Large-scale gene-centric meta-analysis across 32 studies identifies multiple lipid loci

Asselbergs, F.W. et al. (2012) Large-scale gene-centric meta-analysis across 32 studies identifies multiple lipid loci. American Journal of Human Genetics, 91(5), pp. 823-838. (doi:10.1016/j.ajhg.2012.08.032)

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Abstract

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.

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Hastie, Dr Claire and Dominiczak, Professor Anna and Delles, Professor Christian
Authors: Asselbergs, F.W., Guo, Y., van Iperen, E.P.A., Sivapalaratnam, S., Tragante, V., Lanktree, M.B., Lange, L.A., Almoguera, B., Appelman, Y.E., Barnard, J., Baumert, J., Beitelshees, A.L., Bhangale, T.R., Chen, Y.I., Gaunt, T.R., Gong, Y., Hopewell, J.C., Johnson, T., Kleber, M.E., Langaee, T.Y., Li, M., Li, Y.R., Liu, K., McDonough, C.W., Meijs, M.F.L., Middelberg, R.P.S., Musunuru, K., Nelson, C.P., O’Connell, J.R., Padmanabhan, S., Pankow, J.S., Pankratz, N., Rafelt, S., Rajagopalan, R., Romaine, S.P.R., Schork, N.J., Shaffer, J., Shen, H., Smith, E.N., Tischfield, S.E., van der Most, P.J., van Vliet-Ostaptchouk, J.V., Verweij, N., Volcik, K.A., Zhang, L., Bailey, K.R., Bailey, K.M., Bauer, F., Boer, J.M.A., Braund, P.S., Burt, A., Burton, P.R., Buxbaum, S.G., Chen, W., Cooper-DeHoff, R.M., Cupples, L.A., deJong, J.S., Delles, C., Duggan, D., Fornage, M., Furlong, C.E., Glazer, N., Gums, J.G., Hastie, C., Holmes, M.V., Illig, T., Kirkland, S.A., Kivimaki, M., Klein, R., Klein, B.E., Kooperberg, C., Kottke-Marchant, K., Kumari, M., LaCroix, A.Z., Mallela, L., Murugesan, G., Ordovas, J., Ouwehand, W.H., Post, W.S., Saxena, R., Scharnagl, H., Schreiner, P.J., Shah, T., Shields, D.C., Shimbo, D., Srinivasan, S.R., Stolk, R.P., Swerdlow, D.I., Taylor, H.A., Topol, E.J., Toskala, E., van Pelt, J.L., van Setten, J., Yusuf, S., Whittaker, J.C., Zwinderman, A.H., Anand, S.S., Balmforth, A.J., Berenson, G.S., Bezzina, C.R., Boehm, B.O., Boerwinkle, E., Casas, J.P., Caulfield, M.J., Clarke, R., Connell, J.M., Cruickshanks, K.J., Davidson, K.W., Day, I.N.M., de Bakker, P.I.W., Doevendans, P.A., Dominiczak, A.F., Hall, A.S., Hartman, C.A., Hengstenberg, C., Hillege, H.L., Hofker, M.H., Humphries, S.E., Jarvik, G.P., Johnson, J.A., Kaess, B.M., Kathiresan, S., Koenig, W., Lawlor, D.A., März, W., Melander, O., Mitchell, B.D., Montgomery, G.W., Munroe, P.B., Murray, S.S., Newhouse, S.J., Onland-Moret, N.C., Poulter, N., Psaty, B., Redline, S., Rich, S.S., Rotter, J.I., Schunkert, H., Sever, P., Shuldiner, A.R., Silverstein, R.L., Stanton, A., Thorand, B., Trip, M.D., Tsai, M.Y., van der Harst, P., van der Schoot, E., van der Schouw, Y.T., Verschuren, W.M.M., Watkins, H., Wilde, A.A.M., Wolffenbuttel, B.H.R., Whitfield, J.B., Hovingh, G.K., Ballantyne, C.M., Wijmenga, C., Reilly, M.P., Martin, N.G., Wilson, J.G., Rader, D.J., Samani, N.J., Reiner, A.P., Hegele, R.A., Kastelein, J.J.P., Hingorani, A.D., Talmud, P.J., Hakonarson, H., Elbers, C.C., Keating, B.J., and Drenos, F.
College/School:College of Medical Veterinary and Life Sciences > Institute of Cardiovascular and Medical Sciences
Journal Name:American Journal of Human Genetics
Journal Abbr.:AJHG
Publisher:Elsevier (Cell Press)
ISSN:0002-9297
ISSN (Online):1537-6605
Published Online:11 October 2012

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