PANE: fast and reliable ancestral reconstruction on ancient genotype data with non-negative least square and principal component analysis

IF 10.1 1区生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genome Biology Pub Date : 2025-02-11 DOI:10.1186/s13059-025-03491-z

Luciana de Gennaro, Ludovica Molinaro, Alessandro Raveane, Federica Santonastaso, Sandro Sublimi Saponetti, Michela Carlotta Massi, Luca Pagani, Mait Metspalu, Garrett Hellenthal, Toomas Kivisild, Mario Ventura, Francesco Montinaro

引用次数: 0

Abstract

The history of human populations has been strongly shaped by admixture events, contributing to patterns of observed genetic diversity across populations. In this study, we introduce the Principal component Ancestry proportions using NNLS Estimation (PANE) method that leverages principal component analysis and non-negative least squares to assess the ancestral compositions of admixed individuals given a large set of populations. Our results show its ability to reliably estimate ancestry across several scenarios, even those with a significant proportion of missing genotypes, in a fraction of the time required when using other tools.

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来源期刊

Genome Biology Biochemistry, Genetics and Molecular Biology-Genetics

CiteScore

21.00

自引率

3.30%

发文量

241

审稿时长

2 months

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