Genetic and epigenetic contribution to complex traits

Human Molecular Genetics

Volumn 21, Issue R1, 2012, Pages

  Kilpinen, Helena ^a,b,c   Dermitzakis, Emmanouil T ^a,b,c  

^a UNIVERSITY OF GENEVA MEDICAL SCHOOL   (Switzerland)

^b UNIVERSITY OF GENEVA   (Switzerland)

^c SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; DNA SEQUENCE; EPIGENETICS; GENE CONTROL; GENETIC TRAIT; GENETIC VARIABILITY; GENOME ANALYSIS; GENOMICS; GENOTYPE ENVIRONMENT INTERACTION; HUMAN; INHERITANCE; PHENOTYPE; PRIORITY JOURNAL;

EPIGENESIS, GENETIC; EPIGENOMICS; GENETIC VARIATION; GENOME, HUMAN; HUMANS; PHENOTYPE; QUANTITATIVE TRAIT, HERITABLE; SEQUENCE ANALYSIS, DNA;

EID: 84867133601     PISSN: 09646906     EISSN: 14602083     Source Type: Journal    
DOI: 10.1093/hmg/dds383     Document Type: Article

References (26)

1. Genomes Project Consortium. (2010) A map of human genome variation from population-scale sequencing. Nature, 467, 1061-1073.
2. Hindorff, L.A., Sethupathy, P., Junkins, H.A., Ramos, E.M., Mehta, J.P., Collins, F.S. and Manolio, T.A.;1; (2009) Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc. Natl Acad. Sci. USA, 106, 9362-9367.
3. Birney, E., Stamatoyannopoulos, J.A., Dutta, A., Guigo, R., Gingeras, T.R., Margulies, E.H., Weng, Z., Snyder, M., Dermitzakis, E.T., Thurman, R.E. et al.;1; (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature, 447, 799- 816.
4. Dermitzakis, E.T.;1; (2012) Cellular genomics for complex traits. Nat. Rev. Genet., 13, 215-220.
5. Heijmans, B.T., Tobi, E.W., Stein, A.D., Putter, H., Blauw, G.J., Susser, E.S., Slagboom, P.E. and Lumey, L.H.;1; (2008) Persistent epigenetic differences associated with prenatal exposure to famine in humans. Proc. Natl Acad. Sci. USA, 105, 17046-17049.
6. Zhou, V.W., Goren, A. and Bernstein, B.E.;1; (2011) Charting histone modifications and the functional organization of mammalian genomes. Nat. Rev. Genet., 12, 7-18.
7. Olovnikov, I., Aravin, A.A.;1; and Fejes Toth, K. (2012) Small RNA in the nucleus: the RNA-chromatin ping-pong. Curr. Opin. Genet. Dev., 22, 164-171.
8. Guelen, L., Pagie, L., Brasset, E., Meuleman, W., Faza, M.B., Talhout, W., Eussen,;1; B.H., de Klein, A., Wessels, L., de Laat, W. et al. (2008) Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions. Nature, 453, 948-951.
9. Dixon, J.R., Selvaraj, S., Yue, F., Kim, A., Li, Y., Shen, Y., Hu, M., Liu, J.S. and Ren, B.;1; (2012) Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature, 485, 376-380.
10. Sexton, T., Yaffe, E., Kenigsberg, E., Bantignies, F., Leblanc, B., Hoichman, M., Parrinello, H., Tanay, A. and Cavalli, G.;1; (2012) Three-dimensional folding and functional organization principles of the Drosophila genome. Cell, 148, 458-472.
11. Ernst, J., Kheradpour, P., Mikkelsen, T.S., Shoresh, N., Ward, L.D., Epstein, C.B., Zhang, X., Wang, L., Issner, R., Coyne, M. et al.;1; (2011) Mapping and analysis of chromatin state dynamics in nine human cell types. Nature, 473, 43-49.
12. Filion,;1; G.J., van Bemmel, J.G., Braunschweig, U., Talhout, W., Kind, J., Ward, L.D., Brugman, W., de Castro, I.J., Kerkhoven, R.M., Bussemaker, H.J. et al. (2010) Systematic protein location mapping reveals five principal chromatin types in Drosophila cells. Cell, 143, 212-224.
13. Core, L.J., Waterfall, J.J. and Lis, J.T.;1; (2008) Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science, 322, 1845-1848.
14. Lieberman-Aiden,;1; E., van Berkum, N.L., Williams, L., Imakaev, M., Ragoczy, T., Telling, A., Amit, I., Lajoie, B.R., Sabo, P.J., Dorschner, M.O. et al. (2009) Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science, 326, 289-293.
15. McDaniell, R., Lee, B.K., Song, L., Liu, Z., Boyle, A.P., Erdos, M.R., Scott, L.J., Morken, M.A., Kucera, K.S., Battenhouse, A. et al.;1; (2010) Heritable individual-specific and allele-specific chromatin signatures in humans. Science, 328, 235-239.
16. Manolio, T.A., Collins, F.S., Cox, N.J., Goldstein, D.B., Hindorff, L.A., Hunter, D.J., McCarthy, M.I., Ramos, E.M., Cardon, L.R., Chakravarti, A. et al.;1; (2009) Finding the missing heritability of complex diseases. Nature, 461, 747-753.
17. Eichler, E.E., Flint, J., Gibson, G., Kong, A., Leal, S.M., Moore, J.H. and Nadeau, J.H.;1; (2010) Missing heritability and strategies for finding the underlying causes of complex disease. Nat. Rev. Genet., 11, 446-450.
18. Jirtle, R.L. and Skinner, M.K.;1; (2007) Environmental epigenomics and disease susceptibility. Nat. Rev. Genet., 8, 253-262.
19. Degner, J.F., Pai, A.A., Pique-Regi, R., Veyrieras, J.B., Gaffney, D.J., Pickrell, J.K., De Leon, S., Michelini, K., Lewellen, N., Crawford, G.E. et al.;1; (2012) DNase I sensitivity QTLs are a major determinant of human expression variation. Nature, 482, 390-394.
20. Bell, J.T., Pai, A.A., Pickrell, J.K., Gaffney, D.J., Pique-Regi, R., Degner, J.F., Gilad, Y. and Pritchard, J.K.;1; (2011) DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines. Genome Biol., 12, R10.
21. Ng, S.F., Lin, R.C., Laybutt, D.R., Barres, R., Owens, J.A. and Morris, M.J.;1; (2010) Chronic high-fat diet in fathers programs beta-cell dysfunction in female rat offspring. Nature, 467, 963-966.
22. Rakyan, V.K., Down, T.A., Balding, D.J. and Beck, S.;1; (2011) Epigenome-wide association studies for common human diseases. Nat. Rev. Genet., 12, 529-541.
23. Rakyan, V.K., Beyan, H., Down, T.A., Hawa, M.I., Maslau, S., Aden, D., Daunay, A., Busato, F., Mein, C.A., Manfras, B. et al.;1; (2011) Identification of type 1 diabetes-associated DNA methylation variable positions that precede disease diagnosis. PLoS Genet., 7, e1002300.
24. Breitling, L.P., Yang, R., Korn, B., Burwinkel, B. and Brenner, H.;1; (2011) Tobacco-smoking-related differential DNA methylation: 27K discovery and replication. Am. J. Hum. Genet., 88, 450-457.
25. Bell, J.T., Tsai, P.C., Yang, T.P., Pidsley, R., Nisbet, J., Glass, D., Mangino, M., Zhai, G., Zhang, F., Valdes,;1; A. et al.;1; (2012) Epigenome-wide scans identify differentially methylated regions for age and age-related phenotypes in a healthy ageing population. PLoS Genet., 8, e1002629.
26. International HapMap Consortium. (2005) A haplotype map of the human genome. Nature, 437, 1299-1320.