Forensic DNA Phenotyping: starting point to prediction model in Pernambuco population, Brazil




Pigmentation genes; Miscigenated Population; Brazil; SNPs; Phenotypic prediction; Artificial intelligence.


The study of Externally Visible Characteristics (EVC) of pigmentation associated with SNPs (Single Nucleotide Polymorphisms) has become a target in the forensic field due to the possibility of phenotypically characterizing an individual. In Brazil, there are few data that shows the evaluation of some these markers, so further studies are necessary to understand better the pigmentation process related to genetic markers. The aim of this study was to test the association between 8 SNPs  present in HIrisplex tool and EVC to provide a starting point for the development of prediction models for heterogeneous populations like the one in Pernambuco. Were evaluated 176 individuals by associations between self-reported eye, hair and skin color data and polymorphisms. Artificial intelligence tools were used for the prediction models. Significant associations were found between rs1800404 (OCA2), rs6058017 (ASIP), rs16891982 (SLC45A2) and rs1426654 (SLC24A5) with (EVC). The prediction models evaluated showed satisfactory prediction rates, rates above 60% for skin color and above 70% for eyes and hair. The associations found in our data show the importance of SNPs evaluation used in DNA Phenotyping, because of its ability to provide new information in the context of criminal investigations. Our data indicate that is possible to use molecular information to predict phenotypes in miscigenated populations, like the Brazilian population. These polymorphisms could be possible phenotypic predictors for the Pernambuco population.


Adhikari, K., Mendoza-Revilla, J., Sohail, A., Fuentes-Guajardo, M., Lampert, J., Chacón-Duque, J. C., & Ruiz-Linares, A. (2019). A GWAS in Latin Americans highlights the convergent evolution of lighter skin pigmentation in Eurasia. Nature Communications, 10(1), 358.

Andersen, J. D., Pietroni, C., Johansen, P., Andersen, M. M., Pereira, V., Børsting, C., & Morling, N. (2016). Importance of nonsynonymous OCA2 variants in human eye color prediction. Molecular Genetics & Genomic Medicine, 4(4), 420–430.

Andrade, E. S., Fracasso, N. C. A., Strazza Júnior, P. S., Simões, A. L., & Mendes-Junior, C. T. (2017). Associations of OCA2 - HERC2 SNPs and haplotypes with human pigmentation characteristics in the Brazilian population. Legal Medicine, 24, 78–83.

Ayres, M; Ayres Jr, M; Ayres, D. L.; Santos, A. de A. dos S. (2007). Bioestat 5.0. Belém; Sociedade Civil Mamirauá: cnpq.

Bellono, N. W., Escobar, I. E., Lefkovith, A. J., Marks, M. S., & Oancea, E. (2014). An intracellular anion channel critical for pigmentation. ELife, 3, e04543.

Bin, B.-H., Bhin, J., Yang, S. H., Shin, M., Nam, Y.-J., Choi, D.-H., & Lee, T. R. (2015). Membrane-Associated Transporter Protein (MATP) Regulates Melanosomal pH and Influences Tyrosinase Activity. PLOS ONE, 10(6), e0129273.

Bonilla, C., Boxill, L.-A., Donald, S. A. M., Williams, T., Sylvester, N., Parra, E. J., & Kittles, R. A. (2005). The 8818G allele of the agouti signaling protein (ASIP) gene is ancestral and is associated with darker skin color in African Americans. Human Genetics, 116(5), 402–406.

Branicki, W., Brudnik, U., Kupiec, T., Wolañska-Nowak, P., & Wojas-Pelc, A. (2007). Determination of Phenotype Associated SNPs in the MC1R Gene. Journal of Forensic Sciences, 52(2), 349–354.

Canfield, V. A., Berg, A., Peckins, S., Wentzel, S. M., Ang, K. C., Oppenheimer, S., & Cheng, K. C. (2013). Molecular Phylogeography of a Human Autosomal Skin Color Locus Under Natural Selection. G3: Genes|Genomes|Genetics, 3(11), 2059–2067.

Chaitanya, L., Breslin, K., Zuñiga, S., Wirken, L., Pośpiech, E., Kukla-Bartoszek, M., & Walsh, S. (2018). The HIrisPlex-S system for eye, hair and skin colour prediction from DNA: Introduction and forensic developmental validation. Forensic Science International: Genetics, 35(March), 123–135.

Chen, B., Cole, J. W., & Grond-Ginsbach, C. (2017). Departure from Hardy Weinberg Equilibrium and Genotyping Error. Frontiers in Genetics, 8(OCT), 1–6.

Cook, A. L., Chen, W., Thurber, A. E., Smit, D. J., Smith, A. G., Bladen, T. G., & Sturm, R. A. (2009). Analysis of Cultured Human Melanocytes Based on Polymorphisms within the SLC45A2/MATP, SLC24A5/NCKX5, and OCA2/P Loci. Journal of Investigative Dermatology, 129(2), 392–405.

Crawford, N. G., Kelly, D. E., Hansen, M. E. B., Beltrame, M. H., Fan, S., Bowman, S. L., & Tishkoff, S. A. (2017). Loci associated with skin pigmentation identified in African populations. Science, 358(6365), eaan8433.

D??bniak, T., Scott, R., Masojc, B., Serrano-Fernández, P., Huzarski, T., Byrski, T., & Lubinski, J. (2006). MC1R common variants, CDKN2A and their association with melanoma and breast cancer risk. International Journal of Cancer, 119(11), 2597–2602.

de Araújo Lima, F., de Toledo Gonçalves, F., & Fridman, C. (2015). SLC24A5 and ASIP as phenotypic predictors in Brazilian population for forensic purposes. Legal Medicine, 17(4), 261–266.

Deng, L., & Xu, S. (2018). Adaptation of human skin color in various populations. Hereditas, 155(1), 1.

Donnelly, M. P., Paschou, P., Grigorenko, E., Gurwitz, D., Barta, C., Lu, R.-B., Kidd, K. K. (2012). A global view of the OCA2-HERC2 region and pigmentation. Human Genetics, 131(5), 683–696.

Durso, D. F., Bydlowski, S. P., Hutz, M. H., Suarez-Kurtz, G., Magalhães, T. R., & Junho Pena, S. D. (2014). Association of Genetic Variants with Self-Assessed Color Categories in Brazilians. PLoS ONE, 9(1), e83926.

Ensembl. (n.d.). Retrieved from

Feng, H., Xia, X., Li, C., Song, Y., Qin, C., Zhang, Y., & Lan, X. (2015). TYR as a multifunctional reporter gene regulated by the Tet-on system for multimodality imaging: an in vitro study. Scientific Reports, 5(1), 15502.

Fernandez, L., Milne, R., Bravo, J., Lopez, J., Avilés, J., Longo, M., … Ribas, G. (2007). MC1R: three novel variants identified in a malignant melanoma association study in the Spanish population. Carcinogenesis, 28(8), 1659–1664.

Fracasso, N. C. de A., de Andrade, E. S., Wiezel, C. E. V., Andrade, C. C. F., Zanão, L. R., da Silva, M. S., & Mendes-Junior, C. T. (2017). Haplotypes from the SLC45A2 gene are associated with the presence of freckles and eye, hair and skin pigmentation in Brazil. Legal Medicine, 25, 43–51.

Fridman, C., Cardena, M. M. S. G., Lima, F. D. A., & Gonçalves, F. D. T. (2015). Is it possible to use Forensic DNA phenotyping in Brazilian population? Forensic Science International: Genetics Supplement Series, 5, e378–e380.

Giebel, L. B., & Spritz, R. A. (1990). RFLP for Mbol in the human tyrosinase (TYR) gene detected by PCR. Nucleic Acids Research, 18(10), 3103–3103.

Gomes, M. B., Gabrielli, A. B., Santos, D. C., Pizarro, M. H., Barros, B. S. V., Negrato, C. A., & Silva, D. A. (2018). Self-reported color-race and genomic ancestry in an admixed population: A contribution of a nationwide survey in patients with type 1 diabetes in Brazil. Diabetes Research and Clinical Practice, 140, 245–252.

Graf, J., Voisey, J., Hughes, I., & van Daal, A. (2007). Promoter polymorphisms in the MATP ( SLC45A2 ) gene are associated with normal human skin color variation. Human Mutation, 28(7), 710–717.

GraphPad Prism version 5.04. (n.d.). Retrieved from (

Gu, Y., Yun, L., Zhang, L., Yang, F., & Hou, Y. (2011). The potential forensic utility of two single nucleotide polymorphisms in predicting biogeographical ancestry. Forensic Science International: Genetics Supplement Series, 3(1), e105–e106.

Hart, K. L., Kimura, S. L., Mushailov, V., Budimlija, Z. M., Prinz, M., & Wurmbach, E. (2013). Improved eye- and skin-color prediction based on 8 SNPs. Croatian Medical Journal, 54(3), 248–256.

Hernando, B., Sanz-Page, E., Pitarch, G., Mahiques, L., Valcuende-Cavero, F., & Martinez-Cadenas, C. (2018). Genetic variants associated with skin photosensitivity in a southern European population from Spain. Photodermatology, Photoimmunology & Photomedicine, 34(6), 415–422.

Hohl, D. M., Bezus, B., Ratowiecki, J., & Catanesi, C. I. (2018). Genetic and phenotypic variability of iris color in Buenos Aires population. Genetics and Molecular Biology, 41(1), 50–58.

J Park, AH Talukder, 1 SA Lim, 2 K Kim, 1 K Pan, 1 B Melendez, 1 SD Bradley, 1 KR Jackson, 1 JS Khalili, 1 J Wang, 1 C Creasy, 1 BF Pan, 3 SE Woodman, 1 C Bernatchez, 1 D Hawke, P Hwu, KM Lee, J Roszik, G Lizée, and C. Y., Aboud, K., Kang, H., Cutting, L. E., & Bennett, A. (2016). Medical Image Computing and Computer-Assisted Intervention – MICCAI 2016. In S. Ourselin, L. Joskowicz, M. R. Sabuncu, G. Unal, & W. Wells (Eds.), Cancer Immunol Res.

Jackson, I. J. (2006). Pigmentary Diversity: Identifying the genes causing human diversity. European Journal of Human Genetics, 14(9), 979–980.

Jacobs, L. C., Liu, F., Pardo, L. M., Hofman, A., Uitterlinden, A. G., Kayser, M., & Nijsten, T. (2015). IRF4, MC1R and TYR genes are risk factors for actinic keratosis independent of skin color. Human Molecular Genetics, 24(11), 3296–3303.

Jannot, A.-S., Meziani, R., Bertrand, G., Gérard, B., Descamps, V., Archimbaud, A., & Melan-Cohort. (2005). Allele variations in the OCA2 gene (pink-eyed-dilution locus) are associated with genetic susceptibility to melanoma. European Journal of Human Genetics, 13(8), 913–920.

K, B., & Purohit, R. (2013). Mutational analysis of TYR gene and its structural consequences in OCA1A. Gene, 513(1), 184–195.

Kanetsky, P. A., Swoyer, J., Panossian, S., Holmes, R., Guerry, D., & Rebbeck, T. R. (2002). A Polymorphism in the Agouti Signaling Protein Gene Is Associated with Human Pigmentation. The American Journal of Human Genetics, 70(3), 770–775.

Kayser, M. (2015). Forensic DNA Phenotyping: Predicting human appearance from crime scene material for investigative purposes. Forensic Science International: Genetics, 18, 33–48.

Kayser, M., & Schneider, P. M. (2009). DNA-based prediction of human externally visible characteristics in forensics: Motivations, scientific challenges, and ethical considerations. Forensic Science International: Genetics, 3(3), 154–161.

Kehdy, F. S. G., Gouveia, M. H., Machado, M., Magalhães, W. C. S., Horimoto, A. R., Horta, B. L., & Tarazona-Santos, E. (2015). Origin and dynamics of admixture in Brazilians and its effect on the pattern of deleterious mutations. Proceedings of the National Academy of Sciences, 112(28), 8696–8701.

Koops, B.-J., & Schellekens, M. H. M. (2006). Forensic DNA Phenotyping: Regulatory Issues. SSRN Electronic Journal, 158–202.

Kukla-Bartoszek, M., Pośpiech, E., Woźniak, A., Boroń, M., Karłowska-Pik, J., Teisseyre, P., & Branicki, W. (2019). DNA-based predictive models for the presence of freckles. Forensic Science International: Genetics, 42(June), 252–259.

Lamason, R. L. (2005). SLC24A5, a Putative Cation Exchanger, Affects Pigmentation in Zebrafish and Humans. Science, 310(5755), 1782–1786.

Leite, T. K. M., Fonseca, R. M. C., França, N. M. de, Parra, E. J., & Pereira, R. W. (2011a). Genomic Ancestry, Self-Reported “Color” and Quantitative Measures of Skin Pigmentation in Brazilian Admixed Siblings. PLoS ONE, 6(11), e27162.

Leite, T. K. M., Fonseca, R. M. C., França, N. M. de, Parra, E. J., & Pereira, R. W. (2011b). Genomic Ancestry, Self-Reported “Color” and Quantitative Measures of Skin Pigmentation in Brazilian Admixed Siblings. PLoS ONE, 6(11), e27162.

Magalhães da Silva, T., Sandhya Rani, M. R., de Oliveira Costa, G. N., Figueiredo, M. A., Melo, P. S., Nascimento, J. F., & Blanton, R. E. (2015). The correlation between ancestry and color in two cities of Northeast Brazil with contrasting ethnic compositions. European Journal of Human Genetics, 23(7), 984–989.

Makova, K., & Norton, H. (2005). Worldwide polymorphism at the MC1R locus and normal pigmentation variation in humans. Peptides, 26(10), 1901–1908.

Maroñas, O., Phillips, C., Söchtig, J., Gomez-Tato, A., Cruz, R., Alvarez-Dios, J., & Lareu, M. V. (2014). Development of a forensic skin colour predictive test. Forensic Science International: Genetics, 13, 34–44.

Meziani, R., Descamps, V., Gerard, B., Matichard, E., Bertrand, G., Archimbaud, A., & Bassetseguin, N. (2005). Association study of the g.8818A>G polymorphism of the human agouti gene with melanoma risk and pigmentary characteristics in a French population. Journal of Dermatological Science, 40(2), 133–136.

Motokawa, T., Kato, T., Hashimoto, Y., Hongo, M., Ito, M., Takimoto, H., & Katagiri, T. (2006). Characteristic MC1R polymorphism in the Japanese population. Journal of Dermatological Science.

NCBI. (n.d.).

OEGE - Online Encyclopedia for Genetic Epidemiology studies. (n.d.).

Pena, S. D. J., Di Pietro, G., Fuchshuber-Moraes, M., Genro, J. P., Hutz, M. H., Kehdy, F. de S. G., & Suarez-Kurtz, G. (2011). The Genomic Ancestry of Individuals from Different Geographical Regions of Brazil Is More Uniform Than Expected. PLoS ONE, 6(2), e17063.

Pośpiech, E., Karłowska-Pik, J., Ziemkiewicz, B., Kukla, M., Skowron, M., Wojas-Pelc, A., & Branicki, W. (2016). Further evidence for population specific differences in the effect of DNA markers and gender on eye colour prediction in forensics. International Journal of Legal Medicine, 130(4), 923–934.

Qiao, L., Yang, Y., Fu, P., Hu, S., Zhou, H., Peng, S., & Tang, K. (2018). Genome-wide variants of Eurasian facial shape differentiation and a prospective model of DNA based face prediction. Journal of Genetics and Genomics, 45(8), 419–432.

Queirós, F. (2019). The visibilities and invisibilities of race entangled with forensic DNA phenotyping technology. Journal of Forensic and Legal Medicine, 68(April), 101858.

Rebbeck, T. R., Kanetsky, P. A., Walker, A. H., Holmes, R., Halpern, A. C., Schuchter, L. M., & Guerry, D. (2002). P gene as an inherited biomarker of human eye color. Cancer Epidemiology, Biomarkers & Prevention : A Publication of the American Association for Cancer Research, Cosponsored by the American Society of Preventive Oncology, 11(8), 782–784. Retrieved from

Salzano, F. M., & Sans, M. (2014). Interethnic admixture and the evolution of Latin American populations. Genetics and Molecular Biology, 37(1 suppl 1), 151–170.

Sawitzki, F. R., Rodenbusch, R., Gubert, D. W., Soares, D., Santos, B., Filipe, E., & Silva, A. (2017). SM Gr up Analysis of Eight SNPs in South Brazilian Subjects with Different Skin and Eye Melanin Content. 1(2), 1–6.

Scudder, N., McNevin, D., Kelty, S. F., Walsh, S. J., & Robertson, J. (2018). Forensic DNA phenotyping: Developing a model privacy impact assessment. Forensic Science International: Genetics, 34(June 2017), 222–230.

Serre, C., Busuttil, V., & Botto, J.-M. (2018). Intrinsic and extrinsic regulation of human skin melanogenesis and pigmentation. International Journal of Cosmetic Science, 40(4), 328–347.

Shi, P., Lu, X. M., Luo, H. R., Xiang-Yu, J.-G., & Zhang, Y. P. (2001). Melanocortin-1 receptor gene variants in four Chinese ethnic populations. Cell Research, 11(1), 81–84.

Soejima, M., & Koda, Y. (2006). Population differences of two coding SNPs in pigmentation-related genes SLC24A5 and SLC45A2. International Journal of Legal Medicine, 121(1), 36–39.

Souza, A. M. de, Resende, S. S., Sousa, T. N. de, & Brito, C. F. A. de. (2019). A systematic scoping review of the genetic ancestry of the Brazilian population. Genetics and Molecular Biology, 42(3), 495–508.

Sturm, R. A., & Duffy, D. L. (2012). Human pigmentation genes under environmental selection. Genome Biology, 13(9), 248.

Sulem, P., Gudbjartsson, D. F., Stacey, S. N., Helgason, A., Rafnar, T., Jakobsdottir, M., & Stefansson, K. (2008). Two newly identified genetic determinants of pigmentation in Europeans. Nature Genetics, 40(7), 835–837.

Sulem, P., Gudbjartsson, D. F., Stacey, S. N., Helgason, A., Rafnar, T., Magnusson, K. P., & Stefansson, K. (2007). Genetic determinants of hair, eye and skin pigmentation in Europeans. Nature Genetics, 39(12), 1443–1452.

Valenzuela, R. K., Henderson, M. S., Walsh, M. H., Garrison, N. A., Kelch, J. T., Cohen-Barak, O., & Brilliant, M. H. (2010). Predicting phenotype from genotype: Normal pigmentation. Journal of Forensic Sciences.

Valls, J. H. (2012). Identificación y caracterización de regiones cromosómicas asociadas a melanoma esporádico en el uruguay mediante el método de mapeo por mestizaje : MC1-R como posible gen candidato. Facultad de Medicina UDELAR.

Virmond, M. B., Robert, A. W., Brito, P. B., & Massuda, T. Y. C. (2016). Fenotipagem forense pelo DNA através de SNPs. Revista Brasileira de Criminalística, 5(2), 37.

Voisey, J., Gomez-Cabrera, M. D. C., Smit, D. J., Leonard, J. H., Sturm, R. A., & van Daal, A. (2006). A polymorphism in the agouti signalling protein (ASIP) is associated with decreased levels of mRNA. Pigment Cell Research, 19(3), 226–231.

Walsh, S., Chaitanya, L., Breslin, K., Muralidharan, C., Bronikowska, A., Pospiech, E., & Kayser, M. (2017). Global skin colour prediction from DNA. Human Genetics, 136(7), 847–863.

Walsh, S., Liu, F., Ballantyne, K. N., van Oven, M., Lao, O., & Kayser, M. (2011). IrisPlex: A sensitive DNA tool for accurate prediction of blue and brown eye colour in the absence of ancestry information. Forensic Science International: Genetics, 5(3), 170–180.

Walsh, S., Liu, F., Wollstein, A., Kovatsi, L., Ralf, A., Kosiniak-Kamysz, A., & Kayser, M. (2013). The HIrisPlex system for simultaneous prediction of hair and eye colour from DNA. Forensic Science International: Genetics, 7(1), 98–115.

Whikehart, D. R. (2003). Nucleic Acids. In Biochemistry of the Eye (Vol. 16, pp. 191–229).

Wilde, S., Timpson, A., Kirsanow, K., Kaiser, E., Kayser, M., Unterländer, M., & Burger, J. (2014). Direct evidence for positive selection of skin, hair, and eye pigmentation in Europeans during the last 5,000 y. Proceedings of the National Academy of Sciences, 111(13), 4832–4837.

Yun, L., Gu, Y., Rajeevan, H., & Kidd, K. K. (2014). Application of six IrisPlex SNPs and comparison of two eye color prediction systems in diverse Eurasia populations. International Journal of Legal Medicine, 128(3), 447–453.

Zaorska, K., Zawierucha, P., & Nowicki, M. (2019). Prediction of skin color, tanning and freckling from DNA in Polish population: linear regression, random forest and neural network approaches. Human Genetics, 138(6), 635–647.

Zeigler-Johnson, C., Panossian, S., Gueye, S. M., Jalloh, M., Ofori-Adjei, D., & Kanetsky, P. A. (2004). Population Differences in the Frequency of the Agouti Signaling Protein g.8818A>G Polymorphism. Pigment Cell Research, 17(2), 185–187.




How to Cite

SOUZA, J. M. de .; BASTOS, M. L.; SILVA, B. de O.; LIMA, K. G. G. de; ALBUQUERQUE, G. S. de .; OLIVEIRA, R. S. de .; LIMA, L. P. O. de; DELLALIBERA, E. .; LINS , A. J. da C. C.; MUNIZ, M. T. C. . Forensic DNA Phenotyping: starting point to prediction model in Pernambuco population, Brazil . Research, Society and Development, [S. l.], v. 10, n. 13, p. e262101320955, 2021. DOI: 10.33448/rsd-v10i13.20955. Disponível em: Acesso em: 27 jan. 2022.



Agrarian and Biological Sciences