Research Article| Volume 3, ISSUE 2, P128-137, March 2009

Download started.


Maximizing DNA profiling success from sub-optimal quantities of DNA: A staged approach

Published:February 02, 2009DOI:


      Obtaining genetic profiles from samples containing minimal amounts of DNA can be difficult. In forensic science, the vast majority of genetic profiles are generated using commercial kits that have been optimized for the amplification of a specific range of DNA concentrations. DNA extracted from many forensic samples falls below the kit manufacturers’ specified concentrations either because there is not enough total DNA in the extract or the extract is so dilute that not enough volume of the extract can be added to the PCR. In order to develop a method to maximize SGM Plus® and Identifiler® profiling success from samples with sub-optimal quantities of DNA, thermocycle numbers and/or the amount of PCR product injected during capillary electrophoresis (termed Enhancement) of PCR products were increased. Increasing the number of thermocycles from 28 to 30 and/or two phases of Enhancement of both 28 and 30 thermocycle PCR products resulted in an increased number of scorable peaks. As expected with low template amounts of DNA, many of the samples showed allelic drop-out, heterozygote imbalances and sporadic, large stutter peaks. Enhancement decreased the amount of allelic drop-out observed and did not affect stutter peak or heterozygous peak height ratios. Although the PCR reactions from these samples should always be replicated before a reportable consensus profile is reached, Phase 1 and 2 Enhancement can maximize the profiling success from each reaction. Finally, a flexible, staged approach using 28 or 30 thermocycle PCR in combination with the Enhancement techniques described here is proposed for processing samples with sub-optimal quantities of DNA.


      To read this article in full you will need to make a payment

      Purchase one-time access:

      Academic & Personal: 24 hour online accessCorporate R&D Professionals: 24 hour online access
      One-time access price info
      • For academic or personal research use, select 'Academic and Personal'
      • For corporate R&D use, select 'Corporate R&D Professionals'


      Subscribe to Forensic Science International: Genetics
      Already a print subscriber? Claim online access
      Already an online subscriber? Sign in
      Institutional Access: Sign in to ScienceDirect


        • 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
        • Gill P.
        Application of low copy number DNA profiling.
        Croatian Med. J. 2001; 42: 229-232
        • Whitaker J.P.
        • Cotton E.A.
        • Gill P.
        A comparison of the characteristics of profiles produced with the AMPFISTR® SGM Plus™ multiplex system for both standard and low copy number (LCN) STR DNA analysis.
        Forensic Sci. Int. 2001; 123: 215-223
        • Kloosterman A.D.
        • Kersbergen P.
        Efficacy and limits of genotyping low copy number DNA samples by multiplex PCR of STR loci.
        in: Brinkmann B. Carracedo A. Progress in Forensic Genetics 9. Elsevier, 2003: 795-798
        • Prinz M.
        • Schiffner L.
        • Sebestyen J.
        • Bajda E.
        • Tamariz J.
        • Shaler R.
        • Baum H.
        • Caragine T.
        Maximization of STR DNA typing success for touched objects.
        in: Amorim A. Corte-Real F. Morling N. Progress in Forensic Genetics 11. Elsevier, 2006: 651-653
        • Balogh M.K.
        • Burger J.
        • Bender K.
        • Schneider P.M.
        • Alt K.W.
        STR genotyping and mtDNA sequencing of latent fingerprint on paper.
        Forensic Sci. Int. 2003; 137: 188-195
        • Smith P.J.
        • Ballantyne J.
        Simplified low-copy-number DNA analysis by post-PCR purification.
        J. Forensic Sci. 2007; 52: 820-829
        • Lederer T.
        • Braunschweiger G.
        • Betz P.
        • Seidl S.
        Purification of STR-multiplex-amplified microsamples can enhance signal intensity in capillary electrophoresis.
        Int. J. Legal Med. 2002; 116: 165-169
        • Taberlet P.
        • Griffin S.
        • Goossens B.
        • Questiau S.
        • Manceau V.
        • Escaravage N.
        • Waits L.P.
        • Bouvet J.
        Reliable genotyping of samples with very low DNA quantities using PCR.
        Nucleic Acids Res. 1996; 24: 3189-3194
        • Grubbs F.
        Procedures for detecting outlying observations in samples.
        Technometrics. 1969; 11: 1-21
        • Stefansky W.
        Rejecting outliers in factorial designs.
        Technometrics. 1972; 14: 469-479