Population genomics of human gene expression

Nature Genetics

Volumn 39, Issue 10, 2007, Pages 1217-1224

  Stranger, Barbara E ^a   Nica, Alexandra C ^a   Forrest, Matthew S ^a   Dimas, Antigone ^a   Bird, Christine P ^a   Beazley, Claude ^a   Ingle, Catherine E ^a   Dunning, Mark ^b   Flicek, Paul ^c   Koller, Daphne ^d   Montgomery, Stephen ^a   Tavaré, Simon ^b   Deloukas, Panos ^a   Dermitzakis, Emmanouil T ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^c EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

^d Stanford University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CELL TRANSFORMATION; CIS ISOMER; CONTROLLED STUDY; EPSTEIN BARR VIRUS; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE FREQUENCY; GENE IDENTIFICATION; GENE REPLICATION; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENOMICS; GENOTYPE; HEREDITY; HUMAN; HUMAN CELL; HUMAN GENOME; LYMPHOBLASTOID CELL LINE; POPULATION GENETICS; PRIORITY JOURNAL; SIGNAL TRANSDUCTION; SINGLE NUCLEOTIDE POLYMORPHISM; TRANS ISOMER;

ALLELES; CELL LINE, TUMOR; CHROMOSOMES, HUMAN, PAIR 2; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENETICS, POPULATION; GENOME, HUMAN; GENOMICS; HUMANS; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; REPRESSOR PROTEINS; TRANSCRIPTION INITIATION SITE; VARIATION (GENETICS);

HUMAN HERPESVIRUS 4;

EID: 34548738566     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng2142     Document Type: Article

References (43)

1. Ferrari, S.L. et al. Polymorphisms in the low-density lipoprotein receptor-related protein 5 (LRP5) gene are associated with variation in vertebral bone mass, vertebral bone size, and stature in whites. Am. J. Hum. Genet. 74, 866-875 (2004).
2. Bansal, A. et al. Association testing by DNA pooling: an effective initial screen. Proc. Natl. Acad. Sci. USA 99, 16871-16874 (2002).
3. Mahley, R.W. & Huang, Y. Apolipoprotein E: from atherosclerosis to Alzheimer's disease and beyond. Curr. Opin. Lipidol. 10, 207-217 (1999).
4. Kleinjan, D.A. & van Heyningen, V. Long-range control of gene expression: emerging mechanisms and disruption in disease. Am. J. Hum. Genet. 76, 8-32 (2005).
5. Valentonyte, R. et al. Sarcoidosis is associated with a truncating splice site mutation in BTNL2. Nat. Genet. 37, 357-364 (2005).
6. Saxena, R. et al. Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels. Science 316, 1331-1336 (2007).
7. Zeggini, E. et al. Replication of genome-wide association signals in UK samples reveals risk loci for type 2 diabetes. Science 316, 1336-1341 (2007).
8. Fanciulli, M. et al. FCGR3B copy number variation is associated with susceptibility to systemic, but not organ-specific, autoimmunity. Nat. Genet. 39, 721-723 (2007).
9. Stankiewicz, P. & Lupski, J.R. Genome architecture, rearrangements and genomic disorders. Trends Genet. 18, 74-82 (2002).
10. Merla, G. et al. Submicroscopic deletion in patients with Williams-Beuren syndrome influences expression levels of the nonhemizygous flanking genes. Am. J. Hum. Genet. 79, 332-341 (2006).
11. Li, M. et al. CFH haplotypes without the Y402H coding variant show strong association with susceptibility to age-related macular degeneration. Nat. Genet. 38, 1049-1054 (2006).
12. Hirschhorn, J.N. & Daly, M.J. Genome-wide association studies for common diseases and complex traits. Nat. Rev. Genet. 6, 95-108 (2005).
13. Stranger, B.E. & Dermitzakis, E.T. The genetics of regulatory variation in the human genome. Hum. Genomics 2, 126-131 (2005).
14. Stranger, B.E. & Dermitzakis, E.T. From DNA to RNA to disease and back: the 'central dogma' of regulatory disease variation. Hum. Genomics 2, 383-390 (2006).
15. Doss, S., Schadt, E.E., Drake, T.A. & Lusis, A.J. Cis-acting expression quantitative trait loci in mice. Genome Res. 15, 681-691 (2005).
16. Cheung, V.G. et al. Mapping determinants of human gene expression by regional and genome-wide association. Nature 437, 1365-1369 (2005).
17. Schadt, E.E. et al. Genetics of gene expression surveyed in maize, mouse and man. Nature 422, 297-302 (2003).
18. Stranger, B.E. et al. Genome-wide associations of gene expression variation in humans. PLoS Genet. 1, e78 (2005).
19. Stranger, B.E. et al. Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science 315, 848-853 (2007).
20. Knight, J.C. Regulatory polymorphisms underlying complex disease traits. J. Mol. Med. 83, 97-109 (2005).
21. Monks, S.A. et al. Genetic inheritance of gene expression in human cell lines. Am. J. Hum. Genet. 75, 1094-1105 (2004).
22. The International HapMap Consortium. A haplotype map of the human genome. Nature 437, 1299-1320 (2005).
23. The International HapMap Consortium. The phase II haplotype map of the human genome. Nature (in the press).
24. Dunning, M.J., Smith, D.R., Thorne, N.P. & Tavare, S. beadarray: an R Package to analyse Illumina BeadArrays. R News 6, 17 (2006).
25. Dunning, M.J., Thorne, N.P., Camilier, I., Smith, M.L. & Tavare, S. Quality control and low-level statistical analysis of Illumina BeadArrays. Rev. Stat. 4, 1-30 (2006).
26. Ashburner, M. et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25, 25-29 (2000).
27. Camon, E., Barrell, D., Lee, V., Dimmer, E. & Apweiler, R. The Gene Ontology Annotation (GOA) Database - an integrated resource of GO annotations to the UniProt Knowledgebase. In Silico Biol. 4, 5-6 (2004).
28. Storey, J.D., Akey, J.M. & Kruglyak, L. Multiple locus linkage analysis of genomewide expression in yeast. PLoS Biol. 3, e267 (2005).
29. Lee, S.I., Pe'er, D., Dudley, A.M., Church, G.M. & Koller, D. Identifying regulatory mechanisms using individual variation reveals key role for chromatin modification. Proc. Natl. Acad. Sci. USA 103, 14062-14067 (2006).
30. Koren, M. et al. ATM haplotypes and breast cancer risk in Jewish high-risk women. Br. J. Cancer 94, 1537-1543 (2006).
31. Birney, E. et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447, 799-816 (2007).
32. Hoogendoorn, B. et al. Functional analysis of polymorphisms in the promoter regions of genes on 22q11. Hum. Mutat. 24, 35-42 (2004).
33. Dermitzakis, E.T. et al. Evolutionary discrimination of mammalian conserved non-genic sequences (CNGs). Science 302, 1033-1035 (2003).
34. Drake, J.A. et al. Conserved noncoding sequences are selectively constrained and not mutation cold spots. Nat. Genet. 38, 223-227 (2006).
35. Bejerano, G. et al. Ultraconserved elements in the human genome. Science 304, 1321-1325 (2004).
36. Abbasi, A.A. et al. Human GLI3 intragenic conserved non-coding sequences are tissue-specific enhancers. PLoS ONE 2, e366 (2007).
37. Woolfe, A. et al. Highly conserved non-coding sequences are associated with vertebrate development. PLoS Biol. 3, e7 (2005).
38. Brem, R.B. & Kruglyak, L. The landscape of genetic complexity across 5,700 gene expression traits in yeast. Proc. Natl. Acad. Sci. USA 102, 1572-1577 (2005).
39. Yvert, G. et al. Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors. Nat. Genet. 35, 57-64 (2003).
40. Kuhn, K. et al. A novel, high-performance random array platform for quantitative gene expression profiling. Genome Res. 14, 2347-2356 (2004).
41. Bolstad, B.M., Irizarry, R.A., Astrand, M. & Speed, T.P. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19, 185-193 (2003).
42. Churchill, G.A. & Doerge, R.W. Empirical threshold values for quantitative trait mapping. Genetics 138, 963-971 (1994).
43. Doerge, R.W. & Churchill, G.A. Permutation tests for multiple loci affecting a quantitative character. Genetics 142, 285-294 (1996).