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Research Article| Volume 16, P208-215, May 2015

SNP-microarrays can accurately identify the presence of an individual in complex forensic DNA mixtures

Published:January 29, 2015DOI:https://doi.org/10.1016/j.fsigen.2015.01.009

      Highlights

      • We evaluate the usefulness of SNP-microarrays in forensic DNA mixtures.
      • One can accurately identify the presence of an individual in complex DNA mixtures.
      • A set of 3000 SNPs is sufficient for achieving necessary accuracy.

      Abstract

      Common forensic and mass disaster scenarios present DNA evidence that comprises a mixture of several contributors. Identifying the presence of an individual in such mixtures has proven difficult. In the current study, we evaluate the practical usefulness of currently available “off-the-shelf” SNP microarrays for such purposes. We found that a set of 3000 SNPs specifically selected for this purpose can accurately identify the presence of an individual in complex DNA mixtures of various compositions. For example, individuals contributing as little as 5% to a complex DNA mixture can be robustly identified even if the starting DNA amount was as little as 5.0 ng and had undergone whole-genome amplification (WGA) prior to SNP analysis. The work presented in this study represents proof-of-principle that our previously proposed approach, can work with real “forensic-type” samples. Furthermore, in the absence of a low-density focused forensic SNP microarray, the use of standard, currently available high-density SNP microarrays can be similarly used and even increase statistical power due to the larger amount of available information.

      Keywords

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      References

        • Carracedo A.
        • Schneider P.M.
        • Butler J.
        • Prinz M.
        Focus issue-analysis and biostatistical interpretation of complex and low template DNA samples.
        Forensic Sci. Int. Genet. 2012; 6: 277-278
        • Benschop C.
        • Haned H.
        • Sijen T.
        Consensus and pool profiles to assist in the analysis and interpretation of complex low template DNA mixtures.
        Int. J. Legal. Med. 2011; 127: 11-23
        • Gill P.
        • Curran J.
        • Neumann C.
        • Kirkham A.
        • Clayton T.
        • Whitaker J.
        • et al.
        Interpretation of complex DNA profiles using empirical models and a method to measure their robustness.
        Forensic Sci. Int. Genet. 2008; 2: 91-103
        • Haned H.
        • Slooten K.
        • Gill P.
        Exploratory data analysis for the interpretation of low template DNA mixtures.
        Forensic Sci. Int. Genet. 2012; 6: 762-774
        • Gill P.
        • Gusmao L.
        • Haned H.
        • Mayr W.R.
        • Morling N.
        • Parson W.
        • et al.
        DNA commission of the international society of forensic genetics: recommendations on the evaluation of STR typing results that may include drop-out and/or drop-in using probabilistic methods.
        Forensic Sci. Int. Genet. 2012; 6: 679-688
      1. SWGDAM, SWGDAM interpretation guidelines for autosomal STR typing by forensic DNA testing laboratories (2010).

        • Mitchell A.A.
        • Tamariz J.
        • O'Connell K.
        • Ducasse N.
        • Budimlija Z.
        • Prinz M.
        • et al.
        Validation of a DNA mixture statistics tool incorporating allelic drop-out and drop-in.
        Forensic Sci. Int. Genet. 2012; 6: 749-761
        • Homer N.
        • Szelinger S.
        • Redman M.
        • Duggan D.
        • Tembe W.
        • Muehling J.
        • et al.
        Resolving individuals contributing trace amounts of DNA to highly complex mixtures using high-density SNP genotyping microarrays.
        PLoS Genet. 2008; 4: e1000167
        • Egeland T.
        • Fonnelop A.E.
        • Berg P.R.
        • Kent M.
        • Lien S.
        Complex mixtures: a critical examination of a paper by Homer et al.
        Forensic Sci. Int. Genet. 2012; 6: 64-69
        • Voskoboinik L.
        • Darvasi A.
        Forensic identification of an individual in complex DNA mixtures.
        Forensic Sci. Int. Genet. 2011; 5: 428-435
        • The International HapMap Project
        Nature. 2003; 426: 789-796
        • Cavalli-Sforza L.L.
        The human genome diversity project: past, present and future.
        Nat. Rev. Genet. 2005; 6: 333-340
        • Matise T.C.
        • Chen F.
        • Chen W.
        • De La Vega F.M.
        • Hansen M.
        • He C.
        • et al.
        A second-generation combined linkage physical map of the human genome.
        Genome Res. 2007; 17: 1783-1786
        • Curran J.M.
        • Gill P.
        • Bill M.R.
        Interpretation of repeat measurement DNA evidence allowing for multiple contributors and population substructure.
        Forensic Sci. Int. 2005; 148: 47-53
        • Haned H.
        • Slooten K.
        • Gill P.
        Exploratory data analysis for the interpretation of low template DNA mixtures.
        Forensic Sci. Int. Genet. 2012; 6: 762-774
        • Tvedebrink T.
        • Eriksen P.S.
        • Mogensen H.S.
        • Morling N.
        Estimating the probability of allelic drop-out of STR alleles in forensic genetics.
        Forensic Sci. Int. Genet. 2009; 3: 222-226
        • Lohmueller K.E.
        • Rudin N.
        Calculating the weight of evidence in low-template forensic DNA casework.
        J. Forensic Sci. 2013; 58: S243-249
        • Gill P.
        • Kirkham A.
        • Curran J.
        LoComatioN: a software tool for the analysis of low copy number DNA profiles.
        Forensic Sci. Int. 2007; 166: 128-138
        • Biggs M.C.
        Constrained minimization using recursive quadratic programming.
        in: Dixon L.C.W. Szergo G.P. Towards Global Optimization. Elsevier, North-Holland, Amsterdam1975: 341-349
        • Gill P.
        • Kirkham A.
        Development of a simulation model to assess the impact of contamination in casework using STRs.
        J. Forensic Sci. 2004; 49: 485-491
        • Balding D.J.
        • Buckleton J.
        Interpreting low template DNA profiles.
        Forensic Sci. Int. Genet. 2009; 4: 1-10
        • Zeng Z.
        • Wang L.
        • Feng Q.
        • Zhang L.
        • Lee L.
        • Yue Y.
        • et al.
        Evaluation of 96 SNPs in 14 populations for worldwide individual identification.
        J. Forensic Sci. 2012; 57: 1031-1035
        • Fondevila M.
        • Phillips C.
        • Santos C.
        • Freire Aradas A.
        • Vallone P.M.
        • Butler J.M.
        • et al.
        Revision of the SNPforID 34-plex forensic ancestry test: assay enhancements, standard reference sample genotypes and extended population studies.
        Forensic Sci. Int. Genet. 2012; 7: 63-74
        • Ruiz Y.
        • Phillips C.
        • Gomez-Tato A.
        • Alvarez-Dios J.
        • Casares de Cal M.
        • Cruz R.
        • et al.
        Further development of forensic eye color predictive tests.
        Forensic Sci. Int. Genet. 2012; 7: 28-40
        • Walsh S.
        • Lindenbergh A.
        • Zuniga S.B.
        • Sijen T.
        • de Knijff P.
        • Kayser M.
        • et al.
        Developmental validation of the IrisPlex system: determination of blue and brown iris colour for forensic intelligence.
        Forensic Sci. Int. Genet. 2011; 5: 464-471
        • Branicki W.
        • Brudnik U.
        • Wojas-Pelc A.
        Interactions between HERC2, OCA2 and MC1R may influence human pigmentation phenotype.
        Ann. Hum. Genet. 2009; 73: 160-170
        • Van Neste C.
        • Van Nieuwerburgh F.
        • Van Hoofstat D.
        • Deforce D.
        Forensic STR analysis using massive parallel sequencing.
        Forensic Sci. Int. Genet. 2012; 6: 810-818