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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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“The SLC45A2 variant rs16891982 is included in both the IrisPlex (57–59) and The Snipper 3.5 (60) models, and appeared in our COJO and fine-mapping analyses of rs12913832:GG individuals.”
InfluentialFrom paleness to albinism: Contribution of OCA2 exon 10 skipping to hypopigmentation
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Investigation of the MC1R Gene Sequence Variation Using Oxford Nanopore Sequencing
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“Insertion in position 16:89919342 (c.86.1 insA|p.Asn29fs, rs796296176) is an important marker of RHC included in the HIrisPlex-S predictor widely used in forensics and anthropology [11].”
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InfluentialEllegaard, M. R., Ebenesersdóttir, S. S., Moore, K. H. S., Petersen, A., Vågene, Å. J., Bieker, V. C., Denham, S. D., Cavalleri, G. L., Gilbert, E. H., Werge, T. M., et al. (2024) · iScience · doi:10.1016/j.isci.2024.111076
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Eye and hair color prediction of human DNA recovered from Lucilia sericata larvae
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“FDP could already be inferred for eye, hair, and skin color with accuracy rates approaching 80% [22–25].”
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Deep roots of admixture-related cognitive differences in the USAPreprint
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Using DNA to Develop a Profile of Phenotypic Characteristics of Historic Period Human Remains
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Forensic DNA Phenotyping: starting point to prediction model in Pernambuco population, Brazil
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Artificial intelligence enables scale, consistency, and rigor in forensic identity inference
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“Similarly, computational approaches enabled the prediction of outwardly visible phenotypic features from genetic data (41,42).”
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Self-citationForensic DNA phenotyping; Current updates and future prospects
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“Reckon with this evolutionary bar, a global model was established expanding 36 markers of 16 pigmentation genes (4).”
The present state of forensic identification of animals - a review
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“Forensic DNA Phenotyping (FDP) (e.g. eye and hair color prediction) [12–14] and the inference of biogeographical ancestry (BGA) emerged as valuable FDI tools in the last two decades [6, 15].”
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Self-citationLikelihood Ratios for physical traits in forensic investigations
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“For practicality, the values are selected on the basis of the HIrisPlex classification system [4, 5, 29].”
BackgroundMethodDNA Phenotyping of Remains from Elite Burials of the Khazar Period of Southern Russia
Fesenko, D., Aramova, O., Vdovchenkov, E., Ivanovsky, I., Fesenko, O. E., Polyakov, S. A., Faleeva, T., Filippova, M., Florinskaya, V. S., & Kornienko, I. (2023) · Molecular Biology · doi:10.1134/s0026893323040040 · Cited by 1
“The average length of the amplicons synthesized with a Phenotype Expert primer set (DNA Research Center) is approximately 79 bp, and successful genotyping of degraded ancient DNA is thus more likely than with the closest analog, which utilizes the SNaPshot method [9].”
MethodEVALUATION OF PYROMARK Q48 AUTOPREP WITH HIRISPLEX-S IN AN ITALIAN POPULATION SAMPLE
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“Department of Justice in forensic investigations, and validated on thousands of people from around the world (Chaitanya et al., 2018), the HIrisPlex-S imputes skin, hair, and eye color probabilities from 41 SNPs (with overlaps: 6 for eye color, 22 for hair color, and 36 for skin color), with a high degree of accuracy.”
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“Predictions can presently be made for characteristics such as skin, eye and hair colour as well as the donor’s biogeographical ancestry (Chaitanya et al. 2018; Cheung, Gahan & McNevin 2017, 2018).”
BackgroundSelf-citation[Forensic phenotyping: How far along?]
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Leonova, M. V., Reshetova, I. K., Zhur, K. V., Vashunina, D. A., Sharko, F. S., Maximov, N. G., Dobrovol’skaya, M. V., Makarov, N. A., & Prokhortchouk, E. (2026) · Acta Naturae · doi:10.32607/actanaturae.27986
“The eye, hair, and skin colors were pre - dicted using the HIrisPlex-S online tool [20].”
Early Neolithic genomes suggest a local origin for millet farmers in East Asia
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“Pigmentation phenotypes of hair, skin, and eyes were predicted with the HIrisPlex-S web tool ( 102 , 103 ) for each of the sequenced samples.”
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“…[3]; RetinaFace and ArcFace are widely used for face localization and discriminative embedding generation [4, 5]; and forensic DNA phenotyping systems such as IrisPlex and HIrisPlex-S demonstrate how informative SNPs can support probabilistic inference of externally visible characteristics [6, 7].”
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InfluentialBeentjes, I., de Bruin, D. D. S. H., Haagmans, M. A., van der Gaag, K. J., Rice, G., Kayser, M., Ralf, A., Sijen, T., & Henneman, P. (2026) · Forensic Science International: Genetics · doi:10.1016/j.fsigen.2026.103635
Self-citationHigh resolution of complex kinship cases using a dense SNP array.
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“Initiated in the early 2000s, FDP research initially focused on pigmentation traits such as eye, hair, and skin colour, which have well-understood genetic foundations [21–25].”
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“The phenotype of two individuals with a sequencing depth higher than 1 X , MART97 from the Early Neolithic period and BAL6 associated with the Cerny culture, was estimated using the HIrisPlex-S system (Chaitanya et al. 2018).”
Becerra‐Loaiza, D. S., González-Ortiz, N., Sat-Muñoz, D., Balderas-Peña, L.-M.-A., & Aguilar‐Velázquez, J. A. (2026) · Journal of Genome Biotechnology and Genetics · doi:10.3390/jgbg1020014
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“Phenotypic traits were inferred using the HIrisPlex-S online tool [22, 23].”
Exploring imputation performance of phenotype-associated SNPs for forensic prediction models
Köksal, Z., & Tillmar, A. (2026) · Scientific Reports · doi:10.1038/s41598-026-63340-2
“Among these, 31 test samples with diverse phenotypic traits were selected based on (a) hair, eye and skin colour predictions using the HIrisPlex-S prediction model 22 and (b) biogeographic ancestry (BGA) clusters estimated using the software STRUCTURE v2.”
InfluentialMorelli, S., Nerini, M., Carnemolla, G., Cattaneo, C., Biehler-Gomez, L., Mattia, M., & Pilli, E. (2026) · Forensic Science International: Genetics · doi:10.1016/j.fsigen.2026.103591
DNA Phenotyping: Predicting Physical Characteristics from Genetic Material
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GenoEye: A machine learning‐based framework for the prediction of intermediate eye color phenotypes
Dalfovo, D., Pallafacchina, G., Occhi, G., Marino, A., Vazza, G., Faccinetto, C., & Romanel, A. (2026) · Journal of Forensic Sciences · doi:10.1111/1556-4029.70403
“The success of this model led to the HIrisPlex and HIrisPlex-S systems, which incorporate additional markers for the simultaneous prediction of hair and skin color [ 4 ].”
Diepenbroek, M., Amorim, A., Anslinger, K., Arora, N., Amory, C., Ballard, D., Bekaert, B., Bouakaze, C., Costa, H. A., Decorte, R., et al. (2026) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2026.103576
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BR-FDP-SKIN: Brazilian forensic DNA Skin phenotyping based on machine learning models
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“For instance, Chaitanya et al. (2018) developed the HIrisPlex-S DNA detection system consisting of 41 phenotype-related single-nucleotide polymorphisms, which could predict the eye, hair, and skin colors of unknown individuals.”
Wang, M., Feng, Y., Luo, L., Wang, Z., Chen, J., Sun, Q., Huang, Y., Tang, R., Liu, C., & He, G. (2026) · International Journal of Legal Medicine · doi:10.1007/s00414-026-03798-x · Cited by 1
“The IrisPlex-S system, which leverages massively parallel sequencing and SNaPshot technologies, predicts three phenotypic traits, including skin color, eye color, and hair color, simultaneously making it highly suitable for forensic applications [85, 86].”
Nguidi, M., Amory, C., Xavier, C., Huber, G. E., Simão, F., Martínez, B., Caraballo, L., Gusmão, L., & Parson, W. (2026) · American Journal of Biological Anthropology · doi:10.1002/ajpa.70242
“Since this panel was developed for forensic applications, a set of 41 SNPs known as HIrisPlex-System (Chaitanya et al. 2018) was also incorporated to enable the prediction of externally visible traits.”
Forlenza, B. S., Ferreira, M. A., & Fridman, C. (2026) · Legal Medicine · doi:10.1016/j.legalmed.2026.102830
Impact of Semi-Permanent Nail Polish on Forensic DNA Profiling and Phenotyping from Fingernails
Fazio, G., Amurri, S., Giorgetti, A., Melchionda, F., Turchi, C., Pelotti, S., & Bini, C. (2026) · Genes · doi:10.3390/genes17030322
“Participants were invited to select the categories that best represented their physical appearance, following criteria reported in the literature, with three categories for eye colour, four for hair colour, and five for skin colour [19].”
Genetic affinities between the ancient Greek colony of Amvrakia and its metropolis
Psonis, N., Tabakaki, E., Vassou, D., Papadantonakis, S., Souleles, A., Nafplioti, A., Tsampazis, G. K., Papadopoulou, A., Xanthopoulos, K., Panailidis, P., et al. (2026) · Genome biology · doi:10.1186/s13059-026-03968-5 · Cited by 1
“Phenotypic estimation was performed for hair, eye, and skin color prediction using HirisPlex-S [82], as well as for specific metabolic traits (lactase persistence and sensitivity to fats), human muscle characteristics (muscle contraction type and muscle performance), and the genetic disorder of…”
Fazio, G., Gianfreda, D., Amurri, S., Corradini, B., Ferri, G., Ferrari, F., Borciani, I., Bini, C., Cecchi, R., Pelotti, S., et al. (2026) · Legal Medicine · doi:10.1016/j.legalmed.2026.102802
Using all available evidence to solve kinship cases
Egeland, T., & Marsico, F. L. (2025) · bioRxiv · doi:10.1007/s00414-026-03773-6
“This gives The integration of age-based directional evidence provides a statistical framework that can resolve relationship ambiguities in cases where traditional DNA evidence alone is insufficient.”
RF and ELM Applied to Predicting Hair Color Using DNA
Nowik, M., Baltierra, S., Hohl, D., Martínez, C. A., di Marco, M., García, M., González, R., Catanesi, C., & Barrientos, R. (2025) · International Conference of the Chilean Computer Science Society · doi:10.1109/sccc67219.2025.11420801
“…en t´ecnicas de ML (como por ejemplo, modelos lineales de regresi´on (MLR), bayesianos (NB), Support Vector Machines (SVM), RF, Redes Neuronales (ANN), XGBoost, Ordinal Regression (OR) y Stepwise Regression (SR)) o bien el uso de herramientas como HIrisPlex, HIrisPlex-S [11] y Snipper [12].”
DNA-based prediction of external ear morphology in the Chinese population: an exploratory study
Wang, X., Zhao, Z., Wu, J., Li, Y., Yang, Y., Liu, B., Zhou, C.-Y., Wang, C., Chen, X., & Song, F. (2025) · PeerJ · doi:10.7717/peerj.20169
“…compared to highly predictable traits, including eye color, hair color, and skin color, current ear morphology prediction models remain unsuitable for direct forensic or clinical implementation due to the relatively low accuracy ( Walsh et al., 2011 ; Walsh et al., 2013 ; Chaitanya et al., 2018 ).”
Epigenetika, azaz a „genetikán túl” II. rész
Petrétei, D., Lontai, M., & Pamjav, H. (2025) · Belügyi Szemle · doi:10.38146/bsz-ajia.2025.v73.i8.pp1617-1635
Köksal, Z., & Tillmar, A. (2025) · bioRxiv · doi:10.1101/2025.08.01.668059
“For this, 1,164 unique SNPs were identified that were utilized in 23 phenotypic trait prediction models (32,48–64) (“PredSNPs“; Supplementary Table 1).”
Tan, Y., Wei, S., & Wang, L. (2025) · Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition · doi:10.12182/20250760403
Aktueller Stand der „erweiterten DNA-Analyse“
Fleckhaus, J., Anslinger, K., Lutz-Bonengel, S., Vennemann, M., & Diepenbroek, M. (2025) · Rechtsmedizin · doi:10.1007/s00194-025-00768-2
Watson, J. L., Grisedale, K., Ward, J., & McNevin, D. (2025) · Australian Journal of Forensic Sciences · doi:10.1080/00450618.2025.2491376
“Similarly, the HIrisPlex System also uses MLR and a private database to report p-values for hair and eye colours, as well as hair shades 25–27 .”
InfluentialSapozhnikov, M., Medina-Paz, F., Castagnola, M. J., & Zapico, S. C. (2024) · Forensic Sciences · doi:10.3390/forensicsci4040043 · Cited by 3
Exploring ancestry inference of the Middle EastPreprint
Herrick, N., Ghemrawi, M., Singh, S., Mahfouz, R. A., & Walsh, S. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.08.15.607793
Self-citationVeselovskaya, E., Rashkovskaya, Y. V., Dyomin, A. S., Mustafin, K., & Alborova, I. (2024) · Russian Journal of Genetics · doi:10.1134/s1022795424700248
“According to the NGS data of autosomal SNPs, eye color was predicted using the online program HirisPlex [39].”
MC1R and age heteroclassification of face phenotypes in the Rio Grande do Sul population
Bettim, C. A. R., da Silva, A. V., Kahmann, A., Dorn, M., Alho, C. S., & Avila, E. (2023) · International Journal of Legal Medicine · doi:10.1007/s00414-023-03143-6
“…from DNA samples through prediction systems already developed and validated in the forensic community, such as Irisplex [3], HIrisplex [4], and HIrisplex-S [5] — multiplex assays targeting multiple SNPs in different genes together with statistical prediction models for eyes, hair, and skin color.”
DNA-Phenotyping of Remains from Elite Burials in the South of Russia in the Khazar Period
Fesenko, D., Aramova, O., Vdovchenkov, E., Ivanovsky, I., Fesenko, O. E., Polyakov, S. A., Faleeva, T., Filippova, M., Florinskaya, V. S., & Kornienko, I. V. (2023) · Молекулярная биология · doi:10.31857/s0026898423040055
Dielectrophoresis spectroscopy for nucleotide identification in DNA
Shahriar, M., Kabir, J., & Ding, P.-P. (2023) · Aspects of Molecular Medicine · doi:10.1016/j.amolm.2023.100009
Bronzkori nő szobrászi arcrekonstrukciója Balatonkeresztúr-Réti-dűlő lelőhelyről
Kustár, Á., Gerber, D., Fábián, S., Köhler, K., Mende, B. G., Szécsényi‐Nagy, A., & Kiss, V. (2022) · Anthropologiai Közlemények · doi:10.20330/anthropkozl.2022.63.3 · Cited by 2
Kaczmarek, M., & Zysek, W. (2022) · Postępy Biochemii · doi:10.18388/pb.2021_449 · Cited by 1
“6 [61].”
Doctoring Direct-to-Consumer Genetic Tests with DNA Spike-Ins
Ney, P. M., Bhattacharya, A., Ward, D., Ceze, L., Kohno, T., & Nivala, J. (2022) · bioRxiv · doi:10.1101/2022.04.01.486752
Tambuzzi, S., Maderna, E., Steffenini, D., Gentile, G., & Cattaneo, C. (2022) · Legal Medicine · doi:10.1016/j.legalmed.2022.102058
Not Only Olfaction: The Nose, Protagonist of the Diversity and Individuality of the Human Face
Cilli, E., & Gruppioni, G. (2021) · Human perspectives in health sciences and technology · doi:10.1007/978-3-030-75205-7_3
L’amplification génique : une révolution en médecine légale et en criminalistique
Ludes, B. (2021) · Bulletin de l Académie Nationale de Médecine · doi:10.1016/j.banm.2021.01.021 · Cited by 1
Neue Anwendungen der DNA-Analyse: Chancen und Risiken. Interdisziplinäre Technikfolgenabschätzung
Lang, A., Gschmeidler, B., Gruber, M.-C., Wuketich, M., Kinz, E., Karavas, V., Winkler, F., Schumann, S., Burri, N., & Griessler, E. (2020) · doi:10.3929/ethz-b-000452533
“Mit HIrisPlex-S kann zusätzlich noch die Hautpigmentierung analysiert werden (Breslin et al., 2019; Chaitanya et al., 2018).”
BackgroundAbouelhoda, M. I., & Naït-Ali, A. (2019) · Series in bioengineering · doi:10.1007/978-981-13-0956-4_1 · Cited by 2
Wang, C., Wen, D., Qu, W., Xu, R., Liu, Y., Jia, H., Tang, X., Li, J., & Zha, L. (2026) · Forensic Sciences Research · doi:10.3788/tfsr20230045
“The inference model of pigment-related phenotypes, such as hair colour [17] and skin colour [11], is the most widely studied model.”
Carracedo, Á., Ambroa-Conde, A., Blanco-Verea, A., Brión, M., de la Puente, M., Freire-Aradas, A., Mosquera-Miguel, A., Phillips, C., Rodríguez-López, A., & Lareu, M. (2026) · Forensic Sciences Research · doi:10.3788/tfsr20260061
D’Orio, E., Montagna, P., Mangione, M., & Francione, G. (2021) · Handbook of DNA Profiling · doi:10.1007/978-981-15-9364-2_58-1
Animal Population Ecology: References
Stangl, J., Carbone, D., & Chamard, V. (2021) · Hydraulic Fluid Power · doi:10.1002/9781119569145.ref5
Forensic DNA phenotyping - selected legal issues
Tomaszewski, T., Foremniak-Szadura, B., & Figaszewska, K. (2019) · Issues of Forensic Science · doi:10.34836/pk.2019.303.1
“The newly designed tool for profiling of pigmentation features is to allow making a physical description of a person in a manner that used not be possible to achieve, i.e. faster and less costly, due to simultaneous prediction of the three pigmentation characteristics (Chaitanya et al., 2018).”
Method
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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