Ancestry deconvolution and partial polygenic score can improve susceptibility predictions in recently admixed individuals

• Published in: Nature communications Vol. 11; no. 1; pp. 1628 - 9
• Main Authors: Marnetto, Davide, Pärna, Katri, Läll, Kristi, Molinaro, Ludovica, Montinaro, Francesco, Haller, Toomas, Metspalu, Mait, Mägi, Reedik, Fischer, Krista, Pagani, Luca
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 02.04.2020; Nature Publishing Group; Nature Portfolio
• Subjects: 631/114/2413; 631/208/205; 631/208/457/649; Bias; Deconvolution; Genealogy; Genetic Predisposition to Disease; Genetics, Population; Genomes; Genotype; Humanities and Social Sciences; Humans; Models, Genetic; multidisciplinary; Multifactorial Inheritance; Phenotype; Phenotypes; Polygenic inheritance; Population; Population genetics; Populations; Precision medicine; Predictions; Science; Science (multidisciplinary)
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-020-15464-w

Polygenic Scores (PSs) describe the genetic component of an individual’s quantitative phenotype or their susceptibility to diseases with a genetic basis. Currently, PSs rely on population-dependent contributions of many associated alleles, with limited applicability to understudied populations and recently admixed individuals. Here we introduce a combination of local ancestry deconvolution and partial PS computation to account for the population-specific nature of the association signals in individuals with admixed ancestry. We demonstrate partial PS to be a proxy for the total PS and that a portion of the genome is enough to improve susceptibility predictions for the traits we test. By combining partial PSs from different populations, we are able to improve trait predictability in admixed individuals with some European ancestry. These results may extend the applicability of PSs to subjects with a complex history of admixture, where current methods cannot be applied. Polygenic scores are believed to hold future promise for trait prediction and personalized medicine, but are sensitive to demographic history. Here, Marnetto et al . develop partial polygenic scores supplemented with local ancestry deconvolution which improves prediction accuracy into recently admixed European populations.