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Ripatti P, Rämö JT, Söderlund S, Surakka I, Matikainen N, Pirinen M, Pajukanta P, Sarin AP, Service SK, Laurila PP, Ehnholm C, Salomaa V, Wilson RK, Palotie A, Freimer NB, Taskinen MR, Ripatti S. The Contribution of GWAS Loci in Familial Dyslipidemias. PLoS Genet 2016; 12:e1006078. [PMID: 27227539 PMCID: PMC4882070 DOI: 10.1371/journal.pgen.1006078] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [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: 01/22/2016] [Accepted: 05/03/2016] [Indexed: 01/08/2023] Open
Abstract
Familial combined hyperlipidemia (FCH) is a complex and common familial dyslipidemia characterized by elevated total cholesterol and/or triglyceride levels with over five-fold risk of coronary heart disease. The genetic architecture and contribution of rare Mendelian and common variants to FCH susceptibility is unknown. In 53 Finnish FCH families, we genotyped and imputed nine million variants in 715 family members with DNA available. We studied the enrichment of variants previously implicated with monogenic dyslipidemias and/or lipid levels in the general population by comparing allele frequencies between the FCH families and population samples. We also constructed weighted polygenic scores using 212 lipid-associated SNPs and estimated the relative contributions of Mendelian variants and polygenic scores to the risk of FCH in the families. We identified, across the whole allele frequency spectrum, an enrichment of variants known to elevate, and a deficiency of variants known to lower LDL-C and/or TG levels among both probands and affected FCH individuals. The score based on TG associated SNPs was particularly high among affected individuals compared to non-affected family members. Out of 234 affected FCH individuals across the families, seven (3%) carried Mendelian variants and 83 (35%) showed high accumulation of either known LDL-C or TG elevating variants by having either polygenic score over the 90th percentile in the population. The positive predictive value of high score was much higher for affected FCH individuals than for similar sporadic cases in the population. FCH is highly polygenic, supporting the hypothesis that variants across the whole allele frequency spectrum contribute to this complex familial trait. Polygenic SNP panels improve identification of individuals affected with FCH, but their clinical utility remains to be defined. Familial combined hyperlipidemia (FCH) is a familial dyslipidemia and the most common familial risk factor for premature coronary heart disease. Its genetic architecture is poorly understood. Rare high-impact variants have been identified in some patients, but have not explained a substantial portion of the trait. FCH has previously been speculated to be a polygenic disorder, but genetic data supporting this hypothesis have so far been incomplete. We provide experimental evidence for the polygenicity and heterogeneity of FCH in a large set of affected families using comprehensive genome-wide variant data. Approximately a third of the affected FCH individuals in our sample had high polygenic burden, and only a minority carried high-impact variants identifiable by genotyping. We show that the polygenic burden of affected FCH family members is comparable to that observed in individuals with similar lipid phenotypes in the general population. Genetic variants identified in large-scale population studies can also underlie the typical phenotypes observed in complex familial diseases such as FCH. Advances in genetic diagnosis based on population samples may thus also benefit FCH families. Families without high polygenic burden are good candidates for sequencing studies to identify rare variants not observable with genotyping.
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Affiliation(s)
- Pietari Ripatti
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
| | - Joel T. Rämö
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Psychiatric & Neurodevelopmental Genetics Unit, Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Sanni Söderlund
- Research Programs Unit, Diabetes & Obesity, University of Helsinki, and Heart and Lung Centre, Helsinki University Hospital, Helsinki, Finland
| | - Ida Surakka
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
| | - Niina Matikainen
- Research Programs Unit, Diabetes & Obesity, University of Helsinki, and Heart and Lung Centre, Helsinki University Hospital, Helsinki, Finland
- Endocrinology, Abdominal Center, Helsinki University Hospital, Helsinki, Finland
| | - Matti Pirinen
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
| | - Päivi Pajukanta
- Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California Los Angeles (UCLA), Los Angeles, California, United States of America
| | - Antti-Pekka Sarin
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
- National Institute for Health and Welfare, Helsinki, Finland
| | - Susan K. Service
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, California, United States of America
| | - Pirkka-Pekka Laurila
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
- Public Health Genomics Unit, National Institute for Health and Welfare, Helsinki, Finland
- Department of Medical Genetics, University of Helsinki, Helsinki, Finland
| | - Christian Ehnholm
- Public Health Genomics Unit, National Institute for Health and Welfare, Helsinki, Finland
| | - Veikko Salomaa
- National Institute for Health and Welfare, Helsinki, Finland
| | - Richard K. Wilson
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Aarno Palotie
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Psychiatric & Neurodevelopmental Genetics Unit, Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- The Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Nelson B. Freimer
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, California, United States of America
| | - Marja-Riitta Taskinen
- Research Programs Unit, Diabetes & Obesity, University of Helsinki, and Heart and Lung Centre, Helsinki University Hospital, Helsinki, Finland
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
- Department of Public Health, Clinicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Wellcome Trust Sanger Institute, Cambridge, United Kingdom
- * E-mail:
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