INTERPRETATION OF STR PROFILES
Figure 6.8 The green loci from a profile produced using the AmpFlSTR® SGM Plus® kit. The size of each peak has been calculated along with the peak heights and areas. The first amelogenin peak was detected after 13.13 minutes (which is when data point 3570 was taken) and is estimated to be 103.33 bp long, the peak area is 20712 rfu and the peak height 4058 rfu and require further analysis. This comparison of unknown peaks to the allelic ladder can be done manually or by using the Genotyper® (Figure 6.10) or GeneMapperTM ID software (Applied Biosystems), which will compare all the unknown alleles in the profile to the allelic ladder.
Figure 6.9 The allelic ladder of the AmpFlSTR® SGM Plus® kit contains all the common alleles (see plate section for full-colour version of this figure)
Figure 6.10 The comparison of an unknown allele with the allelic ladder allows the THO1 alleles to be classified as 7 and 9.3. The size of the unknown allele and the allele in the allelic ladder are not identical but fall within 0.5 bp of each other. The 0.5 bp match windows are indicated by the shaded areas. The final result is a profile where alleles have been assigned to all of the peaks in the profile (Figure 6.11). The STR profiles should be identical regardless of the laboratory where the analysis took place or the variations in the methodology that may have been used to generate the profile, such as different DNA extraction and quantification techniques and capillary electrophoresis platforms. Loci that are included in different commercial kits should also produce identical results (Table 6.2).
Figure 6.11 assigns alleles. If the peaks in the profile deviate more than ±0.5 bp from the allelic ladder they are designate ‘off ladder’ (see plate section for full-colour version of this figure)
Table 6.2 Profiles have been generated from the same DNA sample using three commercial kits, the AmpFlSTR® SGM Plus®, AmpFlSTR® Identifiler® and the PowerPlex® 16. The alleles that are detected in the loci that are common between the kits are all identical
Butler J.M. (2005) Forensic DNA Typing: Biology and Technology and Genetics of STR Markers, second edition. Academic Press, London.
Butler J.M. (2006) Genetics and genomics of core short tandem repeat loci used in human identity testing. Journal of Forensic Sciences 51, 253-265.
Ruitberg C.M., Reeder D.J., and Butler J.M. (2001) STRBase: a short tandem repeat DNA database for the human identity testing community. Nucleic Acids Research 29, 320-322. (http://www.cstl.nist.gov/div831/strbase/)
1. Clayton, T.M., et al. (1995) Identification of bodies from the scene of a mass disaster using DNA amplification of short tandem repeat (STR) loci. Forensic Science International 76, 7-15.
2. Hagelberg, E., et al. (1991) Identification of the skeletal remains of a murder victim by DNA analysis. Nature 352, 427-429.
3. Jeffreys, A.J., et al. (1992) Identification of the skeletal remains of Josef Mengele by DNA analysis. Forensic Science International 56, 65-76.
4.Gill,P.,etal.(2004)AnassessmentofwhetherSNPswillreplaceSTRsinnationalDNAdatabases. Science and Justice 44, 51-53.
5.Ruitberg, C.M., et al. (2001) STRBase: a short tandem repeat DNA database for the human identity testing community. Nucleic Acids Research 29, 320-322.
6.Gill, P., et al. (1997) Considerations from the European DNA profiling group (EDNAP) concern- ing STR nomenclature. Forensic Science International 87, 185-192.
7.Andersen, J., et al. (1996) Report on the third EDNAP collaborative STR exercise. Forensic Science International 78, 83-93.
8.Budowle, B., et al. (1998) CODIS and PCR-based short tandem repeat loci: law enforce-ment tools.. In Second European Symposium on Human Identification, Promega Corporation, pp. 73-88.
9.Gill, P., et al. (1997) Report of the European DNA profiling group (EDNAP): an investigation of the complex STR loci D21S11 and HUMFIBRA (FGA). Forensic Science International 86, 25-33.
10.Gill, P., et al. (1994) Report of the European DNA profiling group (EDNAP) – towards standard- ization of short tandem repeat (Str) loci. Forensic Science International 65, 51-59.
11.Gill, P., et al. (2000) Report of the European Network of Forensic Science Institutes (ENSFI): formulation and testing of principles to evaluate STR multiplexes. Forensic Science International 108,1-29.
12.Fregeau,C.J.,etal.(2003)AmpFlSTR(R)ProfilerPIUS(TM)shorttandemrepeatDNAanalysis of casework samples, mixture samples, and nonhuman DNA samples amplified under reduced PCR volume conditions (25 mu L). Journal of Forensic Sciences 48, 1014-1034.
13.Krenke, B.E., et al. (2002) Validation of a 16-locus fluorescent multiplex system. Journal of Forensic Sciences 47, 773-785.
14.LaFountain, M.J., et al. (2001) TWGDAM validation of the AmpFlSTR Profiler Plus and AmpFlSTR COfiler STR multiplex systems using capillary electrophoresis. Journal of Forensic Sciences 46, 1191-1198.
15.Moretti, T.R., et al. (2001) Validation of short tandem repeats (STRs) for forensic usage: Per- formance testing of fluorescent multiplex STR systems and analysis of authentic and simulated forensic samples. Journal of Forensic Sciences 46, 647-660.
16.Moretti, T.R., et al. (2001) Validation of STR typing by capillary electrophoresis. Journal of Forensic Sciences 46, 661-676.
17.Cotton, E.A., et al. (2000) Validation of the AMPFlSTR (R) SGM Plus (TM) system for use in forensic casework. Forensic Science International 112, 151-161.
18.Thomson, J.A., et al. (1999) Validation of short tandem repeat analysis for the investigation of cases of disputed paternity. Forensic Science International 100, 1-16.
19.Wallin, J.M., et al. (1998) TWGDAM validation of the AmpFISTR (TM) Blue PCR amplification kit for forensic casework analysis. Journal of Forensic Sciences 43, 854-870.
20.Clayton, T.M., et al. (1995) Further validation of a quadruplex STR DNA typing system: A collaborative effort to identify victims of a mass disaster. Forensic Science International 76, 17-25.
21.Kimpton, C., et al. (1994) Evaluation of an automated DNA profiling system employing multi- plex amplification of 4 tetrameric Str loci. International Journal of Legal Medicine 106, 302-311.
22.Lygo, J.E., et al. (1994) The validation of short tandem repeat (STR) loci for use in forensic casework. International Journal of Legal Medicine 107, 77-89.
23.Kimpton, C.P., et al. (1996) Validation of highly discriminating multiplex short tandem repeat amplification systems for individual identification. Electrophoresis 17, 1283-1293.
24.Sparkes, R., et al. (1996) The validation of a 7-locus multiplex STR test for use in forensic case-work.2. Artefacts, casework studies and success rates. International Journal of Legal Medicine 109,195-204.
25.Sparkes, R., et al. (1996) The validation of a 7-locus multiplex STR test for use in forensic casework.1. Mixtures, ageing, degradation and species studies. International Journal of Legal Medicine 109, 186-194.
26.Budowle, B., et al. (1999) Population data on the thirteen CODIS core short tandem repeat loci in African Americans, US Caucasians, Hispanics, Bahamians, Jamaicans, and Trinidadians. Journal of Forensic Sciences 44, 1277-1286.
27.Collins, P.J., et al. (2004) Developmental validation of a single-tube amplification of the 13 CODIS STR loci, D2S1338, D19S433, and amelogenin: The AmpFlSTR (R) Identifiler (R) PCR amplification kit. Journal of Forensic Sciences 49, 1265-1277.
28.Sullivan, K.M., et al. (1993) A rapid and quantitative DNA sex test – fluorescence-based Pcr analysis of X-Y homologous gene amelogenin. Biotechniques 15, 636-638.
29.Ziegle, J.S., et al. (1992) Application of automated DNA sizing technology for genotyping microsatellite loci. Genomics 14, 1026-1031.
30.Lins, A.M., et al. (1996) Multiplex sets for the amplification of polymorphic short tandem repeat loci – silver stain and fluorescence detection. Biotechniques 20, 882-889.
31.Sprecher, C.J., et al. (1996) General approach to analysis of polymorphic short tandem repeat loci. Biotechniques 20, 266-267.
32.Buel, E., et al. (1998) Capillary electrophoresis STR analysis: comparison to gel-based systems. Journal of Forensic Sciences 43, 164-170.
33.Butler, J.M., et al. (1995) Application of dual internal standards for precise sizing of polymerase chain-reaction products using capillary electrophoresis. Electrophoresis 16, 974-980.
34.Heiger,D.N.,etal.(1990)SeparationofDNArestrictionfragmentsbyhigh-performancecapillary electrophoresis with low and zero cross-linked polyacrylamide using continuous and pulsed electric-fields. Journal of Chromatography 516, 33-48.
35.Butler, J.M., et al. (2004) Forensic DNA typing by capillary electrophoresis using the ABI Prism 310 and 3100 genetic analyzers for STR analysis. Electrophoresis 25, 1397-1412.
36.Madabhushi, R.S. (1998) Separation of 4-color DNA sequencing extension products in nonco-valently coated capillaries using low viscosity polymer solutions. Electrophoresis 19, 224-230.
37.Rosenblum, B.B., et al. (1997) Improved single-strand DNA sizing accuracy in capillary elec- trophoresis. Nucleic Acids Research 25, 3925-3929.
38.Butler, J. (2001) Forensic DNA Typing: Biology and Technology behind STR Markers. Academic Press.
39.Edwards, A., et al. (1991) DNA typing and genetic-mapping with trimeric and tetrameric tandem repeats. American Journal of Human Genetics 49, 746-756.
40.Hartzell, B., et al. (2003) Response of short tandem repeat systems to temperature and sizing methods. Forensic Science International 133, 228-234.
41.Elder, J.K., and Southern, E.M. (1983) Measurement of DNA length by gel-electrophoresis.2. Comparison of methods for relating mobility to fragment length. Analytical Biochemistry 128, 227-231.
42.Smith, R.N. (1995) Accurate size comparison of short tandem repeat alleles amplified by PCR. Biotechniques 18, 122-128.