SNP genotyping by heteroduplex analysis
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 haplotyp...
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| Format: | Artículo |
| Language: | Inglés |
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Springer
2020
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| Online Access: | 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 |
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| author | Paniego, Norma Beatriz Fusari, Corina Mariana Lia, Veronica Viviana Puebla, Andrea Fabiana |
| author_browse | Fusari, Corina Mariana Lia, Veronica Viviana Paniego, Norma Beatriz Puebla, Andrea Fabiana |
| author_facet | Paniego, Norma Beatriz Fusari, Corina Mariana Lia, Veronica Viviana Puebla, Andrea Fabiana |
| author_sort | Paniego, Norma Beatriz |
| collection | INTA Digital |
| 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. |
| format | Artículo |
| id | INTA8118 |
| institution | Instituto Nacional de Tecnología Agropecuaria (INTA -Argentina) |
| language | Inglés |
| publishDate | 2020 |
| publishDateRange | 2020 |
| publishDateSort | 2020 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | INTA81182020-10-23T14:22:38Z SNP genotyping by heteroduplex analysis Paniego, Norma Beatriz Fusari, Corina Mariana Lia, Veronica Viviana Puebla, Andrea Fabiana Single Nucleotide Polymorphism Electrophoresis Genotypes Polimorfismo de un Solo Nucleótido Electroforesis Genotipos Candidate Genes Heteroduplex Analysis Genes Candidatos Análisis heterodúplex 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 2020-10-23T14:15:12Z 2020-10-23T14:15:12Z 2015-10 info:ar-repo/semantics/artículo info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion 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 eng 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 info:eu-repo/semantics/restrictedAccess application/pdf Springer Methods in Molecular Biology 1245 : 141-150 (Octubre 2015) |
| spellingShingle | Single Nucleotide Polymorphism Electrophoresis Genotypes Polimorfismo de un Solo Nucleótido Electroforesis Genotipos Candidate Genes Heteroduplex Analysis Genes Candidatos Análisis heterodúplex Paniego, Norma Beatriz Fusari, Corina Mariana Lia, Veronica Viviana Puebla, Andrea Fabiana SNP genotyping by heteroduplex analysis |
| title | 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_short | SNP genotyping by heteroduplex analysis |
| title_sort | snp genotyping by heteroduplex analysis |
| topic | Single Nucleotide Polymorphism Electrophoresis Genotypes Polimorfismo de un Solo Nucleótido Electroforesis Genotipos Candidate Genes Heteroduplex Analysis Genes Candidatos Análisis heterodúplex |
| 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 |
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