Population genomics of human gene expression (original) (raw)
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). ArticleCASPubMedPubMed Central Google Scholar
Bansal, A. et al. Association testing by DNA pooling: an effective initial screen. Proc. Natl. Acad. Sci. USA99, 16871–16874 (2002). ArticleCASPubMed Google Scholar
Mahley, R.W. & Huang, Y. Apolipoprotein E: from atherosclerosis to Alzheimer's disease and beyond. Curr. Opin. Lipidol.10, 207–217 (1999). ArticleCASPubMed Google Scholar
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). ArticleCASPubMed Google Scholar
Valentonyte, R. et al. Sarcoidosis is associated with a truncating splice site mutation in BTNL2. Nat. Genet.37, 357–364 (2005). ArticleCASPubMed Google Scholar
Saxena, R. et al. Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels. Science316, 1331–1336 (2007). ArticleCASPubMed Google Scholar
Zeggini, E. et al. Replication of genome-wide association signals in UK samples reveals risk loci for type 2 diabetes. Science316, 1336–1341 (2007). ArticleCASPubMedPubMed Central Google Scholar
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). ArticleCASPubMedPubMed Central Google Scholar
Stankiewicz, P. & Lupski, J.R. Genome architecture, rearrangements and genomic disorders. Trends Genet.18, 74–82 (2002). ArticleCASPubMed Google Scholar
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). ArticleCASPubMedPubMed Central Google Scholar
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). ArticleCASPubMedPubMed Central Google Scholar
Hirschhorn, J.N. & Daly, M.J. Genome-wide association studies for common diseases and complex traits. Nat. Rev. Genet.6, 95–108 (2005). ArticleCASPubMed Google Scholar
Stranger, B.E. & Dermitzakis, E.T. From DNA to RNA to disease and back: the 'central dogma' of regulatory disease variation. Hum. Genomics2, 383–390 (2006). ArticleCASPubMedPubMed Central Google Scholar
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). ArticleCASPubMedPubMed Central Google Scholar
Cheung, V.G. et al. Mapping determinants of human gene expression by regional and genome-wide association. Nature437, 1365–1369 (2005). ArticleCASPubMedPubMed Central Google Scholar
Schadt, E.E. et al. Genetics of gene expression surveyed in maize, mouse and man. Nature422, 297–302 (2003). ArticleCASPubMed Google Scholar
Stranger, B.E. et al. Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science315, 848–853 (2007). ArticleCASPubMedPubMed Central Google Scholar
Knight, J.C. Regulatory polymorphisms underlying complex disease traits. J. Mol. Med.83, 97–109 (2005). ArticleCASPubMed Google Scholar
The International HapMap Consortium. A haplotype map of the human genome. Nature437, 1299–1320 (2005).
The International HapMap Consortium. The phase II haplotype map of the human genome. Nature (in the press).
Dunning, M.J., Smith, D.R., Thorne, N.P. & Tavare, S. beadarray: an R Package to analyse Illumina BeadArrays. R News6, 17 (2006). Google Scholar
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). Google Scholar
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). PubMed Google Scholar
Storey, J.D., Akey, J.M. & Kruglyak, L. Multiple locus linkage analysis of genomewide expression in yeast. PLoS Biol.3, e267 (2005). ArticlePubMedPubMed Central Google Scholar
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. USA103, 14062–14067 (2006). ArticleCASPubMed Google Scholar
Birney, E. et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature447, 799–816 (2007). ArticleCASPubMed Google Scholar
Hoogendoorn, B. et al. Functional analysis of polymorphisms in the promoter regions of genes on 22q11. Hum. Mutat.24, 35–42 (2004). ArticleCASPubMed Google Scholar
Dermitzakis, E.T. et al. Evolutionary discrimination of mammalian conserved non-genic sequences (CNGs). Science302, 1033–1035 (2003). ArticleCASPubMed Google Scholar
Drake, J.A. et al. Conserved noncoding sequences are selectively constrained and not mutation cold spots. Nat. Genet.38, 223–227 (2006). ArticleCASPubMed Google Scholar
Bejerano, G. et al. Ultraconserved elements in the human genome. Science304, 1321–1325 (2004). ArticleCASPubMed Google Scholar
Abbasi, A.A. et al. Human GLI3 intragenic conserved non-coding sequences are tissue-specific enhancers. PLoS ONE2, e366 (2007). ArticlePubMedPubMed Central Google Scholar
Woolfe, A. et al. Highly conserved non-coding sequences are associated with vertebrate development. PLoS Biol.3, e7 (2005). ArticlePubMed Google Scholar
Brem, R.B. & Kruglyak, L. The landscape of genetic complexity across 5,700 gene expression traits in yeast. Proc. Natl. Acad. Sci. USA102, 1572–1577 (2005). ArticleCASPubMed Google Scholar
Yvert, G. et al. Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors. Nat. Genet.35, 57–64 (2003). ArticleCASPubMed Google Scholar
Kuhn, K. et al. A novel, high-performance random array platform for quantitative gene expression profiling. Genome Res.14, 2347–2356 (2004). ArticleCASPubMedPubMed Central Google Scholar
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. Bioinformatics19, 185–193 (2003). ArticleCASPubMed Google Scholar
Churchill, G.A. & Doerge, R.W. Empirical threshold values for quantitative trait mapping. Genetics138, 963–971 (1994). CASPubMedPubMed Central Google Scholar
Doerge, R.W. & Churchill, G.A. Permutation tests for multiple loci affecting a quantitative character. Genetics142, 285–294 (1996). CASPubMedPubMed Central Google Scholar