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Genome-wide haplotype analysis of cis expression quantitative trait loci in monocytes

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Genome-wide haplotype analysis of cis expression quantitative trait loci in monocytes. / Garnier, Sophie; Truong, Vinh; Brocheton, Jessy; Zeller, Tanja; Rovital, Maxime; Wild, Philipp S; Ziegler, Andreas; Munzel, Thomas; Tiret, Laurence; Blankenberg, Stefan; Deloukas, Panos; Erdmann, Jeannette; Hengstenberg, Christian; Samani, Nilesh J; Schunkert, Heribert; Ouwehand, Willem H; Goodall, Alison H; Cambien, François; Trégouët, David-Alexandre; CardioGenics Consortium.

in: PLOS GENET, Jahrgang 9, Nr. 1, 2013, S. e1003240.

Publikationen: SCORING: Beitrag in Fachzeitschrift/Zeitung › SCORING: Zeitschriftenaufsatz › Forschung › Begutachtung

Harvard

Garnier, S, Truong, V, Brocheton, J, Zeller, T, Rovital, M, Wild, PS, Ziegler, A, Munzel, T, Tiret, L, Blankenberg, S, Deloukas, P, Erdmann, J, Hengstenberg, C, Samani, NJ, Schunkert, H, Ouwehand, WH, Goodall, AH, Cambien, F, Trégouët, D-A & CardioGenics Consortium 2013, 'Genome-wide haplotype analysis of cis expression quantitative trait loci in monocytes', PLOS GENET, Jg. 9, Nr. 1, S. e1003240. https://doi.org/10.1371/journal.pgen.1003240

APA

Garnier, S., Truong, V., Brocheton, J., Zeller, T., Rovital, M., Wild, P. S., Ziegler, A., Munzel, T., Tiret, L., Blankenberg, S., Deloukas, P., Erdmann, J., Hengstenberg, C., Samani, N. J., Schunkert, H., Ouwehand, W. H., Goodall, A. H., Cambien, F., Trégouët, D-A., & CardioGenics Consortium (2013). Genome-wide haplotype analysis of cis expression quantitative trait loci in monocytes. PLOS GENET, 9(1), e1003240. https://doi.org/10.1371/journal.pgen.1003240

Vancouver

Garnier S, Truong V, Brocheton J, Zeller T, Rovital M, Wild PS et al. Genome-wide haplotype analysis of cis expression quantitative trait loci in monocytes. PLOS GENET. 2013;9(1):e1003240. https://doi.org/10.1371/journal.pgen.1003240

Bibtex

@article{53b2250def9b405dbc6f1fd0f10a5595,
title = "Genome-wide haplotype analysis of cis expression quantitative trait loci in monocytes",
abstract = "In order to assess whether gene expression variability could be influenced by several SNPs acting in cis, either through additive or more complex haplotype effects, a systematic genome-wide search for cis haplotype expression quantitative trait loci (eQTL) was conducted in a sample of 758 individuals, part of the Cardiogenics Transcriptomic Study, for which genome-wide monocyte expression and GWAS data were available. 19,805 RNA probes were assessed for cis haplotypic regulation through investigation of ~2,1 × 10(9) haplotypic combinations. 2,650 probes demonstrated haplotypic p-values >10(4)-fold smaller than the best single SNP p-value. Replication of significant haplotype effects were tested for 412 probes for which SNPs (or proxies) that defined the detected haplotypes were available in the Gutenberg Health Study composed of 1,374 individuals. At the Bonferroni correction level of 1.2 × 10(-4) (~0.05/412), 193 haplotypic signals replicated. 1000 G imputation was then conducted, and 105 haplotypic signals still remained more informative than imputed SNPs. In-depth analysis of these 105 cis eQTL revealed that at 76 loci genetic associations were compatible with additive effects of several SNPs, while for the 29 remaining regions data could be compatible with a more complex haplotypic pattern. As 24 of the 105 cis eQTL have previously been reported to be disease-associated loci, this work highlights the need for conducting haplotype-based and 1000 G imputed cis eQTL analysis before commencing functional studies at disease-associated loci.",
keywords = "Gene Expression Regulation, Genetic Predisposition to Disease, Genome-Wide Association Study, Haplotypes/genetics, Humans, Monocytes, Polymorphism, Single Nucleotide/genetics, Quantitative Trait Loci/genetics, Regulatory Sequences, Nucleic Acid",
author = "Sophie Garnier and Vinh Truong and Jessy Brocheton and Tanja Zeller and Maxime Rovital and Wild, {Philipp S} and Andreas Ziegler and Thomas Munzel and Laurence Tiret and Stefan Blankenberg and Panos Deloukas and Jeannette Erdmann and Christian Hengstenberg and Samani, {Nilesh J} and Heribert Schunkert and Ouwehand, {Willem H} and Goodall, {Alison H} and Fran{\c c}ois Cambien and David-Alexandre Tr{\'e}gou{\"e}t and {CardioGenics Consortium}",
year = "2013",
doi = "10.1371/journal.pgen.1003240",
language = "English",
volume = "9",
pages = "e1003240",
journal = "PLOS GENET",
issn = "1553-7404",
publisher = "Public Library of Science",
number = "1",

}

RIS

TY - JOUR

T1 - Genome-wide haplotype analysis of cis expression quantitative trait loci in monocytes

AU - Garnier, Sophie

AU - Truong, Vinh

AU - Brocheton, Jessy

AU - Zeller, Tanja

AU - Rovital, Maxime

AU - Wild, Philipp S

AU - Ziegler, Andreas

AU - Munzel, Thomas

AU - Tiret, Laurence

AU - Blankenberg, Stefan

AU - Deloukas, Panos

AU - Erdmann, Jeannette

AU - Hengstenberg, Christian

AU - Samani, Nilesh J

AU - Schunkert, Heribert

AU - Ouwehand, Willem H

AU - Goodall, Alison H

AU - Cambien, François

AU - Trégouët, David-Alexandre

AU - CardioGenics Consortium

PY - 2013

Y1 - 2013

N2 - In order to assess whether gene expression variability could be influenced by several SNPs acting in cis, either through additive or more complex haplotype effects, a systematic genome-wide search for cis haplotype expression quantitative trait loci (eQTL) was conducted in a sample of 758 individuals, part of the Cardiogenics Transcriptomic Study, for which genome-wide monocyte expression and GWAS data were available. 19,805 RNA probes were assessed for cis haplotypic regulation through investigation of ~2,1 × 10(9) haplotypic combinations. 2,650 probes demonstrated haplotypic p-values >10(4)-fold smaller than the best single SNP p-value. Replication of significant haplotype effects were tested for 412 probes for which SNPs (or proxies) that defined the detected haplotypes were available in the Gutenberg Health Study composed of 1,374 individuals. At the Bonferroni correction level of 1.2 × 10(-4) (~0.05/412), 193 haplotypic signals replicated. 1000 G imputation was then conducted, and 105 haplotypic signals still remained more informative than imputed SNPs. In-depth analysis of these 105 cis eQTL revealed that at 76 loci genetic associations were compatible with additive effects of several SNPs, while for the 29 remaining regions data could be compatible with a more complex haplotypic pattern. As 24 of the 105 cis eQTL have previously been reported to be disease-associated loci, this work highlights the need for conducting haplotype-based and 1000 G imputed cis eQTL analysis before commencing functional studies at disease-associated loci.

AB - In order to assess whether gene expression variability could be influenced by several SNPs acting in cis, either through additive or more complex haplotype effects, a systematic genome-wide search for cis haplotype expression quantitative trait loci (eQTL) was conducted in a sample of 758 individuals, part of the Cardiogenics Transcriptomic Study, for which genome-wide monocyte expression and GWAS data were available. 19,805 RNA probes were assessed for cis haplotypic regulation through investigation of ~2,1 × 10(9) haplotypic combinations. 2,650 probes demonstrated haplotypic p-values >10(4)-fold smaller than the best single SNP p-value. Replication of significant haplotype effects were tested for 412 probes for which SNPs (or proxies) that defined the detected haplotypes were available in the Gutenberg Health Study composed of 1,374 individuals. At the Bonferroni correction level of 1.2 × 10(-4) (~0.05/412), 193 haplotypic signals replicated. 1000 G imputation was then conducted, and 105 haplotypic signals still remained more informative than imputed SNPs. In-depth analysis of these 105 cis eQTL revealed that at 76 loci genetic associations were compatible with additive effects of several SNPs, while for the 29 remaining regions data could be compatible with a more complex haplotypic pattern. As 24 of the 105 cis eQTL have previously been reported to be disease-associated loci, this work highlights the need for conducting haplotype-based and 1000 G imputed cis eQTL analysis before commencing functional studies at disease-associated loci.

KW - Gene Expression Regulation

KW - Genetic Predisposition to Disease

KW - Genome-Wide Association Study

KW - Haplotypes/genetics

KW - Humans

KW - Monocytes

KW - Polymorphism, Single Nucleotide/genetics

KW - Quantitative Trait Loci/genetics

KW - Regulatory Sequences, Nucleic Acid

U2 - 10.1371/journal.pgen.1003240

DO - 10.1371/journal.pgen.1003240

M3 - SCORING: Journal article

C2 - 23382694

VL - 9

SP - e1003240

JO - PLOS GENET

JF - PLOS GENET

SN - 1553-7404

IS - 1

ER -