Gene prioritization based on biological plausibility over genome wide association studies renders new loci associated with type 2 diabetes

Autores
Sookoian, Silvia Cristina; Fernández Gianotti, Tomás; Schuman, Mariano Luis; Pirola, Carlos José
Año de publicación
2009
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Purpose: We present an approach to prioritize single nucleotide polymorphisms for further follow-up in genome-wide association studies of type 2 diabetes. Method: The proposed method combines both the use of open data access from two type 2 diabetes-genome-wide association studies (granted by the Diabetes Genetics Initiative and the Welcome Trust Case Control Consortium) and the comprehensive analysis of candidate regions generated by the freely accessible ENDEAVOUR software. Results: The algorithm prioritized all genes of the whole genome in relation to type 2 diabetes. There were six of 1096 single nucleotide polymorphisms in five genes potentially associated with type 2 diabetes: tachykinin receptor 3 (rs1384401), anaplastic lymphoma receptor tyrosine kinase (rs4319896), calcium channel, voltage-dependent, L type, alpha 1D subunit (rs12487452), FOXO1A (rs10507486 and rs7323267), and v-akt murine thymoma viral oncogene homolog 3 (rs897959). We estimated the fixed effect and P values of each single nucleotide polymorphism in the combined dataset by Mantel-Haenszel meta-analysis and we observed significant P values for all single nucleotide polymorphisms except for rs897959 at v-akt murine thymoma viral oncogene homolog 3. Conclusion: The proposed strategy may be used as an alternative tool for optimizing the information of the nearly 500,000 gene variants in which markers with modest significant P value for disease association are currently disregarded. Additionally, the said single nucleotide polymorphisms may be incorporated into the replication of the multistage design involved in the genome-wide association studies.
Fil: Sookoian, Silvia Cristina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones Biomédicas. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones Biomédicas; Argentina
Fil: Fernández Gianotti, Tomás. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones Biomédicas. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones Biomédicas; Argentina
Fil: Schuman, Mariano Luis. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones Biomédicas. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones Biomédicas; Argentina
Fil: Pirola, Carlos José. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones Biomédicas. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones Biomédicas; Argentina
Materia
GENOME-WIDE ASSOCIATION STUDIES
GENES
TYPE 2 DIABETES
ENDEAVOUR
CANDIDATE GENES
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/103282
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/103282
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Gene prioritization based on biological plausibility over genome wide association studies renders new loci associated with type 2 diabetesSookoian, Silvia CristinaFernández Gianotti, TomásSchuman, Mariano LuisPirola, Carlos JoséGENOME-WIDE ASSOCIATION STUDIESGENESTYPE 2 DIABETESENDEAVOURCANDIDATE GENEShttps://purl.org/becyt/ford/1.2https://purl.org/becyt/ford/1https://purl.org/becyt/ford/3.1https://purl.org/becyt/ford/3Purpose: We present an approach to prioritize single nucleotide polymorphisms for further follow-up in genome-wide association studies of type 2 diabetes. Method: The proposed method combines both the use of open data access from two type 2 diabetes-genome-wide association studies (granted by the Diabetes Genetics Initiative and the Welcome Trust Case Control Consortium) and the comprehensive analysis of candidate regions generated by the freely accessible ENDEAVOUR software. Results: The algorithm prioritized all genes of the whole genome in relation to type 2 diabetes. There were six of 1096 single nucleotide polymorphisms in five genes potentially associated with type 2 diabetes: tachykinin receptor 3 (rs1384401), anaplastic lymphoma receptor tyrosine kinase (rs4319896), calcium channel, voltage-dependent, L type, alpha 1D subunit (rs12487452), FOXO1A (rs10507486 and rs7323267), and v-akt murine thymoma viral oncogene homolog 3 (rs897959). We estimated the fixed effect and P values of each single nucleotide polymorphism in the combined dataset by Mantel-Haenszel meta-analysis and we observed significant P values for all single nucleotide polymorphisms except for rs897959 at v-akt murine thymoma viral oncogene homolog 3. Conclusion: The proposed strategy may be used as an alternative tool for optimizing the information of the nearly 500,000 gene variants in which markers with modest significant P value for disease association are currently disregarded. Additionally, the said single nucleotide polymorphisms may be incorporated into the replication of the multistage design involved in the genome-wide association studies.Fil: Sookoian, Silvia Cristina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones Biomédicas. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones Biomédicas; ArgentinaFil: Fernández Gianotti, Tomás. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones Biomédicas. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones Biomédicas; ArgentinaFil: Schuman, Mariano Luis. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones Biomédicas. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones Biomédicas; ArgentinaFil: Pirola, Carlos José. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones Biomédicas. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones Biomédicas; ArgentinaLippincott Williams2009-05info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/103282Sookoian, Silvia Cristina; Fernández Gianotti, Tomás; Schuman, Mariano Luis; Pirola, Carlos José; Gene prioritization based on biological plausibility over genome wide association studies renders new loci associated with type 2 diabetes; Lippincott Williams; Genetics In Medicine; 11; 5; 5-2009; 338-3431098-3600CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1097/GIM.0b013e31819995cainfo:eu-repo/semantics/altIdentifier/url/https://www.nature.com/articles/gim200946info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-10-15T15:24:35Zoai:ri.conicet.gov.ar:11336/103282instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-10-15 15:24:36.281CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Gene prioritization based on biological plausibility over genome wide association studies renders new loci associated with type 2 diabetes
title Gene prioritization based on biological plausibility over genome wide association studies renders new loci associated with type 2 diabetes
spellingShingle Gene prioritization based on biological plausibility over genome wide association studies renders new loci associated with type 2 diabetes
Sookoian, Silvia Cristina
GENOME-WIDE ASSOCIATION STUDIES
GENES
TYPE 2 DIABETES
ENDEAVOUR
CANDIDATE GENES
title_short Gene prioritization based on biological plausibility over genome wide association studies renders new loci associated with type 2 diabetes
title_full Gene prioritization based on biological plausibility over genome wide association studies renders new loci associated with type 2 diabetes
title_fullStr Gene prioritization based on biological plausibility over genome wide association studies renders new loci associated with type 2 diabetes
title_full_unstemmed Gene prioritization based on biological plausibility over genome wide association studies renders new loci associated with type 2 diabetes
title_sort Gene prioritization based on biological plausibility over genome wide association studies renders new loci associated with type 2 diabetes
dc.creator.none.fl_str_mv Sookoian, Silvia Cristina
Fernández Gianotti, Tomás
Schuman, Mariano Luis
Pirola, Carlos José
author Sookoian, Silvia Cristina
author_facet Sookoian, Silvia Cristina
Fernández Gianotti, Tomás
Schuman, Mariano Luis
Pirola, Carlos José
author_role author
author2 Fernández Gianotti, Tomás
Schuman, Mariano Luis
Pirola, Carlos José
author2_role author
author
author
dc.subject.none.fl_str_mv GENOME-WIDE ASSOCIATION STUDIES
GENES
TYPE 2 DIABETES
ENDEAVOUR
CANDIDATE GENES
topic GENOME-WIDE ASSOCIATION STUDIES
GENES
TYPE 2 DIABETES
ENDEAVOUR
CANDIDATE GENES
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.2
https://purl.org/becyt/ford/1
https://purl.org/becyt/ford/3.1
https://purl.org/becyt/ford/3
dc.description.none.fl_txt_mv Purpose: We present an approach to prioritize single nucleotide polymorphisms for further follow-up in genome-wide association studies of type 2 diabetes. Method: The proposed method combines both the use of open data access from two type 2 diabetes-genome-wide association studies (granted by the Diabetes Genetics Initiative and the Welcome Trust Case Control Consortium) and the comprehensive analysis of candidate regions generated by the freely accessible ENDEAVOUR software. Results: The algorithm prioritized all genes of the whole genome in relation to type 2 diabetes. There were six of 1096 single nucleotide polymorphisms in five genes potentially associated with type 2 diabetes: tachykinin receptor 3 (rs1384401), anaplastic lymphoma receptor tyrosine kinase (rs4319896), calcium channel, voltage-dependent, L type, alpha 1D subunit (rs12487452), FOXO1A (rs10507486 and rs7323267), and v-akt murine thymoma viral oncogene homolog 3 (rs897959). We estimated the fixed effect and P values of each single nucleotide polymorphism in the combined dataset by Mantel-Haenszel meta-analysis and we observed significant P values for all single nucleotide polymorphisms except for rs897959 at v-akt murine thymoma viral oncogene homolog 3. Conclusion: The proposed strategy may be used as an alternative tool for optimizing the information of the nearly 500,000 gene variants in which markers with modest significant P value for disease association are currently disregarded. Additionally, the said single nucleotide polymorphisms may be incorporated into the replication of the multistage design involved in the genome-wide association studies.
Fil: Sookoian, Silvia Cristina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones Biomédicas. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones Biomédicas; Argentina
Fil: Fernández Gianotti, Tomás. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones Biomédicas. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones Biomédicas; Argentina
Fil: Schuman, Mariano Luis. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones Biomédicas. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones Biomédicas; Argentina
Fil: Pirola, Carlos José. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones Biomédicas. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones Biomédicas; Argentina
description Purpose: We present an approach to prioritize single nucleotide polymorphisms for further follow-up in genome-wide association studies of type 2 diabetes. Method: The proposed method combines both the use of open data access from two type 2 diabetes-genome-wide association studies (granted by the Diabetes Genetics Initiative and the Welcome Trust Case Control Consortium) and the comprehensive analysis of candidate regions generated by the freely accessible ENDEAVOUR software. Results: The algorithm prioritized all genes of the whole genome in relation to type 2 diabetes. There were six of 1096 single nucleotide polymorphisms in five genes potentially associated with type 2 diabetes: tachykinin receptor 3 (rs1384401), anaplastic lymphoma receptor tyrosine kinase (rs4319896), calcium channel, voltage-dependent, L type, alpha 1D subunit (rs12487452), FOXO1A (rs10507486 and rs7323267), and v-akt murine thymoma viral oncogene homolog 3 (rs897959). We estimated the fixed effect and P values of each single nucleotide polymorphism in the combined dataset by Mantel-Haenszel meta-analysis and we observed significant P values for all single nucleotide polymorphisms except for rs897959 at v-akt murine thymoma viral oncogene homolog 3. Conclusion: The proposed strategy may be used as an alternative tool for optimizing the information of the nearly 500,000 gene variants in which markers with modest significant P value for disease association are currently disregarded. Additionally, the said single nucleotide polymorphisms may be incorporated into the replication of the multistage design involved in the genome-wide association studies.
publishDate 2009
dc.date.none.fl_str_mv 2009-05
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/103282
Sookoian, Silvia Cristina; Fernández Gianotti, Tomás; Schuman, Mariano Luis; Pirola, Carlos José; Gene prioritization based on biological plausibility over genome wide association studies renders new loci associated with type 2 diabetes; Lippincott Williams; Genetics In Medicine; 11; 5; 5-2009; 338-343
1098-3600
CONICET Digital
CONICET
url http://hdl.handle.net/11336/103282
identifier_str_mv Sookoian, Silvia Cristina; Fernández Gianotti, Tomás; Schuman, Mariano Luis; Pirola, Carlos José; Gene prioritization based on biological plausibility over genome wide association studies renders new loci associated with type 2 diabetes; Lippincott Williams; Genetics In Medicine; 11; 5; 5-2009; 338-343
1098-3600
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.1097/GIM.0b013e31819995ca
info:eu-repo/semantics/altIdentifier/url/https://www.nature.com/articles/gim200946
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
application/pdf
application/pdf
application/pdf
dc.publisher.none.fl_str_mv Lippincott Williams
publisher.none.fl_str_mv Lippincott Williams
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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