Disease and Polygenic Architecture: Avoid Trio Design and Appropriately Account for Unscreened Control Subjects for Common Disease

American Journal of Human Genetics

Volumn 98, Issue 2, 2016, Pages 382-391

  Peyrot, Wouter J ^a,b   Boomsma, Dorret I ^c   Penninx, Brenda W J H ^a   Wray, Naomi R ^b  

^a VU UNIVERSITY MEDICAL CENTER   (Netherlands)

^b UNIVERSITY OF QUEENSLAND   (Australia)

^c VU UNIVERSITY AMSTERDAM   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; ASSORTATIVE MATING; ATTENTION DEFICIT DISORDER; AUTISM; CONTROLLED STUDY; GENE FREQUENCY; GENETIC ASSOCIATION; GENETIC CORRELATION; GENETIC MARKER; HERITABILITY; HUMAN; MAJOR DEPRESSION; MENTAL DISEASE; PRIORITY JOURNAL; SCHIZOPHRENIA; SINGLE NUCLEOTIDE POLYMORPHISM; ALLELE; DEPRESSIVE DISORDER, MAJOR; GENE LOCUS; GENETIC ASSOCIATION STUDY; GENETIC PREDISPOSITION; GENETICS; PHENOTYPE; PROCEDURES; QUANTITATIVE TRAIT;

GENETIC MARKER;

ALLELES; DEPRESSIVE DISORDER, MAJOR; GENE FREQUENCY; GENETIC ASSOCIATION STUDIES; GENETIC LOCI; GENETIC MARKERS; GENETIC PREDISPOSITION TO DISEASE; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT, HERITABLE;

EID: 84957812977     PISSN: 00029297     EISSN: 15376605     Source Type: Journal    
DOI: 10.1016/j.ajhg.2015.12.017     Document Type: Article

References (48)

1. R.S. Spielman, and W.J. Ewens The TDT and other family-based tests for linkage disequilibrium and association Am. J. Hum. Genet. 59 1996 983 989
2. S.H. Lee, N.R. Wray, M.E. Goddard, and P.M. Visscher Estimating missing heritability for disease from genome-wide association studies Am. J. Hum. Genet. 88 2011 294 305
3. S. Ripke, B.M. Neale, A. Corvin, J.T.R. Walters, K.-H. Farh, P.A. Holmans, P. Lee, B. Bulik-Sullivan, D.A. Collier, H. Huang, et al. Schizophrenia Working Group of the Psychiatric Genomics Consortium Biological insights from 108 schizophrenia-associated genetic loci Nature 511 2014 421 427
4. N. Cai, T.B. Bigdeli, W. Kretzschmar, Y. Li, J. Liang, L. Song, J. Hu, Q. Li, W. Jin, Z. Hu, et al. CONVERGE consortium Sparse whole-genome sequencing identifies two loci for major depressive disorder Nature 523 2015 588 591
5. S. Ripke, N.R. Wray, C.M. Lewis, S.P. Hamilton, M.M. Weissman, G. Breen, E.M. Byrne, D.H.R. Blackwood, D.I. Boomsma, S. Cichon, et al. Major Depressive Disorder Working Group of the Psychiatric GWAS Consortium A mega-analysis of genome-wide association studies for major depressive disorder Mol. Psychiatry 18 2013 497 511
6. B.M. Neale, S.E. Medland, S. Ripke, P. Asherson, B. Franke, K.-P. Lesch, S.V. Faraone, T.T. Nguyen, H. Schäfer, P. Holmans, et al. Psychiatric GWAS Consortium: ADHD Subgroup Meta-analysis of genome-wide association studies of attention-deficit/hyperactivity disorder J. Am. Acad. Child Adolesc. Psychiatry 49 2010 884 897
7. R. Anney, L. Klei, D. Pinto, R. Regan, J. Conroy, T.R. Magalhaes, C. Correia, B.S. Abrahams, N. Sykes, A.T. Pagnamenta, and et al. A genome-wide scan for common alleles affecting risk for autism Hum. Mol. Genet. 19 2010 4072 4082
8. K. Wang, H. Zhang, D. Ma, M. Bucan, J.T. Glessner, B.S. Abrahams, D. Salyakina, M. Imielinski, J.P. Bradfield, P.M.A. Sleiman, and et al. Common genetic variants on 5p14.1 associate with autism spectrum disorders Nature 459 2009 528 533
9. L.A. Weiss, D.E. Arking, M.J. Daly, A. Chakravarti Gene Discovery Project of Johns Hopkins & the Autism Consortium A genome-wide linkage and association scan reveals novel loci for autism Nature 461 2009 802 808
10. M. Ronemus, I. Iossifov, D. Levy, and M. Wigler The role of de novo mutations in the genetics of autism spectrum disorders Nat. Rev. Genet. 15 2014 133 141
11. S.J. Sanders, M.T. Murtha, A.R. Gupta, J.D. Murdoch, M.J. Raubeson, A.J. Willsey, A.G. Ercan-Sencicek, N.M. DiLullo, N.N. Parikshak, J.L. Stein, and et al. De novo mutations revealed by whole-exome sequencing are strongly associated with autism Nature 485 2012 237 241
12. J. Gratten, P.M. Visscher, B.J. Mowry, and N.R. Wray Interpreting the role of de novo protein-coding mutations in neuropsychiatric disease Nat. Genet. 45 2013 234 238
13. P.F. Sullivan, M.J. Daly, and M. O'Donovan Genetic architectures of psychiatric disorders: the emerging picture and its implications Nat. Rev. Genet. 13 2012 537 551
14. S.H. Lee, S. Ripke, B.M. Neale, S.V. Faraone, S.M. Purcell, R.H. Perlis, B.J. Mowry, A. Thapar, M.E. Goddard, J.S. Witte, et al. Cross-Disorder Group of the Psychiatric Genomics Consortium International Inflammatory Bowel Disease Genetics Consortium (IIBDGC) Genetic relationship between five psychiatric disorders estimated from genome-wide SNPs Nat. Genet. 45 2013 984 994
15. P.F. Sullivan The psychiatric GWAS consortium: big science comes to psychiatry Neuron 68 2010 182 186
16. J. Yang, B. Benyamin, B.P. McEvoy, S. Gordon, A.K. Henders, D.R. Nyholt, P.A. Madden, A.C. Heath, N.G. Martin, G.W. Montgomery, and et al. Common SNPs explain a large proportion of the heritability for human height Nat. Genet. 42 2010 565 569
17. G.-B. Chen Estimating heritability of complex traits from genome-wide association studies using IBS-based Haseman-Elston regression Front. Genet. 5 2014 107
18. M.A.R. Ferreira, P. Sham, M.J. Daly, and S. Purcell Ascertainment through family history of disease often decreases the power of family-based association studies Behav. Genet. 37 2007 631 636
19. M. Li, M. Boehnke, and G.R. Abecasis Efficient study designs for test of genetic association using sibship data and unrelated cases and controls Am. J. Hum. Genet. 78 2006 778 792
20. J. Teng, and N. Risch The relative power of family-based and case-control designs for linkage disequilibrium studies of complex human diseases. II. Individual genotyping Genome Res. 9 1999 234 241
21. N.M. Laird, and C. Lange Family-based designs in the age of large-scale gene-association studies Nat. Rev. Genet. 7 2006 385 394
22. Y.V. Virkud, R.D. Todd, A.M. Abbacchi, Y. Zhang, and J.N. Constantino Familial aggregation of quantitative autistic traits in multiplex versus simplex autism Am. J. Med. Genet. B. Neuropsychiatr. Genet. 150B 2009 328 334
23. J.N. Constantino, and R.D. Todd Intergenerational transmission of subthreshold autistic traits in the general population Biol. Psychiatry 57 2005 655 660
24. P. Lichtenstein, C. Björk, C.M. Hultman, E. Scolnick, P. Sklar, and P.F. Sullivan Recurrence risks for schizophrenia in a Swedish national cohort Psychol. Med. 36 2006 1417 1425
25. D.I. Boomsma, V. Saviouk, J.-J. Hottenga, M.A. Distel, M.H.M. de Moor, J.M. Vink, L.M. Geels, J.H.D.A. van Beek, M. Bartels, E.J.C. de Geus, and G. Willemsen Genetic epidemiology of attention deficit hyperactivity disorder (ADHD index) in adults PLoS ONE 5 2010 e10621
26. E.R. Dempster, and I.M. Lerner Heritability of threshold characters Genetics 35 1950 212 236
27. D. Golan, E.S. Lander, and S. Rosset Measuring missing heritability: inferring the contribution of common variants Proc. Natl. Acad. Sci. USA 111 2014 E5272 E5281
28. D. Falconer, and T. Mackay Introduction to Quantitative Genetics 1996 Longman Essex
29. M. Bulmer The Mathematical Theory of Quantitative Genetics 1985 Clarendon press Oxford
30. G.M. Tallis Ancestral covariance and the Bulmer effect Theor. Appl. Genet. 73 1987 815 820
31. J. Yang, N.R. Wray, and P.M. Visscher Comparing apples and oranges: equating the power of case-control and quantitative trait association studies Genet. Epidemiol. 34 2010 254 257
32. J.S. Witte, P.M. Visscher, and N.R. Wray The contribution of genetic variants to disease depends on the ruler Nat. Rev. Genet. 15 2014 765 776
33. S. Purcell, S.S. Cherny, and P.C. Sham Genetic Power Calculator: design of linkage and association genetic mapping studies of complex traits Bioinformatics 19 2003 149 150
34. G.R. Abecasis, D. Altshuler, A. Auton, L.D. Brooks, R.M. Durbin, R.A. Gibbs, M.E. Hurles, G.A. McVean 1000 Genomes Project Consortium A map of human genome variation from population-scale sequencing Nature 467 2010 1061 1073
35. D. Solter Differential imprinting and expression of maternal and paternal genomes Annu. Rev. Genet. 22 1988 127 146
36. H.J. Cordell Estimation and testing of gene-environment interactions in family-based association studies Genomics 93 2009 5 9
37. W.J. Gauderman, D.C. Thomas, C.E. Murcray, D. Conti, D. Li, and J.P. Lewinger Efficient genome-wide association testing of gene-environment interaction in case-parent trios Am. J. Epidemiol. 172 2010 116 122
38. A.L. Price, N.J. Patterson, R.M. Plenge, M.E. Weinblatt, N.A. Shadick, and D. Reich Principal components analysis corrects for stratification in genome-wide association studies Nat. Genet. 38 2006 904 909
39. J. Yang, N.A. Zaitlen, M.E. Goddard, P.M. Visscher, and A.L. Price Advantages and pitfalls in the application of mixed-model association methods Nat. Genet. 46 2014 100 106
40. R. de Graaf, M. ten Have, C. van Gool, and S. van Dorsselaer Prevalence of mental disorders and trends from 1996 to 2009. Results from the Netherlands Mental Health Survey and Incidence Study-2 Soc. Psychiatry Psychiatr. Epidemiol. 47 2012 203 213
41. B.M. Neale, J. Lasky-Su, R. Anney, B. Franke, K. Zhou, J.B. Maller, A.A. Vasquez, P. Asherson, W. Chen, T. Banaschewski, and et al. Genome-wide association scan of attention deficit hyperactivity disorder Am. J. Med. Genet. B. Neuropsychiatr. Genet. 147B 2008 1337 1344
42. E. Mick, A. Todorov, S. Smalley, X. Hu, S. Loo, R.D. Todd, J. Biederman, D. Byrne, B. Dechairo, A. Guiney, and et al. Family-based genome-wide association scan of attention-deficit/hyperactivity disorder J. Am. Acad. Child Adolesc. Psychiatry 49 2010 898 905. e3
43. J. Elia, X. Gai, H.M. Xie, J.C. Perin, E. Geiger, J.T. Glessner, M. D'arcy, R. deBerardinis, E. Frackelton, C. Kim, and et al. Rare structural variants found in attention-deficit hyperactivity disorder are preferentially associated with neurodevelopmental genes Mol. Psychiatry 15 2010 637 646
44. L. Klei, S.J. Sanders, M.T. Murtha, V. Hus, J.K. Lowe, A.J. Willsey, D. Moreno-De-Luca, T.W. Yu, E. Fombonne, D. Geschwind, and et al. Common genetic variants, acting additively, are a major source of risk for autism Mol. Autism 3 2012 9
45. N.R. Wray, M.L. Pergadia, D.H.R. Blackwood, B.W.J.H. Penninx, S.D. Gordon, D.R. Nyholt, S. Ripke, D.J. MacIntyre, K.A. McGhee, A.W. Maclean, and et al. Genome-wide association study of major depressive disorder: new results, meta-analysis, and lessons learned Mol. Psychiatry 17 2012 36 48
46. N. Risch, and J. Teng The relative power of family-based and case-control designs for linkage disequilibrium studies of complex human diseases I. DNA pooling Genome Res. 8 1998 1273 1288
47. N. Risch Implications of multilocus inheritance for gene-disease association studies Theor. Popul. Biol. 60 2001 215 220
48. W.J. Gauderman Candidate gene association analysis for a quantitative trait, using parent-offspring trios Genet. Epidemiol. 25 2003 327 338