SNP genotyping by heteroduplex analysis

Autores
Paniego, Norma Beatriz; Fusari, Corina Mariana; Lia, Veronica Viviana; Puebla, Andrea Fabiana
Año de publicación
2015
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Heteroduplex-based genotyping methods have proven to be technologically effective and economically efficient for low- to medium-range throughput single-nucleotide polymorphism (SNP) determination. In this chapter we describe two protocols that were successfully applied for SNP detection and haplotype analysis of candidate genes in association studies. The protocols involve (1) enzymatic mismatch cleavage with endonuclease CEL1 from celery, associated with fragment separation using capillary electrophoresis (CEL1 cleavage), and (2) differential retention of the homo/heteroduplex DNA molecules under partial denaturing conditions on ion pair reversed-phase liquid chromatography (dHPLC). Both methods are complementary since dHPLC is more versatile than CEL1 cleavage for identifying multiple SNP per target region, and the latter is easily optimized for sequences with fewer SNPs or small insertion/deletion polymorphisms. Besides, CEL1 cleavage is a powerful method to localize the position of the mutation when fragment resolution is done using capillary electrophoresis.
Instituto de Biotecnología
Fil: Paniego, Norma Beatriz. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Fusari, Corina Mariana. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina
Fil: Lia, Veronica Viviana. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina
Fil: Puebla, Andrea Fabiana. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina
Fuente
Methods in Molecular Biology 1245 : 141-150 (Octubre 2015)
Materia
Single Nucleotide Polymorphism
Electrophoresis
Genotypes
Polimorfismo de un Solo Nucleótido
Electroforesis
Genotipos
Candidate Genes
Heteroduplex Analysis
Genes Candidatos
Análisis heterodúplex
Nivel de accesibilidad
acceso restringido
Condiciones de uso
Repositorio
INTA Digital (INTA)
Institución
Instituto Nacional de Tecnología Agropecuaria
OAI Identificador
oai:localhost:20.500.12123/8118
Acceder
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oai_identifier_str oai:localhost:20.500.12123/8118
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spelling SNP genotyping by heteroduplex analysisPaniego, Norma BeatrizFusari, Corina MarianaLia, Veronica VivianaPuebla, Andrea FabianaSingle Nucleotide PolymorphismElectrophoresisGenotypesPolimorfismo de un Solo NucleótidoElectroforesisGenotiposCandidate GenesHeteroduplex AnalysisGenes CandidatosAnálisis heterodúplexHeteroduplex-based genotyping methods have proven to be technologically effective and economically efficient for low- to medium-range throughput single-nucleotide polymorphism (SNP) determination. In this chapter we describe two protocols that were successfully applied for SNP detection and haplotype analysis of candidate genes in association studies. The protocols involve (1) enzymatic mismatch cleavage with endonuclease CEL1 from celery, associated with fragment separation using capillary electrophoresis (CEL1 cleavage), and (2) differential retention of the homo/heteroduplex DNA molecules under partial denaturing conditions on ion pair reversed-phase liquid chromatography (dHPLC). Both methods are complementary since dHPLC is more versatile than CEL1 cleavage for identifying multiple SNP per target region, and the latter is easily optimized for sequences with fewer SNPs or small insertion/deletion polymorphisms. Besides, CEL1 cleavage is a powerful method to localize the position of the mutation when fragment resolution is done using capillary electrophoresis.Instituto de BiotecnologíaFil: Paniego, Norma Beatriz. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Fusari, Corina Mariana. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; ArgentinaFil: Lia, Veronica Viviana. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; ArgentinaFil: Puebla, Andrea Fabiana. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; ArgentinaSpringer2020-10-23T14:15:12Z2020-10-23T14:15:12Z2015-10info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfhttp://hdl.handle.net/20.500.12123/8118https://link.springer.com/protocol/10.1007/978-1-4939-1966-6_101064-3745https://doi.org/10.1007/978-1-4939-1966-6_10Methods in Molecular Biology 1245 : 141-150 (Octubre 2015)reponame:INTA Digital (INTA)instname:Instituto Nacional de Tecnología Agropecuariaenginfo:eu-repograntAgreement/INTA/AEBIO-245001/AR./Bioinformática aplicada a proyectos genómicos de interés agropecuarioinfo:eu-repograntAgreement/INTA/AEBIO-241351/AR./Mapeo de asociación para características de interés agronómicoinfo:eu-repo/semantics/restrictedAccess2025-09-04T09:48:39Zoai:localhost:20.500.12123/8118instacron:INTAInstitucionalhttp://repositorio.inta.gob.ar/Organismo científico-tecnológicoNo correspondehttp://repositorio.inta.gob.ar/oai/requesttripaldi.nicolas@inta.gob.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:l2025-09-04 09:48:40.142INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuariafalse
dc.title.none.fl_str_mv SNP genotyping by heteroduplex analysis
title SNP genotyping by heteroduplex analysis
spellingShingle SNP genotyping by heteroduplex analysis
Paniego, Norma Beatriz
Single Nucleotide Polymorphism
Electrophoresis
Genotypes
Polimorfismo de un Solo Nucleótido
Electroforesis
Genotipos
Candidate Genes
Heteroduplex Analysis
Genes Candidatos
Análisis heterodúplex
title_short SNP genotyping by heteroduplex analysis
title_full SNP genotyping by heteroduplex analysis
title_fullStr SNP genotyping by heteroduplex analysis
title_full_unstemmed SNP genotyping by heteroduplex analysis
title_sort SNP genotyping by heteroduplex analysis
dc.creator.none.fl_str_mv Paniego, Norma Beatriz
Fusari, Corina Mariana
Lia, Veronica Viviana
Puebla, Andrea Fabiana
author Paniego, Norma Beatriz
author_facet Paniego, Norma Beatriz
Fusari, Corina Mariana
Lia, Veronica Viviana
Puebla, Andrea Fabiana
author_role author
author2 Fusari, Corina Mariana
Lia, Veronica Viviana
Puebla, Andrea Fabiana
author2_role author
author
author
dc.subject.none.fl_str_mv Single Nucleotide Polymorphism
Electrophoresis
Genotypes
Polimorfismo de un Solo Nucleótido
Electroforesis
Genotipos
Candidate Genes
Heteroduplex Analysis
Genes Candidatos
Análisis heterodúplex
topic Single Nucleotide Polymorphism
Electrophoresis
Genotypes
Polimorfismo de un Solo Nucleótido
Electroforesis
Genotipos
Candidate Genes
Heteroduplex Analysis
Genes Candidatos
Análisis heterodúplex
dc.description.none.fl_txt_mv Heteroduplex-based genotyping methods have proven to be technologically effective and economically efficient for low- to medium-range throughput single-nucleotide polymorphism (SNP) determination. In this chapter we describe two protocols that were successfully applied for SNP detection and haplotype analysis of candidate genes in association studies. The protocols involve (1) enzymatic mismatch cleavage with endonuclease CEL1 from celery, associated with fragment separation using capillary electrophoresis (CEL1 cleavage), and (2) differential retention of the homo/heteroduplex DNA molecules under partial denaturing conditions on ion pair reversed-phase liquid chromatography (dHPLC). Both methods are complementary since dHPLC is more versatile than CEL1 cleavage for identifying multiple SNP per target region, and the latter is easily optimized for sequences with fewer SNPs or small insertion/deletion polymorphisms. Besides, CEL1 cleavage is a powerful method to localize the position of the mutation when fragment resolution is done using capillary electrophoresis.
Instituto de Biotecnología
Fil: Paniego, Norma Beatriz. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Fusari, Corina Mariana. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina
Fil: Lia, Veronica Viviana. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina
Fil: Puebla, Andrea Fabiana. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina
description Heteroduplex-based genotyping methods have proven to be technologically effective and economically efficient for low- to medium-range throughput single-nucleotide polymorphism (SNP) determination. In this chapter we describe two protocols that were successfully applied for SNP detection and haplotype analysis of candidate genes in association studies. The protocols involve (1) enzymatic mismatch cleavage with endonuclease CEL1 from celery, associated with fragment separation using capillary electrophoresis (CEL1 cleavage), and (2) differential retention of the homo/heteroduplex DNA molecules under partial denaturing conditions on ion pair reversed-phase liquid chromatography (dHPLC). Both methods are complementary since dHPLC is more versatile than CEL1 cleavage for identifying multiple SNP per target region, and the latter is easily optimized for sequences with fewer SNPs or small insertion/deletion polymorphisms. Besides, CEL1 cleavage is a powerful method to localize the position of the mutation when fragment resolution is done using capillary electrophoresis.
publishDate 2015
dc.date.none.fl_str_mv 2015-10
2020-10-23T14:15:12Z
2020-10-23T14:15:12Z
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/20.500.12123/8118
https://link.springer.com/protocol/10.1007/978-1-4939-1966-6_10
1064-3745
https://doi.org/10.1007/978-1-4939-1966-6_10
url http://hdl.handle.net/20.500.12123/8118
https://link.springer.com/protocol/10.1007/978-1-4939-1966-6_10
https://doi.org/10.1007/978-1-4939-1966-6_10
identifier_str_mv 1064-3745
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repograntAgreement/INTA/AEBIO-245001/AR./Bioinformática aplicada a proyectos genómicos de interés agropecuario
info:eu-repograntAgreement/INTA/AEBIO-241351/AR./Mapeo de asociación para características de interés agronómico
dc.rights.none.fl_str_mv info:eu-repo/semantics/restrictedAccess
eu_rights_str_mv restrictedAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Springer
publisher.none.fl_str_mv Springer
dc.source.none.fl_str_mv Methods in Molecular Biology 1245 : 141-150 (Octubre 2015)
reponame:INTA Digital (INTA)
instname:Instituto Nacional de Tecnología Agropecuaria
reponame_str INTA Digital (INTA)
collection INTA Digital (INTA)
instname_str Instituto Nacional de Tecnología Agropecuaria
repository.name.fl_str_mv INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuaria
repository.mail.fl_str_mv tripaldi.nicolas@inta.gob.ar
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score 12.623145

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