Abstract
Approaches that combine expression quantitative trait loci (eQTLs) and genome-wide association (GWA) studies are offering new functional information about the aetiology of complex human traits and diseases. Improved study designs — which take into account technological advances in resolving the transcriptome, cell history and state, population of origin and diverse endophenotypes — are providing insights into the architecture of disease and the landscape of gene regulation in humans. Furthermore, these advances are helping to establish links between cellular effects and organismal traits.
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References
Manolio, T. A. et al. Finding the missing heritability of complex diseases. Nature 461, 747–753 (2009).
Manolio, T. A. Genomewide association studies and assessment of the risk of disease. N. Engl. J. Med. 363, 166–176 (2010).
Nica, A. C. et al. Candidate causal regulatory effects by integration of expression QTLs with complex trait genetic associations. PLoS Genet. 6, e1000895 (2010).
Nicolae, D. L. et al. Trait-associated SNPs are more likely to be eQTLs: annotation to enhance discovery from GWAS. PLoS Genet. 6, e1000888 (2010).
Montgomery, S. B. et al. Transcriptome genetics using second generation sequencing in a Caucasian population. Nature 464, 773–777 (2010).
Pickrell, A. M. & Moraes, C. T. What role does mitochondrial stress play in neurodegenerative diseases? Methods Mol. Biol. 648, 63–78 (2010).
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).
Heintzman, N. D. et al. Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 459, 108–112 (2009).
Schadt, E. E. et al. Mapping the genetic architecture of gene expression in human liver. PLoS Biol. 6, e107 (2008).
Myers, A. J. et al. A survey of genetic human cortical gene expression. Nature Genet. 39, 1494–1499 (2007).
Emilsson, V. et al. Genetics of gene expression and its effect on disease. Nature 452, 423–428 (2008).
Heinzen, E. L. et al. Tissue-specific genetic control of splicing: implications for the study of complex traits. PLoS Biol. 6, e1 (2008).
Dimas, A. S. et al. Common regulatory variation impacts gene expression in a cell type-dependent manner. Science 325, 1246–1250 (2009).
Gerrits, A. et al. Expression quantitative trait loci are highly sensitive to cellular differentiation state. PLoS Genet. 5, e1000692 (2009).
Grundberg, E. et al. Population genomics in a disease targeted primary cell model. Genome Res. 19, 1942–1952 (2009).
Kwan, T. et al. Tissue effect on genetic control of transcript isoform variation. PLoS Genet. 5, e1000608 (2009).
Altshuler, D. M. et al. Integrating common and rare genetic variation in diverse human populations. Nature 467, 52–58 (2010).
Frazer, K. A. et al. A second generation human haplotype map of over 3.1 million SNPs. Nature 449, 851–861 (2007).
Spielman, R. S. et al. Common genetic variants account for differences in gene expression among ethnic groups. Nature Genet. 39, 226–231 (2007).
Storey, J. D. et al. Gene-expression variation within and among human populations. Am. J. Hum. Genet. 80, 502–509 (2007).
Stranger, B. E. et al. Population genomics of human gene expression. Nature Genet. 39, 1217–1224 (2007).
Zaitlen, N., Pasaniuc, B., Gur, T., Ziv, E. & Halperin, E. Leveraging genetic variability across populations for the identification of causal variants. Am. J. Hum. Genet. 86, 23–33 (2010).
Schadt, E. E. et al. An integrative genomics approach to infer causal associations between gene expression and disease. Nature Genet. 37, 710–717 (2005).
Moffatt, M. F. et al. Genetic variants regulating ORMDL3 expression contribute to the risk of childhood asthma. Nature 448, 470–473 (2007).
Dixon, A. L. et al. A genome-wide association study of global gene expression. Nature Genet. 39, 1202–1207 (2007).
Arnosti, D. N. & Kulkarni, M. M. Transcriptional enhancers: Intelligent enhanceosomes or flexible billboards? J. Cell Biochem. 94, 890–898 (2005).
van Nas, A. et al. Expression quantitative trait loci: replication, tissue- and sex-specificity in mice. Genetics 185, 1059–1068 (2010).
Nica, A. E. A. The architecture of gene regulatory variation across multiple human tissues: the MuTHER Study. PLoS Genet. 7, e1002003 (2011).
Gilad, Y., Rifkin, S. A. & Pritchard, J. K. Revealing the architecture of gene regulation: the promise of eQTL studies. Trends Genet. 24, 408–415 (2008).
Price, A. L. et al. Effects of cis and trans genetic ancestry on gene expression in African Americans. PLoS Genet. 4, e1000294 (2008).
Cheung, V. G. et al. Polymorphic cis- and trans-regulation of human gene expression. PLoS Biol. 8, e1000480 (2010).
Goring, H. H. et al. Discovery of expression QTLs using large-scale transcriptional profiling in human lymphocytes. Nature Genet. 39, 1208–1216 (2007).
Petretto, E. et al. New insights into the genetic control of gene expression using a Bayesian multi-tissue approach. PLoS Comput. Biol. 6, e1000737 (2010).
Yvert, G. et al. Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors. Nature Genet. 35, 57–64 (2003).
Breitling, R. et al. Genetical genomics: spotlight on QTL hotspots. PLoS Genet. 4, e1000232 (2008).
Sun, W., Yu, T. & Li, K. C. Detection of eQTL modules mediated by activity levels of transcription factors. Bioinformatics 23, 2290–2297 (2007).
Wu, C. et al. Gene set enrichment in eQTL data identifies novel annotations and pathway regulators. PLoS Genet. 4, e1000070 (2008).
Ghazalpour, A. et al. Integrating genetic and network analysis to characterize genes related to mouse weight. PLoS Genet. 2, e130 (2006).
Ren, X., Zhou, X., Wu, L. Y. & Zhang, X. S. An information-flow-based model with dissipation, saturation and direction for active pathway inference. BMC Syst. Biol. 4, 72 (2010).
Li, S., Lu, Q. & Cui, Y. A systems biology approach for identifying novel pathway regulators in eQTL mapping. J. Biopharm. Stat. 20, 373–400 (2010).
Rashid, I., McDermott, J. & Samudrala, R. Inferring molecular interactions pathways from eQTL data. Methods Mol. Biol. 541, 211–223 (2009).
Wessel, J., Zapala, M. A. & Schork, N. J. Accommodating pathway information in expression quantitative trait locus analysis. Genomics 90, 132–142 (2007).
Suthram, S., Beyer, A., Karp, R. M., Eldar, Y. & Ideker, T. eQED: an efficient method for interpreting eQTL associations using protein networks. Mol. Syst. Biol. 4, 162 (2008).
Lee, E. & Bussemaker, H. J. Identifying the genetic determinants of transcription factor activity. Mol. Syst. Biol. 6, 412 (2010).
Pickrell, J. K. et al. Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature 464, 768–772 (2010).
McDaniell, R. et al. Heritable individual-specific and allele-specific chromatin signatures in humans. Science 328, 235–239 (2010).
Dubois, P. C. et al. Multiple common variants for celiac disease influencing immune gene expression. Nature Genet. 42, 295–302 (2010).
Speliotes, E. K. et al. Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index. Nature Genet. 42, 937–948 (2010).
Anttila, V. et al. Genome-wide association study of migraine implicates a common susceptibility variant on 8q22.1. Nature Genet. 42, 869–873 (2010).
Yamanaka, S. & Blau, H. M. Nuclear reprogramming to a pluripotent state by three approaches. Nature 465, 704–712 (2010).
Durbin, R. M. et al. A map of human genome variation from population-scale sequencing. Nature 467, 1061–1073 (2010).
Willer, C. J. et al. Six new loci associated with body mass index highlight a neuronal influence on body weight regulation. Nature Genet. 41, 25–34 (2009).
Musunuru, K. et al. From noncoding variant to phenotype via SORT1 at the 1p13 cholesterol locus. Nature 466, 714–719 (2010).
Teslovich, T. M. et al. Biological, clinical and population relevance of 95 loci for blood lipids. Nature 466, 707–713 (2010).
Crawford, N. P. et al. Rrp1b, a new candidate susceptibility gene for breast cancer progression and metastasis. PLoS Genet. 3, e214 (2007).
Libioulle, C. et al. 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 (2007).
Heid, I. M. et al. Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution. Nature Genet. 42, 949–960 (2010).
Lango Allen, H. et al. Hundreds of variants clustered in genomic loci and biological pathways affect human height. Nature 467, 832–838 (2010).
Soranzo, N. et al. Meta-analysis of genome-wide scans for human adult stature identifies novel loci and associations with measures of skeletal frame size. PLoS Genet. 5, e1000445 (2009).
Wheeler, H. E. et al. Sequential use of transcriptional profiling, expression quantitative trait mapping, and gene association implicates MMP20 in human kidney aging. PLoS Genet. 5, e1000685 (2009).
Cunnington, M. S., Santibanez Koref, M., Mayosi, B. M., Burn, J. & Keavney, B. Chromosome 9p21 SNPs associated with multiple disease phenotypes correlate with ANRIL expression. PLoS Genet. 6, e1000899 (2010).
Hsu, Y. H. et al. An integration of genome-wide association study and gene expression profiling to prioritize the discovery of novel susceptibility loci for osteoporosis-related traits. PLoS Genet. 6, e1000977 (2010).
Rivadeneira, F. et al. Twenty bone-mineral-density loci identified by large-scale meta-analysis of genome-wide association studies. Nature Genet. 41, 1199–1206 (2009).
Simon-Sanchez, J. et al. Genome-wide association study reveals genetic risk underlying Parkinson's disease. Nature Genet. 41, 1308–1312 (2009).
Hamza, T. H. et al. Common genetic variation in the HLA region is associated with late-onset sporadic Parkinson's disease. Nature Genet. 42, 781–785 (2010).
Stuart, P. E. et al. Genome-wide association analysis identifies three psoriasis susceptibility loci. Nature Genet. 42, 1000–1004 (2010).
Sotoodehnia, N. et al. Common variants in 22 loci are associated with QRS duration and cardiac ventricular conduction. Nature Genet. 42, 1068–1076 (2010).
Dupuis, J. et al. New genetic loci implicated in fasting glucose homeostasis and their impact on type 2 diabetes risk. Nature Genet. 42, 105–116 (2010).
Voight, B. F. et al. Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis. Nature Genet. 42, 579–589 (2010).
Acknowledgements
We acknowledge funds from the Louis-Jeantet Foundation, the Swiss National Science Foundation and the European Commission and the help and comments of our Functional Population Genomics group in Geneva.
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Montgomery, S., Dermitzakis, E. From expression QTLs to personalized transcriptomics. Nat Rev Genet 12, 277–282 (2011). https://doi.org/10.1038/nrg2969
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DOI: https://doi.org/10.1038/nrg2969
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