Heritability and genomics of gene expression in peripheral blood (original) (raw)
Hindorff, L.A. et al. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc. Natl. Acad. Sci. USA106, 9362–9367 (2009). ArticlePubMedPubMed Central Google Scholar
Majewski, J. & Pastinen, T. The study of eQTL variations by RNA-seq: from SNPs to phenotypes. Trends Genet.27, 72–79 (2011). ArticleCASPubMed Google Scholar
Cookson, W., Liang, L., Abecasis, G., Moffatt, M. & Lathrop, M. Mapping complex disease traits with global gene expression. Nat. Rev. Genet.10, 184–194 (2009). ArticleCASPubMedPubMed Central Google Scholar
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). ArticleCASPubMedPubMed Central Google Scholar
Grundberg, E. et al. Mapping _cis_- and _trans_-regulatory effects across multiple tissues in twins. Nat. Genet.44, 1084–1089 (2012). CASPubMedPubMed Central Google Scholar
Lango Allen, H. et al. Hundreds of variants clustered in genomic loci and biological pathways affect human height. Nature467, 832–838 (2010). ArticleCASPubMedPubMed Central Google Scholar
Emilsson, V. et al. Genetics of gene expression and its effect on disease. Nature452, 423–428 (2008). ArticleCASPubMed Google Scholar
de Jong, S. et al. Expression QTL analysis of top loci from GWAS meta-analysis highlights additional schizophrenia candidate genes. Eur. J. Hum. Genet.20, 1004–1008 (2012). ArticleCASPubMedPubMed Central Google Scholar
Fransen, K. et al. Analysis of SNPs with an effect on gene expression identifies UBE2L3 and BCL3 as potential new risk genes for Crohn's disease. Hum. Mol. Genet.19, 3482–3488 (2010). ArticleCASPubMed Google Scholar
Luo, R. et al. Genome-wide transcriptome profiling reveals the functional impact of rare de novo and recurrent CNVs in autism spectrum disorders. Am. J. Hum. Genet.91, 38–55 (2012). ArticleCASPubMedPubMed Central Google Scholar
Speliotes, E.K. et al. Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index. Nat. Genet.42, 937–948 (2010). ArticleCASPubMedPubMed Central Google Scholar
Xia, K. et al. seeQTL: a searchable database for human eQTLs. Bioinformatics28, 451–452 (2012). ArticleCASPubMed Google Scholar
Fehrmann, R.S. et al. _Trans_-eQTLs reveal that independent genetic variants associated with a complex phenotype converge on intermediate genes, with a major role for the HLA. PLoS Genet.7, e1002197 (2011). ArticleCASPubMedPubMed Central Google Scholar
Min, J.L. et al. The use of genome-wide eQTL associations in lymphoblastoid cell lines to identify novel genetic pathways involved in complex traits. PLoS ONE6, e22070 (2011). ArticleCASPubMedPubMed Central Google Scholar
Gibbs, J.R. et al. Abundant quantitative trait loci exist for DNA methylation and gene expression in human brain. PLoS Genet.6, e1000952 (2010). ArticleCASPubMedPubMed Central Google Scholar
Leek, J.T. et al. Tackling the widespread and critical impact of batch effects in high-throughput data. Nat. Rev. Genet.11, 733–739 (2010). ArticleCASPubMed Google Scholar
Akey, J.M., Biswas, S., Leek, J.T. & Storey, J.D. On the design and analysis of gene expression studies in human populations. Nat. Genet.39, 807–808 (2007). ArticleCASPubMed Google Scholar
Innocenti, F. et al. Identification, replication, and functional fine-mapping of expression quantitative trait loci in primary human liver tissue. PLoS Genet.7, e1002078 (2011). ArticleCASPubMedPubMed Central Google Scholar
Fairfax, B.P. et al. Genetics of gene expression in primary immune cells identifies cell type–specific master regulators and roles of HLA alleles. Nat. Genet.44, 502–510 (2012). ArticleCASPubMedPubMed Central Google Scholar
Flutre, T., Wen, X., Pritchard, J. & Stephens, M. A statistical framework for joint eQTL analysis in multiple tissues. PLoS Genet.9, e1003486 (2013). ArticleCASPubMedPubMed Central Google Scholar
Westra, H.J. et al. Systematic identification of trans eQTLs as putative drivers of known disease associations. Nat. Genet.45, 1238–1243 (2013). ArticleCASPubMedPubMed Central Google Scholar
Powell, J.E. et al. Genetic control of gene expression in whole blood and lymphoblastoid cell lines is largely independent. Genome Res.22, 456–466 (2012). ArticleCASPubMedPubMed Central Google Scholar
Choy, E. et al. Genetic analysis of human traits in vitro: drug response and gene expression in lymphoblastoid cell lines. PLoS Genet.4, e1000287 (2008). ArticleCASPubMedPubMed Central Google Scholar
van Dongen, J., Slagboom, P.E., Draisma, H.H., Martin, N.G. & Boomsma, D.I. The continuing value of twin studies in the omics era. Nat. Rev. Genet.13, 640–653 (2012). ArticleCASPubMed Google Scholar
Rossin, E.J. et al. Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology. PLoS Genet.7, e1001273 (2011). ArticleCASPubMedPubMed Central Google Scholar
Huang, W. et al. DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists. Nucleic Acids Res.35, W169–W175 (2007). ArticlePubMedPubMed Central Google Scholar
Grossman, S.R. et al. A composite of multiple signals distinguishes causal variants in regions of positive selection. Science327, 883–886 (2010). ArticleCASPubMed Google Scholar
Nickel, G.C., Tefft, D. & Adams, M.D. Human PAML browser: a database of positive selection on human genes using phylogenetic methods. Nucleic Acids Res.36, D800–D808 (2008). ArticleCASPubMed Google Scholar
Voight, B.F., Kudaravalli, S., Wen, X. & Pritchard, J.K. A map of recent positive selection in the human genome. PLoS Biol.4, e72 (2006). ArticlePubMedPubMed Central Google Scholar
Visscher, P.M., Hill, W.G. & Wray, N.R. Heritability in the genomics era—concepts and misconceptions. Nat. Rev. Genet.9, 255–266 (2008). ArticleCASPubMed Google Scholar
Yang, J., Lee, S.H., Goddard, M.E. & Visscher, P.M. GCTA: a tool for genome-wide complex trait analysis. Am. J. Hum. Genet.88, 76–82 (2011). ArticleCASPubMedPubMed Central Google Scholar
Powell, J.E. et al. Congruence of additive and non-additive effects on gene expression estimated from pedigree and SNP data. PLoS Genet.9, e1003502 (2013). ArticleCASPubMedPubMed Central 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
Montgomery, S.B. et al. Transcriptome genetics using second generation sequencing in a Caucasian population. Nature464, 773–777 (2010). ArticleCASPubMed Google Scholar
Pickrell, J.K. et al. Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature464, 768–772 (2010). ArticleCASPubMedPubMed Central Google Scholar
Spielman, R.S. et al. Common genetic variants account for differences in gene expression among ethnic groups. Nat. Genet.39, 226–231 (2007). ArticleCASPubMedPubMed Central Google Scholar
Gatti, D.M., Barry, W.T., Nobel, A.B., Rusyn, I. & Wright, F.A. Heading down the wrong pathway: on the influence of correlation within gene sets. BMC Genomics11, 574 (2010). ArticlePubMedPubMed Central Google Scholar
McLaren, W. et al. Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics26, 2069–2070 (2010). ArticleCASPubMedPubMed Central Google Scholar
Sun, W., Ibrahim, J.G. & Zou, F. Genomewide multiple-loci mapping in experimental crosses by iterative adaptive penalized regression. Genetics185, 349–359 (2010). ArticleCASPubMedPubMed Central Google Scholar
Marfil, V. et al. Interaction between Hhex and SOX13 modulates Wnt/TCF activity. J. Biol. Chem.285, 5726–5737 (2010). ArticleCASPubMed Google Scholar
Betancur, C. Etiological heterogeneity in autism spectrum disorders: more than 100 genetic and genomic disorders and still counting. Brain Res.1380, 42–77 (2011). ArticleCASPubMed Google Scholar
Chiurazzi, P., Schwartz, C.E., Gecz, J. & Neri, G. XLMR genes: update 2007. Eur. J. Hum. Genet.16, 422–434 (2008). ArticleCASPubMed Google Scholar
Sullivan, P.F., Daly, M.J. & O'Donovan, M. Genetic architectures of psychiatric disorders: the emerging picture and its implications. Nat. Rev. Genet.13, 537–551 (2012). ArticleCASPubMedPubMed Central Google Scholar
Wise, A.L., Gyi, L. & Manolio, T.A. eXclusion: toward integrating the X chromosome in genome-wide association analyses. Am. J. Hum. Genet.92, 643–647 (2013). ArticleCASPubMedPubMed Central Google Scholar
Xavier, R.J. & Rioux, J.D. Genome-wide association studies: a new window into immune-mediated diseases. Nat. Rev. Immunol.8, 631–643 (2008). ArticleCASPubMedPubMed Central Google Scholar
Hurst, L.D., Pal, C. & Lercher, M.J. The evolutionary dynamics of eukaryotic gene order. Nat. Rev. Genet.5, 299–310 (2004). ArticleCASPubMed Google Scholar
Osborne, C.S. et al. Active genes dynamically colocalize to shared sites of ongoing transcription. Nat. Genet.36, 1065–1071 (2004). ArticleCASPubMed Google Scholar
Sproul, D., Gilbert, N. & Bickmore, W.A. The role of chromatin structure in regulating the expression of clustered genes. Nat. Rev. Genet.6, 775–781 (2005). ArticleCASPubMed Google Scholar
Hentges, K.E., Pollock, D.D., Liu, B. & Justice, M.J. Regional variation in the density of essential genes in mice. PLoS Genet.3, e72 (2007). ArticleCASPubMedPubMed Central Google Scholar
Cai, J.J., Macpherson, J.M., Sella, G. & Petrov, D.A. Pervasive hitchhiking at coding and regulatory sites in humans. PLoS Genet.5, e1000336 (2009). ArticleCASPubMedPubMed Central Google Scholar
Davidson, S., Starkey, A. & MacKenzie, A. Evidence of uneven selective pressure on different subsets of the conserved human genome; implications for the significance of intronic and intergenic DNA. BMC Genomics10, 614 (2009). ArticleCASPubMedPubMed Central Google Scholar
Willemsen, G. et al. The Netherlands Twin Register biobank: a resource for genetic epidemiological studies. Twin Res. Hum. Genet.13, 231–245 (2010). ArticlePubMed Google Scholar
Penninx, B.W. et al. The Netherlands Study of Depression and Anxiety (NESDA): rationales, objectives and methods. Int. J. Methods Psychiatr. Res.17, 121–140 (2008). ArticlePubMedPubMed Central Google Scholar
Boomsma, D.I. et al. Netherlands Twin Register: from twins to twin families. Twin Res. Hum. Genet.9, 849–857 (2006). ArticlePubMed Google Scholar
Boomsma, D.I. et al. Genome-wide association of major depression: description of samples for the GAIN major depressive disorder study: NTR and NESDA Biobank Projects. Eur. J. Hum. Genet.16, 335–342 (2008). ArticleCASPubMed Google Scholar
Sullivan, P.F. et al. Genomewide association for major depressive disorder: a possible role for the presynaptic protein piccolo. Mol. Psychiatry14, 359–375 (2009). ArticleCASPubMed Google Scholar
Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol.10, R25 (2009). ArticleCASPubMedPubMed Central Google Scholar
Altshuler, D.M. et al. Integrating common and rare genetic variation in diverse human populations. Nature467, 52–58 (2010). ArticleCASPubMed Google Scholar
1000 Genomes Project Consortium. A map of human genome variation from population-scale sequencing. Nature467, 1061–1073 (2010).
Schadt, E.E., Woo, S. & Hao, K. Bayesian method to predict individual SNP genotypes from gene expression data. Nat. Genet.44, 603–608 (2012). ArticleCASPubMed Google Scholar
Leek, J.T. & Storey, J.D. Capturing heterogeneity in gene expression studies by surrogate variable analysis. PLoS Genet.3, 1724–1735 (2007). ArticleCASPubMed Google Scholar
Neale, M.C. & Cardon, L.R. Methodology for the Study of Twins and Families (Kluwer Academic Publisher Group, Dordrecht, The Netherlands, 1992).
Wang, X., Guo, X., He, M. & Zhang, H. Statistical inference in mixed models and analysis of twin and family data. Biometrics67, 987–995 (2011). ArticlePubMedPubMed Central Google Scholar
Visscher, P.M. et al. Assumption-free estimation of heritability from genome-wide identity-by-descent sharing between full siblings. PLoS Genet.2, e41 (2006). ArticleCASPubMedPubMed Central Google Scholar
Wright, F.A. The phenotypic difference discards sib-pair QTL linkage information. Am. J. Hum. Genet.60, 740–742 (1997). CASPubMedPubMed Central Google Scholar
Abecasis, G.R., Cherny, S.S., Cookson, W.O. & Cardon, L.R. Merlin—rapid analysis of dense genetic maps using sparse gene flow trees. Nat. Genet.30, 97–101 (2002). ArticleCASPubMed Google Scholar
Barry, W.T., Nobel, A.B. & Wright, F.A. A statistical framework for testing functional categories in microarray data. Ann. Appl. Stat.2, 286–315 (2008). Article Google Scholar