Expression quantitative trait loci detected in cell lines are often present in primary tissues

Human Molecular Genetics

Volumn 18, Issue 22, 2009, Pages 4296-4303

  Bullaughey, Kevin ^a   Chavarria, Claudia I ^a   Coop, Graham ^a,b   Gilad, Yoav ^a,c  

^a UNIVERSITY OF CHICAGO   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c NONE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CANCER CELL CULTURE; CONTROLLED STUDY; CYTODIAGNOSIS; EXPRESSION QUANTITATIVE TRAIT LOCUS; GENE EXPRESSION REGULATION; GENE MAPPING; GENETIC VARIABILITY; GENOTYPE; HAPLOTYPE MAP; HEART; HUMAN; HUMAN TISSUE; LIVER; LUNG; LYMPHOBLASTOID CELL LINE; PRIORITY JOURNAL; QUANTITATIVE TRAIT LOCUS; TESTIS;

ADULT; CELL LINE; FEMALE; GENE EXPRESSION PROFILING; GENOTYPE; HUMANS; KIDNEY; LIVER; LUNG; MALE; QUANTITATIVE TRAIT LOCI; TESTIS;

EID: 70350683774     PISSN: 09646906     EISSN: 14602083     Source Type: Journal    
DOI: 10.1093/hmg/ddp382     Document Type: Article

References (42)

1. Gilad, Y., Rifkin, S.A. and Pritchard, J.K. (2008) Revealing the architecture of gene regulation: The promise of eQTL studies. Trends Genet., 24, 408-415.
2. Deutsch, S., Lyle, R., Dermitzakis, E.T., Attar, H., Subrahmanyan, L., Gehrig, C., Parand, L., Gagnebin, M., Rougemont, J., Jongeneel, C.V. et al. (2005) Gene expression variation and expression quantitative trait mapping of human chromosome 21 genes. Hum. Mol. Genet., 14, 3741-3749.
3. Dixon, A.L., Liang, L., Moffatt, M.F., Chen, W., Heath, S., Wong, K.C.C., Taylor, J., Burnett, E., Gut, I., Farrall, M. et al. (2007) A genome-wide association study of global gene expression. Nat. Genet., 39, 1202-1207.
4. Duan, S., Huang, R.S., Zhang, W., Bleibel, W.K., Roe, C.A., Clark, T.A., Chen, T.X., Schweitzer, A.C., Blume, J.E., Cox, N.J. et al. (2008) Genetic architecture of transcript-level variation in humans. Am. J. Hum. Genet., 82, 1101-1113.
5. Huang, R.S., Duan, S., Kistner, E.O., Zhang, W., Bleibel, W.K., Cox, N.J. and Dolan, M.E. (2008) Identification of genetic variants and gene expression relationships associated with pharmacogenes in humans. Pharmacogenet. Genomics, 18, 545-549.
6. Veyrieras, J.-B., Kudaravalli, S., Kim, S.Y., Dermitzakis, E.T., Gilad, Y., Stephens, M. and Pritchard, J.K. (2008) High-resolution mapping of expression-QTLs yields insight into human gene regulation. PLoS Genet., 4, e1000214.
7. The HapMap Consortium (2005) A haplotype map of the human genome. Nature, 437, 1299-1320.
8. Hayden, E.C. (2008) International genome project launched. Nature, 451, 378-379.
9. Redon, R., Ishikawa, S., Fitch, K.R., Feuk, L., Perry, G.H., Andrews, T.D., Fiegler, H., Shapero, M.H., Carson, A.R., Chen, W. et al. (2006) Global variation in copy number in the human genome. Nature 444, 444-454.
10. Hannula, K., Lipsanen-Nyman, M., Scherer, S.W., Holmberg, C., Höglund, P. and Kere, J. (2001) Maternal and paternal chromosomes 7 show differential methylation of many genes in lymphoblast DNA. Genomics, 73, 1-9.
11. Akey, J.M., Biswas, S., Leek, J.T. and Storey, J.D. (2007) On the design and analysis of gene expression studies in human populations. Nat. Genet., 39, 807-808.
12. Choy, E., Yelensky, R., Bonakdar, S., Plenge, R.M., Saxena, R., De Jager, P.L., Shaw, S.Y., Wolfish, C.S., Slavik, J.M., Cotsapas, C. et al. (2008) Genetic analysis of human traits in vitro: Drug response and gene expression in lymphoblastoid cell lines. PLoS Genet., 4, e1000287.
13. Carter, K.L., Cahir-McFarland, E. and Kieff, E. (2002) Epstein-Barr virus-induced changes in B-lymphocyte gene expression. J. Virol., 76, 10427-10436.
14. Arnone, M.I. and Davidson, E.H. (1997) The hardwiring of development: organization and function of genomic regulatory systems. Development 124, 1851-1864.
15. Wray, G.A. (2007) The evolutionary significance of cis-regulatory mutations. Nat. Rev. Genet., 8, 206-216.
16. Smirnov, D.A. and Cheung, V.G. (2008) ATM gene mutations result in both recessive and dominant expression phenotypes of genes and micrornas. Am. J. Hum. Genet., 83, 243-253.
17. Fritsche, L.G., Loenhardt, T., Janssen, A., Fisher, S.A., Rivera, A., Keilhauer, C.N. and Weber, B.H.F. (2008) Age-related macular degeneration is associated with an unstable ARMS2 (LOC387715) mRNA. Nat. Genet., 40, 892-896.
18. Graham, D.S.C., Graham, R.R., Manku, H., Wong, A.K., Whittaker, J.C., Gaffney, P.M., Moser, K.L., Rioux, J.D., Altshuler, D., Behrens, T.W. et al. (2008) Polymorphism at the TNF superfamily gene TNFSF4 confers susceptibility to systemic lupus erythematosus. Nat. Genet., 40 83-89.
19. Hunt, K.A., Zhernakova, A., Turner, G., Heap, G.A.R., Franke, L., Bruinenberg, M., Romanos, J., Dinesen, L.C., Ryan, A.W., Panesar, D. et al. (2008) Newly identified genetic risk variants for celiac disease related to the immune response. Nat. Genet., 40, 395-402.
20. Lettre, G., Jackson, A.U., Gieger, C., Schumacher, F.R., Berndt, S.I., Sanna, S., Eyheramendy, S., Voight, B.F., Butler, J.L., Guiducci, C. et al. (2008) Identification of ten loci associated with height highlights new biological pathways in human growth. Nat. Genet., 40, 584-591.
21. McCarroll, S., Huett, A., Kuballa, P., Chilewski, S., Landry, A., Goyette, P., Zody, M., Hall, J., Brant, S., Cho, J. et al. (2008) Deletion polymorphism upstream of IRGM associated with altered IRGM expression and Crohn's disease. Nat. Genet., 40, 1107-1112.
22. Miyagawa, T., Kawashima, M., Nishida, N., Ohashi, J., Kimura, R., Fujimoto, A., Shimada, M., Morishita, S., Shigeta, T., Lin, L. et al. (2008) Variant between CPT1B and CHKB associated with susceptibility to narcolepsy. Nat. Genet., 40, 1324-1328.
23. Miyamoto, Y., Mabuchi, A., Shi, D., Kubo, T., Takatori, Y., Saito, S., Fujioka, M., Sudo, A., Uchida, A., Yamamoto, S. et al. (2007) A functional polymorphism in the 5′-UTR of GDF5 is associated with susceptibility to osteoarthritis. Nat. Genet., 39, 529-533.
24. Suzuki, A., Yamada, R., Kochi, Y., Sawada, T., Okada, Y., Matsuda, K., Kamatani, Y., Mori, M., Shimane, K., Hirabayashi, Y. et al. (2008) Functional SNPs in CD244 increase the risk of rheumatoid arthritis in a Japanese population. Nat. Genet., 40, 1224-1229.
25. Emilsson, V., Thorleifsson, G., Zhang, B., Leonardson, A.S., Zink, F., Zhu, J., Carlson, S., Helgason, A., Walters, G.B., Gunnarsdottir, S. et al. (2008) Genetics of gene expression and its effect on disease. Nature, 452, 423-428.
26. Schadt, E.E., Molony, C., Chudin, E., Hao, K., Yang, X., Lum, P.Y., Kasarskis, A., Zhang, B., Wang, S., Suver, C. et al. (2008) Mapping the genetic architecture of gene expression in human liver. PLoS Biol., 6, e107.
27. Myers, A.J., Gibbs, J.R., Webster, J.A., Rohrer, K., Zhao, A., Marlowe, L., Kaleem, M., Leung, D., Bryden, L., Nath, P. et al. (2007) A survey of genetic human cortical gene expression. Nat. Genet., 39, 1494-1499.
28. Heinzen, E.L., Ge, D., Cronin, K.D., Maia, J.M., Shianna, K.V., Gabriel, W.N., Welsh-Bohmer, K.A., Hulette, C.M., Denny, T.N. and Goldstein, D.B. (2008) Tissue-specific genetic control of splicing: Implications for the study of complex traits. PLoS Biol., 6, e1.
29. Pastinen, T., Ge, B. and Hudson, T.J. (2006) Influence of human genome polymorphism on gene expression. Hum. Mol. Genet., 15 (Spec No 1), R9-R16.
30. Yan, H. and Zhou, W. (2004) Allelic variations in gene expression. Curr. Opin. Oncol., 16, 39-43.
31. Lo, H.S., Wang, Z., Hu, Y., Yang, H.H., Gere, S., Buetow, K.H. and Lee, M.P. (2003) Allelic variation in gene expression is common in the human genome. Genome Res., 13, 1855-1862.
32. Verlaan, D.J., Ge, B., Grundberg, E., Hoberman, R., Lam, K.C.L., Koka, V., Dias, J., Gurd, S., Martin, N.W., Mallmin, H. et al. (2009) Targeted screening of cis-regulatory variation in human haplotypes. Genome Res., 19, 118-127.
33. Stranger, B.E., Forrest, M.S., Dunning, M., Ingle, C.E., Beazley, C., Thorne, N., Redon, R., Bird, C.P., de Grassi, A., Lee, C. et al. (2007) Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science, 315, 848-853.
34. Gibson, G., Riley-Berger, R., Harshman, L., Kopp, A., Vacha, S., Nuzhdin, S. and Wayne, M. (2004) Extensive sex-specific nonadditivity of gene expression in drosophila melanogaster. Genetics, 167, 1791-1799.
35. Storey, J. (2002) A direct approach to false discovery rates. J. R. Stat. Soc. Series B Stat. Methodol., 64, 479-498.
36. Zollner, S. and Pritchard, J.K. (2007) Overcoming the winner's curse: estimating penetrance parameters from case-control data. Am. J. Hum. Genet., 80, 605-615.
37. Heintzman, N.D., Hon, G.C., Hawkins, R.D., Kheradpour, P., Stark, A., Harp, L.F., Ye, Z., Lee, L.K., Stuart, R.K., Ching, C.W. et al. (2009) Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature, 459, 108-112.
38. Hovatta, I., Zapala, M.A., Broide, R.S., Schadt, E.E., Libiger, O., Schork, N.J., Lockhart, D.J. and Barlow, C. (2007) DNA variation and brain region-specific expression profiles exhibit different relationships between inbred mouse strains: Implications for eQTL mapping studies. Genome Biol., 8, R25.
39. Bento, J.L., Bowden, D.W., Mychaleckyj, J.C., Hirakawa, S., Rich, S.S., Freedman, B.I. and Segade, F. (2005) Genetic analysis of the GLUT10 glucose transporter (SLC2A10) polymorphisms in Caucasian American type 2 diabetes. BMC Med. Genet., 6, 42.
40. Spielman, R.S., Bastone, L.A., Burdick, J.T., Morley, M., Ewens, W.J. and Cheung, V.G. (2007) Common genetic variants account for differences in gene expression among ethnic groups. Nat. Genet., 39, 226-231.
41. Price, A.L., Patterson, N., Hancks, D.C., Myers, S., Reich, D., Cheung, V.G. and Spielman, R.S. (2008) Effects of cis and trans genetic ancestry on gene expression in African Americans. PLoS Genet. 4, e1000294.
42. R Development Core Team (2008) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria, ISBN 3-900051-07-0.