LoCIM-tool: An expert's assistant for inferring the major contributor's alleles in mixed consensus DNA profiles

When dealing with mixed DNA profiles where contributors have donated DNA in unequal amounts, it is often useful to deduce the genotype of the major contributor. Inference of a major contributor's genotype empowers storage of the DNA profile in a DNA database (DDB), which is especially of interest in cases without a suspect. When a major contributor's genotype cannot be inferred straightforwardly, for instance because low level components are present, replicate analyses can be prepared and combined into a consensus profile [1]. Here we describe an automated and freely available tool to deduce the major component's alleles in mixed consensus DNA profiles. In these consensus profiles, theoretical peak heights (PHs) are assigned to the alleles using the sum of the PHs in the individual amplifications. The LoCIM-tool (Locus Classification & Inference of the Major-tool) uses these PHs plus parameters on the stochastic threshold, heterozygote balance (HB) and major to minor(s) ratio to classify every locus as a type 1, type 2 or type 3 locus, which represent classes of increasing complexity. Based on the type of locus, the LoCIM-tool applies an inclusion percentage to deduce the alleles for the major contributor. Using the LoCIM-tool, 99.9% of all type 1 loci and 96.7% of all type 2 loci were inferred correctly from a large set of consensus DNA profiles that were generated from mixtures varying for the mixture ratio, amount of DNA per contributor, number of contributors, quality of DNA, and allele sharing among the contributors. For type 3 loci, we aimed at inferring the major contributor's alleles and possibly extra alleles, which occurred for 87.2% of all type 3 loci analysed using the LoCIM-tool. When compared to the overall results of manual inference by a group of forensic scientists, the LoCIM-tool obtains a higher percentage of correctly inferred loci. From our results, we conclude that the LoCIM-tool presents an objective, uniform and fast method to reliably deduce alleles of a major component.