Prediction of eye and hair pigmentation phenotypes using the HIrisPlex system in a Brazilian admixed population sample

Abstract

Human pigmentation is a complex trait, probably involving more than 100 genes. Predicting phenotypes using SNPs present in those genes is important for forensic purpose. For this, the HIrisPlex tool was developed for eye and hair color prediction, with both models achieving high accuracy among Europeans. Its evaluation in admixed populations is important, since they present a higher frequency of intermediate phenotypes, and HIrisPlex has demonstrated limitations in such predictions; therefore, the performance of this tool may be impaired in such populations. Here, we evaluate the set of 24 markers from the HIrisPlex system in 328 individuals from Ribeirão Preto (SP) region, predicting eye and hair color and comparing the predictions with their real phenotypes. We used the HaloPlex Target Enrichment System and MiSeq Personal Sequencer platform for massively parallel sequencing. The prediction of eye and hair color was accomplished by the HIrisPlex online tool, using the default prediction settings. Ancestry was estimated using the SNPforID 34-plex to observe if and how an individual’s ancestry background would affect predictions in this admixed sample. Our sample presented major European ancestry (70.5%), followed by African (21.1%) and Native American/East Asian (8.4%). HIrisPlex presented an overall sensitivity of 0.691 for hair color prediction, with sensitivities ranging from 0.547 to 0.782. The lowest sensitivity was observed for individuals with black hair, who present a reduced European contribution (48.4%). For eye color prediction, the overall sensitivity was 0.741, with sensitivities higher than 0.85 for blue and brown eyes, although it failed in predicting intermediate eye color. Such struggle in predicting this phenotype category is in accordance with what has been seen in previous studies involving HIrisPlex. Individuals with brown eye color are more admixed, with European ancestry decreasing to 62.6%; notwithstanding that, sensitivity for brown eyes was almost 100%. Overall sensitivity increases to 0.791 when a 0.7 threshold is set, though 12.5% of the individuals become undefined. When combining eye and hair prediction, hit rates between 51.3 and 68.9% were achieved. Despite the difficulties with intermediate phenotypes, we have shown that HIrisPlex results can be very helpful when interpreted with caution.

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Fig. 1

Data availability

The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request.

Code availability

Not applicable.

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Acknowledgments

We thank André Justino, Juliana Doblas Massaro, Sandra Rodrigues, and Flavia Tremeschin de Almeida for technical assistance.

Funding

This study was supported by CNPq/Brazil (Conselho Nacional de Desenvolvimento Científico e Tecnológico) Grant #448242/2014–1, and FAPESP/Brazil (Fundação de Amparo à Pesquisa do Estado de São Paulo) Grant #2013/15447–0. This study was financed in part by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior—Brasil (CAPES)—Finance Code 001. C.T.M.J. (#312802/2018–8) and E.C.C. (#302590/2016–1) are supported by Research fellowships from CNPq/Brazil.

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Conceptualization: Celso Teixeira Mendes-Junior; Methodology: Thássia Mayra Telles Carratto, Letícia Marcorin, Guilherme do Valle-Silva; Maria Luiza Guimarães de Oliveira Formal analysis and investigation: Thássia Mayra Telles Carratto, Celso Teixeira Mendes-Junior; Writing—original draft preparation: Thássia Mayra Telles Carratto, Celso Teixeira Mendes Junior; Writing—review and editing: Letícia Marcorin, Guilherme do Valle-Silva, Maria Luiza Guimarães de Oliveira, Eduardo Antônio Donadi, Aguinaldo Luiz Simões, Erick C. Castelli, Funding acquisition: Eduardo Antônio Donadi, Aguinaldo Luiz Simões, Erick C. Castelli, Celso Teixeira Mende-Junior; Resources: Eduardo Antônio Donadi, Aguinaldo Luiz Simões, Erick C. Castelli, Celso Teixeira Mendes-Junior

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Correspondence to Celso Teixeira Mendes-Junior.

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Carratto, T.M.T., Marcorin, L., do Valle-Silva, G. et al. Prediction of eye and hair pigmentation phenotypes using the HIrisPlex system in a Brazilian admixed population sample. Int J Legal Med 135, 1329–1339 (2021). https://doi.org/10.1007/s00414-021-02554-7

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Keywords

  • SNPs
  • Massively parallel sequencing
  • DNA phenotyping
  • Forensic DNA phenotyping
  • Forensic genetics