Relationship between CAD risk genotype in the chromosome 9p21 locus and gene expression. Identification of eight new ANRIL splice variants.
<h4>Background</h4>Several genome-wide association studies have recently linked a group of single nucleotide polymorphisms in the 9p21 region with cardiovascular disease. The molecular mechanisms of this link are not fully understood. We investigated five different expression microarray...
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2009
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oai:doaj.org-article:4e6a32a404894831a2dc98e5e9b686a02021-11-25T06:28:23ZRelationship between CAD risk genotype in the chromosome 9p21 locus and gene expression. Identification of eight new ANRIL splice variants.1932-620310.1371/journal.pone.0007677https://doaj.org/article/4e6a32a404894831a2dc98e5e9b686a02009-11-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/19888323/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>Several genome-wide association studies have recently linked a group of single nucleotide polymorphisms in the 9p21 region with cardiovascular disease. The molecular mechanisms of this link are not fully understood. We investigated five different expression microarray datasets in order to determine if the genotype had effect on expression of any gene transcript in aorta, mammary artery, carotid plaque and lymphoblastoid cells.<h4>Methodology/principal findings</h4>After multiple testing correction, no genes were found to have relation to the rs2891168 risk genotype, either on a genome-wide scale or on a regional (8 MB) scale. The neighbouring ANRIL gene was found to have eight novel transcript variants not previously known from literature and these varied by tissue type. We therefore performed a detailed probe-level analysis and found small stretches of significant relation to genotype but no consistent associations. In all investigated tissues we found an inverse correlation between ANRIL and the MTAP gene and a positive correlation between ANRIL and CDKN2A and CDKN2B.<h4>Conclusions/significance</h4>Investigation of relation of the risk genotype to gene expression is complicated by the transcript complexity of the locus. With our investigation of a range of relevant tissue we wish to underscore the need for careful attention to the complexity of the alternative splicing issues in the region and its implications to the design of future gene expression studies.Lasse FolkersenTheodosios KyriakouAnuj GoelJohn PedenAnders MälarstigGabrielle Paulsson-BerneAnders HamstenHugh WatkinsAnders Franco-CerecedaAnders GabrielsenPer ErikssonPROCARDIS consortiaPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 4, Iss 11, p e7677 (2009) |
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Medicine R Science Q |
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Medicine R Science Q Lasse Folkersen Theodosios Kyriakou Anuj Goel John Peden Anders Mälarstig Gabrielle Paulsson-Berne Anders Hamsten Hugh Watkins Anders Franco-Cereceda Anders Gabrielsen Per Eriksson PROCARDIS consortia Relationship between CAD risk genotype in the chromosome 9p21 locus and gene expression. Identification of eight new ANRIL splice variants. |
| description |
<h4>Background</h4>Several genome-wide association studies have recently linked a group of single nucleotide polymorphisms in the 9p21 region with cardiovascular disease. The molecular mechanisms of this link are not fully understood. We investigated five different expression microarray datasets in order to determine if the genotype had effect on expression of any gene transcript in aorta, mammary artery, carotid plaque and lymphoblastoid cells.<h4>Methodology/principal findings</h4>After multiple testing correction, no genes were found to have relation to the rs2891168 risk genotype, either on a genome-wide scale or on a regional (8 MB) scale. The neighbouring ANRIL gene was found to have eight novel transcript variants not previously known from literature and these varied by tissue type. We therefore performed a detailed probe-level analysis and found small stretches of significant relation to genotype but no consistent associations. In all investigated tissues we found an inverse correlation between ANRIL and the MTAP gene and a positive correlation between ANRIL and CDKN2A and CDKN2B.<h4>Conclusions/significance</h4>Investigation of relation of the risk genotype to gene expression is complicated by the transcript complexity of the locus. With our investigation of a range of relevant tissue we wish to underscore the need for careful attention to the complexity of the alternative splicing issues in the region and its implications to the design of future gene expression studies. |
| format |
article |
| author |
Lasse Folkersen Theodosios Kyriakou Anuj Goel John Peden Anders Mälarstig Gabrielle Paulsson-Berne Anders Hamsten Hugh Watkins Anders Franco-Cereceda Anders Gabrielsen Per Eriksson PROCARDIS consortia |
| author_facet |
Lasse Folkersen Theodosios Kyriakou Anuj Goel John Peden Anders Mälarstig Gabrielle Paulsson-Berne Anders Hamsten Hugh Watkins Anders Franco-Cereceda Anders Gabrielsen Per Eriksson PROCARDIS consortia |
| author_sort |
Lasse Folkersen |
| title |
Relationship between CAD risk genotype in the chromosome 9p21 locus and gene expression. Identification of eight new ANRIL splice variants. |
| title_short |
Relationship between CAD risk genotype in the chromosome 9p21 locus and gene expression. Identification of eight new ANRIL splice variants. |
| title_full |
Relationship between CAD risk genotype in the chromosome 9p21 locus and gene expression. Identification of eight new ANRIL splice variants. |
| title_fullStr |
Relationship between CAD risk genotype in the chromosome 9p21 locus and gene expression. Identification of eight new ANRIL splice variants. |
| title_full_unstemmed |
Relationship between CAD risk genotype in the chromosome 9p21 locus and gene expression. Identification of eight new ANRIL splice variants. |
| title_sort |
relationship between cad risk genotype in the chromosome 9p21 locus and gene expression. identification of eight new anril splice variants. |
| publisher |
Public Library of Science (PLoS) |
| publishDate |
2009 |
| url |
https://doaj.org/article/4e6a32a404894831a2dc98e5e9b686a0 |
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