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The HIrisPlex-S system for eye, hair and skin colour prediction from DNA: Introduction and forensic developmental validation
Open accessAbstract
Forensic DNA Phenotyping (FDP), i.e. the prediction of human externally visible traits from DNA, has become a fast growing subfield within forensic genetics due to the intelligence information it can provide from DNA traces. FDP outcomes can help focus police investigations in search of unknown perpetrators, who are generally unidentifiable with standard DNA profiling. Therefore, we previously developed and forensically validated the IrisPlex DNA test system for eye colour prediction and the HIrisPlex system for combined eye and hair colour prediction from DNA traces. Here we introduce and forensically validate the HIrisPlex-S DNA test system (S for skin) for the simultaneous prediction of eye, hair, and skin colour from trace DNA. This FDP system consists of two SNaPshot-based multiplex assays targeting a total of 41 SNPs via a novel multiplex assay for 17 skin colour predictive SNPs and the previous HIrisPlex assay for 24 eye and hair colour predictive SNPs, 19 of which also contribute to skin colour prediction. The HIrisPlex-S system further comprises three statistical prediction models, the previously developed IrisPlex model for eye colour prediction based on 6 SNPs, the previous HIrisPlex model for hair colour prediction based on 22 SNPs, and the recently introduced HIrisPlex-S model for skin colour prediction based on 36 SNPs. In the forensic developmental validation testing, the novel 17-plex assay performed in full agreement with the Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines, as previously shown for the 24-plex assay. Sensitivity testing of the 17-plex assay revealed complete SNP profiles from as little as 63 pg of input DNA, equalling the previously demonstrated sensitivity threshold of the 24-plex HIrisPlex assay. Testing of simulated forensic casework samples such as blood, semen, saliva stains, of inhibited DNA samples, of low quantity touch (trace) DNA samples, and of artificially degraded DNA samples as well as concordance testing, demonstrated the robustness, efficiency, and forensic suitability of the new 17-plex assay, as previously shown for the 24-plex assay. Finally, we provide an update to the publically available HIrisPlex website https://hirisplex.erasmusmc.nl/, now allowing the estimation of individual probabilities for 3 eye, 4 hair, and 5 skin colour categories from HIrisPlex-S input genotypes. The HIrisPlex-S DNA test represents the first forensically validated tool for skin colour prediction, and reflects the first forensically validated tool for simultaneous eye, hair and skin colour prediction from DNA.
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“Skin color (assessed genetically with the highly accurate predictor [79,93] was associated with cognitive ability (Model 1b, Table 5), but made no significant incremental contribution when ancestry was also in the model (Model 2, Table 5).”
From Global Ancestry and Cognitive Ability (2019) · cites this paper as [79]
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“Skin color (assessed genetically with the highly accurate predictor [79,93] was associated with cognitive ability (Model 1b, Table 5), but made no significant incremental contribution when ancestry was also in the model (Model 2, Table 5).”
From Global Ancestry and Cognitive Ability (2019) · cites this paper as [79]
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“A prediction was accepted without further explanation if in both runs the same phenotype showed a probability R 0.7 (Chaitanya et al., 2018).”
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“We investigated genotypes of 72 SNPs associated with phenotypes of interest in all individuals 42,63 , including the HIris-Plex-S SNPs to predict the pigmentation of skin, eyes and hair 64–66 .”
Bronze and Iron Age population movements underlie Xinjiang population history
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Self-citationDevelopments in forensic DNA analysis
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“We compared our dataset with the 41 SNPs published as HIrisPlex-S (Chaitanya et al., 2018;Walsh et al., 2017) and found an overlap of 30 SNPs (Table S1, ‘‘Nuclear capture’’ tab).”
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“Recently, a non-commercial MPS application of the HIrisPlex-S SNP panel for simultaneous prediction of eye, hair and skin color was published [25] for both the AmpliSeq-based Ion S5 System (Thermo Fisher Scientific) as well as the MiSeq FGx (Illumina) MPS platforms.”
MethodSelf-citationA genetic probe into the ancient and medieval history of Southern Europe and West Asia
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“Ancestry and admixture were assessed using principal component analyses, unsupervised ADMIXTURE [41], and admixture proportions were estimated using ADMIXTOOLS’ qpWave and qpAdm [1,44], and phenotypic variation was investigated [61,62].”
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“The simultaneous prediction of eye, hair, and skin color has already been validated forensically (20).”
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“Observations about the weak amplification rate of rs1470608 have been previously reported in the development of the SNapShot and MPS versions of the HIrisPlex-S (HPS) Panel [11,17,56].”
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“Examples include the extensively researched study of single nucleotide polymorphisms (SNPs) predictive for eye, hair, skin color, and biogeographical ancestry [35,36], which has become the most accurate and widely used in Forensic DNA Phenotyping.”
BackgroundGenetic ancestry plays a central role in population pharmacogenomics
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Self-citationEvaluation of supervised machine-learning methods for predicting appearance traits from DNA
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Self-citationGlobal Ancestry and Cognitive Ability
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“Skin color (assessed genetically with the highly accurate predictor [79,93] was associated with cognitive ability (Model 1b, Table 5), but made no significant incremental contribution when ancestry was also in the model (Model 2, Table 5).”
BackgroundMethodGenomic ancestry and social dynamics of the last hunter-gatherers of Atlantic France
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Self-citationPopulation relationships based on 170 ancestry SNPs from the combined Kidd and Seldin panels
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Self-citationMolecular markers used in forensic genetics
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“[43] (see appendix 5 FAQs) require that informed consent cover that the donor understands and agrees that the sample may be searched in national and non-national databases.”
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Self-citationExternal visible characteristics prediction through SNPs analysis in the forensic setting: a review
Tozzo, P., Politi, C., Delicati, A., Gabbin, A., & Caenazzo, L. (2021) · Frontiers in Bioscience-Landmark · doi:10.52586/4991 · Cited by 33
“rs2378249 ASIP/PIGU 20 Hair colour [37, 49]”
Kukla-Bartoszek, M., Szargut, M., Pośpiech, E., Diepenbroek, M., Zielińska, G., Jarosz, A., Piniewska-Róg, D., Arciszewska, J., Cytacka, S., Spólnicka, M., et al. (2020) · Forensic Science International: Genetics · doi:10.1016/j.fsigen.2020.102301 · Cited by 25
Self-citationForensic DNA phenotyping: Inferring phenotypic traits from crime scene DNA
Dabas, P., Jain, S. G., Khajuria, H., & Nayak, B. P. (2022) · Journal of Forensic and Legal Medicine · doi:10.1016/j.jflm.2022.102351 · Cited by 25
Salvo, N. M., Janssen, K., Kirsebom, M. K., Meyer, O. S., Berg, T., & Olsen, G. (2021) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2021.102620 · Cited by 24
Performance of four models for eye color prediction in an Italian population sample.
Salvoro, C., Faccinetto, C., Zucchelli, L., Porto, M., Marino, A., Occhi, G., Campos, G. D. L., & Vazza, G. (2019) · Forensic Science International: Genetics · doi:10.1016/j.fsigen.2019.03.008 · Cited by 24
Mandape, S. N., Budowle, B., Mittelman, K., & Mittelman, D. (2024) · Croatian Medical Journal · doi:10.3325/cmj.2024.65.249 · Cited by 27
“Since then, the capability of phenotypic SNPs to identify markers directly related to traits has progressed in their utility to predict visible traits, such as facial shape, skin pigmentation, eye color, hair color, baldness, and freckles, to name a few (78-81).”
Gerber, D., Szeifert, B., Székely, O., Egyed, B., Gyuris, B., Giblin, J. I., Horváth, A., Köhler, K., Kulcsár, G., Kustár, Á., et al. (2023) · Molecular Biology and Evolution · doi:10.1093/molbev/msad182 · Cited by 30
“For inferring pigmentation of the studied individuals, we used the HIrisPlex (Chaitanya et al., 2018) system supplemented with further variants obtained from SNPedia database (Cariaso and Lennon, 2012).”
MethodPredicting Physical Appearance from DNA Data—Towards Genomic Solutions
Pośpiech, E., Teisseyre, P., Mielniczuk, J., & Branicki, W. (2022) · Genes · doi:10.3390/genes13010121 · Cited by 25
“The IrisPlex tool for the genotyping and prediction of eye colour evolved to HIrisPlex [106] and finally to the HIrisPlex-S tool [109], which were developed based on the same strategy as IrisPlex.”
MethodSelf-citationFrom flesh to bones: Multi‐omics approaches in forensic science
Procopio, N., & Bonicelli, A. (2024) · PROTEOMICS · doi:10.1002/pmic.202200335 · Cited by 32
“Similarly, but using the HIrisPlex system, Chaitanya et al. analysed the SNPs profiles for 49 samples originated from bones or teeth from the World War II and obtained and eye and hair color predictions from all the skeletal samples analysed [342].”
MethodNortheastern Asian and Jomon-related genetic structure in the Three Kingdoms period of Gimhae, Korea
Gelabert, P., Blažytė, A., Chang, Y., Fernandes, D., Jeon, S., Hong, J. G., Yoon, J., Ko, Y., Oberreiter, V., Cheronet, O., et al. (2022) · Current Biology · doi:10.1016/j.cub.2022.06.004 · Cited by 22
Pushing the Boundaries: Forensic DNA Phenotyping Challenged by Single-Cell Sequencing
Diepenbroek, M., Bayer, B., & Anslinger, K. (2021) · Genes · doi:10.3390/genes12091362 · Cited by 23
“Furthermore, skin color is the most complex phenotypic trait to predict, and incomplete profiles make it even more difficult [34,35].”
BackgroundStephens, K., Barta, R., Fleming, K., Pérez, J. C., Wu, S., Snedecor, J., Holt, C., LaRue, B., & Budowle, B. (2023) · Forensic Science International: Genetics · doi:10.1016/j.fsigen.2023.102851 · Cited by 21
Gross, T., Fleckhaus, J., & Schneider, P. (2021) · Zeitschrift für Rechtsmedizin · doi:10.1007/s00414-021-02569-0 · Cited by 21
Prediction of eye, hair and skin colour in Latin Americans
Palmal, S., Adhikari, K., Mendoza‐Revilla, J., Fuentes‐Guajardo, M., de Cerqueira, C. C. S., Bonfante, B., Chacón-Duque, J. C., Sohail, A., Hurtado, M., Villegas, V., et al. (2021) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2021.102517 · Cited by 25
“…studies on prediction of pigmentation traits, exploiting GWAS findings, focused on eye colour [20–23] and these analyses were subsequently extended to hair [24,25] and skin [26]. r As a result, sets of SNPs have now been proposed for the simultaneous prediction of eye, hair and skin colour[27,28].”
Optimizing the genetic prediction of the eye and hair color for North Eurasian populations
Balanovska, E. V., Lukianova, E., Kagazezheva, J., Maurer, A. M., Leybova, N., Agdzhoyan, A., Gorin, I., Petrushenko, V., Zhabagin, M. K., Pylev, V. Y., et al. (2020) · BMC Genomics · doi:10.1186/s12864-020-06923-1 · Cited by 24
Forensic DNA phenotyping: a review on SNP panels, genotyping techniques, and prediction models
Terrado-Ortuño, N., & May, P. (2024) · Forensic Sciences Research · doi:10.1093/fsr/owae013 · Cited by 19
Staadig, A., Hedman, J., & Tillmar, A. (2023) · Genes · doi:10.3390/genes14040818 · Cited by 20
“The phenotype and ancestry informative markers have previously been identified and found to be informative [53,59,60].”
BackgroundMeyer, O., Lunn, M. M. B., Garcia, S. L., Kjærbye, A. B., Morling, N., Børsting, C., & Andersen, J. D. (2020) · PLoS ONE · doi:10.1371/journal.pone.0239131 · Cited by 20
“rs1126809 has previously been used as a marker for skin pigmentation [5, 44, 45].”
A review of the method and validation of the MiSeq FGx™ Forensic Genomics Solution
England, R., & Harbison, S. (2019) · WIREs Forensic Science · doi:10.1002/wfs2.1351 · Cited by 20
Ragazzo, M., Puleri, G., Errichiello, V., Manzo, L., Luzzi, L., Potenza, S., Strafella, C., Peconi, C., Nicastro, F., Caputo, V., et al. (2021) · Genes · doi:10.3390/genes12020221 · Cited by 19
“The HIrisPlex-S panel and the related software were previously validated elsewhere [16,19].”
BackgroundMethodOpening up forensic DNA phenotyping: the logics of accuracy, commonality and valuing
Hopman, R. (2020) · doi:10.1080/14636778.2020.1755638 · Cited by 19
“And indeed in 2012 and 2017 additional tests for eye- and hair color respectively were legalized, with skin color to be added in the near future (Chaitanya et al. 2018). Within the Dutch forensic context, I move from the research lab where researchers are working on the discovery of biomarkers that affect physical app…”
BackgroundOff-target phenotypes in forensic DNA phenotyping and biogeographic ancestry inference: A resource
Bradbury, C., Köttgen, A., & Staubach, F. (2018) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2018.10.010 · Cited by 22
Resutik, P., Aeschbacher, S., Krützen, M., Kratzer, A., Haas, C., Phillips, C., & Arora, N. (2023) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2023.102850 · Cited by 14
Advancement in Human Face Prediction Using DNA
Alshehhi, A., Almarzooqi, A., Alhammadi, K., Werghi, N., Tay, G. K., & AlSafar, H. S. (2023) · Genes · doi:10.3390/genes14010136 · Cited by 18
Searching for improvements in predicting human eye colour from DNA
Kukla‐Bartoszek, M., Teisseyre, P., Pośpiech, E., Karłowska-Pik, J., Zieliński, P., Woźniak, A., Boroń, M., Dąbrowski, M., Zubańska, M., Jarosz, A., et al. (2021) · International Journal of Legal Medicine · doi:10.1007/s00414-021-02645-5 · Cited by 19
Self-citationPrediction of Eye Colour in Scandinavians Using the EyeColour 11 (EC11) SNP Set
Meyer, O., Salvo, N. M., Kjærbye, A. B., Kjersem, M., Andersen, M. M., Sørensen, E., Ullum, H., Janssen, K., Morling, N., Børsting, C., et al. (2021) · Genes · doi:10.3390/genes12060821 · Cited by 16
Carratto, T. M. T., Marcorin, L., Valle-Silva, G. D., de Oliveira, M. D., Donadi, E., Simões, A., Castelli, E., & Mendes-Junior, C. (2021) · Zeitschrift für Rechtsmedizin · doi:10.1007/s00414-021-02554-7 · Cited by 16
“The HIrisPlex-S system was developed to predict skin color based on 36 SNPs, in addition to the previous models for eye and hair color prediction [39, 40].”
MethodLasisi, T. (2021) · American Journal of Physical Anthropology · doi:10.1002/ajpa.24264 · Cited by 20
“Davenport and Davenport (1907), for instance, claimed that “blue/grey and brown suffice”, the DNA phenotyping tool HIrisPlex-S claims to be able to predict eye color as being blue brown or “intermediate” (Chaitanya et al., 2018), and a recent genome-wide association study (GWAS) on admixed Latin Americans used the cat…”
BackgroundInfluentialChen, Y., Branicki, W., Walsh, S., Nothnagel, M., Kayser, M., & Liu, F. (2020) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2020.102395 · Cited by 15
Self-citationNimbkar, P. H., & Bhatt, V. D. (2022) · Forensic Science International · doi:10.1016/j.forsciint.2022.111352 · Cited by 15
Forensic DNA phenotyping: A promising tool to aid forensic investigation. Current situation
Serrano, A. C. (2020) · Revista Española de Medicina Legal · doi:10.1016/j.remle.2020.01.002 · Cited by 15
Marano, L. A., Andersen, J. D., Gonçalves, F., Garcia, A. L., & Fridman, C. (2019) · doi:10.1016/j.fsigss.2019.10.038 · Cited by 15
Forensic genetic investigation of human skeletal remains recovered from the La Belle shipwreck.
Ambers, A., Bus, M., King, J., Jones, B. M., Durst, J., Bruseth, J., Gill-King, H., & Budowle, B. (2019) · Forensic Science International · doi:10.1016/j.forsciint.2019.110050 · Cited by 15
Investigating the genetic architecture of eye colour in a Canadian cohort
Lona‐Durazo, F., Thakur, R., Pairo‐Castineira, E., Funderburk, K. M., Zhang, T., Kovacs, M. A., Choi, J., Jackson, I. J., Brown, K. M., & Parra, E. J. (2022) · iScience · doi:10.1016/j.isci.2022.104485 · Cited by 16
A review of scientific research in defensive cyberspace operation tools and technologies
Goethals, P., & Hunt, M. E. (2019) · Journal of Cyber Security Technology · doi:10.1080/23742917.2019.1601889 · Cited by 14
A review on the role of emerging revolutionary nanotechnology in forensic investigations
Tambo, F., & Ablateye, D. N. O. (2020) · doi:10.31018/jans.v12i4.2415 · Cited by 14
“However, eye, hair and skin color from DNA can be predicted using HirisPlex-S systems which in conjunction with SNP genotyping achieve essentially useful accuracies and have been validated for forensic analysis (Wirken et al., 2018).”
BackgroundPilli, E., Palamenghi, A., & Cattaneo, C. (2025) · Annals of the New York Academy of Sciences · doi:10.1111/nyas.15398 · Cited by 17
Sobral, A. F., Dinis‐Oliveira, R. J., & Barbosa, D. J. (2024) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2024.103163 · Cited by 14
Melchionda, F., Silvestrini, B., Robino, C., Bini, C., Fattorini, P., Martínez-Labarga, C., Angelis, F. D., Tagliabracci, A., & Turchi, C. (2022) · Genes · doi:10.3390/genes13101688 · Cited by 13
“The 41 SNPs of HirisPlex-S systems [2] were analysed in this study.”
BackgroundMethodInfluentialAt the beginnings of the funerary Megalithism in Iberia at Campo de Hockey necropolis
Vila, E. V., Bonilla, M. D., Morell, B., Olalde, Í., Muñoz, L. P. S.-B., Bella, S. D., Emslie, S. D., Martín, S. B., Salvador, Á. R., Fernández-Sánchez, D., et al. (2022) · Scientific Reports · doi:10.1038/s41598-022-13014-6 · Cited by 15
Wendt, F. R., Pathak, G. A., & Polimanti, R. (2022) · Nature Communications · doi:10.1038/s41467-022-35423-x · Cited by 12
Ravasini, F., Kabral, H., Solnik, A., de Gennaro, L., Montinaro, F., Hui, R., Delpino, C., Finocchi, S., Giroldini, P., Mei, O., et al. (2024) · Genome biology · doi:10.1186/s13059-024-03430-4 · Cited by 12
Life history and ancestry of the late Upper Palaeolithic infant from Grotta delle Mura, Italy
Higgins, O. A., Modi, A., Cannariato, C., Diroma, M. A., Lugli, F., Ricci, S., Zaro, V., Vai, S., Vazzana, A., Romandini, M., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-51150-x · Cited by 15
“Based on data from the 41 SNPs in the HIrisPlex-S panel 51 , the infantmostlikelyhadblueeyes,darkskinandcurlydarkbrown/almost black hair (Supplementary Data 23).”
Metadata
- Authors
- Chaitanya, L., Breslin, K., Zuñiga, S., Wirken, L., Pośpiech, E., Kukla-Bartoszek, M., Sijen, T., Knijff, P. D., Liu, F., Branicki, W., Kayser, M., & Walsh, S.
- Affiliations
- Erasmus MC (NL)
- Indiana University – Purdue University Indianapolis (US)
- Leiden University Medical Center (NL)
- Jagiellonian University (PL)
- Netherlands Forensic Institute (NL)
- Chinese Academy of Sciences (CN)
- Corresponding author
- Kayser, Manfred
- Walsh, Susan
- ORCID
- Venue
- Forensic Science International: Genetics
- Publisher
- Elsevier BV
- Published
- 2018-07
- Volume
- 35
- Pages
- 123-135
- ISSN
- 1872-4973 (ISSN-L)
- OpenAlex
- W2796803633
- Cited by
- 335
- References
- 58
- Citations by year
- 2026: 48 · 2025: 37 · 2024: 42 · 2023: 45 · 2022: 51 · 2021: 39 · 2020: 33 · 2019: 30 · 2018: 9
- FWCI
- 16.98
- Type
- journal article
- Language
- en
- Open access
- green
- ruj.uj.edu.pl
- Licence
- Locations
- Forensic Science International Genetics (publishedVersion)
- PubMed (publishedVersion)
- Homo Politicus (Academy of Humanities and Economics in Lodz) (submittedVersion, cc-by-nc-nd)
- EUR Research Repository (Erasmus University Rotterdam) (submittedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion)
- Leiden Repository (Leiden University) (submittedVersion)
- IUScholarWorks (Indiana University) (submittedVersion)
- Purdue University Indianapolis (Indiana University) (submittedVersion)
- Funders
- Indiana University-Purdue University Indianapolis
- Fundacja na rzecz Nauki Polskiej
- National Institute of Justice (2014-DN-BX-K031)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Keywords
- trace DNA, degraded DNA, statistical forecasting models, suspect identification, genotype probabilities
- MeSH terms
- Animals, DNA, Eye Color, Hair Color, Humans, Phenotype, Skin Pigmentation, Species Specificity, Reproducibility of Results, Polymerase Chain Reaction, Polymorphism, Single Nucleotide, Forensic Genetics, Genotyping Techniques
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