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Mapping the genetic architecture of gene expression in human liver

Schadt, EE and Molony, C and Chudin, E and Hao, K and Yang, X and Lum, PY and Kasarskis, A and Zhang, B and Wang, S and Suver, C and Zhu, J and Millstein, J and Sieberts, S and Lamb, J and GuhaThakurta, D and Derry, J and Storey, JD and Avila-Campillo, I and Kruger, MJ and Johnson, JM and Rohl, CA and Van Nas, A and Mehrabian, M and Drake, TA and Lusis, AJ and Smith, RC and Guengerich, FP and Strom, SC and Schuetz, E and Rushmore, TH and Ulrich, R (2008) Mapping the genetic architecture of gene expression in human liver. PLoS Biology, 6 (5). 1020 - 1032. ISSN 1544-9173

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Genetic variants that are associated with common human diseases do not lead directly to disease, but instead act on intermediate, molecular phenotypes that in turn induce changes in higher-order disease traits. Therefore, identifying the molecular phenotypes that vary in response to changes in DNA and that also associate with changes in disease traits has the potential to provide the functional information required to not only identify and validate the susceptibility genes that are directly affected by changes in DNA, but also to understand the molecular networks in which such genes operate and how changes in these networks lead to changes in disease traits. Toward that end, we profiled more than 39,000 transcripts and we genotyped 782,476 unique single nucleotide polymorphisms (SNPs) in more than 400 human liver samples to characterize the genetic architecture of gene expression in the human liver, a metabolically active tissue that is important in a number of common human diseases, including obesity, diabetes, and atherosclerosis. This genome-wide association study of gene expression resulted in the detection of more than 6,000 associations between SNP genotypes and liver gene expression traits, where many of the corresponding genes identified have already been implicated in a number of human diseases. The utility of these data for elucidating the causes of common human diseases is demonstrated by integrating them with genotypic and expression data from other human and mouse populations. This provides much-needed functional support for the candidate susceptibility genes being identified at a growing number of genetic loci that have been identified as key drivers of disease from genome-wide association studies of disease. By using an integrative genomics approach, we highlight how the gene RPS26 and not ERBB3 is supported by our data as the most likely susceptibility gene for a novel type 1 diabetes locus recently identified in a large-scale, genome-wide association study. We also identify SORT1 and CELSR2 as candidate susceptibility genes for a locus recently associated with coronary artery disease and plasma low-density lipoprotein cholesterol levels in the process. © 2008 Schadt et al.


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Item Type: Article
Status: Published
CreatorsEmailPitt UsernameORCID
Schadt, EE
Molony, C
Chudin, E
Hao, K
Yang, X
Lum, PY
Kasarskis, A
Zhang, B
Wang, S
Suver, C
Zhu, J
Millstein, J
Sieberts, S
Lamb, J
GuhaThakurta, D
Derry, J
Storey, JD
Avila-Campillo, I
Kruger, MJ
Johnson, JM
Rohl, CA
Van Nas, A
Mehrabian, M
Drake, TA
Lusis, AJ
Smith, RC
Guengerich, FP
Strom, SCstrom@pitt.eduSTROM
Schuetz, E
Rushmore, TH
Ulrich, R
ContributionContributors NameEmailPitt UsernameORCID
Date: 1 May 2008
Date Type: Publication
Journal or Publication Title: PLoS Biology
Volume: 6
Number: 5
Page Range: 1020 - 1032
DOI or Unique Handle: 10.1371/journal.pbio.0060107
Refereed: Yes
ISSN: 1544-9173
PubMed ID: 18462017
Date Deposited: 18 Jul 2012 20:35
Last Modified: 02 Feb 2019 16:58


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