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Prediction of eye, hair and skin colour in Latin Americans.

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dc.contributor.author Palmal, Sagnik
dc.contributor.author Adhikari, Kaustubh
dc.contributor.author Mendoza-Revilla, Javier
dc.contributor.author Fuentes-Guajardo, Macarena
dc.contributor.author Silva de Cerqueira, Caio Cesar
dc.contributor.author Bonfante, Betty
dc.contributor.author Chacón-Duque, Juan Camilo
dc.contributor.author Sohail, Anood
dc.contributor.author Hurtado, Malena
dc.contributor.author Villegas, Valeria
dc.contributor.author Granja, Vanessa
dc.contributor.author Jaramillo, Claudia
dc.contributor.author Arias, William
dc.contributor.author Lozano, Rodrigo Barquera
dc.contributor.author Everardo-Martínez, Paola
dc.contributor.author Gómez-Valdés, Jorge
dc.contributor.author Villamil-Ramírez, Hugo
dc.contributor.author Hünemeier, Tábita
dc.contributor.author Ramallo, Virginia
dc.contributor.author Parolin, Maria-Laura
dc.contributor.author Gonzalez-José, Rolando
dc.contributor.author Schüler-Faccini, Lavinia
dc.contributor.author Bortolini, Maria-Cátira
dc.contributor.author Acuña-Alonzo, Victor
dc.contributor.author Canizales-Quinteros, Samuel
dc.contributor.author Gallo López-Aliaga, Carla Maria
dc.contributor.author Poletti, Giovanni
dc.contributor.author Bedoya, Gabriel
dc.contributor.author Rothhammer, Francisco
dc.contributor.author Balding, David
dc.contributor.author Faux, Pierre
dc.contributor.author Ruiz-Linares, Andrés
dc.date.accessioned 2021-05-18T21:44:16Z
dc.date.available 2021-05-18T21:44:16Z
dc.date.issued 2021
dc.identifier.uri https://hdl.handle.net/20.500.12866/9395
dc.description.abstract Here we evaluate the accuracy of prediction for eye, hair and skin pigmentation in a dataset of > 6500 individuals from Mexico, Colombia, Peru, Chile and Brazil (including genome-wide SNP data and quantitative/categorical pigmentation phenotypes - the CANDELA dataset CAN). We evaluated accuracy in relation to different analytical methods and various phenotypic predictors. As expected from statistical principles, we observe that quantitative traits are more sensitive to changes in the prediction models than categorical traits. We find that Random Forest or Linear Regression are generally the best performing methods. We also compare the prediction accuracy of SNP sets defined in the CAN dataset (including 56, 101 and 120 SNPs for eye, hair and skin colour prediction, respectively) to the well-established HIrisPlex-S SNP set (including 6, 22 and 36 SNPs for eye, hair and skin colour prediction respectively). When training prediction models on the CAN data, we observe remarkably similar performances for HIrisPlex-S and the larger CAN SNP sets for the prediction of hair (categorical) and eye (both categorical and quantitative), while the CAN sets outperform HIrisPlex-S for quantitative, but not for categorical skin pigmentation prediction. The performance of HIrisPlex-S, when models are trained in a world-wide sample (although consisting of 80% Europeans, https://hirisplex.erasmusmc.nl), is lower relative to training in the CAN data (particularly for hair and skin colour). Altogether, our observations are consistent with common variation of eye and hair colour having a relatively simple genetic architecture, which is well captured by HIrisPlex-S, even in admixed Latin Americans (with partial European ancestry). By contrast, since skin pigmentation is a more polygenic trait, accuracy is more sensitive to prediction SNP set size, although here this effect was only apparent for a quantitative measure of skin pigmentation. Our results support the use of HIrisPlex-S in the prediction of categorical pigmentation traits for forensic purposes in Latin America, while illustrating the impact of training datasets on its accuracy en_US
dc.language.iso eng
dc.publisher Elsevier
dc.relation.ispartofseries Forensic Science International. Genetics
dc.rights info:eu-repo/semantics/restrictedAccess
dc.rights.uri https://creativecommons.org/licenses/by-nc-nd/4.0/deed.es
dc.subject Admixture en_US
dc.subject DNA phenotyping en_US
dc.subject Eye-colour en_US
dc.subject Hair-colour en_US
dc.subject Latin Americans en_US
dc.subject Pigmentation prediction en_US
dc.subject Skin-colour en_US
dc.title Prediction of eye, hair and skin colour in Latin Americans. en_US
dc.type info:eu-repo/semantics/article
dc.identifier.doi https://doi.org/10.1016/j.fsigen.2021.102517
dc.subject.ocde https://purl.org/pe-repo/ocde/ford#3.01.02
dc.relation.issn 1878-0326


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