Estimated allele substitution effects underlying genomic evaluation models depend on the scaling of allele counts

Bouwman, Aniek C., Hayes, Ben J. and Calus, Mario P. L. (2017) Estimated allele substitution effects underlying genomic evaluation models depend on the scaling of allele counts. Genetics, Selection, Evolution, 49 1: 79. doi:10.1186/s12711-017-0355-9


Author Bouwman, Aniek C.
Hayes, Ben J.
Calus, Mario P. L.
Title Estimated allele substitution effects underlying genomic evaluation models depend on the scaling of allele counts
Journal name Genetics, Selection, Evolution   Check publisher's open access policy
ISSN 1297-9686
0999-193X
Publication date 2017-10-30
Year available 2017
Sub-type Article (original research)
DOI 10.1186/s12711-017-0355-9
Open Access Status DOI
Volume 49
Issue 1
Start page 79
Total pages 13
Place of publication London, United Kingdom
Publisher BioMed Central
Language eng
Abstract Background: Genomic evaluation is used to predict direct genomic values (DGV) for selection candidates in breeding programs, but also to estimate allele substitution effects (ASE) of single nucleotide polymorphisms (SNPs). Scaling of allele counts influences the estimated ASE, because scaling of allele counts results in less shrinkage towards the mean for low minor allele frequency (MAF) variants. Scaling may become relevant for estimating ASE as more low MAF variants will be used in genomic evaluations. We show the impact of scaling on estimates of ASE using real data and a theoretical framework, and in terms of power, model fit and predictive performance.
Keyword Wide Association
Complex Traits
Technical-Note
Sequence Data
Heritability
Predictions
Information
Accuracy
Cattle
Q-Index Code C1
Q-Index Status Provisional Code
Grant ID 317697
BO-22.04-011-001-ASG-LR
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: HERDC Pre-Audit
Queensland Alliance for Agriculture and Food Innovation
 
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Created: Wed, 08 Nov 2017, 12:03:21 EST