Resources by Module

• Amplification Overview
• Locus Selection
• Multiplexing
• Contamination

Amplification Overview

Works Cited

1. Haas, S. A., M. Hild, A. P. Wright, T. Hain, D. Talibi, and M. M. Vingron. 2003. Genome-scale design of PCR primers and long oligomers for DNA microarrays. Nucleic Acids Res 31 (19): 5576–81
2. Farley, Mark A., and James J. Harrington, eds. 1991. Forensic DNA technology. Chelsea, MI: Lewis Publishers.
3. National Research Council, Committee on DNA Technology in Forensic Science. 1996. The evaluation of forensic DNA evidence: An update. Washington, D.C.: National Academy Press.
4. Butler, John M. 2005. Forensic DNA typing: Biology, technology, and genetics of STR markers. 2nd ed. Burlington, MA: Elsevier Academic Press.
5. Innis, Michael A., David H. Gelfand, and John J. Sninsky, eds. 1995. PCR strategies. San Diego, CA: Academic Press.
6. PREMIER Biosoft International. PCR primer design guidelines. http://www.premierbiosoft.com/tech_notes/PCR_Primer_Design
   (accessed August 31, 2006).
7. Burke, J. F. 1996. PCR: Essential techniques. Chichester, West Sussex, U.K.: John Wiley & Sons.
8. Erlich, Henry A., ed. 1989. PCR technology: Principles and applications for DNA amplification. New York: Stockton Press.
9. Newton, C. R., and A Graham. 1994. PCR. Oxford, U.K.: BIOS Scientific Publishers.
10. Haas, S. A., M. Hild, A. P. Wright, T. Hain, D. Talibi, and M. M. Vingron. 2003. Genome-scale design of PCR primers and long oligomers for DNA microarrays. Nucleic Acids Res 31 (19): 5576–81.
11. Sugimoto, N., S. Nakano, M. Yoneyama, and K. Honda. 1996. Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes. Nucleic Acids Res 24 (22): 4501–5.
12. Innis, Michael A., David H. Gelfand, John J. Sninsky, and Thomas J. White, eds. 1990. PCR protocols: A guide to methods and applications. San Diego, CA: Academic Press.
13. Rychlik, W., W. J. Spencer, and R. E. Rhoads. 1990. Optimization of the annealing temperature for DNA amplification in vitro. Nucleic Acids Res 18 (21): 6409–12.
14. Edwards, M., and R. Gibbs. PCR Methods and Applications, 3, S65-S75.
15. Mitsuhashi, M. 1996. Technical report: Part 2; Basic requirements for designing optimal PCR primers. J Clin Lab Anal 10 (5): 285–93.
16. Vallone, P. M., and J. M. Butler. 2004. AutoDimer: A screening tool for primer-dimer and hairpin structures. Biotechniques 37 (2): 226–31.

Online Links

• Applied Biosystems
  http://www.appliedbiosystems.com/
• AutoDimer homepage
  http://www.cstl.nist.gov/div831/strbase/AutoDimerHomepage/ AutoDimerProgramHomepage.htm
• BLAST
  http://www.ncbi.nlm.nih.gov/blast
• UNAFold download (was mFold)
  http://dinamelt.bioinfo.rpi.edu/download.php
• Oligonucleotide Properties Calculator
  http://www.basic.northwestern.edu/biotools/oligocalc.html
• Primer Design Software Packages
  http://www.cstl.nist.gov/div831/strbase/primer.htm

Locus Selection

Works Cited

1. U.S. Congress. House. 1994. The Violent Crime Control and Law Enforcement Act of 1994. Public Law 103-322.
2. Budowle, B. 2000. STR allele concordance between different primer sets: A brief summary. Profiles in DNA, Promega publication 3 (3):10–11. http://www.promega.com/profiles/303/ ProfilesinDNA_303_10.pdf.
3. Sparkes, R., C. Kimpton, S. Watson, N. Oldroyd, T. Clayton, L. Barnett, and J. Arnold, et al. 1996. The validation of a 7-locus multiplex STR test for use in forensic casework. (I). Mixtures, ageing, degradation and species studies. Int J Legal Med 109 (4): 186–94.
4. Sparkes, R., C. Kimpton, S. Gilbard, P. Carne, J. Andersen, N. Oldroyd, D. Thomas, A. Urquhart, and P. Gill. 1996. The validation of a 7-locus multiplex STR test for use in forensic casework. (II). Artefacts, casework studies and success rates. Int J Legal Med 109 (4): 195–204.
5. Kayser, M. et al. 1997. Evaluation of Y-chromosomal STRs: A multicenter study. International Journal of Legal Medicine 110(3): 125-133, 141-149.
6. Applied Biosystems. 2005. AmpFlSTR® SGM Plus® PCR Amplification Kit User's Manual.
7. Gill, P., L. Fereday, N. Morling, and P. M. Schneider. 2006. The evolution of DNA databases: Recommendations for new European STR loci. Forensic Sci Int 156 (2–3): 242–44.
8. Scientific Working Group on DNA Analysis Methods (SWGDAM) Y-STR Subcommittee. 2004. Report on the current activities of the Scientific Working Group on DNA Analysis Methods Y-STR Subcommittee. Forensic Science Communications 6 (3). http://www.fbi.gov/hq/lab/fsc/backissu/july2004/standards/ 2004_03_standards03.htm.
9. Kayser, M., A. Caglia, D. Corach, N. Fretwell, C. Gehrig, G. Graziosi, F. Heidorn, et al. 1997. Evaluation of Y-chromosomal STRs: A multicenter study. Int J Legal Med 110 (3): 125–33, 141–49.

Online Links

• ENFSI
  http://www.enfsi.org/
• FBI Laboratory Services
  http://www.fbi.gov/hq/lab/labhome.htm
• Forensic Science Service
  http://www.forensic.gov.uk/
• Human Genome Project
  http://ornl.gov/swci/techresources/Human_Genome/home.shtml
• INTERPOL
  http://www.interpol.int/

Multiplexing

Works Cited

1. Applied Biosystems. 1998. AmpFℓSTR® Profiler Plus™ PCR Amplification Kit user's manual.
2. Budowle, B. 2000. STR allele concordance between different primer sets: A brief summary. Profiles in DNA, Promega publication 3 (3): 10–1. http://www.promega.com/profiles/303/ ProfilesinDNA_303_10.pdf.
3. Applied Biosystems. 1998. AmpFℓSTR® Profiler Plus™ PCR Amplification Kit user's manual.
4. Applied Biosystems. 2005. AmpFℓSTR COfiler® PCR Amplification Kit user bulletin.
5. Applied Biosystems. 2005. AmpFℓSTR® Identifiler™ PCR Amplification Kit user's manual.
6. Grossman, P. D., W. Bloch, E. Brinson, C. C. Chang, F. A. Eggerding, S. Fung, D. M. Iovannisci, S. Woo, and E. S. Winn-Deen. 1994. High-density multiplex detection of nucleic acid sequences: Oligonucleotide ligation assay and sequence-coded separation. Nucleic Acids Res 22 (21): 4527–34.
7. Baron H., S. Fung, A. Aydin, S. Bahring, F. C. Luft, and H. Schuster. 1996. Oligonucleotide ligation assay (OLA) for the diagnosis of familial hypercholesterolemia. Nat Biotechnol 14 (10): 1279–82.
8. Applied Biosystems. 2005. AmpFℓSTR® Yfiler™ PCR Amplification Kit product bulletin.
9. Promega Corporation. 2001. PowerPlex® 1.1 System technical manual.
10. Promega Corporation. 2002. PowerPlex® 1.2 System technical manual.
11. Promega Corporation. 2001. PowerPlex® 2.1 System technical manual.
12. Promega Corporation. 2002. PowerPlex® 16 System technical manual.
13. Applied Biosystems. 1998. AmpFℓSTR® Profiler Plus™ PCR Amplification Kit user's manual.
14. Promega, PowerPlex^® 16 System Technical Manual, (2002).
15. Fregeau, C. J., K. L. Bowen, B. Leclair, I. Trudel, L. Bishop, and R. M. Fourney. 2003. AmpFℓSTR Profiler Plus short tandem repeat DNA analysis of casework samples, mixture samples, and nonhuman DNA samples amplified under reduced PCR volume conditions (25 microL). J Forensic Sci 48 (5): 1014–34.

Contamination

Works Cited

1. Jobling, M. A., and P. Gill. 2004. Encoded evidence: DNA in forensic analysis. Nature Reviews Genetics 5 (10): 739–51.
2. Gill, P., and A. Kirkham. 2004. Development of a simulation model to assess the impact of contamination in casework using STRs. J Sci 49 (3): 485–91.
3. Gill, P., J. Whitaker, C. Flaxman, N. Brown, and J. Buckleton. 2000. An investigation of the rigor of interpretation rules for STRs derived from less than 100 pg of DNA. Forensic Sci Int 112 (1): 17–40.
4. Gil, P. 2002. Role of short tandem repeat DNA in forensic casework in the UK: Past, present, and future perspectives. Biotechniques 32 (2): 366–8, 370, 372 passim.
5. Scherczinger, C. A., C. Ladd, M. T. Bourke, M. S. Adamowicz, P. M. Johannes, R. Scherczinger, T. Beesley, and H. C. Lee. 1999. A systematic analysis of PCR contamination. J Forensic Sci 44 (5): 1042–5.
6. Butler, John M. 2005. Forensic DNA typing: Biology, technology, and genetics of STR markers . 2nd ed. Burlington, MA: Elsevier Academic Press.

Online Links

• Forensic Science Service
  http://www.forensic.gov.uk/
• Section 6, Facilities, of the QAS
  http://www.fbi.gov/hq/lab/codis/forensic.htm