A resampling-based approach to share reference panels.

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Version: Final published version
License: CC BY 4.0
Serval ID
serval:BIB_981E899095A4
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
A resampling-based approach to share reference panels.
Journal
Nature computational science
Author(s)
Cavinato T., Rubinacci S., Malaspinas A.S., Delaneau O.
ISSN
2662-8457 (Electronic)
ISSN-L
2662-8457
Publication state
Published
Issued date
05/2024
Peer-reviewed
Oui
Volume
4
Number
5
Pages
360-366
Language
english
Notes
Publication types: Journal Article
Publication Status: ppublish
Abstract
For many genome-wide association studies, imputing genotypes from a haplotype reference panel is a necessary step. Over the past 15 years, reference panels have become larger and more diverse, leading to improvements in imputation accuracy. However, the latest generation of reference panels is subject to restrictions on data sharing due to concerns about privacy, limiting their usefulness for genotype imputation. In this context, here we propose RESHAPE, a method that employs a recombination Poisson process on a reference panel to simulate the genomes of hypothetical descendants after multiple generations. This data transformation helps to protect against re-identification threats and preserves data attributes, such as linkage disequilibrium patterns and, to some degree, identity-by-descent sharing, allowing for genotype imputation. Our experiments on gold-standard datasets show that simulated descendants up to eight generations can serve as reference panels without substantially reducing genotype imputation accuracy.
Keywords
Humans, Genome-Wide Association Study/methods, Genotype, Linkage Disequilibrium, Haplotypes/genetics, Polymorphism, Single Nucleotide/genetics, Information Dissemination/methods, Computer Simulation, Models, Genetic, Algorithms, Genome, Human/genetics, Poisson Distribution
Pubmed
Web of science
Open Access
Yes
Create date
16/05/2024 14:29
Last modification date
14/06/2024 7:14
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