Application of Forensic DNA Phenotyping for Prediction of Eye, Hair and Skin Colour in Highly Decomposed Bodies

Abstract

In the last few years, predicting externally visible characteristics (EVCs) by adopting informative DNA molecular markers has become a method in forensic genetics that has increased its value, giving rise to an interesting field called "Forensic DNA Phenotyping" (FDP). The most meaningful forensic applications of EVCs prediction are those in which, having only a DNA sample isolated from highly decomposed remains, it is essential to reconstruct the physical appearance of a person. Through this approach, we set out to evaluate 20 skeletal remains of Italian provenance in order to associate them with as many cases of missing persons as possible. To achieve the intended goal, in this work we applied the HIrisPlex-S multiplex system through the conventional short tandem repeats (STR) method to confirm the expected identity of subjects by evaluating phenotypic features. To investigate the reliability and accuracy of the DNA-based EVCs prediction, pictures of the cases were compared as they were available to researchers. Results showed an overall prediction accuracy greater than 90% for all three phenotypic features-iris, hair, and skin colour-at a probability threshold of 0.7. The experimental analysis showed inconclusive results in only two cases; this is probably due to the characteristics of subjects who had an intermediate eye and hair colour, for which the DNA-based system needs to improve the prediction accuracy.

Keywords: HIrisPlex-S; eye colour; forensic DNA phenotyping; hair colour; identification; predictive DNA analysis; skin colour.

Figure 1

Illustration of the workflow for multiplex PCR phenotyping. Outlining of the main work steps: (a) sampling, (b) gDNA extraction, (c) multiplex PCR, purification of amplicons with exonuclease, SBE reactions, enzymatic purification with SAP, capillary electrophoresis, (d) integration of genetic data in the on-line table to obtain phenotypic results, and finally, comparison of these with the photograms of the individuals.

Figure 2

HIrisPlex-S SNP electropherogram obtained from sample I1. The electropherogram shows the amplified SNPs in the same order as those reported in Figure 3. Peaks show the different DNA bases, pointed using the following colour code: green (adenine), black (cytosine), blue (guanine), and red (timine).

Figure 3

Phenotype and trait prediction shown by samples I7, shown on the left, and I10, shown on the right. Charts taken from entering data in the tool available on the website https://HIrisPlex.erasmusmc.nl (last accessed on 17 February 2023). In the figure, “0” indicates if the input allele is not present; “1” indicates the presence of heterozygosity; and “2” shows the presence of the homozygous input allele; “NA” shows missing SNP.