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      Estimating the number of contributors to two-, three-, and four-person mixtures containing DNA in high template and low template amounts

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          Abstract

          Aim

          To develop guidelines to estimate the number of contributors to two-, three-, and four-person mixtures containing either high template DNA (HT-DNA) or low template DNA (LT-DNA) amounts.

          Methods

          Seven hundred and twenty-eight purposeful two-, three-, and four-person mixtures composed of 85 individuals of various ethnicities with template amounts ranging from 10 to 500 pg were examined. The number of alleles labeled at each locus and the number of labeled different and repeating alleles at each locus as well over all loci for 2 HT-DNA or 3 LT-DNA replicates were determined. Guidelines based on these data were then evaluated with 117 mixtures generated from items handled by known individuals.

          Results

          The number of different alleles over all loci and replicates was used to initially categorize mixtures. Ranges were established based on the averages plus and minus 2 standard deviations, and to encompass all observations, the maximum and the minimum values. To differentiate samples that could be classified in more than one grouping, the number of loci with 4 or more repeating or different alleles, which were specific to three- and four-person mixtures, were verified. Misclassified samples showed an extraordinary amount of allele sharing or stutter.

          Conclusions

          These guidelines proved to be useful tools to distinguish low template and high template two-, three-, and four-person mixtures. Due to the inherent higher probability of allele sharing, four-person mixtures were more challenging. Because of allelic drop-out, this was also the case for samples with very low amounts of template DNA or extreme mixture ratios.

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          Most cited references26

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          An investigation of the rigor of interpretation rules for STRs derived from less than 100 pg of DNA.

          By increasing the PCR amplification regime to 34 cycles, we have demonstrated that it is possible routinely to analyse <100 pg DNA. The success rate was not improved (without impairing quality) by increasing cycle number further. Compared to amplification of 1 ng DNA at 28 cycles, it was shown that increased imbalance of heterozygotes occurred, along with an increase in the size (peak area) of stutters. The analysis of mixtures by peak area measurement becomes increasingly difficult as the sample size is reduced. Laboratory-based contamination cannot be completely avoided, even when analysis is carried out under stringent conditions of cleanliness. A set of guidelines that utilises duplication of results to interpret profiles originating from picogram levels of DNA is introduced. We demonstrate that the duplication guideline is robust by applying a statistical theory that models three key parameters - namely the incidence of allele drop-out, laboratory contamination and stutter. The advantage of the model is that the critical levels for each parameter can be calculated. This information may be used (for example) to determine levels of contamination that can be tolerated within the strategy employed. In addition we demonstrate that interpreting one banded loci, where allele dropout could have occurred, using LR=1/2f(a) was conservative provided that the band was low in peak area. Furthermore, we demonstrate that an apparent mis-match between crime-stain and a suspect DNA profile does not necessarily result in an exclusion. The method used is complex, yet can be converted into an expert system. We envisage this to be the next step.
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            Interpreting low template DNA profiles.

            We discuss the interpretation of DNA profiles obtained from low template DNA samples. The most important challenge to interpretation in this setting arises when either or both of "drop-out" and "drop-in" create discordances between the crime scene DNA profile and the DNA profile expected under the prosecution allegation. Stutter and unbalanced peak heights are also problematic, in addition to the effects of masking from the profile of a known contributor. We outline a framework for assessing such evidence, based on likelihood ratios that involve drop-out and drop-in probabilities, and apply it to two casework examples. Our framework extends previous work, including new approaches to modelling homozygote drop-out and uncertainty in allele calls for stutter, masking and near-threshold peaks. We show that some current approaches to interpretation, such as ignoring a discrepant locus or reporting a "Random Man Not Excluded" (RMNE) probability, can be systematically unfair to defendants, sometimes extremely so. We also show that the LR can depend strongly on the assumed value for the drop-out probability, and there is typically no approximation that is useful for all values. We illustrate that ignoring the possibility of drop-in is usually unfair to defendants, and argue that under circumstances in which the prosecution relies on drop-out, it may be unsatisfactory to ignore any possibility of drop-in.
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              Development of an Alu-based, real-time PCR method for quantitation of human DNA in forensic samples.

              Determining the amount of human DNA extracted from a crime scene sample is an important step in DNA profiling. The forensic community relies almost entirely upon a technique (slot blot) to quantitate human DNA that is imprecise, time consuming, and labor intensive. We have previously described a method for quantitation of human DNA based on PCR amplification of a repetitive Alu sequence that uses a fluorescence plate reader. This manuscript describes and validates a variation of this assay using real-time PCR and SYBR Green I for quantitation. The advantages of the real-time assay over the plate reader assay are: reduced hands-on time, lower assay cost, and a greater dynamic range. The main disadvantage is the cost of the real-time instrument. However, for those forensic laboratories with access to a real-time instrument, this Alu-based assay has a dynamic range of 16 ng to 1 pg, is sensitive, specific, fast, quantitative, and uses only 2 microL of sample.
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                Author and article information

                Journal
                Croat Med J
                CMJ
                Croatian Medical Journal
                Croatian Medical Schools
                0353-9504
                1332-8166
                June 2011
                : 52
                : 3
                : 314-326
                Affiliations
                [1]Office of Chief Medical Examiner of the City of New York, The Department of Forensic Biology, New York, NY, USA
                Author notes
                Correspondence to:
Theresa Caragine
Department of Forensic Biology
Office of Chief Medical Examiner
421 East 26th Street
New York, NY 10016
 tcaragine@ 123456ocme.nyc.gov
                Article
                CroatMedJ_52_0314
                10.3325/cmj.2011.52.314
                3118719
                21674827
                e5cc899f-248a-4e1f-9786-091ccc343007
                Copyright © 2011 by the Croatian Medical Journal. All rights reserved.

                This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 29 April 2011
                : 31 May 2011
                Categories
                Forensic Science

                Medicine
                Medicine

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