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Björnsson E, Thorgeirsson G, Helgadóttir A, Thorleifsson G, Sveinbjörnsson G, Kristmundsdóttir S, Jónsson H, Jónasdóttir A, Jónasdóttir Á, Sigurðsson Á, Guðnason T, Ólafsson Í, Sigurðsson EL, Sigurðardóttir Ó, Viðarsson B, Baldvinsson M, Bjarnason R, Danielsen R, Matthíasson SE, Thórarinsson BL, Grétarsdóttir S, Steinthórsdóttir V, Halldórsson BV, Andersen K, Arnar DO, Jónsdóttir I, Guðbjartsson DF, Hólm H, Thorsteinsdóttir U, Sulem P, Stefánsson K. Large-Scale Screening for Monogenic and Clinically Defined Familial Hypercholesterolemia in Iceland. Arterioscler Thromb Vasc Biol 2021; 41:2616-2628. [PMID: 34407635 PMCID: PMC8454500 DOI: 10.1161/atvbaha.120.315904] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 08/02/2021] [Indexed: 01/07/2023]
Abstract
Objective: Familial hypercholesterolemia (FH) is traditionally defined as a monogenic disease characterized by severely elevated LDL-C (low-density lipoprotein cholesterol) levels. In practice, FH is commonly a clinical diagnosis without confirmation of a causative mutation. In this study, we sought to characterize and compare monogenic and clinically defined FH in a large sample of Icelanders. Approach and Results: We whole-genome sequenced 49 962 Icelanders and imputed the identified variants into an overall sample of 166 281 chip-genotyped Icelanders. We identified 20 FH mutations in LDLR, APOB, and PCSK9 with combined prevalence of 1 in 836. Monogenic FH was associated with severely elevated LDL-C levels and increased risk of premature coronary disease, aortic valve stenosis, and high burden of coronary atherosclerosis. We used a modified version of the Dutch Lipid Clinic Network criteria to screen for the clinical FH phenotype among living adult participants (N=79 058). Clinical FH was found in 2.2% of participants, of whom only 5.2% had monogenic FH. Mutation-negative clinical FH has a strong polygenic basis. Both individuals with monogenic FH and individuals with mutation-negative clinical FH were markedly undertreated with cholesterol-lowering medications and only a minority attained an LDL-C target of <2.6 mmol/L (<100 mg/dL; 11.0% and 24.9%, respectively) or <1.8 mmol/L (<70 mg/dL; 0.0% and 5.2%, respectively), as recommended for primary prevention by European Society of Cardiology/European Atherosclerosis Society cholesterol guidelines. Conclusions: Clinically defined FH is a relatively common phenotype that is explained by monogenic FH in only a minority of cases. Both monogenic and clinical FH confer high cardiovascular risk but are markedly undertreated.
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Affiliation(s)
- Eythór Björnsson
- deCODE genetics/Amgen, Inc, Reykjavík, Iceland (E.B., G. Thorgeirsson, A.H., G. Thorleifsson, G.S., S.K., H.J., Aðalbjörg Jónasdóttir, Áslaug Jónasdóttir, A.S., S.G., V.S., B.V.H., D.O.A., I.J., D.F.G., H.H., U.T., P.S., K.S.)
- Faculty of Medicine, University of Iceland, Reykjavík (E.B., E.L.S., R.B., K.A., D.O.A., I.J., U.T., K.S.)
- Department of Internal Medicine (E.B.), Landspítali-The National University Hospital of Iceland, Reykjavík
| | - Guðmundur Thorgeirsson
- deCODE genetics/Amgen, Inc, Reykjavík, Iceland (E.B., G. Thorgeirsson, A.H., G. Thorleifsson, G.S., S.K., H.J., Aðalbjörg Jónasdóttir, Áslaug Jónasdóttir, A.S., S.G., V.S., B.V.H., D.O.A., I.J., D.F.G., H.H., U.T., P.S., K.S.)
- Division of Cardiology, Department of Internal Medicine (G. Thorgeirsson, R.D., K.A., D.O.A.), Landspítali-The National University Hospital of Iceland, Reykjavík
| | - Anna Helgadóttir
- deCODE genetics/Amgen, Inc, Reykjavík, Iceland (E.B., G. Thorgeirsson, A.H., G. Thorleifsson, G.S., S.K., H.J., Aðalbjörg Jónasdóttir, Áslaug Jónasdóttir, A.S., S.G., V.S., B.V.H., D.O.A., I.J., D.F.G., H.H., U.T., P.S., K.S.)
| | - Guðmar Thorleifsson
- deCODE genetics/Amgen, Inc, Reykjavík, Iceland (E.B., G. Thorgeirsson, A.H., G. Thorleifsson, G.S., S.K., H.J., Aðalbjörg Jónasdóttir, Áslaug Jónasdóttir, A.S., S.G., V.S., B.V.H., D.O.A., I.J., D.F.G., H.H., U.T., P.S., K.S.)
| | - Garðar Sveinbjörnsson
- deCODE genetics/Amgen, Inc, Reykjavík, Iceland (E.B., G. Thorgeirsson, A.H., G. Thorleifsson, G.S., S.K., H.J., Aðalbjörg Jónasdóttir, Áslaug Jónasdóttir, A.S., S.G., V.S., B.V.H., D.O.A., I.J., D.F.G., H.H., U.T., P.S., K.S.)
| | - Snaedís Kristmundsdóttir
- deCODE genetics/Amgen, Inc, Reykjavík, Iceland (E.B., G. Thorgeirsson, A.H., G. Thorleifsson, G.S., S.K., H.J., Aðalbjörg Jónasdóttir, Áslaug Jónasdóttir, A.S., S.G., V.S., B.V.H., D.O.A., I.J., D.F.G., H.H., U.T., P.S., K.S.)
| | - Hákon Jónsson
- deCODE genetics/Amgen, Inc, Reykjavík, Iceland (E.B., G. Thorgeirsson, A.H., G. Thorleifsson, G.S., S.K., H.J., Aðalbjörg Jónasdóttir, Áslaug Jónasdóttir, A.S., S.G., V.S., B.V.H., D.O.A., I.J., D.F.G., H.H., U.T., P.S., K.S.)
| | - Aðalbjörg Jónasdóttir
- deCODE genetics/Amgen, Inc, Reykjavík, Iceland (E.B., G. Thorgeirsson, A.H., G. Thorleifsson, G.S., S.K., H.J., Aðalbjörg Jónasdóttir, Áslaug Jónasdóttir, A.S., S.G., V.S., B.V.H., D.O.A., I.J., D.F.G., H.H., U.T., P.S., K.S.)
| | - Áslaug Jónasdóttir
- deCODE genetics/Amgen, Inc, Reykjavík, Iceland (E.B., G. Thorgeirsson, A.H., G. Thorleifsson, G.S., S.K., H.J., Aðalbjörg Jónasdóttir, Áslaug Jónasdóttir, A.S., S.G., V.S., B.V.H., D.O.A., I.J., D.F.G., H.H., U.T., P.S., K.S.)
| | - Ásgeir Sigurðsson
- deCODE genetics/Amgen, Inc, Reykjavík, Iceland (E.B., G. Thorgeirsson, A.H., G. Thorleifsson, G.S., S.K., H.J., Aðalbjörg Jónasdóttir, Áslaug Jónasdóttir, A.S., S.G., V.S., B.V.H., D.O.A., I.J., D.F.G., H.H., U.T., P.S., K.S.)
| | | | - Ísleifur Ólafsson
- Department of Clinical Biochemistry (I.O.), Landspítali-The National University Hospital of Iceland, Reykjavík
| | - Emil L. Sigurðsson
- Faculty of Medicine, University of Iceland, Reykjavík (E.B., E.L.S., R.B., K.A., D.O.A., I.J., U.T., K.S.)
- Development Centre for the Primary Care, Reykjavík, Iceland (E.L.S.)
| | | | - Brynjar Viðarsson
- Department of Hematology (B.V.), Landspítali-The National University Hospital of Iceland, Reykjavík
- The Laboratory in Mjódd, Reykjavík, Iceland (B.V.)
| | | | - Ragnar Bjarnason
- Faculty of Medicine, University of Iceland, Reykjavík (E.B., E.L.S., R.B., K.A., D.O.A., I.J., U.T., K.S.)
- Children’s Medical Center (R.B.), Landspítali-The National University Hospital of Iceland, Reykjavík
| | - Ragnar Danielsen
- Division of Cardiology, Department of Internal Medicine (G. Thorgeirsson, R.D., K.A., D.O.A.), Landspítali-The National University Hospital of Iceland, Reykjavík
| | | | - Björn L. Thórarinsson
- Department of Neurology (B.L.T.), Landspítali-The National University Hospital of Iceland, Reykjavík
| | - Sólveig Grétarsdóttir
- deCODE genetics/Amgen, Inc, Reykjavík, Iceland (E.B., G. Thorgeirsson, A.H., G. Thorleifsson, G.S., S.K., H.J., Aðalbjörg Jónasdóttir, Áslaug Jónasdóttir, A.S., S.G., V.S., B.V.H., D.O.A., I.J., D.F.G., H.H., U.T., P.S., K.S.)
| | - Valgerður Steinthórsdóttir
- deCODE genetics/Amgen, Inc, Reykjavík, Iceland (E.B., G. Thorgeirsson, A.H., G. Thorleifsson, G.S., S.K., H.J., Aðalbjörg Jónasdóttir, Áslaug Jónasdóttir, A.S., S.G., V.S., B.V.H., D.O.A., I.J., D.F.G., H.H., U.T., P.S., K.S.)
| | - Bjarni V. Halldórsson
- deCODE genetics/Amgen, Inc, Reykjavík, Iceland (E.B., G. Thorgeirsson, A.H., G. Thorleifsson, G.S., S.K., H.J., Aðalbjörg Jónasdóttir, Áslaug Jónasdóttir, A.S., S.G., V.S., B.V.H., D.O.A., I.J., D.F.G., H.H., U.T., P.S., K.S.)
| | - Karl Andersen
- Faculty of Medicine, University of Iceland, Reykjavík (E.B., E.L.S., R.B., K.A., D.O.A., I.J., U.T., K.S.)
- Division of Cardiology, Department of Internal Medicine (G. Thorgeirsson, R.D., K.A., D.O.A.), Landspítali-The National University Hospital of Iceland, Reykjavík
| | - Davíð O. Arnar
- deCODE genetics/Amgen, Inc, Reykjavík, Iceland (E.B., G. Thorgeirsson, A.H., G. Thorleifsson, G.S., S.K., H.J., Aðalbjörg Jónasdóttir, Áslaug Jónasdóttir, A.S., S.G., V.S., B.V.H., D.O.A., I.J., D.F.G., H.H., U.T., P.S., K.S.)
- Faculty of Medicine, University of Iceland, Reykjavík (E.B., E.L.S., R.B., K.A., D.O.A., I.J., U.T., K.S.)
- Division of Cardiology, Department of Internal Medicine (G. Thorgeirsson, R.D., K.A., D.O.A.), Landspítali-The National University Hospital of Iceland, Reykjavík
| | - Ingileif Jónsdóttir
- deCODE genetics/Amgen, Inc, Reykjavík, Iceland (E.B., G. Thorgeirsson, A.H., G. Thorleifsson, G.S., S.K., H.J., Aðalbjörg Jónasdóttir, Áslaug Jónasdóttir, A.S., S.G., V.S., B.V.H., D.O.A., I.J., D.F.G., H.H., U.T., P.S., K.S.)
- Faculty of Medicine, University of Iceland, Reykjavík (E.B., E.L.S., R.B., K.A., D.O.A., I.J., U.T., K.S.)
| | - Daníel F. Guðbjartsson
- deCODE genetics/Amgen, Inc, Reykjavík, Iceland (E.B., G. Thorgeirsson, A.H., G. Thorleifsson, G.S., S.K., H.J., Aðalbjörg Jónasdóttir, Áslaug Jónasdóttir, A.S., S.G., V.S., B.V.H., D.O.A., I.J., D.F.G., H.H., U.T., P.S., K.S.)
- School of Engineering and Natural Sciences, University of Iceland, Reykjavík (D.F.G.)
| | - Hilma Hólm
- deCODE genetics/Amgen, Inc, Reykjavík, Iceland (E.B., G. Thorgeirsson, A.H., G. Thorleifsson, G.S., S.K., H.J., Aðalbjörg Jónasdóttir, Áslaug Jónasdóttir, A.S., S.G., V.S., B.V.H., D.O.A., I.J., D.F.G., H.H., U.T., P.S., K.S.)
| | - Unnur Thorsteinsdóttir
- deCODE genetics/Amgen, Inc, Reykjavík, Iceland (E.B., G. Thorgeirsson, A.H., G. Thorleifsson, G.S., S.K., H.J., Aðalbjörg Jónasdóttir, Áslaug Jónasdóttir, A.S., S.G., V.S., B.V.H., D.O.A., I.J., D.F.G., H.H., U.T., P.S., K.S.)
- Faculty of Medicine, University of Iceland, Reykjavík (E.B., E.L.S., R.B., K.A., D.O.A., I.J., U.T., K.S.)
| | - Patrick Sulem
- deCODE genetics/Amgen, Inc, Reykjavík, Iceland (E.B., G. Thorgeirsson, A.H., G. Thorleifsson, G.S., S.K., H.J., Aðalbjörg Jónasdóttir, Áslaug Jónasdóttir, A.S., S.G., V.S., B.V.H., D.O.A., I.J., D.F.G., H.H., U.T., P.S., K.S.)
| | - Kári Stefánsson
- deCODE genetics/Amgen, Inc, Reykjavík, Iceland (E.B., G. Thorgeirsson, A.H., G. Thorleifsson, G.S., S.K., H.J., Aðalbjörg Jónasdóttir, Áslaug Jónasdóttir, A.S., S.G., V.S., B.V.H., D.O.A., I.J., D.F.G., H.H., U.T., P.S., K.S.)
- Faculty of Medicine, University of Iceland, Reykjavík (E.B., E.L.S., R.B., K.A., D.O.A., I.J., U.T., K.S.)
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3
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Björnsson E, Thorleifsson G, Helgadóttir A, Guðnason T, Guðbjartsson T, Andersen K, Grétarsdóttir S, Ólafsson Í, Tragante V, Ólafsson ÓH, Jónsdóttir B, Eyjólfsson GI, Sigurðardóttir Ó, Thorgeirsson G, Guðbjartsson DF, Thorsteinsdóttir U, Hólm H, Stefánsson K. Association of Genetically Predicted Lipid Levels With the Extent of Coronary Atherosclerosis in Icelandic Adults. JAMA Cardiol 2021; 5:13-20. [PMID: 31746962 PMCID: PMC6902100 DOI: 10.1001/jamacardio.2019.2946] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Importance Genetic studies have evaluated the influence of blood lipid levels on the risk of coronary artery disease (CAD), but less is known about how they are associated with the extent of coronary atherosclerosis. Objective To estimate the contributions of genetically predicted blood lipid levels on the extent of coronary atherosclerosis. Design, Setting, and Participants This genetic study included Icelandic adults who had undergone coronary angiography or assessment of coronary artery calcium using cardiac computed tomography. The study incorporates data collected from January 1987 to December 2017 in Iceland in the Swedish Coronary Angiography and Angioplasty Registry and 2 registries of individuals who had undergone percutaneous coronary interventions and coronary artery bypass grafting. For each participant, genetic scores were calculated for levels of non-high-density lipoprotein cholesterol (non-HDL-C), low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), and triglycerides, based on reported effect sizes of 345 independent, lipid-associated variants. The genetic scores' predictive ability for lipid levels was assessed in more than 87 000 Icelandic adults. A mendelian randomization approach was used to estimate the contribution of each lipid trait. Exposures Genetic scores for levels of non-HDL-C, LDL-C, HDL-C, and triglycerides. Main Outcomes and Measures The extent of angiographic CAD and coronary artery calcium quantity. Results A total of 12 460 adults (mean [SD] age, 65.1 [10.7] years; 8383 men [67.3%]) underwent coronary angiography, and 4837 had coronary artery calcium assessed by computed tomography. A genetically predicted increase in non-HDL-C levels by 1 SD (38 mg/dL [to convert to millimoles per liter, multiply by 0.0259]) was associated with greater odds of obstructive CAD (odds ratio [OR], 1.83 [95% CI, 1.63-2.07]; P = 2.8 × 10-23). Among patients with obstructive CAD, there were significant associations with multivessel disease (OR, 1.26 [95% CI, 1.11-1.44]; P = 4.1 × 10-4) and 3-vessel disease (OR, 1.47 [95% CI, 1.26-1.72]; P = 9.2 × 10-7). There were also significant associations with the presence of coronary artery calcium (OR, 2.04 [95% CI, 1.70-2.44]; P = 5.3 × 10-15) and loge-transformed coronary artery calcium (effect, 0.70 [95% CI, 0.53-0.87]; P = 1.0 × 10-15). Genetically predicted levels of non-HDL-C remained associated with obstructive CAD and coronary artery calcium extent even after accounting for the association with LDL-C. Genetically predicted levels of HDL-C and triglycerides were associated individually with the extent of coronary atherosclerosis, but not after accounting for the association with non-HDL cholesterol. Conclusions and Relevance In this study, genetically predicted levels of non-HDL-C were associated with the extent of coronary atherosclerosis as estimated by 2 different methods. The association was stronger than for genetically predicted levels of LDL-C. These findings further support the notion that non-HDL-C may be a better marker of the overall burden of atherogenic lipoproteins than LDL-C.
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Affiliation(s)
- Eythór Björnsson
- deCODE genetics/Amgen Inc, Reykjavík, Iceland.,Faculty of Medicine, University of Iceland, Reykjavík, Iceland.,Division of Cardiology, Landspítali-The National University Hospital of Iceland, Reykjavík, Iceland
| | | | | | - Thórarinn Guðnason
- Division of Cardiology, Landspítali-The National University Hospital of Iceland, Reykjavík, Iceland
| | - Tómas Guðbjartsson
- Faculty of Medicine, University of Iceland, Reykjavík, Iceland.,Division of Cardiothoracic Surgery, Landspítali-The National University Hospital of Iceland, Reykjavík, Iceland
| | - Karl Andersen
- Faculty of Medicine, University of Iceland, Reykjavík, Iceland.,Division of Cardiology, Landspítali-The National University Hospital of Iceland, Reykjavík, Iceland
| | | | - Ísleifur Ólafsson
- Department of Clinical Biochemistry, Landspítali-The National University Hospital of Iceland, Reykjavík, Iceland
| | - Vinicius Tragante
- deCODE genetics/Amgen Inc, Reykjavík, Iceland.,Division of Heart & Lungs, Department of Cardiology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Ólafur Hreiðar Ólafsson
- deCODE genetics/Amgen Inc, Reykjavík, Iceland.,Faculty of Medicine, University of Iceland, Reykjavík, Iceland
| | | | | | | | - Guðmundur Thorgeirsson
- deCODE genetics/Amgen Inc, Reykjavík, Iceland.,Faculty of Medicine, University of Iceland, Reykjavík, Iceland.,Division of Cardiology, Landspítali-The National University Hospital of Iceland, Reykjavík, Iceland
| | - Daníel F Guðbjartsson
- deCODE genetics/Amgen Inc, Reykjavík, Iceland.,School of Engineering and Natural Sciences, University of Iceland, Reykjavík, Iceland
| | - Unnur Thorsteinsdóttir
- deCODE genetics/Amgen Inc, Reykjavík, Iceland.,Faculty of Medicine, University of Iceland, Reykjavík, Iceland
| | - Hilma Hólm
- deCODE genetics/Amgen Inc, Reykjavík, Iceland
| | - Kári Stefánsson
- deCODE genetics/Amgen Inc, Reykjavík, Iceland.,Faculty of Medicine, University of Iceland, Reykjavík, Iceland
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5
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Swaminathan B, Thorleifsson G, Jöud M, Ali M, Johnsson E, Ajore R, Sulem P, Halvarsson BM, Eyjolfsson G, Haraldsdottir V, Hultman C, Ingelsson E, Kristinsson SY, Kähler AK, Lenhoff S, Masson G, Mellqvist UH, Månsson R, Nelander S, Olafsson I, Sigurðardottir O, Steingrimsdóttir H, Vangsted A, Vogel U, Waage A, Nahi H, Gudbjartsson DF, Rafnar T, Turesson I, Gullberg U, Stefánsson K, Hansson M, Thorsteinsdóttir U, Nilsson B. Variants in ELL2 influencing immunoglobulin levels associate with multiple myeloma. Nat Commun 2015; 6:7213. [PMID: 26007630 PMCID: PMC4455110 DOI: 10.1038/ncomms8213] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 04/20/2015] [Indexed: 02/07/2023] Open
Abstract
Multiple myeloma (MM) is characterized by an uninhibited, clonal growth of plasma cells. While first-degree relatives of patients with MM show an increased risk of MM, the genetic basis of inherited MM susceptibility is incompletely understood. Here we report a genome-wide association study in the Nordic region identifying a novel MM risk locus at ELL2 (rs56219066T; odds ratio (OR)=1.25; P=9.6 × 10(-10)). This gene encodes a stoichiometrically limiting component of the super-elongation complex that drives secretory-specific immunoglobulin mRNA production and transcriptional regulation in plasma cells. We find that the MM risk allele harbours a Thr298Ala missense variant in an ELL2 domain required for transcription elongation. Consistent with a hypomorphic effect, we find that the MM risk allele also associates with reduced levels of immunoglobulin A (IgA) and G (IgG) in healthy subjects (P=8.6 × 10(-9) and P=6.4 × 10(-3), respectively) and, potentially, with an increased risk of bacterial meningitis (OR=1.30; P=0.0024).
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Affiliation(s)
- Bhairavi Swaminathan
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, BMC B13, SE-221 84 Lund, Sweden
| | | | - Magnus Jöud
- 1] Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, BMC B13, SE-221 84 Lund, Sweden [2] Clinical Immunology and Transfusion Medicine, Laboratory Medicine, Office of Medical Services, Akutgatan 8, SE-221 85 Lund, Sweden
| | - Mina Ali
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, BMC B13, SE-221 84 Lund, Sweden
| | - Ellinor Johnsson
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, BMC B13, SE-221 84 Lund, Sweden
| | - Ram Ajore
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, BMC B13, SE-221 84 Lund, Sweden
| | - Patrick Sulem
- deCODE genetics, Sturlugata 8, IS-101 Reykjavik, Iceland
| | - Britt-Marie Halvarsson
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, BMC B13, SE-221 84 Lund, Sweden
| | | | - Vilhelmina Haraldsdottir
- Department of Hematology, Landspitali, The National University Hospital of Iceland, IS-101 Reykjavik, Iceland
| | - Christina Hultman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Erik Ingelsson
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden
| | | | - Anna K Kähler
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Stig Lenhoff
- Hematology Clinic, Skåne University Hospital, SE-221 85 Lund, Sweden
| | - Gisli Masson
- deCODE genetics, Sturlugata 8, IS-101 Reykjavik, Iceland
| | - Ulf-Henrik Mellqvist
- Section of Hematology, Sahlgrenska University Hospital, SE-413 45 Gothenburg, Sweden
| | - Robert Månsson
- Center for Hematology and Regenerative Medicine, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Sven Nelander
- Department of Immunology, Pathology and Genetics, Uppsala University, Rudbeck Laboratory, SE-751 05 Uppsala, Sweden
| | - Isleifur Olafsson
- Department of Clinical Biochemistry, Landspitali, The National University Hospital of Iceland, IS-101 Reykjavik, Iceland
| | - Olof Sigurðardottir
- Department of Clinical Biochemistry, Akureyri Hospital, IS-600 Akureyri, Iceland
| | - Hlif Steingrimsdóttir
- Department of Hematology, Landspitali, The National University Hospital of Iceland, IS-101 Reykjavik, Iceland
| | - Annette Vangsted
- Department of Haematology, University Hospital of Copenhagen at Rigshospitalet, Blegdamsvej 9, DK-2100 Copenhagen, Denmark
| | - Ulla Vogel
- National Research Centre for the Working Environment, Lersø Parkallé 105, DK-2100 Copenhagen, Denmark
| | - Anders Waage
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Box 8905, N-7491 Trondheim, Norway
| | - Hareth Nahi
- Center for Hematology and Regenerative Medicine, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | | | - Thorunn Rafnar
- deCODE genetics, Sturlugata 8, IS-101 Reykjavik, Iceland
| | - Ingemar Turesson
- Hematology Clinic, Skåne University Hospital, SE-221 85 Lund, Sweden
| | - Urban Gullberg
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, BMC B13, SE-221 84 Lund, Sweden
| | | | - Markus Hansson
- 1] Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, BMC B13, SE-221 84 Lund, Sweden [2] Hematology Clinic, Skåne University Hospital, SE-221 85 Lund, Sweden
| | | | - Björn Nilsson
- 1] Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, BMC B13, SE-221 84 Lund, Sweden [2] Clinical Immunology and Transfusion Medicine, Laboratory Medicine, Office of Medical Services, Akutgatan 8, SE-221 85 Lund, Sweden [3] Broad Institute, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
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Walters RG, Coin LJM, Ruokonen A, de Smith AJ, El-Sayed Moustafa JS, Jacquemont S, Elliott P, Esko T, Hartikainen AL, Laitinen J, Männik K, Martinet D, Meyre D, Nauck M, Schurmann C, Sladek R, Thorleifsson G, Thorsteinsdóttir U, Valsesia A, Waeber G, Zufferey F, Balkau B, Pattou F, Metspalu A, Völzke H, Vollenweider P, Stefansson K, Järvelin MR, Beckmann JS, Froguel P, Blakemore AIF. Rare genomic structural variants in complex disease: lessons from the replication of associations with obesity. PLoS One 2013; 8:e58048. [PMID: 23554873 PMCID: PMC3595275 DOI: 10.1371/journal.pone.0058048] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Accepted: 01/30/2013] [Indexed: 01/19/2023] Open
Abstract
The limited ability of common variants to account for the genetic contribution to complex disease has prompted searches for rare variants of large effect, to partly explain the ‘missing heritability’. Analyses of genome-wide genotyping data have identified genomic structural variants (GSVs) as a source of such rare causal variants. Recent studies have reported multiple GSV loci associated with risk of obesity. We attempted to replicate these associations by similar analysis of two familial-obesity case-control cohorts and a population cohort, and detected GSVs at 11 out of 18 loci, at frequencies similar to those previously reported. Based on their reported frequencies and effect sizes (OR≥25), we had sufficient statistical power to detect the large majority (80%) of genuine associations at these loci. However, only one obesity association was replicated. Deletion of a 220 kb region on chromosome 16p11.2 has a carrier population frequency of 2×10−4 (95% confidence interval [9.6×10−5–3.1×10−4]); accounts overall for 0.5% [0.19%–0.82%] of severe childhood obesity cases (P = 3.8×10−10; odds ratio = 25.0 [9.9–60.6]); and results in a mean body mass index (BMI) increase of 5.8 kg.m−2 [1.8–10.3] in adults from the general population. We also attempted replication using BMI as a quantitative trait in our population cohort; associations with BMI at or near nominal significance were detected at two further loci near KIF2B and within FOXP2, but these did not survive correction for multiple testing. These findings emphasise several issues of importance when conducting rare GSV association, including the need for careful cohort selection and replication strategy, accurate GSV identification, and appropriate correction for multiple testing and/or control of false discovery rate. Moreover, they highlight the potential difficulty in replicating rare CNV associations across different populations. Nevertheless, we show that such studies are potentially valuable for the identification of variants making an appreciable contribution to complex disease.
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Affiliation(s)
- Robin G. Walters
- Department of Genomics of Common Disease, Imperial College London, London, United Kingdom
- Clinical Trial Service Unit and Epidemiological Studies Unit, University of Oxford, Oxford, United Kingdom
| | - Lachlan J. M. Coin
- Department of Genomics of Common Disease, Imperial College London, London, United Kingdom
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Aimo Ruokonen
- Institute of Diagnostics, Clinical Chemistry, University of Oulu, Oulu, Finland
- Oulu University Hospital, Oulu, Finland
| | - Adam J. de Smith
- Department of Genomics of Common Disease, Imperial College London, London, United Kingdom
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, United States of America
| | | | - Sebastien Jacquemont
- Service of Medical Genetics, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Paul Elliott
- Department of Epidemiology and Biostatistics, Imperial College London, London, United Kingdom
- MRC Health Protection Agency (HPA) Centre for Environment and Health, Imperial College London, London, United Kingdom
| | - Tõnu Esko
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Anna-Liisa Hartikainen
- Institute of Clinical Sciences/Obstetrics and Gynecology, University of Oulu, Oulu, Finland
| | | | - Katrin Männik
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- The Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Danielle Martinet
- Service of Medical Genetics, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - David Meyre
- CNRS 8199-Institute of Biology, Pasteur Institute, Lille, France
- Department of Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, Ontario, Canada
| | - Matthias Nauck
- Institute of Clinical Chemistry and Laboratory Medicine, Ernst-Moritz-Arndt-University, Greifswald, Germany
| | - Claudia Schurmann
- Interfaculty Institute for Genetics and Functional Genomics, Ernst-Moritz-Arndt-University, Greifswald, Germany
| | - Rob Sladek
- McGill University and Genome Quebec Innovation Centre, Montreal, Canada
- Department of Medicine and Human Genetics, McGill University, Montreal, Canada
| | | | - Unnur Thorsteinsdóttir
- deCODE Genetics, Reykjavík, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Armand Valsesia
- Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Gerard Waeber
- Department of Internal Medicine, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Flore Zufferey
- Service of Medical Genetics, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Beverley Balkau
- INSERM, CESP Centre for Research in Epidemiology and Population Health, U1018, Villejuif, France
- University Paris Sud 11, UMRS 1018, Villejuif, France
| | - François Pattou
- INSERM U859, Lille, France
- Université Lille Nord de France, Centre Hospitalier Universitaire Lille, Lille, France
| | - Andres Metspalu
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Henry Völzke
- Institute for Community Medicine, Ernst-Moritz-Arndt-University, Greifswald, Germany
| | - Peter Vollenweider
- Department of Internal Medicine, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Kári Stefansson
- deCODE Genetics, Reykjavík, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Marjo-Riitta Järvelin
- Department of Epidemiology and Biostatistics, Imperial College London, London, United Kingdom
- MRC Health Protection Agency (HPA) Centre for Environment and Health, Imperial College London, London, United Kingdom
- Institute of Health Sciences, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Department of Lifecourse and Services, National Institute for Health and Welfare, Oulu, Finland
| | - Jacques S. Beckmann
- Service of Medical Genetics, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
- Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland
| | - Philippe Froguel
- Department of Genomics of Common Disease, Imperial College London, London, United Kingdom
- CNRS 8199-Institute of Biology, Pasteur Institute, Lille, France
- * E-mail: (AIFB); (PF)
| | - Alexandra I. F. Blakemore
- Department of Genomics of Common Disease, Imperial College London, London, United Kingdom
- Section of Investigative Medicine, Imperial College London, London, United Kingdom
- * E-mail: (AIFB); (PF)
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