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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
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:...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Korea Genome Organization
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4330263/ https://www.ncbi.nlm.nih.gov/pubmed/25705167 http://dx.doi.org/10.5808/GI.2014.12.4.254 |
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author | Lee, Young-Sup Kim, Hyeon-Jeong Cho, Seoae Kim, Heebal |
author_facet | Lee, Young-Sup Kim, Hyeon-Jeong Cho, Seoae Kim, Heebal |
author_sort | Lee, Young-Sup |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-4330263 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | Korea Genome Organization |
record_format | MEDLINE/PubMed |
spelling | pubmed-43302632015-02-22 The Usage of an SNP-SNP Relationship Matrix for Best Linear Unbiased Prediction (BLUP) Analysis Using a Community-Based Cohort Study Lee, Young-Sup Kim, Hyeon-Jeong Cho, Seoae Kim, Heebal Genomics Inform Original Article 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. Korea Genome Organization 2014-12 2014-12-31 /pmc/articles/PMC4330263/ /pubmed/25705167 http://dx.doi.org/10.5808/GI.2014.12.4.254 Text en Copyright © 2014 by the Korea Genome Organization http://creativecommons.org/licenses/by-nc/3.0/ It is identical to the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/). |
spellingShingle | Original Article Lee, Young-Sup Kim, Hyeon-Jeong Cho, Seoae Kim, Heebal The Usage of an SNP-SNP Relationship Matrix for Best Linear Unbiased Prediction (BLUP) Analysis Using a Community-Based Cohort Study |
title | The Usage of an SNP-SNP Relationship Matrix for Best Linear Unbiased Prediction (BLUP) Analysis Using a Community-Based Cohort Study |
title_full | The Usage of an SNP-SNP Relationship Matrix for Best Linear Unbiased Prediction (BLUP) Analysis Using a Community-Based Cohort Study |
title_fullStr | The Usage of an SNP-SNP Relationship Matrix for Best Linear Unbiased Prediction (BLUP) Analysis Using a Community-Based Cohort Study |
title_full_unstemmed | The Usage of an SNP-SNP Relationship Matrix for Best Linear Unbiased Prediction (BLUP) Analysis Using a Community-Based Cohort Study |
title_short | The Usage of an SNP-SNP Relationship Matrix for Best Linear Unbiased Prediction (BLUP) Analysis Using a Community-Based Cohort Study |
title_sort | usage of an snp-snp relationship matrix for best linear unbiased prediction (blup) analysis using a community-based cohort study |
topic | Original Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4330263/ https://www.ncbi.nlm.nih.gov/pubmed/25705167 http://dx.doi.org/10.5808/GI.2014.12.4.254 |
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