Abstract
Metabolic syndrome is a complex human disorder characterized by a cluster of conditions (increased blood pressure, hyperglycemia, excessive body fat around the waist, and abnormal cholesterol or triglyceride levels). Any of these conditions increases the risk of serious disorders such as diabetes or cardiovascular disease. Currently, the degree of genetic regulation of this syndrome is under debate and partially unknown. The principal aim of this study was to estimate the genetic component and the common environmental effects in different populations using full pedigree and genomic information. We used three large populations (Gubbio, ARIC, and Ogliastra cohorts) to estimate the heritability of metabolic syndrome. Due to both pedigree and genotyped data, different approaches were applied to summarize relatedness conditions. Linear mixed models (LLM) using average information restricted maximum likelihood (AIREML) algorithm were applied to partition the variances and estimate heritability (h2) and common sib–household effect (c2). Globally, results obtained from pedigree information showed a significant heritability (h2: 0.286 and 0.271 in Gubbio and Ogliastra, respectively), whereas a lower, but still significant heritability was found using SNPs data (\(h_{\text{SNP}}^{2}\): 0.167 and 0.254 in ARIC and Ogliastra). The remaining heritability between h2 and \(h_{\text{SNP}}^{2}\) ranged between 0.031 and 0.237. Finally, the common environmental c2 in Gubbio and Ogliastra were also significant accounting for about 11% of the phenotypic variance. Availability of different kinds of populations and data helped us to better understand what happened when heritability of metabolic syndrome is estimated and account for different possible confounding. Furthermore, the opportunity of comparing different results provided more precise and less biased estimation of heritability.
Similar content being viewed by others
References
Abou Ziki MD, Mani A (2016) Metabolic syndrome: genetic insights into disease pathogenesis. Curr Opin Lipidol 27(2):162–171. https://doi.org/10.1097/MOL.0000000000000276
Almasy L, Blangero J (1998) Multipoint quantitative-trait linkage analysis in general pedigrees. Am J Hum Genet 62(5):1198–1211. https://doi.org/10.1086/301844
Andreassi MG, Botto N (2003) DNA damage as a new emerging risk factor in atherosclerosis. Trends Cardiovasc Med 13(7):270–275
Bellia A, Giardina E, Lauro D, Tesauro M, Di Fede G, Cusumano G et al (2009) “The Linosa Study”: epidemiological and heritability data of the metabolic syndrome in a Caucasian genetic isolate. Nutr Metab Cardiovasc Dis 19(7):455–461. https://doi.org/10.1016/j.numecd.2008.11.002
Bennett RL, Steinhaus KA, Uhrich SB, O’Sullivan CK, Resta RG, Lochner-Doyle D et al (1995) Recommendations for standardized human pedigree nomenclature. Pedigree Standardization Task Force of the National Society of Genetic Counselors. Am J Hum Genet 56(3):745–752
Biino G, Balduini CL, Casula L, Cavallo P, Vaccargiu S, Parracciani D, Pirastu M (2011) Analysis of 12,517 inhabitants of a Sardinian geographic isolate reveals that predispositions to thrombocytopenia and thrombocytosis are inherited traits. Haematologica 96(1):96–101. https://doi.org/10.3324/haematol.2010.029934
Biino G, Concas MP, Cena H, Parracciani D, Vaccargiu S, Cosso M, Pirastu M (2015) Dissecting metabolic syndrome components: data from an epidemiologic survey in a genetic isolate. Springerplus 4:324. https://doi.org/10.1186/s40064-015-1049-9
Blanco-Gomez A, Castillo-Lluva S, Del Mar Saez-Freire M, Hontecillas-Prieto L, Mao JH, Castellanos-Martin A, Perez-Losada J (2016) Missing heritability of complex diseases: enlightenment by genetic variants from intermediate phenotypes. BioEssays 38(7):664–673. https://doi.org/10.1002/bies.201600084
Bonati MT, Graziano F, Monti MC, Crocamo C, Terradura-Vagnarelli O, Cirillo M, Zanchetti A (2014) Heritability of blood pressure through latent curve trajectories in families from the Gubbio population study. J Hypertens 32(11):2179–2187. https://doi.org/10.1097/hjh.0000000000000311
Bosy-Westphal A, Onur S, Geisler C, Wolf A, Korth O, Pfeuffer M, Muller MJ (2007) Common familial influences on clustering of metabolic syndrome traits with central obesity and insulin resistance: the Kiel obesity prevention study. Int J Obes (Lond) 31(5):784–790. https://doi.org/10.1038/sj.ijo.0803481
Bourrat P, Lu Q (2017) Dissolving the missing heritability problem. Philos Sci 84(5):1055–1067
Chen F, He J, Zhang J, Chen GK, Thomas V, Ambrosone CB, Stram DO (2015) Methodological considerations in estimation of phenotype heritability using genome-wide SNP data, illustrated by an analysis of the heritability of height in a large sample of african ancestry adults. PLoS One 10(6):e0131106. https://doi.org/10.1371/journal.pone.0131106
Cirillo M, Terradura-Vagnarelli O, Mancini M, Menotti A, Zanchetti A, Laurenzi M (2014) Cohort profile: the Gubbio population study. Int J Epidemiol 43(3):713–720. https://doi.org/10.1093/ije/dyt025
Collins FS, Cox NJ, Goldstein DB, Hindorff LA, Hunter DJ et al (2009) Finding the missing heritability of complex diseases. Nature. https://doi.org/10.1038/nature08494
Conomos M, Thornton T, Gogarten S (2017) GENESIS: GENetic EStimation and Inference in Structured samples (GENESIS): statistical methods for analyzing genetic data from samples with population structure and/or relatedness. R package version 2.2. 7. 2017
Covarrubias-Pazaran G (2016) Genome-assisted prediction of quantitative traits using the R package sommer. PLoS One 11(6):e0156744. https://doi.org/10.1371/journal.pone.0156744
Dandine-Roulland C, Perdry H (2017) Genome-wide data manipulation, association analysis and heritability estimates in R with gaston 1.5. In: Human heredity, vol. 83, Allschwilerstrasse 10, Ch-4009 Basel, Switzerland, Karger, p. 6
Evans LM, Tahmasbi R, Vrieze SI, Abecasis GR, Das S, Gazal S et al (2018) Comparison of methods that use whole genome data to estimate the heritability and genetic architecture of complex traits. Nat Genet 50(5):737–745. https://doi.org/10.1038/s41588-018-0108-x
Gilmour AR, Thompson R, Cullis BR (1995) Average information REML: an efficient algorithm for variance parameter estimation in linear mixed models. Biometrics 51(4):1440–1450
Graziano F, Grassi M, Sacco S, Concas MP, Vaccargiu S, Pirastu M, Biino G (2015) Probing the factor structure of metabolic syndrome in Sardinian genetic isolates. Nutr Metab Cardiovasc Dis 25(6):548–555. https://doi.org/10.1016/j.numecd.2015.02.004
Graziano F, Grassi M, Bonati MT, Zanchetti A, Biino G (2016) External validation of the MetS score, a prediction tool for metabolic syndrome. Nutr Metab Cardiovasc Dis 26(4):359–360. https://doi.org/10.1016/j.numecd.2015.12.014
Henneman P, Aulchenko YS, Frants RR, van Dijk KW, Oostra BA, van Duijn CM (2008) Prevalence and heritability of the metabolic syndrome and its individual components in a Dutch isolate: the Erasmus Rucphen Family study. J Med Genet 45(9):572–577. https://doi.org/10.1136/jmg.2008.058388
Hill WG, Maki-Tanila A (2015) Expected influence of linkage disequilibrium on genetic variance caused by dominance and epistasis on quantitative traits. J Anim Breed Genet 132(2):176–186. https://doi.org/10.1111/jbg.12140
Investigators A (1989) The atherosclerosis risk in communities (ARIC) study: design and objectives. Am J Epidemiol 129(4):687–702
Khan RJ, Gebreab SY, Sims M, Riestra P, Xu R, Davis SK (2015) Prevalence, associated factors and heritabilities of metabolic syndrome and its individual components in African Americans: the Jackson heart study. BMJ Open 5(10):e008675. https://doi.org/10.1136/bmjopen-2015-008675
Khoury MJ, Beaty TH, Cohen BH (1993) Fundamentals of genetic epidemiology, vol 22. Oxford University Press, Oxford
Lee JJ, Chow CC (2014) Conditions for the validity of SNP-based heritability estimation. Hum Genet 133(8):1011–1022. https://doi.org/10.1007/s00439-014-1441-5
Legarra A, Aguilar I, Misztal I (2009) A relationship matrix including full pedigree and genomic information. J Dairy Sci 92(9):4656–4663. https://doi.org/10.3168/jds.2009-2061
Makowsky R, Pajewski NM, Klimentidis YC, Vazquez AI, Duarte CW, Allison DB, de los Campos G (2011) Beyond missing heritability: prediction of complex traits. PLoS Genet 7(4): e1002051
Menotti A, Lanti M, Angeletti M, Botta G, Cirillo M, Laurenzi M et al (2009) Twenty-year cardiovascular and all-cause mortality trends and changes in cardiovascular risk factors in Gubbio, Italy: the role of blood pressure changes. J Hypertens 27(2):266–274. https://doi.org/10.1097/HJH.0b013e32831cbb0b
Misztal I, Legarra A, Aguilar I (2009) Computing procedures for genetic evaluation including phenotypic, full pedigree, and genomic information. J Dairy Sci 92(9):4648–4655. https://doi.org/10.3168/jds.2009-2064
Müller S, Scealy JL, Welsh AH (2013) Model selection in linear mixed models. Stat Sci 28(2):135–167
Shetty PB, Qin H, Namkung J, Elston RC, Zhu X (2011) Estimating heritability using family and unrelated individuals data. BMC Proc 5:S34
Sinnwell JP, Therneau TM, Schaid DJ (2014) The kinship2 R package for pedigree data. Hum Hered 78(2):91–93. https://doi.org/10.1159/000363105
Speed D, Cai N, Johnson MR, Nejentsev S, Balding DJ (2017) Reevaluation of SNP heritability in complex human traits. Nat Genet. https://doi.org/10.1038/ng.3865
TeamR, RC (2018) A language and environment for statistical computing. 2015. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/. Accessed 26 Nov
Teran-Garcia M, Bouchard C (2007) Genetics of the metabolic syndrome. Appl Physiol Nutr Metab 32(1):89–114. https://doi.org/10.1139/h06-102
Tucker G, Loh PR, MacLeod IM, Hayes BJ, Goddard ME, Berger B, Price AL (2015) Two-variance-component model improves genetic prediction in family datasets. Am J Hum Genet 97(5):677–690. https://doi.org/10.1016/j.ajhg.2015.10.002
Varilo T, Peltonen L (2004) Isolates and their potential use in complex gene mapping efforts. Curr Opin Genet Dev 14(3):316–323. https://doi.org/10.1016/j.gde.2004.04.008
Vattikuti S, Guo J, Chow CC (2012) Heritability and genetic correlations explained by common SNPs for metabolic syndrome traits. PLoS Genet 8(3):e1002637
Vinkhuyzen AA, Wray NR, Yang J, Goddard ME, Visscher PM (2013) Estimation and partition of heritability in human populations using whole-genome analysis methods. Annu Rev Genet 47:75–95. https://doi.org/10.1146/annurev-genet-111212-133258
Visscher PM, Medland SE, Ferreira MA, Morley KI, Zhu G, Cornes BK, Martin NG (2006) Assumption-free estimation of heritability from genome-wide identity-by-descent sharing between full siblings. PLoS Genet 2(3):e41. https://doi.org/10.1371/journal.pgen.0020041
Visscher PM, Hill WG, Wray NR (2008) Heritability in the genomics era—concepts and misconceptions. Nat Rev Genet. https://doi.org/10.1038/nrg2322
Witte JS, Visscher PM, Wray NR (2014) The contribution of genetic variants to disease depends on the ruler. Nat Rev Genet 15:765–776
Wright AF, Carothers AD, Pirastu M (1999) Population choice in mapping genes for complex diseases. Nat Genet 23(4):397–404. https://doi.org/10.1038/70501
Xia C, Amador C, Huffman J, Trochet H, Campbell A, Porteous D, Haley CS (2016) Pedigree- and SNP-associated genetics and recent environment are the major contributors to anthropometric and cardiometabolic trait variation. PLoS Genet 12(2):e1005804. https://doi.org/10.1371/journal.pgen.1005804
Yang J, Benyamin B, McEvoy BP, Gordon S, Henders AK, Nyholt DR et al (2010) Common SNPs explain a large proportion of the heritability for human height. Nat Genet. https://doi.org/10.1038/ng.608
Yang J, Lee SH, Goddard ME, Visscher PM (2011a) GCTA: a tool for genome-wide complex trait analysis. Am J Hum Genet 88:76–82
Yang J, Manolio TA, Pasquale LR, Boerwinkle E, Caporaso N, Cunningham JM et al (2011b) Genome partitioning of genetic variation for complex traits using common SNPs. Nat Genet 43(6):519–525. https://doi.org/10.1038/ng.823
Yang J, Bakshi A, Zhu Z, Hemani G, Vinkhuyzen AA, Lee SH, Visscher PM (2015) Genetic variance estimation with imputed variants finds negligible missing heritability for human height and body mass index. Nat Genet 47(10):1114–1120. https://doi.org/10.1038/ng.3390
Zaitlen N, Kraft P, Patterson N, Pasaniuc B, Bhatia G, Pollack S, Price AL (2013) Using extended genealogy to estimate components of heritability for 23 quantitative and dichotomous traits. PLoS Genet 9(5):e1003520
Zheng X, Levine D, Shen J, Gogarten SM, Laurie C, Weir BS (2012) A high-performance computing toolset for relatedness and principal component analysis of SNP data. Bioinformatics 28(24):3326–3328. https://doi.org/10.1093/bioinformatics/bts606
Zuk O, Hechter E, Sunyaev SR, Lander ES (2012) The mystery of missing heritability: genetic interactions create phantom heritability. Proc Natl Acad Sci USA 109(4):1193–1198. https://doi.org/10.1073/pnas.1119675109
Acknowledgements
The authors thank the staff and participants of the ARIC, Gubbio, and Ogliastra studies for their important contributions. The ARIC study was carried out as a collaborative study supported by the National Heart, Lung, and Blood Institute contracts (HHSN26820 1100005C, HHSN268201100006C, HHSN268201100007C, HHSN268201100008C, HHSN268201100009C, HHSN26820 1100010C, HHSN268201100011C, and HHSN268201100012C). The Gubbio study was originally funded by Merck Sharp and Dohme, Italy, and the Department of Outcome Research of Merck & Co Inc., USA. Funds were also obtained from Grant # R01HL40397 – 02 of the National Heart Lung and Blood Institute, Bethesda, Maryland, USA, and Ministero Italiano di Università e Ricerca (Grant # 068034, PRIN 2004). The present analyses were done in the context of the Istituto Auxologico Italiano participation to EU MASCARA project/EC-7th Framework Program contract no. 278249. The Ogliastra study was supported by a grant from the Italian Ministry of Education, University and Research: MERIT RBNE08NKH7_007.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest
The authors declare no conflict of interest.
Additional information
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Alberto Zanchetti: Deceased.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Graziano, F., Biino, G., Bonati, M.T. et al. Estimation of metabolic syndrome heritability in three large populations including full pedigree and genomic information. Hum Genet 138, 739–748 (2019). https://doi.org/10.1007/s00439-019-02024-6
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00439-019-02024-6