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. 2022 Sep 21;13(10):1688.
doi: 10.3390/genes13101688.

Development and Validation of MPS-Based System for Human Appearance Prediction in Challenging Forensic Samples

Filomena Melchionda  1 , Beatrice Silvestrini  1   2 , Carlo Robino  3   4 , Carla Bini  5 , Paolo Fattorini  6 , Cristina Martinez-Labarga  7 , Flavio De Angelis  7 , Adriano Tagliabracci  1 , Chiara Turchi  1
Affiliations

Development and Validation of MPS-Based System for Human Appearance Prediction in Challenging Forensic Samples

Filomena Melchionda et al. Genes (Basel). .

Abstract

Forensic DNA phenotyping (FDP) provides the ability to predict the human external traits from unknown sample donors, directly from minute amounts of DNA found at the crime scene. We developed a MPS multiplex assay, with the aim of genotyping all 41 DNA markers included in the HIrisPlex-S system for simultaneous prediction of eye, hair and skin colours. Forensic samples such as blood, skeletal remains, touch DNA, saliva swab, artificially degraded samples together with individuals with known phenotypes and a set of 2800 M control DNA were sequenced on the Ion Torrent platform in order to evaluate the concordance testing results and the forensic suitability of the 41-plex MPS assay. The panel was evaluated by testing a different number of PCR cycles and the volume of reagents for library preparation. The study demonstrated that full and reliable profiles were obtained with 0.1-5 ng, even with high degraded DNA. The increment of the number of PCR cycles results in an improvement of correctly genotyping and phenotyping for samples with low amounts of degraded DNA but higher frequencies of artefacts were found. The high DNA degradation level did not influence the correct genotyping and phenotyping and the critical parameter affecting the result is the quantity of input DNA. Eye and hair colour was predicted in 92.60% of individuals and skin colour in 85.15% of individuals. The results suggest that this MPS assay is robust, highly sensitive and useful for human pigmentation prediction in the forensic genetic field.

Keywords: HIrisPlex-S system; MPS; degraded DNA; externally visible trait; forensic DNA phenotyping.

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Conflict of interest statement

The authors have declared no conflicts of interest.

Figures

Figure 1
Figure 1
Comparison of rDoC distribution observed in non-degraded samples pooled in two groups according to the DNA input used for amplification, named as follows: DNA input > 0.5 ng and DNA input < 0.5 ng. X-axis: polymorphisms included in the amplicons; Y-axis: value relative depth of coverage (rDoC).
Figure 2
Figure 2
Comparison of average rDoC distribution observed in non-degraded samples (DNA input > 0.5 ng and DNA input < 0.5 ng) and DNA degraded samples. X-axis: mean relative depth of coverage (rDoC) value; Y-axis: polymorphisms included in the amplicons together with the amplicon size.
Figure 3
Figure 3
Visualization of sequence alignment to hg19 for AMPL7160226302 (rs6119471) with IGV software. In the circle, the dimers present in the samples.
Figure 4
Figure 4
The figure shows the assessment of 41-SNPs panel sensitivity on control DNA samples. Reliable profiles were observed with 100 pg DNA input or higher. An increase in allelic drop-out events and decrease in no-call were observed with lower amount of DNA. * Libraries prepared with half reaction volume.
See this image and copyright information in PMC

References

    1. Kayser M. Forensic DNA Phenotyping: Predicting human appearance from crime scene material for investigative purposes. Forensic Sci. Int. Genet. 2015;18:33–48. doi: 10.1016/j.fsigen.2015.02.003. - DOI - PubMed
    1. Chaitanya L., Breslin K., Zuñiga S., Wirken L., Pośpiech E., Kukla-Bartoszek M., Sijen T., de Knijff P., Liu F., Branicki W., et al. The HIrisPlex-S system for eye, hair and skin colour prediction from DNA: Introduction and forensic developmental validation. Forensic Sci. Int. Genet. 2018;35:123–135. doi: 10.1016/j.fsigen.2018.04.004. - DOI - PubMed
    1. Walsh S., Liu F., Ballantyne K.N., van Oven M., Lao O., Kayser M. IrisPlex: A sensitive DNA tool for accurate prediction of blue and brown eye colour in the absence of ancestry information. Forensic Sci. Int. Genet. 2011;5:170–180. doi: 10.1016/j.fsigen.2010.02.004. - DOI - PubMed
    1. Walsh S., Liu F., Wollstein A., Kovatsi L., Ralf A., Kosiniak-Kamysz A., Branicki W., Kayser M. The HIrisPlex system for simultaneous prediction of hair and eye colour from DNA. Forensic Sci. Int. Genet. 2013;7:98–115. doi: 10.1016/j.fsigen.2012.07.005. - DOI - PubMed
    1. Børsting C., Morling N. Next generation sequencing and its applications in forensic genetics. Forensic Sci. Int. Genet. 2015;18:78–89. doi: 10.1016/j.fsigen.2015.02.002. - DOI - PubMed

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