Describing the genetic architecture of epilepsy through heritability analysis

Brain

Volumn 137, Issue 10, 2014, Pages 2680-2689

  Speed, Doug ^a   O'Brien, Terence J ^b   Palotie, Aarno ^c,d,e   Shkura, Kirill ^f   Marson, Anthony G ^g   Balding, David J ^a   Johnson, Michael R ^f  

^a UNIVERSITY COLLEGE LONDON   (United Kingdom)

^b UNIVERSITY OF MELBOURNE   (Australia)

^c UNIVERSITY OF HELSINKI   (Finland)

^d BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^e HELSINKI UNIVERSITY CENTRAL HOSPITAL   (Finland)

^f IMPERIAL COLLEGE LONDON   (United Kingdom)

^g UNIVERSITY OF LIVERPOOL   (United Kingdom)

Author keywords

Association studies; Complex trait prediction; Epilepsy; Heritability analysis

Indexed keywords

ALGORITHM; AREA UNDER THE CURVE; ARTICLE; ASIAN; ASSOCIATION STUDIES; CAUCASIAN; COMPLEX TRAIT PREDICTION; EPILEPSY; GENE LOCUS; GENETIC ASSOCIATION; GENETIC PREDISPOSITION; GENETICS; GENOTYPE; GENOTYPING TECHNIQUE; HERITABILITY ANALYSIS; HUMAN; ONSET AGE; PATHOPHYSIOLOGY; POPULATION; QUANTITATIVE TRAIT; RECEIVER OPERATING CHARACTERISTIC; SEIZURE; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL MODEL;

ASSOCIATION STUDIES; COMPLEX TRAIT PREDICTION; EPILEPSY; HERITABILITY ANALYSIS;

AGE OF ONSET; ALGORITHMS; AREA UNDER CURVE; ASIAN CONTINENTAL ANCESTRY GROUP; EPILEPSY; EUROPEAN CONTINENTAL ANCESTRY GROUP; GENETIC LOCI; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; GENOTYPING TECHNIQUES; HUMANS; MODELS, STATISTICAL; POLYMORPHISM, SINGLE NUCLEOTIDE; POPULATION; QUANTITATIVE TRAIT, HERITABLE; ROC CURVE; SEIZURES;

EID: 84908391631     PISSN: 00068950     EISSN: 14602156     Source Type: Journal    
DOI: 10.1093/brain/awu206     Document Type: Article

References (38)

1. Astle W, Balding DJ. Population structure and cryptic relatedness in genetic association studies. Stat Sci 2009; 24: 451-71.
2. Banerjee P, Filippi D, Allen Hauser W. The descriptive epidemiology of epilepsy - a review. Epilepsy Res 2009; 85: 31-45.
3. Berg AT, Berkovic SF, Brodie MJ, Buchhalter J, Cross JH, van Emde Boas W, et al. Revised terminology and concepts for organization of seizures and epilepsies: report of the ILAE Commission on Classification and Terminology. Epilepsia 2010; 51: 676-85.
4. Commission on Classification and Terminology of the International League Against Epilepsy. Proposal for revised classification of epilepsies and epileptic syndromes. Epilepsia 1989; 30: 389-99.
5. de Kovel CG, Trucks H, Helbig I, Mefford HC, Baker C, Leu C, et al. Recurrent microdeletions at 15q11.2 and 16p13.11 predispose to idiopathic generalized epilepsies. Brain 2010; 133: 23-32.
6. Dempster E, Lerner I. Heritability of threshold characters. Genetics 1950; 35: 212-36.
7. Dibbens LM, Mullen S, Helbig I, Mefford HC, Bayly MA, Bellows S, et al. Familial and sporadic 15q13.3 microdeletions in idiopathic generalized epilepsy: precedent for disorders with complex inheritance. Hum Mol Genet 2009; 18: 3626-31.
8. Dickson SP, Wang K, Krantz I, Hakonarson H, Goldstein DB. Rare variants create synthetic genome-wide associations. PLoS Biol 2010; 8: e1000294.
9. Epi4K Consortium; Epilepsy Phenome/Genome Project, Allen A, Berkovic S, Cossette P, Delanty N, et al. de novo mutations in epileptic encephalopahties. Nature 2013; 501: 217-21.
10. EPICURE Consortium; EMINet Consortium; Steffens M, Leu C, Ruppert AK, Zara F, et al. Genome-wide association analysis of genetic generalized epilepsies implicates susceptibility loci at 1q43, 216.1, 2q22.3 and 17q21.32. Hum Mol Genet 2012; 21: 5359-72.
11. Falconer D, Mackay T. Introduction to quantitative genetics. 4th edn. Pearson, Harlow; 1996.
12. Fisher R, Acevedo C, Arzimanoglou A, Bogacz A, Cross J, Elger C, et al. ILAE official report: a practical clinical definition of epilepsy. Epilepsia 2014; 55: 475-82.
13. Fisher RS, van Emde Boas W, Blume W, Elger C, Genton P, Lee P, et al. Epileptic seizures and epilepsy: definitions proposed by the International League Against Epilepsy (ILAE) and the International Bureau for Epilepsy (IBE). Epilepsia 2005; 46: 470-2.
14. Goldstein D. Common genetic variation and human traits. N Engl J Med 2008; 360: 1696-8.
15. Guo Y, Baum LW, Sham PC, Wong V, Ng PW, Lui CH, et al. Two-stage genome-wide association study identifies variants in CAMSAP1L1 as susceptibility loci for epilepsy in Chinese. Hum Mol Genet 2011; 21: 1184-9.
16. Hauser WA, Rich SS, Lee JR, Annegers JF, Anderson VE. Risk of recurrent seizures after two unprovoked seizures. N Engl J Med 1998; 429-34.
17. Heinzen E, Depondt C, Cavalleri G, Ruzzo E, Walley N, Need A, et al. Exome sequencing followed by large-scale genotyping fails to identify single rare variants of large effect in idiopathic generalized epilepsy. Am J Hum Genet 2012; 91: 293-302.
18. Heinzen EL, Radtke RA, Urban TJ, Cavalleri GL, Depondt C, Need AC, et al. Rare deletions at 16p13.11 predispose to a diverse spectrum of sporadic epilepsy syndromes. Am J Hum Genet 2010; 15: 707-18.
19. Hildebrand M, Dahl H, Damiano J, Smith R, Scheffer I, Berkovic S. Recent advances in the molecular genetics of epilepsy. J Med Genet 2013; 50: 271-9.
20. Howie B, Marchini J, Stephens M. Genotype imputation with thousands of genomes. G3 2011; 1: 457-70.
21. Janssens A, Aulchenko Y, Elefante S, Borsboom G, Steyerberg E, van Duijn C. Predictive testing for complex diseases using multiple genes: fact or fiction? Genet Med 2006; 8: 395-400.
22. Kasperavičirūtė D, Catrino CB, Heinzen EL, Depondt C, Cavalleri GL, Caboclo LO, et al. Common genetic variation and susceptibility to partial epilepsies: a genome-wide association study. Brain 2010; 133 (Pt 7): 2136-47.
23. Kemper K, Visscher P, Goddard M. Genetic architecture of body size in mammals. Genome Biol 2012; 13: 244-56.
24. Kjeldsen MJ, Kyvik KO, Christensen K, Friis ML. Genetic and environmental factors in epilepsy: a population-based study of 11,900 Danish twin pairs. Epilepsy Res 2001; 44: 167-78.
25. Korff CM, Scheffer IE. Epilepsy classification: a cycle of evolution and revolution. Curr Opin Neurol 2013; 26: 163-7.
26. Lee SH, Yang J, Goddard ME, Visscher PM, Wray NR. Estimation of pleiotropy between complex diseases using single-nucleotide polymorphism-derived genomic relationships and restricted maximum likelihood. Bioinformatics 2012; 28: 2540-2.
27. Makowsky R, Pajewski N, Klimentidis Y, Vazquez A, Duarte C, Allison D, et al. Beyond missing heritability: prediction of complex traits. PLoS Genet 2011; 7: e1002051.
28. Miller LL, Pellock JM, De Lorenzo RJ, Meyer JM, Corey LA. Univariate genetic analyses of epilepsy and seizures in a population-based twin study: the Virginia Twin Registry. Genet Epidemiol 1998; 15: 33-49.
29. Ottman R, Lee JH, Hauser WA, Risch N. Are generalized and localization-related epilepsies genetically distinct? Arch Neurol 1998; 55: 339-44.
30. Peljto A, Barker-Cummings C, Vasoli V, Leibson C, Hauser A, Buchhalter J, et al. Familial risk of epilepsy: a population-based study. Brain 2014; 137: 795-805.
31. Speed D, Hemani G, Johnson MR, Balding DJ. Improved heritability estimation from genome-wide SNP data. Am J Hum Genet 2012; 91: 1011-21.
32. Speed D, Hoggart C, Petrovski S, Tachmazidou I, Coffey A, Jorgensen A, et al. A genome-wide association study and biological pathway analysis of epilepsy prognosis in a prospective cohort of newly treated epilepsy. Hum Mol Genet 2014; 1: 247-58.
33. The 1000 Genomes Project Consortium. A map of human genome variation from population-scale sequencing. Nature 2010; 467: 1061-73.
34. The Wellcome Trust Case Control Consortium. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 2007; 447: 661-78.
35. Wray NR, Yang J, Goddard ME, Visscher PM. The genetic interpretation of area under the {ROC} curve in genetic profiling. PLoS Genet 2010; 6: e1000864.
36. Yang J, Benjamin B, McEvoy BP, Gordon S, Henders AK, Nyholt DR, et al. Common SNPs explain a large proportion of the heritability for human height. Nat Genet 2010; 42: 565-9.
37. Yang J, Lee SH, Goddard ME, Visscher PM. GCTA: a tool for genome-wide complex trait analysis. Am J Hum Genet 2011; 88: 76-82.
38. Zuk O, Hechter E, Sunyaev S, Lander E. The mystery of missing heritability: genetic interactions create phantom heritability. Proc Natl Acad Sci USA 2012; 24: 1193-8.