD, Butler JM. Characterization of new miniSTR loci to aid analysis of degraded DNA. J Forensic Sci. 2005; 50: 43-53. Medline:15830996 doi:10.1520/JFS2004216
39. Parsons TJ, Huel R, Davoren J, Katzmarzyk C, Milos A, Selmanovic A, et al. Application of novel "mini-amplicon" STR multiplexes to high volume casework on degraded skeletal remains. Forensic Sci Int; Genet. 2007; 1: 175-9. Medline:19083751 doi:10.1016/j.fsigen. 2007.02.003