Newly identified loci that influence lipid concentrations and risk of coronary artery disease
Open accessAbstract
To identify genetic variants influencing plasma lipid concentrations, we first used genotype imputation and meta-analysis to combine three genome-wide scans totaling 8,816 individuals and comprising 6,068 individuals specific to our study (1,874 individuals from the FUSION study of type 2 diabetes and 4,184 individuals from the SardiNIA study of aging-associated variables) and 2,758 individuals from the Diabetes Genetics Initiative, reported in a companion study in this issue. We subsequently examined promising signals in 11,569 additional individuals. Overall, we identify strongly associated variants in eleven loci previously implicated in lipid metabolism (ABCA1, the APOA5-APOA4-APOC3-APOA1 and APOE-APOC clusters, APOB, CETP, GCKR, LDLR, LPL, LIPC, LIPG and PCSK9) and also in several newly identified loci (near MVK-MMAB and GALNT2, with variants primarily associated with high-density lipoprotein (HDL) cholesterol; near SORT1, with variants primarily associated with low-density lipoprotein (LDL) cholesterol; near TRIB1, MLXIPL and ANGPTL3, with variants primarily associated with triglycerides; and a locus encompassing several genes near NCAN, with variants strongly associated with both triglycerides and LDL cholesterol). Notably, the 11 independent variants associated with increased LDL cholesterol concentrations in our study also showed increased frequency in a sample of coronary artery disease cases versus controls.
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Different haplotypes of APOA5 and APOC3 have been considered to be independently associated with TG levels.
“Although APOA1, APOC3, APOA4, and APOA5 cluster together in 11q23, different haplotypes of APOA5 and APOC3 have been considered to be independently associated with TG levels [100].”
From Fenofibrate and metabolic syndrome (2010) · cites this paper as [100]
The Results (Genome-wide association scans and Follow-up of initial findings; page not provided) associate variants near the APOA5–APOA4–APOC3–APOA1 cluster with triglyceride levels. They do not establish that distinct APOA5 and APOC3 haplotypes are independently associated with those levels. (LLM, conf=0.85)
Experimental — accuracy not yet measuredSeveral genome-wide association studies have linked the rs4420638 and rs10402271 SNPs of the APOE-APOC cluster with higher serum LDL cholesterol levels and an increased risk of coronary artery disease.
“Indeed, several GWAS have linked the rs4420638 and rs10402271 SNPs of the APOE–APOC cluster with higher serum LDL cholesterol levels and an increased risk of coronary artery disease84,85.”
From Multifaceted roles of APOE in Alzheimer disease (2024) · cites this paper as [84]
Variants in loci implicated in Mendelian disorders also contribute to susceptibility to more common forms of disease.
“There are now several examples where variants in loci implicated in Mendelian disorders also contribute to susceptibility to more common forms of disease; these include discoveries related to the genetics of blood lipid levels and coronary artery disease (83, 162), genetics of obesity (100, 163), and the genetics of height (96, 159).”
From Unraveling a Multifactorial Late-Onset Disease: From Genetic Susceptibility to Disease Mechanisms for Age-Related Macular Degeneration (2009) · cites this paper as [162]
A single locus can harbor both common variants of weak effect and rare variants of large effect; of 19 lipid loci, nine were already known to carry rare Mendelian mutations with large effects.
“6) A single locus can harbor both common variants of weak effect and rare variants of large effect. In recent GWASs, studies of common SNPs enabled the identification of 19 loci as influencing low- or high-density lipoprotein (LDL, HDL) or triglycerides (84, 85). Nine of these 19 were already known to carry rare Mendelian mutations with large effects, such as the loci for the LDL receptor (LDLR)”
From Genetic Mapping in Human Disease (2008) · cites this paper as [85]
A subset of associations involve genes previously related to the disease; of 19 loci meeting genome-wide significance in a recent GWAS of LDL, HDL, or triglycerides, 12 contained genes with known functions in lipid biology.
“1) A subset of associations involve genes previously related to the disease. Of 19 loci meeting genome-wide significance in a recent GWAS of LDL, HDL, or triglyceride levels, 12 contained genes with known functions in lipid biology (84, 85).”
From Genetic Mapping in Human Disease (2008) · cites this paper as [85]
GWASs have shown that common genetic variation in LDLR and HMGCR influences LDL levels.
“More recently, GWASs have shown that common genetic variation in LDLR and HMGCR influences LDL levels (84, 85).”
From Genetic Mapping in Human Disease (2008) · cites this paper as [85]
SNPs in HMGCR have only a small effect (~5%) on LDL levels, whereas drugs targeting the encoded protein decrease LDL levels by a much greater extent (~30%).
“Although SNPs in HMGCR have only a small effect (~5%) on LDL levels, drugs targeting the encoded protein decrease LDL levels by a much greater extent (~30%).”
From Genetic Mapping in Human Disease (2008) · cites this paper as [85]
Newly described variants on chromosome 1 near SORT1 are associated both with levels of LDL cholesterol and with risk of myocardial infarction.
“For example, newly described variants on chromosome 1 (near SORTI) are associated both with levels of LDL cholesterol (84, 85) and with risk of myocardial infarction (106);”
From Genetic Mapping in Human Disease (2008) · cites this paper as [85]
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- Authors
- Willer, C. J., Sanna, S., Jackson, A. U., Scuteri, A., Bonnycastle, L. L., Clarke, R., Heath, S. C., Timpson, N. J., Najjar, S. S., Stringham, H. M., Strait, J., Duren, W. L., Maschio, A., Busonero, F., Mulas, A., Albai, G., Swift, A. J., Morken, M. A., Narisu, N., Bennett, D., Parish, S., Shen, H., Galan, P., Meneton, P., Hercberg, S., Zelenika, D., Chen, W.-M., Li, Y., Scott, L. J., Scheet, P. A., Sundvall, J., Watanabe, R. M., Nagaraja, R., Ebrahim, S., Lawlor, D. A., Ben-Shlomo, Y., Davey-Smith, G., Shuldiner, A. R., Collins, R., Bergman, R. N., Uda, M., Tuomilehto, J., Cao, A., Collins, F. S., Lakatta, E., Lathrop, G. M., Boehnke, M., Schlessinger, D., Mohlke, K. L., & Abecasis, G. R.
- Affiliations
- University of Michigan (US)
- National Institute on Aging (US)
- National Human Genome Research Institute (US)
- University of Oxford (GB)
- Commissariat à l'Énergie Atomique et aux Énergies Alternatives (FR)
- University of Bristol (GB)
- Institute of Genetic and Biomedical Research (IT)
- University of Maryland, Baltimore (US)
- Inserm (FR)
- University of Southern California (US)
- London School of Hygiene & Tropical Medicine (GB)
- University of Helsinki (FI)
- University of North Carolina at Chapel Hill (US)
- Corresponding author
- Mohlke, Karen L
- Abecasis, Gonçalo R
- ORCID
- Willer, Cristen J
- Sanna, Serena
- Jackson, Anne U
- Scuteri, Angelo
- Bonnycastle, Lori L
- Clarke, Robert
- Heath, Simon C
- Timpson, Nicholas J
- Najjar, Samer S
- Stringham, Heather M
- Strait, James
- Maschio, Andrea
- Busonero, Fabio
- Mulas, Antonella
- Narisu, Narisu
- Bennett, Derrick
- Parish, Sarah
- Shen, Haiqing
- Galan, Pilar
- Meneton, Pierre
- Chen, Wei-Min
- Li, Yun
- Scott, Laura J
- Scheet, Paul A
- Watanabe, Richard M
- Nagaraja, Ramaiah
- Ebrahim, Shah
- Lawlor, Debbie A
- Shuldiner, Alan R
- Collins, Rory
- Bergman, Richard N
- Uda, Manuela
- Tuomilehto, Jaakko
- Collins, Francis S
- Lakatta, Edward
- Boehnke, Michael
- Schlessinger, David
- Mohlke, Karen L
- Abecasis, Gonçalo R
- Venue
- Nature Genetics
- Published
- 2008-01-13
- Volume
- 40
- Issue
- 2
- Pages
- 161-169
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- PMC
- PMC5206900
- OpenAlex
- W2142769596
- Cited by
- 1,585
- References
- 59
- Citations by year
- 2026: 9 · 2025: 29 · 2024: 33 · 2023: 32 · 2022: 46 · 2021: 63 · 2020: 55 · 2019: 58 · 2018: 75 · 2017: 67 · 2016: 78 · 2015: 88 · 2014: 112 · 2013: 115 · 2012: 139
- FWCI
- 18.13
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Genetics (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Carolina Digital Repository (University of North Carolina at Chapel Hill) (submittedVersion)
- UNICA IRIS Institutional Research Information System (University of Cagliari) (submittedVersion)
- UnissResearch (Università degli Studi di Sassari) (submittedVersion)
- Explore Bristol Research (submittedVersion)
- Bristol Research (University of Bristol) (submittedVersion)
- Funders
- Wellcome Trust (076113)
- National Institutes of Health (n01hg065403-000, 1z01ag000235-01, Z01 AG000235)
- National Human Genome Research Institute (N01 HG065403, N01 HG-65403)
- National Institute of Diabetes and Digestive and Kidney Diseases (R01DK072193, R01DK029867)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Health Sciences › Medicine › Surgery › Lipoproteins and Cardiovascular Health
- Health Sciences › Medicine › Cardiology and Cardiovascular Medicine › Lipid metabolism and disorders
- Keywords
- plasma lipid concentrations, coronary artery disease, genetic loci, LDL cholesterol, HDL cholesterol, triglycerides, SORT1, ANGPTL3, GALNT2, neurocan, apolipoprotein E, apolipoprotein C-III, APOA5, PCSK9, LDL receptor, lipoprotein lipase, GCKR, cholesteryl ester transfer protein, hepatic lipase, endothelial lipase, type 2 diabetes, aging
- MeSH terms
- Alleles, Computer Simulation, Coronary Artery Disease, Gene Frequency, Haplotypes, Humans, Lipids, Cholesterol, HDL, Cholesterol, LDL, Markov Chains, Probability, Risk Factors, Triglycerides, Genetic Variation, Cohort Studies, Genome, Human, Likelihood Functions, Case-Control Studies, Polymorphism, Single Nucleotide
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