et al. Missing heritability and strategies for finding the underlying causes of complex disease. Nat. Rev. Genet.
11, 446–450 (2010).
et al. Mapping determinants of human gene expression by regional and genome-wide association. Nature
437, 1365–1369 (2005).
et al. Discovery of expression QTLs using large-scale transcriptional profiling in human lymphocytes. Nat. Genet.
39, 1208–1216 (2007).
et al. Population genomics in a disease targeted primary cell model. Genome Res.
19, 1942–1952 (2009).
et al. Population genomics of human gene expression. Nat. Genet.
39, 1217–1224 (2007).
et al. A survey of genetic human cortical gene expression. Nat. Genet.
39, 1494–1499 (2007).
et al. Mapping the genetic architecture of gene expression in human liver. PLoS Biol.
6, e107 (2008).
et al. Genetics of gene expression and its effect on disease. Nature
452, 423–428 (2008).
et al. Common regulatory variation impacts gene expression in a cell type–dependent manner. Science
325, 1246–1250 (2009).
et al. A survey of the genetics of stomach, liver, and adipose gene expression from a morbidly obese cohort. Genome Res.
21, 1008–1016 (2011).
et al. The architecture of gene regulatory variation across multiple human tissues: the MuTHER study. PLoS Genet.
7, e1002003 (2011).
et al. Genetics and beyond—the transcriptome of human monocytes and disease susceptibility. PLoS ONE
5, e10693 (2010).
et al. Gene expression in skin and lymphoblastoid cells: refined statistical method reveals extensive overlap in cis-eQTL signals. Am. J. Hum. Genet.
87, 779–789 (2010).
et al. Candidate causal regulatory effects by integration of expression QTLs with complex trait genetic associations. PLoS Genet.
6, e1000895 (2010).
et al. A genome-wide association study of global gene expression. Nat. Genet.
39, 1202–1207 (2007).
et al. Single-tissue and cross-tissue heritability of gene expression via identity-by-descent in related or unrelated individuals. PLoS Genet.
7, e1001317 (2011).
Spector, T.D. & Williams, F.M.
The UK Adult Twin Registry (TwinsUK). Twin Res. Hum. Genet.
9, 899–906 (2006).
et al. Are twins and singletons comparable? A study of disease-related and lifestyle characteristics in adult women. Twin Res.
4, 464–477 (2001).
Visscher, P.M., Benyamin, B. & White, I.
The use of linear mixed models to estimate variance components from data on twin pairs by maximum likelihood. Twin Res.
7, 670–674 (2004).
Storey, J.D. & Tibshirani, R.
Statistical significance for genomewide studies. Proc. Natl. Acad. Sci. USA
100, 9440–9445 (2003).
et al. Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts. Nat. Genet.
41, 47–55 (2009).
et al. Variants in ADCY5 and near CCNL1 are associated with fetal growth and birth weight. Nat. Genet.
42, 430–435 (2010).
et al. Common sequence variants on 20q11.22 confer melanoma susceptibility. Nat. Genet.
40, 838–840 (2008).
et al. Genetic determinants of hair, eye and skin pigmentation in Europeans. Nat. Genet.
39, 1443–1452 (2007).
Anderson, C.A., Soranzo, N., Zeggini, E. & Barrett, J.C.
Synthetic associations are unlikely to account for many common disease genome-wide association signals. PLoS Biol.
9, e1000580 (2011).
et al. Rare variants create synthetic genome-wide associations. PLoS Biol.
8, e1000294 (2010).
et al. Genetic control of gene expression in whole blood and lymphoblastoid cell lines is largely independent. Genome Res.
22, 456–466 (2012).
et al. A trans-acting locus regulates an anti-viral expression network and type 1 diabetes risk. Nature
467, 460–464 (2010).
et al. Identification of an imprinted master trans regulator at the KLF14 locus related to multiple metabolic phenotypes. Nat. Genet.
43, 561–564 (2011).
et al. Regulation of ploidy and senescence by the AMPK-related kinase NUAK1. EMBO J.
29, 376–386 (2010).
Li, H., Ruan, J. & Durbin, R.
Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res.
18, 1851–1858 (2008).
et al. A genotype calling algorithm for the Illumina BeadArray platform. Bioinformatics
23, 2741–2746 (2007).
Aulchenko, Y.S., de Koning, D.J. & Haley, C.
Genomewide rapid association using mixed model and regression: a fast and simple method for genomewide pedigree-based quantitative trait loci association analysis. Genetics
177, 577–585 (2007).
Chen, W.M. & Abecasis, G.R.
Family-based association tests for genomewide association scans. Am. J. Hum. Genet.
81, 913–926 (2007).
Aulchenko, Y.S., Ripke, S., Isaacs, A. & van Duijn, C.M.
GenABEL: an R library for genome-wide association analysis. Bioinformatics
23, 1294–1296 (2007).
Aulchenko, Y.S., Struchalin, M.V. & van Duijn, C.M.
ProbABEL package for genome-wide association analysis of imputed data. BMC Bioinformatics
11, 134 (2010).
R Development Core Team. R: A Language and Environment for Statistical Computing. (R Foundation for Statistical Computing, Vienna, 2010).
et al. The fine-scale structure of recombination rate variation in the human genome. Science
304, 581–584 (2004).
lme4: Linear Mixed-Effects Models Using S4 Classes. (R Foundation for Statistical Computing, Vienna, 2010).
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).
et al. The use of genome-wide eQTL associations in lymphoblastoid cell lines to identify novel genetic pathways involved in complex traits. PLoS ONE
6, e22070 (2011).
Golding, J., Pembrey, M. & Jones, R.
ALSPAC—the Avon Longitudinal Study of Parents and Children. I. Study methodology. Paediatr. Perinat. Epidemiol.
15, 74–87 (2001).
et al. MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes. Genet. Epidemiol.
34, 816–834 (2010).