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:...
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BioMed Central
2014-12-01
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| Series: | Genomics & Informatics |
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| Online Access: | http://genominfo.org/upload/pdf/gni-12-254.pdf |
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| author | Young-Sup Lee Hyeon-Jeong Kim Seoae Cho Heebal Kim |
| author_facet | Young-Sup Lee Hyeon-Jeong Kim Seoae Cho Heebal Kim |
| author_sort | Young-Sup Lee |
| collection | DOAJ |
| 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 | Article |
| id | doaj-art-6ad86a65ab9d46a985d90101e9b32147 |
| institution | Kabale University |
| issn | 1598-866X 2234-0742 |
| language | English |
| publishDate | 2014-12-01 |
| publisher | BioMed Central |
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| series | Genomics & Informatics |
| spelling | doaj-art-6ad86a65ab9d46a985d90101e9b321472025-02-02T15:55:32ZengBioMed CentralGenomics & Informatics1598-866X2234-07422014-12-0112425426010.5808/GI.2014.12.4.254117The Usage of an SNP-SNP Relationship Matrix for Best Linear Unbiased Prediction (BLUP) Analysis Using a Community-Based Cohort StudyYoung-Sup Lee0Hyeon-Jeong Kim1Seoae Cho2Heebal Kim3Department of Natural Science, Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-747, Korea.C&K Genomics, Seoul 151-742, Korea.C&K Genomics, Seoul 151-742, Korea.Department of Natural Science, Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-747, Korea.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.http://genominfo.org/upload/pdf/gni-12-254.pdfbest linear unbiased estimation (BLUE)best linear unbiased prediction (BLUP)SNP genomic best linear unbiased prediction (SNP-GBLUP)SNP-SNP relationship matrix |
| spellingShingle | Young-Sup Lee Hyeon-Jeong Kim Seoae Cho Heebal Kim The Usage of an SNP-SNP Relationship Matrix for Best Linear Unbiased Prediction (BLUP) Analysis Using a Community-Based Cohort Study Genomics & Informatics best linear unbiased estimation (BLUE) best linear unbiased prediction (BLUP) SNP genomic best linear unbiased prediction (SNP-GBLUP) SNP-SNP relationship matrix |
| 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 | best linear unbiased estimation (BLUE) best linear unbiased prediction (BLUP) SNP genomic best linear unbiased prediction (SNP-GBLUP) SNP-SNP relationship matrix |
| url | http://genominfo.org/upload/pdf/gni-12-254.pdf |
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