The Significance of Non-Replication of Gene-Phenotype Associations

Handbook of Developmental Science, Behavior, and Genetics

Volumn , Issue , 2010, Pages 466-490

  Halpern, Carolyn Tucker ^a  

^a UNIVERSITY OF NORTH CAROLINA   (United States)

Author keywords

Concept of replication having different meanings; Developmental aspects of gene phenotype associations; Explanations of non replication and inconsistency in gene phenotype associations; Genome wide association studies (GWAS); Non replication in gene phenotype association literature and "inconsistency"; Notion of probabilistic epigenesis, direct or strict replication by definition, not possible; Population genetics, on quantitative analysis variance partitioning of genetic and environmental contributions to individual differences; Significance of non replication gene phenotype associations

Indexed keywords

EID: 84884141632     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9781444327632.ch15     Document Type: Chapter

References (94)

1. Amos, C. I., Wu, X., Broderick, P., Gorlov, I. P., Gu, J., Eisen, T., et al. (2008). Genome-wide association scan of tag SNPs identifies a susceptibility locus for lung cancer at 15q25.1. Nature Genetics, 40, 616-622.
2. Barr, C. S., Newman, T. K., Shannon, C., Parker, C., Dvoskin, R. L., Becker, M. L., et al. (2004). Rearing condition and the rh5-HTTLPR interact to influence limbichypthalamic- pituitary-adrenal axis response to stress in infant macaques. Biological Psychiatry, 55, 733-738.
3. Beloussov, L. V. (1998). The dynamic architecture of a developing organism: An interdisciplinary approach to the development of organisms, Dordrecht: Kluwer.
4. Bobb, A. J., Castellanos, F. X., Addington, A. M.,&Rapoport, J. L. (2006). Molecular genetic studies of ADHD: 1991 to 2004. American Journal of Medical Genetics Part B (Neuropsychiatric Genetics), 141ß, 551-565.
5. Bryan, J. (2004). Problems in gene clustering based on gene expression data. Journal of Multivariate Analysis, 90, 44-66.
6. Cairns, R. B., & Rodkin, P. C. (1997). Phenomena regained: From configuration to pathways. In R. B. Cairns, L. R. Bergman, & J. Kagan (Eds.), Methods and models for studying the individual (pp. 245-264). Thousand Oaks, CA: Sage.
7. Cameron, N., Del Corpo, A., Diorio, J., McAllister, K., Sharma, S., & Meaney, M. J. (2008). Maternal programming of sexual behavior and hypothalamic-pituitary-gonadal function in the female rat. PLoSONE, 3(5), e2210. doi: 10.1371/journal.pone.0002210.
8. Campbell, H., & Manolio, T. (2007). Commentary: Rare alleles, modest genetic effects and the need for collaboration. International Journal of Epidemiology, 36, 445-448.
9. Cardon, L. R., & Bell, J. L. (2001). Association study designs for complex diseases. Nature Reviews Genetics, 2, 91-99.
10. Cardon, L. R., & Palmer, L. J. (2003). Population stratification and spurious allelic association. The Lancet, 361, 598-604.
11. Caspi, A., McClay, J., Moffitt, T. E., Mill, J., Martin, J., Craig, I. W., et al. (2002). Role of genotype in the cycle of violence in maltreated children. Science, 297, 851-854.
12. Caspi, A., Sugden, K., Moffitt, T. E., Taylor, A., Craig, I. W., Harrington, H., et al. (2003). Influence of life stress on depression: Moderation by a polymorphism in the 5-HTT gene. Science, 301(5631), 386-389.
13. Chanock, S. J., & Hunter, D. J. (2008). When the smoke clears. Nature, 452(3), 537-538.
14. Chanock, S. J., Manolio, T., Boehnke, M., Boerwinkle, E., Hunter, G. T., Thomas, G., et al. (2007). Replicating genotype-phenotype associations: What constitutes replication of a genotype-phenotype association, and how best can it be achieved?. Nature, 447, 655-660.
15. Clark, A. G., Boerwinkle, E., Hixson, J., & Sing, F. F. (2005). Determinants of the success of whole-genome association testing. Genome Research, 15, 1463-1467.
16. Colhoun, H. M., McKeigue, P. M.,&Davey Smith, G. (2003). Problems of reporting genetic associations with complex outcomes. Lancet, 361, 865-872.
17. Cumming, G.,&Fidler, F. (2009). Confidence intervals: Better answers to better questions. Journal of Psychology, 217(1), 15-26.
18. Danziger, K.,&Shermer, P. (1994). The varieties of replication:Ahistorical introduction. In R. van der Veer, M. van Ijzendoorn., & J. Valsiner, J. (Eds.), Reconstructing the mind: Replicability in research on human development (pp. 17-36). Norwood, NJ: Ablex Publishing.
19. Dewey, J., & Bentley, A. F. (1949). Knowing and the known. Boston: Beacon.
20. Dimas, A. S., Deutsch, S., Stranger, B. E., Montgomery, S. B., Bore, C., Attar-Cohen, H., et al. (2009). Common regulator variation impacts gene expression in a cell typedependent manner. Science Express, 30 July; 10.1126/science.1174148.
21. D'Souza, U. M., & Craig, I. W. (2006). Functional polymorphisms in dopamine and serotonin pathway genes. Human Mutation, 27(1), 1-13.
22. Ennis, S., Goverdhan, S., Cree, A. J., Hoh, J., Collins, A., & Lotery, A. J. (2007). Fine scale linkage disequilibrium mapping of age-related macular degeneration in the complement factor H gene region. British Journal of Ophthalmology, 91, 966-970.
23. Gest, S. D., Mahoney, J. L.,&Cairns, R. B. (1999). A developmental approach to prevention research: Configural antecedents of early parenthood. American Journal of Community Psychology, 27(4), 543-565.
24. Goldstein, D. B. (2009). Common genetic variation and human traits. The New England Journal of Medicine, 360(17), 1696-1698.
25. Gottlieb, G. (1991). Experiential canalization of behavioral development: Theory. Developmental Psychology, 27, 4-13.
26. Gottlieb, G. (1995). Some conceptual deficiencies in "developmental" behavioral genetics. Human Development, 38, 131-141.
27. Gottlieb, G. (1998). Normally occurring environmental and behavioral influences on gene activity: Fromcentral dogma to probabilistic epigenesis. Psychological Review, 105(4), 792-802.
28. Gottlieb, G. (2002). Individual development and evolution: The genesis of novel behavior. Mahwah, NJ: Erlbaum.
29. Gottlieb, G. (2003). On making behavioral genetics truly developmental. Human Development, 46, 337-355.
30. Gottlieb, G. (2007). Developmental neurobehavioral genetics: Development as explanation. In B. C. Jones & P. Mormede (Eds.), Neurobehavioral genetics: Methods and applications ( 2nd ed., pp. 17-27). Boca Raton, FL: CRC/Taylor & Francis.
31. Gottlieb, G.,&Halpern, C. T. (2002). A relational view of causality in normal and abnormal development. Development and Psychopathology, 46, 421-435.
32. Gudbjartsson, D. F., Walters, G. B., Thorleifsson, G., Stefansson, H., Halldorsson, B. V., Zusmanovich, P., et al. (2008). Many sequence variants affecting diversity of adult human height. Nature Genetics, 40(5), 609-615.
33. Gudmundsson, J., Sulem, P., Manolescu, A., Amundadottir, L. T., Gudbjarttsson, D., Helgaston, A., et al. (2007). Genome-wide association study identifies a second prostate cancer susceptibility variant at 8q24. Nature Genetics, 39, 631-637.
34. Hauber, M. E., Sewell, M. A., & Zuk, M. (2008). Gender genomics and equality. Heredity, 101, 395.
35. Hirschhorn, J. N.,&Altshuler, D. (2002). Once and again - Issues surrounding replication in genetic association studies. Journal of Clinical Endocrinology and Metabolism, 87, 4438-4441.
36. Hirschhorn, J. N., Lohmueller, K., Byrne, E., & Hirschhorn, K. (2002). A comprehensive review of genetic association studies. Genetics in Medicine, 4, 45-61.
37. Hung, R. J., McKay, J. D., Gaborieau, V., Boffetta, P., Hashibe, M., Zaridze, D., et al. (2008). Asusceptibility locus for lung cancer maps to nicotinic acetylcholine receptor subunit genes on 15q25. Nature, 452(3), 633-637.
38. Hunter, D. J. (2005). Gene- environment interactions in human diseases. Nature Reviews Genetics, 6(4), 287-298.
39. Ioannidis, J. P. A. (2007). Non-replication and inconsistency in the genome-wide association setting. Human Heredity, 64, 203-213.
40. Ioannidis, J. P. A. (2008). Why most discovered true associations are inflated. Epidemiology, 19(5), 640-648.
41. Ioannidis, J. P. A., Ntzani, E. E., Trikalinos, T. A., & Contopoulos-Ioannidis, D. G. (2001). Replication validity of genetic association studies. Nature Genetics, 29, 306-309.
42. Kalin, N. H., Shelton, S. E., Fox, A. S., Rogers, J.,Oakes, T. R., & Davidson, R. J. (2008). The serotonin transporter genotype is associated with intermediate brain phenotypes that depend on the context of an eliciting stressor. Molecular Psychiatry, 13, 1021-1027.
43. Khoury, M. J., Little, J., Gwinn, M., & Ioannidis, J. P. A. (2007). On the synthesis and interpretation of consistent but weak gene-disease association in the era of genomewide association studies. International Journal of Epidemiology, 36, 439-45.
44. Killeen, P. R. (2005). An alternative to null-hypothesis significance tests. Psychological Science, 16(5), 345-353.
45. Kindermann, T. A., & Valsiner, J. (1995). Directions for the study of developing personcontext relations. In T. A. Kindermann & J. Valsiner, J. (Eds.), Development of personcontext relations (pp 227-240). Hillsdale, NJ: Erlbaum.
46. Kraft, P. (2008). Curses - winner's and otherwise - in genetic epidemiology. Epidemiology, 19(5), 649-651.
47. Kraft, P.,&Hunter, D. J. (2009). Genetic risk prediction - Are we there yet? The New England Journal of Medicine, 360(17), 1701-1703.
48. Ku, K. C., & Chia, C. K. (2008). The success of the genome-wide association approach: A brief story of a long struggle. European Journal of Human Genetics, 16, 554-564.
49. Lerner, R. M. (1995). Developing individuals within changing contexts: Implications of developmental contextualism for human research, policy, and programs. In T. A. Kindermann & J. Valsiner, J. (Eds.), Development of person-context relations (pp 13-37). Hillsdale, NJ: Erlbaum.
50. Lerner, R. M., & Kaufman, M. B. (1985). The concept of development in contextualism. Developmental Review, 5, 309-333.
51. Lettre, G., Jackson, A. U., Gieger, C., Schumacher, F. R., Berndt, S. I., Sanna, S., et al. (2008). Identification of ten loci associated with height highlights new biological pathways in human growth. Nature Genetics, 40(5), 584-591.
52. Libioulle, C., Louis, E., Hansoul, S., Sandor, S., Farnir, F., Franchimont, D., et al. (2007). Novel Crohn disease locus identified by genome-wide association maps to a gene desert on 5p13.1 and modulates expression of PTGER4. PLoS Genet. 3: e58.
53. Lin, P. I., Vance, J. M., Pericak-Vance, M. A., & Martin, E. R. (2007). No gene is an island: The flip-flop phenomenon. The American Journal of Human Genetics, 80, 531-538.
54. Mackay, T. F. C., & Anholt, R. R. H. (2006). Of flies and man: Drosophila as a model for human complex traits. Annual Review of Genomics and Human Genetics, 7, 339-367.
55. Manolio, T. A. (2009). Cohort studies and the genetics of complex disease. Nature Genetics, 41(1), 5-6.
56. Marchini, J., Howie, B., Myers, S., McVean, G., & Donnelly, P. (2007). A new multipoint method for genome-wide association studies by imputation of genotypes. Nature Genetics, 39(7), 906-913.
57. Moffitt, T. E., Caspi, A., & Rutter, M. (2005). Strategy for investigating interactions between measured genes and measured environments. Archives of General Psychiatry, 62, 473-481.
58. Molenaar, P. C. M., & Campbell, C. G. (2009). The new person-specific paradigm in psychology. Current Directions in Psychological Science, 18(2), 112-117.
59. Molenaar, P. C. M., Huizenga, H. M., & Nesselroade, J. R. (2003). The relationship between the structure of inter-individual and intra-individual variability: A theoretical and empirical vindication of developmental systems theory. In U. M. Staudinger & U. Lindenberger (Eds.), Understanding Human Development (pp. 339-360). Boston: Kluwer.
60. Monroe, S. M., & Reid, M. W. (2008). Gene-environment interactions in depression research: Genetic polymorphisms and life stress polyprocedures. Psychological Science, 19(10), 947-956.
61. Munafo ,M. R., Durrant, C., Lewis, G.,&Flint, J. (2009). Gene-environment interactions at the serotonin transporter locus. Biological Psychiatry, 65, 211-219.
62. Munafò, M. R., Matheson, I. J., & Flint, J. (2007). Association of the DRD2 gene Taq1A polymorphism and alcoholism: A meta-analysis of case-control studies and evidence of publication bias. Molecular Psychiatry, 12, 454-461.
63. National Institutes of Health (NIH) (2007). Policy for sharing of data obtained in NIH supported or conducted genome-wide association studies (GWAS). Federal Register, 72(166), 49290-49297.
64. Neale, B. M., & Sham, P. C. (2004). The future of association studies: Gene-based analysis and replication. American Journal of Human Genetics, 75(3), 353-362.
65. Ober, C., Loisel, D. A., & Gilad, Y. (2008). Sex-specific genetic architecture of human disease. Nature Reviews Genetics, 9, 911-922.
66. O'Donovan, M. C., Craddock, N. Norton, N., Williams, H., Peirce, T., et al., (2008). Identification of loci associated with schizophrenia by genome-wide association and follow-up. Nature Genetics, 40(9) 1053-1055.
67. Pearson, T. A.,&Manolio, T. A. (2008). Howto interpret a genome-wide association study. Journal of the American Medical Association, 299(11), 1335-1344.
68. Radder,H. (1992). Experimental reproducibility and the experimenters' regress. In D.Hull, M. Forbes, & K. Okruhlik (Eds.), Proceedings of the 1992 biennial meeting of the philosophy of science association (pp. 63-73). East Lansing, MI: Philosophy of Science Association.
69. Risch, N., Herrell, R., Lehner, T., Liang, K. -Y., Eaves, L., Hoh, J., et al. (2009). Interaction between the serotonin transporter gene (5-HTTLPR), stressful life events, and risk of depression: A meta-analysis. Journal of the American Medical Association, 301(23), 2462-2471.
70. Rosenthal, R. (1990). Replication in behavioral research. Journal of Social Behavior and Personality, 5(4), 1-30.
71. Rutter, M., Pickles, A., Murray, R., & Eaves, L. (2001). Testing hypotheses on specific environmental causal effects on behavior. Psychological Bulletin, 127, 291-324.
72. Sameroff, A. (1983). Developmental systems. In W. Kessen (Ed.), Handbook of child psychology: History, theory, and methods: Vol. 1 ( 4th ed., pp. 237-294). New York: Wiley.
73. Saxena, R., Voight, B. F., Lyssenko, V., Burrt, N. P., de Bakker, P. I. W., Chen, H., et al. (2007). Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels. Science, 316, 1331-1336.
74. Schmidt, S. (2009). Shall we really do it again? The powerful concept of replication is neglected in the social sciences. Review of General Psychology, 13(2), 90-100.
75. Spencer, C. C. A., Su, Z., Donnelly, P., & Marchini, J. (2009). Designing genome-wide association studies: Sample size, power, imputation, and the choice of genotyping chip. PLOS Genetics, 5(5), e1000477. 1-13.
76. Talkowski, M. E., Bamne, M., Mansour, H., & Nimgaonkar, V. L. (2007). Dopamine genes and schizophrenia: Case closed or evidence pending? Schizophrenia Bulletin, 33(5), 1071-1081.
77. Taylor, A., & Kim-Cohen, J. (2007). Meta-analysis of gene-environment interactions in developmental psychopathology. Development and Psychopathology, 19, 1029-1037.
78. Thorgeirsson, T. E., Geller, F., Sulem, P., Rafnar, T., Wiste, A., Magnusson, K. P., et al. (2008). A variant associated with nicotine dependence, lung cancer and peripheral arterial disease. Nature, 452(3), 638-641.
79. Todd, J. A. (2006). Statistical false positive or true disease pathway? Nature Genetics, 38(7), 731-733.
80. Uher, R., & McGuffin, P. (2008). The moderation by the serotonin transporter gene of environmental adversity in the aetiology of mental illness: Review and methodological analysis. Molecular Psychiatry, 13, 131-146.
81. Valsiner, J. (1987). Culture and the development of children's action. New York: Wiley.
82. Valsiner, J. (2007). Gilbert Gottleib's theory of probabilistic epigenesis: Probabilities and realities in development. Developmental Psychobiology, 49(8), 832-840.
83. Van den Oord, E. J. C. G. (2008). Controlling false discoveries in genetic studies. American Journal of Medical Genetics Part B (Neuropsychiatric Genetics), 147, 637-644.
84. van der Veer, R., van Ijzendoorn, M., & Valsiner, J. (1994). General introduction. In R. van der Veer, M. van Ijzendoorn & J. Valsiner (Eds.), Reconstructing the mind: Replicability in research on human development (pp. 1-9). Norwoord, NJ: Ablex Publishing.
85. Visscher, P. M. (2008). Sizing up human height variation. Nature Genetics, 40(5), 489-490.
86. Visscher, P. M., Hill, W. G., & Wray, N. R. (2008). Heritability in the genomics era - concepts and misconceptions. Nature Reviews, 9, 255-266.
87. Wahlsten, D. (1990). Insensitivity of the analysis of variance to heredity-environment interaction. Behavioral and Brain Sciences, 13, 109-161.
88. Wahlsten, D. (2003). Genetics and the development of brain and behavior. In J. Valsiner and K. J. Connolly (Eds.), Handbook of developmental psychology (pp. 18-47). London: Sage.
89. Weedon, M. N., Lango, H., Lindgren, C. M., Wallace, C., Evans, D., Mangino, M., et al. (2008). Genome-wide association analysis identifies 20 loci that influence adult height. Nature Genetics, 40(5), 575-583.
90. Weedon, M. N., Lettre, G., Freathy, R. M., Lindgren, C. M., Voight, B. F., Perry, J. R. B., et al. (2007). A common variant of HMGA2 is associated with adult and childhood height in the general population. Nature Genetics, 39(10), 1245-1250.
91. Weiss, L. A., Pan, L., Abney, M., & Ober, C. (2006). The sex-specific genetic architecture of quantitative traits in humans. Nature Genetics, 38, 218-222.
92. Wong, A. H. C., Buckle, C. E., & Van Tol, H. H. M. (2000). Polymorphisms in dopamine receptors: What do they tell us? European Journal of Pharmacology, 410, 183-203.
93. Wong, M. Y., Day, N. E., Luan, J. A., Chan, K. P.,&Wareham, N. J. (2003). The detection of gene-environment interaction for continuous traits: Should we deal with measurement error by bigger studies or better measurement? Internationl Journal of Epidemiology, 32, 51-57.
94. Zollner, S.,&Pritchard, J. K. (2007). Overcoming the winner's curse: estimating penetrance parameters from case-control data. American Journal of Human Genetics, 80, 605-615.