Large-scale gene-centric meta-analysis across 32 studies identifies multiple lipid loci
Genome-wide association studies (GWASs) have identified many SNPs underlying variations in plasma-lipid levels. We explore whether additional loci associated with plasma-lipid phenotypes, such as high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), total cholest...
| Main Authors: | , , , , , , , , , , , , , , , , , , |
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| Format: | Journal article |
| Published: |
2012
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| _version_ | 1797069428834172928 |
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| author | Asselbergs, F Asselbergs, F Asselbergs, F Guo, Y Guo, Y Van Iperen, E Van Iperen, E Sivapalaratnam, S Tragante, V Tragante, V Lanktree, M Lange, L Almoguera, B Appelman, Y Barnard, J Baumert, J Beitelshees, A Bhangale, T Chen, Y Gaunt, T Gong, Y Hopewell, J Johnson, T Kleber, M Kleber, M |
| author_facet | Asselbergs, F Asselbergs, F Asselbergs, F Guo, Y Guo, Y Van Iperen, E Van Iperen, E Sivapalaratnam, S Tragante, V Tragante, V Lanktree, M Lange, L Almoguera, B Appelman, Y Barnard, J Baumert, J Beitelshees, A Bhangale, T Chen, Y Gaunt, T Gong, Y Hopewell, J Johnson, T Kleber, M Kleber, M |
| author_sort | Asselbergs, F |
| collection | OXFORD |
| description | Genome-wide association studies (GWASs) have identified many SNPs underlying variations in plasma-lipid levels. We explore whether additional loci associated with plasma-lipid phenotypes, such as high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), total cholesterol (TC), and triglycerides (TGs), can be identified by a dense gene-centric approach. Our meta-analysis of 32 studies in 66,240 individuals of European ancestry was based on the custom ∼50,000 SNP genotyping array (the ITMAT-Broad-CARe array) covering ∼2,000 candidate genes. SNP-lipid associations were replicated either in a cohort comprising an additional 24,736 samples or within the Global Lipid Genetic Consortium. We identified four, six, ten, and four unreported SNPs in established lipid genes for HDL-C, LDL-C, TC, and TGs, respectively. We also identified several lipid-related SNPs in previously unreported genes: DGAT2, HCAR2, GPIHBP1, PPARG, and FTO for HDL-C; SOCS3, APOH, SPTY2D1, BRCA2, and VLDLR for LDL-C; SOCS3, UGT1A1, BRCA2, UBE3B, FCGR2A, CHUK, and INSIG2 for TC; and SERPINF2, C4B, GCK, GATA4, INSR, and LPAL2 for TGs. The proportion of explained phenotypic variance in the subset of studies providing individual-level data was 9.9% for HDL-C, 9.5% for LDL-C, 10.3% for TC, and 8.0% for TGs. This large meta-analysis of lipid phenotypes with the use of a dense gene-centric approach identified multiple SNPs not previously described in established lipid genes and several previously unknown loci. The explained phenotypic variance from this approach was comparable to that from a meta-analysis of GWAS data, suggesting that a focused genotyping approach can further increase the understanding of heritability of plasma lipids. © 2012 The American Society of Human Genetics. |
| first_indexed | 2024-03-06T22:24:19Z |
| format | Journal article |
| id | oxford-uuid:562471ef-1f19-449a-ae4a-e15851ddf2ae |
| institution | University of Oxford |
| last_indexed | 2024-03-06T22:24:19Z |
| publishDate | 2012 |
| record_format | dspace |
| spelling | oxford-uuid:562471ef-1f19-449a-ae4a-e15851ddf2ae2022-03-26T16:48:40ZLarge-scale gene-centric meta-analysis across 32 studies identifies multiple lipid lociJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:562471ef-1f19-449a-ae4a-e15851ddf2aeSymplectic Elements at Oxford2012Asselbergs, FAsselbergs, FAsselbergs, FGuo, YGuo, YVan Iperen, EVan Iperen, ESivapalaratnam, STragante, VTragante, VLanktree, MLange, LAlmoguera, BAppelman, YBarnard, JBaumert, JBeitelshees, ABhangale, TChen, YGaunt, TGong, YHopewell, JJohnson, TKleber, MKleber, MGenome-wide association studies (GWASs) have identified many SNPs underlying variations in plasma-lipid levels. We explore whether additional loci associated with plasma-lipid phenotypes, such as high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), total cholesterol (TC), and triglycerides (TGs), can be identified by a dense gene-centric approach. Our meta-analysis of 32 studies in 66,240 individuals of European ancestry was based on the custom ∼50,000 SNP genotyping array (the ITMAT-Broad-CARe array) covering ∼2,000 candidate genes. SNP-lipid associations were replicated either in a cohort comprising an additional 24,736 samples or within the Global Lipid Genetic Consortium. We identified four, six, ten, and four unreported SNPs in established lipid genes for HDL-C, LDL-C, TC, and TGs, respectively. We also identified several lipid-related SNPs in previously unreported genes: DGAT2, HCAR2, GPIHBP1, PPARG, and FTO for HDL-C; SOCS3, APOH, SPTY2D1, BRCA2, and VLDLR for LDL-C; SOCS3, UGT1A1, BRCA2, UBE3B, FCGR2A, CHUK, and INSIG2 for TC; and SERPINF2, C4B, GCK, GATA4, INSR, and LPAL2 for TGs. The proportion of explained phenotypic variance in the subset of studies providing individual-level data was 9.9% for HDL-C, 9.5% for LDL-C, 10.3% for TC, and 8.0% for TGs. This large meta-analysis of lipid phenotypes with the use of a dense gene-centric approach identified multiple SNPs not previously described in established lipid genes and several previously unknown loci. The explained phenotypic variance from this approach was comparable to that from a meta-analysis of GWAS data, suggesting that a focused genotyping approach can further increase the understanding of heritability of plasma lipids. © 2012 The American Society of Human Genetics. |
| spellingShingle | Asselbergs, F Asselbergs, F Asselbergs, F Guo, Y Guo, Y Van Iperen, E Van Iperen, E Sivapalaratnam, S Tragante, V Tragante, V Lanktree, M Lange, L Almoguera, B Appelman, Y Barnard, J Baumert, J Beitelshees, A Bhangale, T Chen, Y Gaunt, T Gong, Y Hopewell, J Johnson, T Kleber, M Kleber, M Large-scale gene-centric meta-analysis across 32 studies identifies multiple lipid loci |
| title | Large-scale gene-centric meta-analysis across 32 studies identifies multiple lipid loci |
| title_full | Large-scale gene-centric meta-analysis across 32 studies identifies multiple lipid loci |
| title_fullStr | Large-scale gene-centric meta-analysis across 32 studies identifies multiple lipid loci |
| title_full_unstemmed | Large-scale gene-centric meta-analysis across 32 studies identifies multiple lipid loci |
| title_short | Large-scale gene-centric meta-analysis across 32 studies identifies multiple lipid loci |
| title_sort | large scale gene centric meta analysis across 32 studies identifies multiple lipid loci |
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