Detecting differential allelic expression using high-resolution melting curve analysis: application to the breast cancer susceptibility gene CHEK2
<p>Abstract</p> <p>Background</p> <p>The gene <it>CHEK2 </it>encodes a checkpoint kinase playing a key role in the DNA damage pathway. Though <it>CHEK2 </it>has been identified as an intermediate breast cancer susceptibility gene, only a small pr...
| Main Authors: | , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2011-05-01
|
| Series: | BMC Medical Genomics |
| Online Access: | http://www.biomedcentral.com/1755-8794/4/39 |
| _version_ | 1818902437133549568 |
|---|---|
| author | Sinilnikova Olga McKay-Chopin Sandrine Forey Nathalie Michelon Jocelyne Jordheim Lars P Nguyen-Dumont Tú Le Calvez-Kelm Florence Southey Melissa C Tavtigian Sean V Lesueur Fabienne |
| author_facet | Sinilnikova Olga McKay-Chopin Sandrine Forey Nathalie Michelon Jocelyne Jordheim Lars P Nguyen-Dumont Tú Le Calvez-Kelm Florence Southey Melissa C Tavtigian Sean V Lesueur Fabienne |
| author_sort | Sinilnikova Olga |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>The gene <it>CHEK2 </it>encodes a checkpoint kinase playing a key role in the DNA damage pathway. Though <it>CHEK2 </it>has been identified as an intermediate breast cancer susceptibility gene, only a small proportion of high-risk families have been explained by genetic variants located in its coding region. Alteration in gene expression regulation provides a potential mechanism for generating disease susceptibility. The detection of differential allelic expression (DAE) represents a sensitive assay to direct the search for a functional sequence variant within the transcriptional regulatory elements of a candidate gene. We aimed to assess whether <it>CHEK2 </it>was subject to DAE in lymphoblastoid cell lines (LCLs) from high-risk breast cancer patients for whom no mutation in <it>BRCA1</it> or <it>BRCA2</it> had been identified.</p> <p>Methods</p> <p>We implemented an assay based on high-resolution melting (HRM) curve analysis and developed an analysis tool for DAE assessment.</p> <p>Results</p> <p>We observed allelic expression imbalance in 4 of the 41 LCLs examined. All four were carriers of the truncating mutation 1100delC. We confirmed previous findings that this mutation induces non-sense mediated mRNA decay. In our series, we ruled out the possibility of a functional sequence variant located in the promoter region or in a regulatory element of <it>CHEK2 </it>that would lead to DAE in the transcriptional regulatory milieu of freely proliferating LCLs.</p> <p>Conclusions</p> <p>Our results support that HRM is a sensitive and accurate method for DAE assessment. This approach would be of great interest for high-throughput mutation screening projects aiming to identify genes carrying functional regulatory polymorphisms.</p> |
| first_indexed | 2024-12-19T20:35:38Z |
| format | Article |
| id | doaj.art-3eff200091044fa2a7177354845cac22 |
| institution | Directory Open Access Journal |
| issn | 1755-8794 |
| language | English |
| last_indexed | 2024-12-19T20:35:38Z |
| publishDate | 2011-05-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Medical Genomics |
| spelling | doaj.art-3eff200091044fa2a7177354845cac222022-12-21T20:06:33ZengBMCBMC Medical Genomics1755-87942011-05-01413910.1186/1755-8794-4-39Detecting differential allelic expression using high-resolution melting curve analysis: application to the breast cancer susceptibility gene CHEK2Sinilnikova OlgaMcKay-Chopin SandrineForey NathalieMichelon JocelyneJordheim Lars PNguyen-Dumont TúLe Calvez-Kelm FlorenceSouthey Melissa CTavtigian Sean VLesueur Fabienne<p>Abstract</p> <p>Background</p> <p>The gene <it>CHEK2 </it>encodes a checkpoint kinase playing a key role in the DNA damage pathway. Though <it>CHEK2 </it>has been identified as an intermediate breast cancer susceptibility gene, only a small proportion of high-risk families have been explained by genetic variants located in its coding region. Alteration in gene expression regulation provides a potential mechanism for generating disease susceptibility. The detection of differential allelic expression (DAE) represents a sensitive assay to direct the search for a functional sequence variant within the transcriptional regulatory elements of a candidate gene. We aimed to assess whether <it>CHEK2 </it>was subject to DAE in lymphoblastoid cell lines (LCLs) from high-risk breast cancer patients for whom no mutation in <it>BRCA1</it> or <it>BRCA2</it> had been identified.</p> <p>Methods</p> <p>We implemented an assay based on high-resolution melting (HRM) curve analysis and developed an analysis tool for DAE assessment.</p> <p>Results</p> <p>We observed allelic expression imbalance in 4 of the 41 LCLs examined. All four were carriers of the truncating mutation 1100delC. We confirmed previous findings that this mutation induces non-sense mediated mRNA decay. In our series, we ruled out the possibility of a functional sequence variant located in the promoter region or in a regulatory element of <it>CHEK2 </it>that would lead to DAE in the transcriptional regulatory milieu of freely proliferating LCLs.</p> <p>Conclusions</p> <p>Our results support that HRM is a sensitive and accurate method for DAE assessment. This approach would be of great interest for high-throughput mutation screening projects aiming to identify genes carrying functional regulatory polymorphisms.</p>http://www.biomedcentral.com/1755-8794/4/39 |
| spellingShingle | Sinilnikova Olga McKay-Chopin Sandrine Forey Nathalie Michelon Jocelyne Jordheim Lars P Nguyen-Dumont Tú Le Calvez-Kelm Florence Southey Melissa C Tavtigian Sean V Lesueur Fabienne Detecting differential allelic expression using high-resolution melting curve analysis: application to the breast cancer susceptibility gene CHEK2 BMC Medical Genomics |
| title | Detecting differential allelic expression using high-resolution melting curve analysis: application to the breast cancer susceptibility gene CHEK2 |
| title_full | Detecting differential allelic expression using high-resolution melting curve analysis: application to the breast cancer susceptibility gene CHEK2 |
| title_fullStr | Detecting differential allelic expression using high-resolution melting curve analysis: application to the breast cancer susceptibility gene CHEK2 |
| title_full_unstemmed | Detecting differential allelic expression using high-resolution melting curve analysis: application to the breast cancer susceptibility gene CHEK2 |
| title_short | Detecting differential allelic expression using high-resolution melting curve analysis: application to the breast cancer susceptibility gene CHEK2 |
| title_sort | detecting differential allelic expression using high resolution melting curve analysis application to the breast cancer susceptibility gene chek2 |
| url | http://www.biomedcentral.com/1755-8794/4/39 |
| work_keys_str_mv | AT sinilnikovaolga detectingdifferentialallelicexpressionusinghighresolutionmeltingcurveanalysisapplicationtothebreastcancersusceptibilitygenechek2 AT mckaychopinsandrine detectingdifferentialallelicexpressionusinghighresolutionmeltingcurveanalysisapplicationtothebreastcancersusceptibilitygenechek2 AT foreynathalie detectingdifferentialallelicexpressionusinghighresolutionmeltingcurveanalysisapplicationtothebreastcancersusceptibilitygenechek2 AT michelonjocelyne detectingdifferentialallelicexpressionusinghighresolutionmeltingcurveanalysisapplicationtothebreastcancersusceptibilitygenechek2 AT jordheimlarsp detectingdifferentialallelicexpressionusinghighresolutionmeltingcurveanalysisapplicationtothebreastcancersusceptibilitygenechek2 AT nguyendumonttu detectingdifferentialallelicexpressionusinghighresolutionmeltingcurveanalysisapplicationtothebreastcancersusceptibilitygenechek2 AT lecalvezkelmflorence detectingdifferentialallelicexpressionusinghighresolutionmeltingcurveanalysisapplicationtothebreastcancersusceptibilitygenechek2 AT southeymelissac detectingdifferentialallelicexpressionusinghighresolutionmeltingcurveanalysisapplicationtothebreastcancersusceptibilitygenechek2 AT tavtigianseanv detectingdifferentialallelicexpressionusinghighresolutionmeltingcurveanalysisapplicationtothebreastcancersusceptibilitygenechek2 AT lesueurfabienne detectingdifferentialallelicexpressionusinghighresolutionmeltingcurveanalysisapplicationtothebreastcancersusceptibilitygenechek2 |