The interpretation of trace DNA analyses is currently the most controversial aspect of its use within the medico-legal systems. In placing a profile obtained from trace amounts of biological material found at the crime-scene into context, the analyst should take into account the potential for transfer of the material, the possible cellular origin of the DNA profile in question, the stochastic nature of the collection and analytical procedures and the possibility of artefacts confounding the true result. In most laboratories the analytical methods and statistical calculations employed for standard DNA typing are used for trace DNA - a process which is statistically and scientifically incorrect and which can bias calculations heavily against the defendant. In 2007, a high-profile case in Northern Ireland [180] raised questions regarding the appropriate interpretation methods of low template DNA and the subsequent UK Forensic Regulator's report recommended the development and validation of methods specific to trace DNA amounts [181].
Interpretation methods specific for trace DNA
Guidelines and models for the interpretation of trace level DNA profiles have existed for over a decade [77] but there has been no widespread implementation across laboratories performing low template analysis. Instead, the same profile interpretation and statistical methods are used as for high quantity samples. However, it is imperative that any analysis of a trace profile considers the four most common features of trace amplification: allele drop-out, decreased heterozygote balance, allele drop-in (stutter) and contamination, as described above. The effects of these can be minimized by the implementation of strict interpretation guidelines and specialized statistical models and can give the user reliable and robust results from trace DNA.
The most common method of ensuring the reliability of trace DNA profiles involves the use of detection thresholds. In order to eliminate background noise, a ~50 RFU threshold is commonly used as a calling threshold, termed the limit of detection (LOD). To ensure allelic drop-out does not result in false homozygote calls, a separate threshold, referred to as the low-template DNA threshold, T [182], the MIT (match interpretation threshold) [183], or the limit of quantitation (LOQ) [184] is set at 150-200 RFU. Only peaks above this threshold may be called as homozygous. The purpose behind this decision is to ensure that the probability of allele drop-out (Pr(D)) is minimized and so the probability of defining either a mixture as a single-source, or a heterozygote as a homozygote, is low. However, even with a strict threshold, drop-out may still occur. Therefore, it has been recommended that, instead of thresholds, a more continuous measure should be used which is modelled on the risk of dropout based on peak heights. In this manner, the evidence intensity can be included in the exclusion calculation and informative alleles below an arbitrary threshold value do not have to be automatically ignored
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Mixed trace DNA profiles add yet another level of complexity to the interpretative process. Mixed samples may be composed of one or more major contributors with high quantities of DNA and with a minor contributor present only at trace levels. Alternatively, all contributors' DNA within the mixture may be at trace levels. Furthermore, DNA truly derived from a single source could be treated as a mixture due to high stutter peaks being present and, therefore, wrongly interpreted as coming from multiple individuals. Given the high probability of drop-in, drop-out and increased stutter, estimating the number of contributors can be problematic, as can separating the contributors' genotypes at any given locus. Amplification bias may cause the minor contributor's alleles to drop out entirely at some loci or may cause over-amplification of some alleles, creating the appearance of a separate contributor. In particular, the increased stutter seen with trace DNA amplification [77,78,179] creates formidable problems for mixture interpretation. Although there are locus-specific stutter percentage guidelines for standard template amounts, none exist for trace DNA amounts. In addition, there is evidence that both forward and backward stutter increases with increasing allele length within a locus [20,194-196]. A difference in stutter percentage of 12% has been reported between alleles 10 and 17 at a commonly used locus [20]. From the limited data available, peak heights of backwards stutter may increase from 0%-4% at the smallest allele within a locus, to 12%-20% at the largest [194]. This difference may create a bias during interpretation, with longer molecular weight stutters being more likely to exceed thresholds and to be incorrectly designated as real. Alternatively, a peak at a stutter location of a small allele could potentially be perceived as a stutter when actually it represents a true allele from another source. Further efforts toward more precisely defining stutter peak expectations based on the laboratory specific methodologies in use, DNA template amount and allele height should assist profile interpretation.