Genomics & Informatics

Korea Genome Organization (한국유전체학회)
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The Usage of an SNP-SNP Relationship Matrix for Best Linear Unbiased Prediction (BLUP) Analysis Using a Community-Based Cohort Study

  • Lee, Young-Sup (Department of Natural Science, Interdisciplinary Program in Bioinformatics, Seoul National University) ;
  • Kim, Hyeon-Jeong (C&K Genomics) ;
  • Cho, Seoae (C&K Genomics) ;
  • Kim, Heebal (Department of Natural Science, Interdisciplinary Program in Bioinformatics, Seoul National University)
  • Received : 2014.07.12
  • Accepted : 2014.09.16
  • Published : 2014.12.31
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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.

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References

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