Research paper| Volume 25, P227-239, November 2016

Encoding of low-quality DNA profiles as genotype probability matrices for improved profile comparisons, relatedness evaluation and database searches

Published:September 21, 2016DOI:


      • Complex DNA profiles encoded as probability distributions for the genotypes of one or more contributors.
      • Formulas for calculating likelihood ratios for comparisons of genotype probability matrices.
      • Compare a reference profile with a complex profile or two complex profiles.
      • Database searches performed rapidly with uncertain genotypes both as query and included in the database.
      • Open-source software available.


      Many DNA profiles recovered from crime scene samples are of a quality that does not allow them to be searched against, nor entered into, databases. We propose a method for the comparison of profiles arising from two DNA samples, one or both of which can have multiple donors and be affected by low DNA template or degraded DNA. We compute likelihood ratios to evaluate the hypothesis that the two samples have a common DNA donor, and hypotheses specifying the relatedness of two donors. Our method uses a probability distribution for the genotype of the donor of interest in each sample. This distribution can be obtained from a statistical model, or we can exploit the ability of trained human experts to assess genotype probabilities, thus extracting much information that would be discarded by standard interpretation rules. Our method is compatible with established methods in simple settings, but is more widely applicable and can make better use of information than many current methods for the analysis of mixed-source, low-template DNA profiles. It can accommodate uncertainty arising from relatedness instead of or in addition to uncertainty arising from noisy genotyping. We describe a computer program GPMDNA, available under an open source licence, to calculate LRs using the method presented in this paper.


      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


        • Butler J.
        Advanced Topics in Forensic DNA Typing: Interpretation.
        Academic Press, 2014 (ISBN 9780124052130)
        • Steele C.D.
        • Balding D.J.
        Statistical evaluation of forensic DNA profile evidence.
        Annu. Rev. Stat. Appl. 2014; 1: 361-384
      1. P. Gill, J. Guiness, S. Iveson, The interpretation of DNA evidence (including low-template DNA). (July 2012).

      2. Scientific Working Group on DNA Analysis Methods, SWGDAM Interpretation Guidelines for Autosomal STR Typing., 2010.

        • Puch-Solis R.
        • Kirkham A.J.
        • Gill P.
        • Read J.
        • Watson S.
        • Drew D.
        Practical determination of the low template DNA threshold.
        Forensic Sci. Int. Genet. 2011; 5: 422-427
        • Robertson B.
        • Vignaux G.
        Interpreting Evidence: Evaluating Forensic Science in the Courtroom.
        Wiley, 1995
        • Balding D.
        • Steele C.
        Weight of Evidence for Forensic DNA Profiles.
        2nd ed. Wiley, 2015
        • Taroni F.
        • Biedermann A.
        • Bozza S.
        • Garbolino P.
        • Aitken C.
        Bayesian Networks for Probabilistic Inference and Decision Analysis in Forensic Science.
        Wiley, Chichester, UK2014
        • Fung W.K.
        • Hu Y.Q.
        Statistical DNA Forensics: Theory, Methods, Computation.
        Wiley Chichester, UK2008
        • Lu D.
        • Liu Q.
        • Wu W.
        • Zhao H.
        Mutation analysis of 24 short tandem repeats in Chinese Han population.
        Int. J. Legal Med. 2012; 126: 331-335
        • National Research Council
        The Evaluation of Forensic DNA Evidence.
        National Academy Press, Washington DC1996
        • Bright J.-A.
        • Evett I.W.
        • Taylor D.
        • Curran J.M.
        • Buckleton J.
        A series of recommended tests when validating probabilistic DNA profile interpretation software.
        Forensic Sci. Int. Genet. 2015; 5: 125-131
        • Cowell R.G.
        • Graversen T.
        • Lauritzen S.L.
        • Mortera J.
        Analysis of forensic DNA mixtures with artefacts.
        Appl. Statist. 2015; 64: 1-48
        • Gill P.
        • Buckleton J.
        A universal strategy to interpret DNA profiles that does not require a definition of low-copy- number.
        Forensic Sci. Int. Genet. 2010; 4: 221-227
        • 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
        • Buckleton J.
        • Triggs C.
        • Walsh S.
        Forensic DNA Evidence Interpretation.
        CRC Press, Boca Raton, Florida2005
        • O’Hagan A.
        • Buck C.
        • Daneshkhah A.
        • Eiser J.
        • Garthwaite P.
        • Jenkinson D.
        • Oakley J.
        • Rakow T.
        Uncertain Judgements Eliciting Experts’ Probabilities.
        Wiley, Chichester, UK2006
        • Cooke R.
        Experts in Uncertainty: Opinion and Subjective Probability in Science.
        Oxford University Press, New York1991
        • Buckleton J.
        • Kelly H.
        • Bright J.-A.
        • Taylor D.
        • Tvedebrink T.
        • Curran J.M.
        Utilising allelic dropout probabilities estimated by logistic regression in casework.
        Forensic Sci. Int. Genet. 2014; 9: 9-11

      Linked Article