Forensic Science International: Genetics
Volume 2, Issue 2 , Pages 108-125 , March 2008

A quadruplex real-time qPCR assay for the simultaneous assessment of total human DNA, human male DNA, DNA degradation and the presence of PCR inhibitors in forensic samples: A diagnostic tool for STR typing

Received 28 February 2007 ,Revised 14 August 2007 ,Accepted 20 September 2007.

References 

  1. Walker JA, Hedges DJ, Perodeau BP, Landry KE, Stoilova N, Laborde ME, et al. Multiplex polymerase chain reaction for simultaneous quantitation of human nuclear, mitochondrial, and male Y-chromosome DNA: application in human identification. Anal. Biochem. 2005;337:89–97
  2. Alonso A, Martin P. A real-time PCR protocol to determine the number of Amelogenin (X-Y) gene copies from forensic DNA samples. Methods Mol. Biol. 2005;297:31–44
  3. Horsman KM, Hickey JA, Cotton RW, Landers JP, Maddox LO. Development of a human-specific real-time PCR assay for the simultaneous quantitation of total genomic and male DNA. J. Forensic Sci. 2006;51:758–765
  4. Nicklas JA, Buel E. Simultaneous determination of total human and male DNA using a duplex real-time PCR assay. J. Forensic Sci. 2006;51:1005–1015
  5. Niederstätter H, Köchl S, Grubweiser 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
  6. Butler JM, Shen Y, McCord B. The development of reduced size STR amplicons as tools for analysis of degraded DNA. J. Forensic Sci. 2003;48:1054–1064
  7. Shewale J, Nasir H, Schneida E, Gross AM, Budowle B, Sinha S. Y-chromosome STR system, Y-PLEX™ 12 for forensic casework: development and validation. J. Forensic Sci. 2004;49:1278–1290
  8. Krenke BE, Viculis L, Richard ML, Prinz M, Milne SC, Ladd C, et al. Validation of a male-specific, 12-locus fluorescent short tandem repeat (STR) multiplex. Forensic Sci. Int. 2006;151:111–124
  9. Mulero JJ, Chang CW, Calandro LM, Green RL, Li Y, Johnson CL, et al. Development and validation of the AmpFlSTR® Yfiler™ PCR amplification kit: a male specific, single amplification 17 Y-STR multiplex system. J. Forensic Sci. 2006;51:64–75
  10. Anderson S, Bankier AT, Barrell BG, de Bruijn MHL, Coulson AR, Drouin J, et al. Sequence and organization of the mitochondrial genome. Nature. 1981;290:457–465
  11. Holland MM, Parsons TJ. Mitochondrial DNA sequence analysis—validation and use for forensic casework. Forensic Sci. Rev. 1999;11(1):21–50
  12. Reynolds R, Walker K, Varlaro J, Allen M, Clark E, Alvararen M, et al. Detection of sequence variation in the HVII region of the human mitochondrial genome in 689 individuals using immobilized sequence specific oligonucleotide probes. J. Forensic Sci. 2000;45:1210–1231
  13. Date Chong M, Calloway CD, Klein SB, Orrego C, Buoncristiani MR. Optimization of a duplex amplification and sequencing strategy for the HVI/HVII regions of human mitochondrial DNA for forensic casework. Forensic Sci. Int. 2005;154:137–148
  14. Sobrino B, Brion M, Carracedo A. SNPs in forensic genetics: a review on SNP typing methodologies. Forensic Sci. Int. 2005;154:181–194
  15. Ray DA, Walker JA, Hall A, Llewllyn B, Ballantyne J, Christian AT, et al. Inference of human geographic origins using Alu insertion polymorphisms. Forensic Sci. Int. 2005;153:117–124
  16. Sun G, Kaushal R, Pal P, Wolujewicz M, Smelser D, Cheng H, et al. Whole genome amplification: relative efficiencies of the current methods. Leg. Med. 2005;7:279–286
  17. Swango KL, Timken MD, Date Chong M, Buoncristiani MR. A quantitative PCR assay for the assessment of DNA degradation in forensic samples. Forensic Sci. Int. 2006;158:14–26
  18. Swango KL, Hudlow WR, Timken MD, Buoncristiani MR. Developmental validation of a multiplex qPCR assay for assessing the quantity and quality of nuclear DNA in forensic samples. Forensic Sci. Int. 2007;170:35–45
  19. Revised Validation Guidelines, Scientific Working Group on DNA Analysis Methods (SWGDAM), Forensic Sci. Comm. 6 (3) (2004), http://www.fbi.gov/hq/lab/fsc/backissu/july2004/standards/2004_03_standards02.htm.
  20. Lo YMD, Tein MSC, Lau TK, Haines CJ, Leung TN, Poon PMK, et al. Quantitative analysis of fetal DNA in maternal plasma and serum: implications for noninvasive prenatal diagnosis. Am. J. Hum. Genet. 1998;62:768–775
  21. Gill P, Jeffreys AJ, Werrett DJ. Forensic application of DNA ‘fingerprints’. Nature. 1985;318:577–579
  22. Efficiency of PCR Reactions, Stratagene Application Note #10 for the Mx4000 Multiplex Quantitative PCR System, http://www.stratagene.com/lit_items/appnotes10.pdf.
  23. M.D. Timken, K.L. Swango, C. Orrego, M. Date Chong, M.R. Buoncristiani, Quantitation of DNA for forensic DNA typing by qPCR (quantitative PCR): singleplex and multiple modes for nuclear and mitochondrial genomes, and the Y chromosome, National Criminal Justice Reference Service, 2005, NCJ publication number 210302.
  24. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank: update. Nucleic Acids Res. 2004;32:Database issue: D23–D26
  25. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, et al. The human genome browser at UCSC. Genome Res. 2002;12:996–1006
  26. van Oorschot RAH, Gutowski SJ, Robinson SL. HUMTH01: amplification, species specificity, population genetics and forensic applications. Int. J. Legal Med. 1994;107:121–126
  27. Crouse CA, Schumm J. Investigation of species specificity using nine PCR-based human STR systems. J. Forensic Sci. 1995;40:952–956
  28. User's Manual Quantifiler Kits, Applied Biosystems part number 4344790 Rev. B, 2003.
  29. Hoorfar J, Malorny B, Abdulmawjood A, Cook N, Wagner M, Fach P. Practical considerations in design of internal amplification controls for diagnostic PCR assays. J. Clin. Microbiol. 2004;42:1863–1868

PII: S1872-4973(07)00159-7

doi: 10.1016/j.fsigen.2007.09.001

Forensic Science International: Genetics
Volume 2, Issue 2 , Pages 108-125 , March 2008