Mapping the genetic architecture of gene regulation in whole blood

PLoS ONE

Volumn 9, Issue 4, 2014, Pages

  Schramm, Katharina ^a,b   Marzi, Carola ^a,c   Schurmann, Claudia ^d   Carstensen, Maren ^e,f   Reinmaa, Eva ^g,h   Biffar, Reiner ^d   Eckstein, Gertrud ^a   Gieger, Christian ^a   Grabe, Hans Jörgen ^d   Homuth, Georg ^d   Kastenmüller, Gabriele ^a   Mägi, Reedik ^h   Metspalu, Andres ^g,h   Mihailov, Evelin ^h   Peters, Annette ^b   Petersmann, Astrid ⁱ   Roden, Michael ^e,f,j   Strauch, Konstantin ^a,k   Suhre, Karsten ^a,l   Teumer, Alexander ^d   Völker, Uwe ^d   Völzke, Henry ^d   Wang Sattler, Rui ^a   Waldenberger, Melanie ^a   Meitinger, Thomas ^a,b,m   Illig, Thomas ⁿ   Herder, Christian ^e,f   Grallert, Harald ^a,c   Prokisch, Holger ^a,b   more..

^a INSTITUTE OF EPIDEMIOLOGY   (Germany)

^b TECHNICAL UNIVERSITY OF MUNICH   (Germany)

^c GERMAN CENTER FOR DIABETES RESEARCH DZD   (Germany)

^d UNIVERSITY MEDICINE GREIFSWALD   (Germany)

^e HEINRICH HEINE UNIVERSITY   (Germany)

^f LEIBNIZ CENTER FOR DIABETES RESEARCH AT HEINRICH HEINE UNIVERSITY DÜSSELDORF   (Germany)

^g UNIVERSITY OF TARTU   (Estonia)

^h UNIVERSITY OF TARTU   (Estonia)

ⁱ Institute of Clinical Chemistry and Laboratory Medicine   (Germany)

^j UNIVERSITY HOSPITAL DÜSSELDORF   (Germany)

^k UNIVERSITY OF MUNICH   (Germany)

^l WEILL CORNELL MEDICAL COLLEGE   (Qatar)

^m Munich Heart Alliance   (Germany)

ⁿ HANNOVER MEDICAL SCHOOL   (Germany)

more..

Author keywords

[No Author keywords available]

Indexed keywords

HEMOGLOBIN BETA CHAIN; GENETIC MARKER;

ADULT; AGED; ARTICLE; BLOOD CELL; CELL SPECIFICITY; CHROMOSOME 11; CHROMOSOME 12; CHROMOSOME 13; CHROMOSOME 2; DISEASE PREDISPOSITION; DNA MODIFICATION; FEMALE; GENE EXPRESSION REGULATION; GENE INTERACTION; GENE LINKAGE DISEQUILIBRIUM; GENE LOCATION; HUMAN; HUMAN CELL; IMMUNE RESPONSE; MAJOR CLINICAL STUDY; MALE; QUANTITATIVE TRAIT LOCUS MAPPING; SINGLE NUCLEOTIDE POLYMORPHISM; TRANSCRIPTION INITIATION SITE; TRANSCRIPTION REGULATION; BLOOD; CHROMOSOME MAP; GENE REGULATORY NETWORK; GENETIC ASSOCIATION; GENETIC MARKER; METABOLISM; QUANTITATIVE TRAIT LOCUS; STATISTICAL MODEL;

BLOOD; CHROMOSOME MAPPING; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORKS; GENETIC ASSOCIATION STUDIES; GENETIC MARKERS; HUMANS; LINEAR MODELS; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI;

EID: 84899694686     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0093844     Document Type: Article

References (36)

1. Jones BL, Swallow DM (2011) The impact of cis-acting polymorphisms on the human phenotype. Hugo J 5: 13-23.
2. Fehrmann RS, Jansen RC, Veldink JH, Westra HJ, Arends D, et al. (2011) 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.
3. Sasayama D, Hori H, Nakamura S, Miyata R, Teraishi T, et al. (2013) Identification of single nucleotide polymorphisms regulating peripheral blood mRNA expression with genome-wide significance: an eQTL study in the Japanese population. PLoS One 8: e54967.
4. Mehta D, Heim K, Herder C, Carstensen M, Eckstein G, et al. (2013) Impact of common regulatory single-nucleotide variants on gene expression profiles in whole blood. Eur J Hum Genet 21: 48-54.
5. Menke A, Rex-Haffner M, Klengel T, Binder EB, Mehta D (2012) Peripheral blood gene expression: it all boils down to the RNA collection tubes. BMC Res Notes 5: 1.
6. Fairfax BP, Makino S, Radhakrishnan J, Plant K, Leslie S, et al. (2012) Genetics of gene expression in primary immune cells identifies cell type-specific master regulators and roles of HLA alleles. Nat Genet 44: 502-510.
7. Zeller T, Wild P, Szymczak S, Rotival M, Schillert A, et al. (2010) Genetics and beyond - the transcriptome of human monocytes and disease susceptibility. PLoS One 5: e10693.
8. Schadt EE, Molony C, Chudin E, Hao K, Yang X, et al. (2008) Mapping the genetic architecture of gene expression in human liver. PLoS Biol 6: e107.
9. Stranger BE, Nica AC, Forrest MS, Dimas A, Bird CP, et al. (2007) Population genomics of human gene expression. Nat Genet 39: 1217-1224. (Pubitemid 47482691)
10. Innocenti F, Cooper GM, Stanaway IB, Gamazon ER, Smith JD, et al. (2011) Identification, replication, and functional fine-mapping of expression quantitative trait loci in primary human liver tissue. PLoS Genet 7: e1002078.
11. Dixon AL, Liang L, Moffatt MF, Chen W, Heath S, et al. (2007) A genome-wide association study of global gene expression. Nat Genet 39: 1202-1207. (Pubitemid 47482680)
12. Hao K, Bosse Y, Nickle DC, Pare PD, Postma DS, et al. (2012) Lung eQTLs to help reveal the molecular underpinnings of asthma. PLoS Genet 8: e1003029.
13. Ding J, Gudjonsson JE, Liang L, Stuart PE, Li Y, et al. (2010) Gene expression in skin and lymphoblastoid cells: Refined statistical method reveals extensive overlap in cis-eQTL signals. Am J Hum Genet 87: 779-789.
14. Nica AC, Parts L, Glass D, Nisbet J, Barrett A, et al. (2011) The architecture of gene regulatory variation across multiple human tissues: the MuTHER study. PLoS Genet 7: e1002003.
15. Powell JE, Henders AK, McRae AF, Wright MJ, Martin NG, et al. (2012) Genetic control of gene expression in whole blood and lymphoblastoid cell lines is largely independent. Genome Res 22: 456-466.
16. 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.
17. Flutre T, Wen X, Pritchard J, Stephens M (2013) A statistical framework for joint eQTL analysis in multiple tissues. PLoS Genet 9: e1003486.
18. Simonis M, Klous P, Splinter E, Moshkin Y, Willemsen R, et al. (2006) Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat Genet 38: 1348-1354. (Pubitemid 44646300)
19. Schoenfelder S, Sexton T, Chakalova L, Cope NF, Horton A, et al. (2010) Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells. Nat Genet 42: 53-61.
20. Dastani Z, Hivert MF, Timpson N, Perry JR, Yuan X, et al. (2012) Novel loci for adiponectin levels and their influence on type 2 diabetes and metabolic traits: a multi-ethnic meta-analysis of 45,891 individuals. PLoS Genet 8: e1002607.
21. Simon-Sanchez J, Scholz S, Matarin Mdel M, Fung HC, Hernandez D, et al. (2008) Genomewide SNP assay reveals mutations underlying Parkinson disease. Hum Mutat 29: 315-322. (Pubitemid 351240605)
22. Gudbjartsson DF, Walters GB, Thorleifsson G, Stefansson H, Halldorsson BV, et al. (2008) Many sequence variants affecting diversity of adult human height. Nat Genet 40: 609-615. (Pubitemid 351601211)
23. Imboden M, Bouzigon E, Curjuric I, Ramasamy A, Kumar A, et al. (2012) Genome-wide association study of lung function decline in adults with and without asthma. J Allergy Clin Immunol 129: 1218-1228.
24. Turner ST, Schwartz GL, Chapman AB, Beitelshees AL, Gums JG, et al. (2010) Plasma renin activity predicts blood pressure responses to beta-blocker and thiazide diuretic as monotherapy and add-on therapy for hypertension. Am J Hypertens 23: 1014-1022.
25. Chambers JC, Zhang W, Lord GM, van der Harst P, Lawlor DA, et al. (2010) Genetic loci influencing kidney function and chronic kidney disease. Nat Genet 42: 373-375.
26. Wain LV, Verwoert GC, O'Reilly PF, Shi G, Johnson T, et al. (2011) Genomewide association study identifies six new loci influencing pulse pressure and mean arterial pressure. Nat Genet 43: 1005-1011.
27. Kottgen A, Pattaro C, Boger CA, Fuchsberger C, Olden M, et al. (2010) New loci associated with kidney function and chronic kidney disease. Nat Genet 42: 376-384.
28. Meisinger C, Prokisch H, Gieger C, Soranzo N, Mehta D, et al. (2009) A genome-wide association study identifies three loci associated with mean platelet volume. Am J Hum Genet 84: 66-71.
29. Soranzo N, Spector TD, Mangino M, Kuhnel B, Rendon A, et al. (2009) A genome-wide meta-analysis identifies 22 loci associated with eight hematological parameters in the HaemGen consortium. Nat Genet 41: 1182-1190.
30. Suhre K, Gieger C (2012) Genetic variation in metabolic phenotypes: study designs and applications. Nat Rev Genet 13: 759-769.
31. Illig T, Gieger C, Zhai G, Romisch-Margl W, Wang-Sattler R, et al. (2010) A genome-wide perspective of genetic variation in human metabolism. Nat Genet 42: 137-141.
32. Suhre K, Shin SY, Petersen AK, Mohney RP, Meredith D, et al. (2011) Human metabolic individuality in biomedical and pharmaceutical research. Nature 477: 54-60.
33. Rathmann W, Strassburger K, Heier M, Holle R, Thorand B, et al. (2009) Incidence of Type 2 diabetes in the elderly German population and the effect of clinical and lifestyle risk factors: KORA S4/F4 cohort study. Diabet Med 26: 1212-1219.
34. Holle R, Happich M, Lowel H, Wichmann HE, Group MKS (2005) KORA - a research platform for population based health research. Gesundheitswesen 67 Suppl 1: S19-25.
35. Volzke H, Alte D, Schmidt CO, Radke D, Lorbeer R, et al. (2011) Cohort profile: the study of health in Pomerania. Int J Epidemiol 40: 294-307.
36. Schurmann C, Heim K, Schillert A, Blankenberg S, Carstensen M, et al. (2012) Analyzing illumina gene expression microarray data from different tissues: methodological aspects of data analysis in the metaxpress consortium. PLoS One 7: e50938