The Brisbane Systems Genetics Study: genetical genomics meets complex trait genetics.

There is growing evidence that genetic risk factors for common disease are caused by hereditary changes of gene regulation acting in complex pathways. Clearly understanding the molecular genetic relationships between genetic control of gene expression and its effect on complex diseases is essential....

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Autores principales: Joseph E Powell, Anjali K Henders, Allan F McRae, Anthony Caracella, Sara Smith, Margaret J Wright, John B Whitfield, Emmanouil T Dermitzakis, Nicholas G Martin, Peter M Visscher, Grant W Montgomery
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Publicado: Public Library of Science (PLoS) 2012
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spelling oai:doaj.org-article:d1b75fe252724fe98f4681497c3ce6762021-11-18T07:20:49ZThe Brisbane Systems Genetics Study: genetical genomics meets complex trait genetics.1932-620310.1371/journal.pone.0035430https://doaj.org/article/d1b75fe252724fe98f4681497c3ce6762012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22563384/?tool=EBIhttps://doaj.org/toc/1932-6203There is growing evidence that genetic risk factors for common disease are caused by hereditary changes of gene regulation acting in complex pathways. Clearly understanding the molecular genetic relationships between genetic control of gene expression and its effect on complex diseases is essential. Here we describe the Brisbane Systems Genetics Study (BSGS), a family-based study that will be used to elucidate the genetic factors affecting gene expression and the role of gene regulation in mediating endophenotypes and complex diseases.BSGS comprises of a total of 962 individuals from 314 families, for which we have high-density genotype, gene expression and phenotypic data. Families consist of combinations of both monozygotic and dizygotic twin pairs, their siblings, and, for 72 families, both parents. A significant advantage of the inclusion of parents is improved power to disentangle environmental, additive genetic and non-additive genetic effects of gene expression and measured phenotypes. Furthermore, it allows for the estimation of parent-of-origin effects, something that has not previously been systematically investigated in human genetical genomics studies. Measured phenotypes available within the BSGS include blood phenotypes and biochemical traits measured from components of the tissue sample in which transcription levels are determined, providing an ideal test case for systems genetics approaches.We report results from an expression quantitative trait loci (eQTL) analysis using 862 individuals from BSGS to test for associations between expression levels of 17,926 probes and 528,509 SNP genotypes. At a study wide significance level approximately 15,000 associations were observed between expression levels and SNP genotypes. These associations corresponded to a total of 2,081 expression quantitative trait loci (eQTL) involving 1,503 probes. The majority of identified eQTL (87%) were located within cis-regions.Joseph E PowellAnjali K HendersAllan F McRaeAnthony CaracellaSara SmithMargaret J WrightJohn B WhitfieldEmmanouil T DermitzakisNicholas G MartinPeter M VisscherGrant W MontgomeryPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 4, p e35430 (2012)
institution DOAJ
collection DOAJ
language EN
topic Medicine
R
Science
Q
spellingShingle Medicine
R
Science
Q
Joseph E Powell
Anjali K Henders
Allan F McRae
Anthony Caracella
Sara Smith
Margaret J Wright
John B Whitfield
Emmanouil T Dermitzakis
Nicholas G Martin
Peter M Visscher
Grant W Montgomery
The Brisbane Systems Genetics Study: genetical genomics meets complex trait genetics.
description There is growing evidence that genetic risk factors for common disease are caused by hereditary changes of gene regulation acting in complex pathways. Clearly understanding the molecular genetic relationships between genetic control of gene expression and its effect on complex diseases is essential. Here we describe the Brisbane Systems Genetics Study (BSGS), a family-based study that will be used to elucidate the genetic factors affecting gene expression and the role of gene regulation in mediating endophenotypes and complex diseases.BSGS comprises of a total of 962 individuals from 314 families, for which we have high-density genotype, gene expression and phenotypic data. Families consist of combinations of both monozygotic and dizygotic twin pairs, their siblings, and, for 72 families, both parents. A significant advantage of the inclusion of parents is improved power to disentangle environmental, additive genetic and non-additive genetic effects of gene expression and measured phenotypes. Furthermore, it allows for the estimation of parent-of-origin effects, something that has not previously been systematically investigated in human genetical genomics studies. Measured phenotypes available within the BSGS include blood phenotypes and biochemical traits measured from components of the tissue sample in which transcription levels are determined, providing an ideal test case for systems genetics approaches.We report results from an expression quantitative trait loci (eQTL) analysis using 862 individuals from BSGS to test for associations between expression levels of 17,926 probes and 528,509 SNP genotypes. At a study wide significance level approximately 15,000 associations were observed between expression levels and SNP genotypes. These associations corresponded to a total of 2,081 expression quantitative trait loci (eQTL) involving 1,503 probes. The majority of identified eQTL (87%) were located within cis-regions.
format article
author Joseph E Powell
Anjali K Henders
Allan F McRae
Anthony Caracella
Sara Smith
Margaret J Wright
John B Whitfield
Emmanouil T Dermitzakis
Nicholas G Martin
Peter M Visscher
Grant W Montgomery
author_facet Joseph E Powell
Anjali K Henders
Allan F McRae
Anthony Caracella
Sara Smith
Margaret J Wright
John B Whitfield
Emmanouil T Dermitzakis
Nicholas G Martin
Peter M Visscher
Grant W Montgomery
author_sort Joseph E Powell
title The Brisbane Systems Genetics Study: genetical genomics meets complex trait genetics.
title_short The Brisbane Systems Genetics Study: genetical genomics meets complex trait genetics.
title_full The Brisbane Systems Genetics Study: genetical genomics meets complex trait genetics.
title_fullStr The Brisbane Systems Genetics Study: genetical genomics meets complex trait genetics.
title_full_unstemmed The Brisbane Systems Genetics Study: genetical genomics meets complex trait genetics.
title_sort brisbane systems genetics study: genetical genomics meets complex trait genetics.
publisher Public Library of Science (PLoS)
publishDate 2012
url https://doaj.org/article/d1b75fe252724fe98f4681497c3ce676
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