Meta-imputation: An efficient method to combine genotype data after imputation with multiple reference panels.
genome-wide association study
genotype imputation
Journal
American journal of human genetics
ISSN: 1537-6605
Titre abrégé: Am J Hum Genet
Pays: United States
ID NLM: 0370475
Informations de publication
Date de publication:
02 06 2022
02 06 2022
Historique:
received:
08
11
2021
accepted:
01
04
2022
pubmed:
5
5
2022
medline:
9
6
2022
entrez:
4
5
2022
Statut:
ppublish
Résumé
Genotype imputation is an integral tool in genome-wide association studies, in which it facilitates meta-analysis, increases power, and enables fine-mapping. With the increasing availability of whole-genome-sequence datasets, investigators have access to a multitude of reference-panel choices for genotype imputation. In principle, combining all sequenced whole genomes into a single large panel would provide the best imputation performance, but this is often cumbersome or impossible due to privacy restrictions. Here, we describe meta-imputation, a method that allows imputation results generated using different reference panels to be combined into a consensus imputed dataset. Our meta-imputation method requires small changes to the output of existing imputation tools to produce necessary inputs, which are then combined using dynamically estimated weights that are tailored to each individual and genome segment. In the scenarios we examined, the method consistently outperforms imputation using a single reference panel and achieves accuracy comparable to imputation using a combined reference panel.
Identifiants
pubmed: 35508176
pii: S0002-9297(22)00150-1
doi: 10.1016/j.ajhg.2022.04.002
pmc: PMC9247833
pii:
doi:
Types de publication
Journal Article
Meta-Analysis
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
1007-1015Subventions
Organisme : Medical Research Council
ID : MC_PC_17228
Pays : United Kingdom
Organisme : Medical Research Council
ID : MC_QA137853
Pays : United Kingdom
Informations de copyright
Copyright © 2022 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.
Déclaration de conflit d'intérêts
Declaration of interests G.R.A. is an employee of Regeneron Pharmaceuticals and owns stock and stock options in Regeneron Pharmaceuticals.
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