Eye and Hair Color Prediction of Ancient and Second World War Skeletal Remains Using a Forensic PCR-MPS Approach

Abstract

To test the usefulness of the forensic PCR-MPS approach to eye and hair color prediction for aged skeletons, a customized version of the PCR-MPS HIrisPlex panel was used on two sets of samples. The first set contained 11 skeletons dated from the 3rd to the 18th centuries AD, and for each of them at least four bone types were analyzed (for a total of 47 samples). In the second set, 24 skeletons from the Second World War were analyzed, and only petrous bones from the skulls were tested. Good-quality libraries were achieved in 83.3% of the cases for the ancient skeletons and in all Second World War petrous bones, with 94.7% and 100% of the markers, respectively, suitable for SNP typing. Consensus typing was achieved for about 91.7% of the markers in 10 out of 11 ancient skeletons, and the HIrisPlex-S webtool was then used to generate phenotypic predictions. Full predictions were achieved for 3 (27.3%) ancient skeletons and 12 (50%) Second World War petrous bones. In the remaining cases, different levels of AUC (area under the receiver operating curve) loss were computed because of no available data (NA) for 8.3% of markers in ancient skeletons and 4.2% of markers in Second World War petrous bones. Although the PCR-based approach has been replaced with new techniques in ancient DNA studies, the results show that customized forensic technologies can be successfully applied to aged bone remains, highlighting the role of the template in the success of PCR-MPS analysis. However, because several typical errors of ancient DNA sequencing were scored, replicate tests and accurate evaluation by an expert remain indispensable tools.

SNP analysis of challenging bone DNA samples using the HID-Ion AmpliSeq™ Identity Panel: facts and artefacts

“…The origin of the allelic drop-in events in the analysis of SNP markers via PCR-MPS has been questioned by numerous researchers [ 10 , 12 , 25 , 27 , 42 , 43 ]. The error rate generated by the Ion Torrent technology is quite high (≥ 1%), but they consisted mainly in insertion/deletion artefacts [ 44 ] (whilst the Illumina technology is mainly subjected to misinsertions [ 45 ]).…”

Forensic DNA Phenotyping: Genes and Genetic Variants for Eye Color Prediction

“…In 2008, three studies highlighted the role of HERC2 and described the SNP located in intron 86, rs12913832:A/G, as a major eye color predictor strongly associated with OCA2 expression levels [ 13 , 24 , 25 , 41 ]. More recently, it was experimentally demonstrated that this SNP acts as an enhancer, regulating OCA2 transcription by distantly modulating chromatin folding [ 27 ].…”

“…Significant progress has been made with the implementation of next generation sequencing (NGS) technology to provide precious information about identity, biogeographic ancestry, paternity, and the possibility of adding massive parallel sequencing (MPS) with many DNA predictors, useful for forensic purposes such as FDP [ 8 , 9 , 10 ]. There are currently available a variety of genotyping assays based on MPS technologies developed to predict EVCs from DNA recovered in a crime scene, i.e., to reconstruct the appearance traits from highly decomposed remains, the biogeographic ancestry, the estimation of the age of the subject, and the age of bone remains, which certainly allow a more comprehensive approach toward the FDP applications [ 11 , 12 , 13 ]. The development of the MPS multiplex assay and the introduction of single-cell sequencing consent to enhance the EVC prediction, especially when low amounts of DNA or mixed traces were collected [ 14 , 15 ].…”

Cartilage Tissue in Forensic Science—State of the Art and Future Research Directions

“…Genetic phenotyping using next-generation sequencing (NGS) technology seems to be another interesting aspect of DNA isolation [86]. So far, DNA isolated from human remains from World War II allowed for determination of the eye and hair color in 100% of the studied cases [87]. Furthermore, cartilage tissue was used in phenotyping, attempting to reconstruct the deceased's face using alar cartilage dimensions, among other things [88].…”