Patterns of Cis regulatory variation in diverse human populations

PLoS Genetics

Volumn 8, Issue 4, 2012, Pages

  Stranger, Barbara E ^a,b,c,d   Montgomery, Stephen B ^a,e,f   Dimas, Antigone S ^a,e,f,g,h   Parts, Leopold ^a   Stegle, Oliver ^h   Ingle, Catherine E ^a   Sekowska, Magda ^a   Smith, George Davey ⁱ   Evans, David ⁱ   Gutierrez Arcelus, Maria ^e,f   Price, Alkes ^c,j   Raj, Towfique ^b,c,k   Nisbett, James ^a   Nica, Alexandra C ^a,e,f   Beazley, Claude ^a   Durbin, Richard ^a   Deloukas, Panos ^a   Dermitzakis, Emmanouil T ^a,e,f  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^b BRIGHAM AND WOMEN S HOSPITAL   (United States)

^c MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^d HARVARD MEDICAL SCHOOL   (United States)

^e UNIVERSITY OF GENEVA MEDICAL SCHOOL   (Switzerland)

^f Institute of Genetics and Genomics in Geneva (iGE3)   (Switzerland)

^g UNIVERSITY OF OXFORD   (United Kingdom)

^h MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY   (Germany)

ⁱ UNIVERSITY OF BRISTOL   (United Kingdom)

^j HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^k MASSACHUSETTS GENERAL HOSPITAL   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

CIS ACTING ELEMENT;

ARTICLE; GENE EXPRESSION REGULATION; GENE FREQUENCY; GENETIC ASSOCIATION; GENETIC DISTANCE; GENETIC VARIABILITY; GENOTYPE; HUMAN; HUMAN CELL; LYMPHOBLASTOID CELL LINE; PHENOTYPE; POPULATION DIFFERENTIATION; POPULATION GENETICS; QUANTITATIVE TRAIT LOCUS; SINGLE NUCLEOTIDE POLYMORPHISM; TRANSCRIPTION INITIATION SITE; ASIAN; CAUCASIAN; CELL LINE; GENETICS; HAPLOTYPE MAP; HUMAN GENOME; NEGRO; REGULATORY SEQUENCE;

AFRICAN CONTINENTAL ANCESTRY GROUP; ASIAN CONTINENTAL ANCESTRY GROUP; CELL LINE; EUROPEAN CONTINENTAL ANCESTRY GROUP; GENE EXPRESSION REGULATION; GENETICS, POPULATION; GENOME, HUMAN; HAPMAP PROJECT; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI; REGULATORY SEQUENCES, NUCLEIC ACID; TRANSCRIPTION INITIATION SITE;

EID: 84860596557     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1002639     Document Type: Article

References (37)

1. Bustamante CD, Fledel-Alon A, Williamson S, Nielsen R, Hubisz MT, et al. (2005) Natural selection on protein-coding genes in the human genome. Nature 437: 1153-1157.
2. Boyko AR, Williamson SH, Indap AR, Degenhardt JD, Hernandez RD, et al. (2008) Assessing the evolutionary impact of amino acid mutations in the human genome. PLoS Genet 4: e1000083 doi:10.1371/journal.pgen.1000083.
3. Kudaravalli S, Veyrieras JB, Stranger BE, Dermitzakis ET, Pritchard JK, (2009) Gene expression levels are a target of recent natural selection in the human genome. Mol Biol Evol 26: 649-658.
4. Torgerson DG, Boyko AR, Hernandez RD, Indap A, Hu X, et al. (2009) Evolutionary processes acting on candidate cis-regulatory regions in humans inferred from patterns of polymorphism and divergence. PLoS Genet 5: e1000592 doi:10.1371/journal.pgen.1000592.
5. Nica AC, Montgomery SB, Dimas AS, Stranger BE, Beazley C, et al. (2010) Candidate causal regulatory effects by integration of expression QTLs with complex trait genetic associations. PLoS Genet 6: e1000895 doi:10.1371/journal.pgen.1000895.
6. Nicolae DL, Gamazon E, Zhang W, Duan S, Dolan ME, et al. (2010) Trait-associated SNPs are more likely to be eQTLs: annotation to enhance discovery from GWAS. PLoS Genet 6: e1000888 doi:10.1371/journal.pgen.1000888.
7. Gamazon ER, Nicolae DL, Cox NJ, (2011) A study of CNVs as trait-associated polymorphisms and as expression quantitative trait loci. PLoS Genet 7: e1001292 doi:10.1371/journal.pgen.1001292.
8. King MC, Wilson AC, (1975) Evolution at two levels in humans and chimpanzees. Science 188: 107-116.
9. Blekhman R, Marioni JC, Zumbo P, Stephens M, Gilad Y, (2010) Sex-specific and lineage-specific alternative splicing in primates. Genome Res 20: 180-189.
10. Blekhman R, Oshlack A, Gilad Y, (2009) Segmental duplications contribute to gene expression differences between humans and chimpanzees. Genetics 182: 627-630.
11. Cheung VG, Spielman RS, Ewens KG, Weber TM, Morley M, et al. (2005) Mapping determinants of human gene expression by regional and genome-wide association. Nature 437: 1365-1369.
12. Morley M, Molony CM, Weber TM, Devlin JL, Ewens KG, et al. (2004) Genetic analysis of genome-wide variation in human gene expression. Nature 430: 743-747.
13. Stranger BE, Forrest MS, Clark AG, Minichiello MJ, Deutsch S, et al. (2005) Genome-wide associations of gene expression variation in humans. PLoS Genet 1: e78 doi:10.1371/journal.pgen.0010078.
14. Stranger BE, Forrest MS, Dunning M, Ingle CE, Beazley C, et al. (2007) Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science 315: 848-853.
15. Stranger BE, Nica AC, Forrest MS, Dimas A, Bird CP, et al. (2007) Population genomics of human gene expression. Nat Genet 39: 1217-1224.
16. Emilsson V, Thorleifsson G, Zhang B, Leonardson AS, Zink F, et al. (2008) Genetics of gene expression and its effect on disease. Nature 452: 423-428.
17. Grundberg E, Kwan T, Ge B, Lam KC, Koka V, et al. (2009) Population genomics in a disease targeted primary cell model. Genome Res 19: 1942-1952.
18. Myers AJ, Gibbs JR, Webster JA, Rohrer K, Zhao A, et al. (2007) A survey of genetic human cortical gene expression. Nat Genet 39: 1494-1499.
19. Dimas AS, Deutsch S, Stranger BE, Montgomery SB, Borel C, et al. (2009) Common regulatory variation impacts gene expression in a cell type-dependent manner. Science 325: 1246-1250.
20. Kwan T, Grundberg E, Koka V, Ge B, Lam KC, et al. (2009) Tissue effect on genetic control of transcript isoform variation. PLoS Genet 5: e1000608 doi:10.1371/journal.pgen.1000608.
21. Spielman RS, Bastone LA, Burdick JT, Morley M, Ewens WJ, et al. (2007) Common genetic variants account for differences in gene expression among ethnic groups. Nat Genet 39: 226-231.
22. Kuhn K, Baker SC, Chudin E, Lieu MH, Oeser S, et al. (2004) A novel, high-performance random array platform for quantitative gene expression profiling. Genome Res 14: 2347-2356.
23. Bolstad BM, Irizarry RA, Astrand M, Speed TP, (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19: 185-193.
24. Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, et al. (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 38: 904-909.
25. Pemberton TJ, Wang C, Li JZ, Rosenberg NA, (2010) Inference of unexpected genetic relatedness among individuals in HapMap Phase III. Am J Hum Genet 87: 457-464.
26. Stegle O, Kannan A, Durbin R, Winn J, (2008) Accounting for Non-genetic Factors Improves the Power of eQTL Studies. In: Vingron M, Wong L, editors. pp. 411-422 Research in Computational Molecular Biology: Springer Berlin/ Heidelberg.
27. Stegle O, Parts L, Durbin R, Winn J, (2010) A Bayesian framework to account for complex non-genetic factors in gene expression levels greatly increases power in eQTL studies. PLoS Comput Biol 6: e1000770 doi:10.1371/journal.pcbi.1000770.
28. Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, et al. (2006) Global variation in copy number in the human genome. Nature 444: 444-454.
29. Montgomery SB, Sammeth M, Gutierrez-Arcelus M, Lach RP, Ingle C, et al. (2010) Transcriptome genetics using second generation sequencing in a Caucasian population. Nature 464: 773-777.
30. Churchill GA, Doerge RW, (1994) Empirical threshold values for quantitative trait mapping. Genetics 138: 963-971.
31. Spitz F, Gonzalez F, Peichel C, Vogt TF, Duboule D, et al. (2001) Large scale transgenic and cluster deletion analysis of the HoxD complex separate an ancestral regulatory module from evolutionary innovations. Genes Dev 15: 2209-2214.
32. Mackay TF, Stone EA, Ayroles JF, (2009) The genetics of quantitative traits: challenges and prospects. Nat Rev Genet 10: 565-577.
33. Stranger BE, Dermitzakis ET, (2006) From DNA to RNA to disease and back: the 'central dogma' of regulatory disease variation. Hum Genomics 2: 383-390.
34. Musunuru K, Strong A, Frank-Kamenetsky M, Lee NE, Ahfeldt T, et al. (2010) From noncoding variant to phenotype via SORT1 at the 1p13 cholesterol locus. Nature 466: 714-719.
35. Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, et al. (2009) Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci U S A 106: 9362-9367.
36. Hindorff LA, Junkins HA, Hall PN, Mehta JP, Manolio TA, A Catalog of Published Genome-Wide Association Studies.
37. Yang TP, Beazley C, Montgomery SB, Dimas AS, Gutierrez-Arcelus M, et al. (2010) Genevar: a database and Java application for the analysis and visualization of SNP-gene associations in eQTL studies. Bioinformatics 26: 2474-2476.