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Deelen J, Beekman M, Uh HW, Helmer Q, Kuningas M, Christiansen L, Kremer D, van der Breggen R, Suchiman HED, Lakenberg N, van den Akker EB, Passtoors WM, Tiemeier H, van Heemst D, de Craen AJ, Rivadeneira F, de Geus EJ, Perola M, van der Ouderaa FJ, Gunn DA, Boomsma DI, Uitterlinden AG, Christensen K, van Duijn CM, Heijmans BT, Houwing-Duistermaat JJ, Westendorp RGJ, Slagboom PE. Genome-wide association study identifies a single major locus contributing to survival into old age; the APOE locus revisited. Aging Cell 2011; 10:686-98. [PMID: 21418511 PMCID: PMC3193372 DOI: 10.1111/j.1474-9726.2011.00705.x] [Citation(s) in RCA: 208] [Impact Index Per Article: 16.0] [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] [Indexed: 12/19/2022] Open
Abstract
By studying the loci that contribute to human longevity, we aim to identify mechanisms that contribute to healthy aging. To identify such loci, we performed a genome-wide association study (GWAS) comparing 403 unrelated nonagenarians from long-living families included in the Leiden Longevity Study (LLS) and 1670 younger population controls. The strongest candidate SNPs from this GWAS have been analyzed in a meta-analysis of nonagenarian cases from the Rotterdam Study, Leiden 85-plus study, and Danish 1905 cohort. Only one of the 62 prioritized SNPs from the GWAS analysis (P < 1 × 10−4) showed genome-wide significance with survival into old age in the meta-analysis of 4149 nonagenarian cases and 7582 younger controls [OR = 0.71 (95% CI 0.65–0.77), P = 3.39 × 10−17]. This SNP, rs2075650, is located in TOMM40 at chromosome 19q13.32 close to the apolipoprotein E (APOE) gene. Although there was only moderate linkage disequilibrium between rs2075650 and the ApoE ε4 defining SNP rs429358, we could not find an APOE-independent effect of rs2075650 on longevity, either in cross-sectional or in longitudinal analyses. As expected, rs429358 associated with metabolic phenotypes in the offspring of the nonagenarian cases from the LLS and their partners. In addition, we observed a novel association between this locus and serum levels of IGF-1 in women (P = 0.005). In conclusion, the major locus determining familial longevity up to high age as detected by GWAS was marked by rs2075650, which tags the deleterious effects of the ApoE ε4 allele. No other major longevity locus was found.
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Affiliation(s)
- Joris Deelen
- Section of Molecular Epidemiology, Leiden University Medical CenterPO Box 9600, 2300 RC Leiden, The Netherlands
- Netherlands Consortium for Healthy Ageing, Leiden University Medical CenterPO Box 9600, 2300 RC Leiden, The Netherlands
| | - Marian Beekman
- Section of Molecular Epidemiology, Leiden University Medical CenterPO Box 9600, 2300 RC Leiden, The Netherlands
- Netherlands Consortium for Healthy Ageing, Leiden University Medical CenterPO Box 9600, 2300 RC Leiden, The Netherlands
| | - Hae-Won Uh
- Section of Medical Statistics, Leiden University Medical CenterPO Box 9600, 2300 RC Leiden, The Netherlands
| | - Quinta Helmer
- Section of Medical Statistics, Leiden University Medical CenterPO Box 9600, 2300 RC Leiden, The Netherlands
| | - Maris Kuningas
- Department of Epidemiology, Erasmus Medical CenterPO Box 2040, 3015 CE Rotterdam, The Netherlands
| | - Lene Christiansen
- Department of Epidemiology, University of Southern DenmarkJ.B. Winsløws Vej 9, DK-5000 Odense C, Denmark
- The Danish Aging Research Center, Institute of Public Health-EpidemiologyJ.B. Winsløws Vej 9 B, st. tv, DK-5000 Odense C, Denmark
- Department of Clinical Genetics and Department of Clinical Biochemistry and Pharmacology, Odense University HospitalDK-5000 Odense C, Denmark
| | - Dennis Kremer
- Section of Molecular Epidemiology, Leiden University Medical CenterPO Box 9600, 2300 RC Leiden, The Netherlands
| | - Ruud van der Breggen
- Section of Molecular Epidemiology, Leiden University Medical CenterPO Box 9600, 2300 RC Leiden, The Netherlands
| | - H Eka D Suchiman
- Section of Molecular Epidemiology, Leiden University Medical CenterPO Box 9600, 2300 RC Leiden, The Netherlands
| | - Nico Lakenberg
- Section of Molecular Epidemiology, Leiden University Medical CenterPO Box 9600, 2300 RC Leiden, The Netherlands
| | - Erik B van den Akker
- Section of Molecular Epidemiology, Leiden University Medical CenterPO Box 9600, 2300 RC Leiden, The Netherlands
- Department of Mediamatics, Delft Bioinformatics Lab, Delft University of TechnologyPO Box 5031, 2600 GA Delft, The Netherlands
| | - Willemijn M Passtoors
- Section of Molecular Epidemiology, Leiden University Medical CenterPO Box 9600, 2300 RC Leiden, The Netherlands
| | - Henning Tiemeier
- Department of Epidemiology, Erasmus Medical CenterPO Box 2040, 3015 CE Rotterdam, The Netherlands
- Department of Child and Adolescent Psychiatry, Erasmus Medical Center and Sophia Children's HospitalPO Box 2040, 3015 CE Rotterdam, The Netherlands
| | - Diana van Heemst
- Department of Gerontology and Geriatrics, Leiden University Medical CenterPO Box 9600, 2300 RC Leiden, The Netherlands
| | - Anton J de Craen
- Department of Gerontology and Geriatrics, Leiden University Medical CenterPO Box 9600, 2300 RC Leiden, The Netherlands
| | - Fernando Rivadeneira
- Department of Epidemiology, Erasmus Medical CenterPO Box 2040, 3015 CE Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus Medical CenterPO Box 2040, 3015 CE Rotterdam, The Netherlands
| | - Eco J de Geus
- Department of Biological Psychology, VU University AmsterdamVan der Boechorststraat 1, 1081 BT Amsterdam, The Netherlands
| | - Markus Perola
- National Institute for Health and WelfarePO Box 30, 00271 Helsinki, Finland
| | - Frans J van der Ouderaa
- Netherlands Consortium for Healthy Ageing, Leiden University Medical CenterPO Box 9600, 2300 RC Leiden, The Netherlands
- Department of Gerontology and Geriatrics, Leiden University Medical CenterPO Box 9600, 2300 RC Leiden, The Netherlands
| | - David A Gunn
- Unilever DiscoverColworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, UK
| | - Dorret I Boomsma
- Department of Biological Psychology, VU University AmsterdamVan der Boechorststraat 1, 1081 BT Amsterdam, The Netherlands
| | - André G Uitterlinden
- Netherlands Consortium for Healthy Ageing, Leiden University Medical CenterPO Box 9600, 2300 RC Leiden, The Netherlands
- Department of Epidemiology, Erasmus Medical CenterPO Box 2040, 3015 CE Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus Medical CenterPO Box 2040, 3015 CE Rotterdam, The Netherlands
| | - Kaare Christensen
- The Danish Aging Research Center, Institute of Public Health-EpidemiologyJ.B. Winsløws Vej 9 B, st. tv, DK-5000 Odense C, Denmark
- Department of Clinical Genetics and Department of Clinical Biochemistry and Pharmacology, Odense University HospitalDK-5000 Odense C, Denmark
| | - Cornelia M van Duijn
- Netherlands Consortium for Healthy Ageing, Leiden University Medical CenterPO Box 9600, 2300 RC Leiden, The Netherlands
- Department of Epidemiology, Erasmus Medical CenterPO Box 2040, 3015 CE Rotterdam, The Netherlands
| | - Bastiaan T Heijmans
- Section of Molecular Epidemiology, Leiden University Medical CenterPO Box 9600, 2300 RC Leiden, The Netherlands
| | | | - Rudi G J Westendorp
- Netherlands Consortium for Healthy Ageing, Leiden University Medical CenterPO Box 9600, 2300 RC Leiden, The Netherlands
- Department of Gerontology and Geriatrics, Leiden University Medical CenterPO Box 9600, 2300 RC Leiden, The Netherlands
| | - P Eline Slagboom
- Section of Molecular Epidemiology, Leiden University Medical CenterPO Box 9600, 2300 RC Leiden, The Netherlands
- Netherlands Consortium for Healthy Ageing, Leiden University Medical CenterPO Box 9600, 2300 RC Leiden, The Netherlands
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Stokowski RP, Pant PVK, Dadd T, Fereday A, Hinds DA, Jarman C, Filsell W, Ginger RS, Green MR, van der Ouderaa FJ, Cox DR. A genomewide association study of skin pigmentation in a South Asian population. Am J Hum Genet 2007; 81:1119-32. [PMID: 17999355 DOI: 10.1086/522235] [Citation(s) in RCA: 196] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2007] [Accepted: 08/01/2007] [Indexed: 01/26/2023] Open
Abstract
We have conducted a multistage genomewide association study, using 1,620,742 single-nucleotide polymorphisms to systematically investigate the genetic factors influencing intrinsic skin pigmentation in a population of South Asian descent. Polymorphisms in three genes--SLC24A5, TYR, and SLC45A2--yielded highly significant replicated associations with skin-reflectance measurements, an indirect measure of melanin content in the skin. The associations detected in these three genes, in an additive manner, collectively account for a large fraction of the natural variation of skin pigmentation in a South Asian population. Our study is the first to interrogate polymorphisms across the genome, to find genetic determinants of the natural variation of skin pigmentation within a human population.
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