title: The Usage of an SNP-SNP Relationship Matrix for Best Linear Unbiased Prediction (BLUP) Analysis Using a Community-Based Cohort Study.
abstract: Best linear unbiased prediction (BLUP) has been used to estimate the fixed effects and random effects of complex traits. Traditionally, genomic relationship matrix-based (GRM) and random marker-based BLUP analyses are prevalent to estimate the genetic values of complex traits. We used three methods: GRM-based prediction (G-BLUP), random marker-based prediction using an identity matrix (so-called single-nucleotide polymorphism [SNP]-BLUP), and SNP-SNP variance-covariance matrix (so-called SNP-GBLUP). We used 35,675 SNPs and R package "rrBLUP" for the BLUP analysis. The SNP-SNP relationship matrix was calculated using the GRM and Sherman-Morrison-Woodbury lemma. The SNP-GBLUP result was very similar to G-BLUP in the prediction of genetic values. However, there were many discrepancies between SNP-BLUP and the other two BLUPs. SNP-GBLUP has the merit to be able to predict genetic values through SNP effects.
authors.affiliation: Department of Natural Science, Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-747, Korea.
authors.forename: Young-Sup
authors.initials: YS
authors.lastname: Lee
authors.affiliation: C&K Genomics, Seoul 151-742, Korea.
authors.forename: Hyeon-Jeong
authors.initials: HJ
authors.lastname: Kim
authors.affiliation: C&K Genomics, Seoul 151-742, Korea.
authors.forename: Seoae
authors.initials: S
authors.lastname: Cho
authors.affiliation: Department of Natural Science, Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-747, Korea. ; C&K Genomics, Seoul 151-742, Korea. ; Department of Agricultural Biotechnology, Animal Biotechnology, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea.
authors.forename: Heebal
authors.initials: H
authors.lastname: Kim
keywords: SNP genomic best linear unbiased prediction (SNP-GBLUP); SNP-SNP relationship matrix; best linear unbiased estimation (BLUE); best linear unbiased prediction (BLUP)