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Research article - Peer-reviewed, 2022

MetaGS: an accurate method to impute and combine SNP effects across populations using summary statistics

Jighly, Abdulqader; Benhajali, Haifa; Liu, Zengting; Goddard, Mike E.

Abstract

Background Meta-analysis describes a category of statistical methods that aim at combining the results of multiple studies to increase statistical power by exploiting summary statistics. Different industries that use genomic prediction do not share their raw data due to logistic or privacy restrictions, which can limit the size of their reference populations and creates a need for a practical meta-analysis method. Results We developed a meta-analysis, named MetaGS, that duplicates the results of multi-trait best linear unbiased prediction (mBLUP) analysis without accessing raw data. MetaGS exploits the correlations among different populations to produce more accurate population-specific single nucleotide polymorphism (SNP) effects. The method improves SNP effect estimations for a given population depending on its relations to other populations. MetaGS was tested on milk, fat and protein yield data of Australian Holstein and Jersey cattle and it generated very similar genomic estimated breeding values to those produced using the mBLUP method for all traits in both breeds. One of the major difficulties when combining SNP effects across populations is the use of different variants for the populations, which limits the applications of meta-analysis in practice. We solved this issue by developing a method to impute missing summary statistics without using raw data. Our results showed that imputing summary statistics can be done with high accuracy (r > 0.9) even when more than 70% of the SNPs were missing with a minimal effect on prediction accuracy. Conclusions We demonstrated that MetaGS can replace the mBLUP model when raw data cannot be shared, which can lead to more flexible collaborations compared to the single-trait BLUP model.

Published in

Genetics Selection Evolution
2022, volume: 54, article number: 37
Publisher: BMC

Authors' information

Jighly, Abdulqader
Agriculture Victoria
Benhajali, Haifa (Splittorff, Haifa)
Swedish University of Agricultural Sciences, Department of Animal Breeding and Genetics
Liu, Zengting
IT solutions for animal production (vit)
Goddard, Mike
Agriculture Victoria
Goddard, Mike E.
University of Melbourne

UKÄ Subject classification

Genetics and Breeding

Publication Identifiers

DOI: https://doi.org/10.1186/s12711-022-00725-7

URI (permanent link to this page)

https://res.slu.se/id/publ/117562