Polymorphism genotyping based on loop-mediated isothermal amplification and smartphone detection

[EN] The genotyping of a single-nucleotide polymorphism (SNP) is addressed through methods based on loop-mediated isothermal amplification (LAMP) combined with user-friendly optical read-outs to cover the current demand for point-of-care DNA biomarker detection. The modification of primer design and...

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Detalles Bibliográficos
Autores: YAMANAKA, ERIC-SEITI, Tortajada-Genaro, Luis Antonio|||0000-0003-4021-5607, Pastor Navarro, Nuria, Maquieira, Angel|||0000-0003-4641-4957
Tipo de recurso: artículo
Fecha de publicación:2018
País:España
Institución:Universitat Politècnica de València (UPV)
Repositorio:RiuNet. Repositorio Institucional de la Universitat Politécnica de Valéncia
Idioma:inglés
OAI Identifier:oai:riunet.upv.es:10251/142518
Acceso en línea:https://riunet.upv.es/handle/10251/142518
Access Level:acceso abierto
Palabra clave:Single-nucleotide polymorphism
Loop-mediated isothermal amplification
Point-of-care optical testing
Smartphone
Phannacogenomics
QUIMICA ANALITICA
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spelling Polymorphism genotyping based on loop-mediated isothermal amplification and smartphone detectionYAMANAKA, ERIC-SEITITortajada-Genaro, Luis Antonio|||0000-0003-4021-5607Pastor Navarro, NuriaMaquieira, Angel|||0000-0003-4641-4957Single-nucleotide polymorphismLoop-mediated isothermal amplificationPoint-of-care optical testingSmartphonePhannacogenomicsQUIMICA ANALITICA[EN] The genotyping of a single-nucleotide polymorphism (SNP) is addressed through methods based on loop-mediated isothermal amplification (LAMP) combined with user-friendly optical read-outs to cover the current demand for point-of-care DNA biomarker detection. The modification of primer design and reaction composition improved the assay selectivity yielding allele-specific results and reducing false-positive frequency. Furthermore, the reduced cost, ease of use and effectiveness of calorimetric detection (solution and hybridisation chip formats) were availed for the image capture by a smartphone, reching high sensitivity. In order to evaluate their discriminating capacities, LAMP-based methods were applied to human samples to genotype a SNP biomarker (rs1954787) located in the GRIK4 gene and related to the treatment response to anti-depressants drugs. Sensitive (limit of detection: 100 genomic DNA copies), reproducible ( < 15% error), fast (around 70 min) and low-cost assays were accomplished. Patient subgroups were correctly discriminated, agreeing with reference sequencing techniques. The achieved analytical performances using the developed amplification-detection principles confirmed the approach potential for point-of-care optical DNA testing.The authors acknowledge the financial support received from the Generalitat Valenciana (Project GVA-PROMETEOII/2014/040 and GRISOLIA/2014/024 Ph.D. grant) and from the Spanish Ministry of Economy and Competitiveness (MINECO CTQ2013-45875-R Project).ElsevierDepartamento de QuímicaInstituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo TecnológicoEscuela Técnica Superior de Ingeniería Agronómica y del Medio NaturalGeneralitat ValencianaMinisterio de Economía, Industria y CompetitividadRepositorio Institucional de la Universitat Politècnica de València Riunet20182018-06-01journal articlehttp://purl.org/coar/resource_type/c_6501VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleapplication/pdfapplication/pdfhttps://riunet.upv.es/handle/10251/142518reponame:RiuNet. Repositorio Institucional de la Universitat Politécnica de Valénciainstname:Universitat Politècnica de València (UPV)InglésengGeneralitat Valenciana https://doi.org/10.13039/501100003359 GRISOLIA%2F2014%2F024Generalitat Valenciana https://doi.org/10.13039/501100003359 PROMETEOII%2F2014%2F040 Estudio de estrategias fisico-químicas para el desarrollo de biosensores interferométricos en soportes interactivos de aplicación en clínicaMinisterio de Economía y Competitividad http://dx.doi.org/10.13039/501100003329 CTQ2013-45875-R BIOSENSADO EN SOPORTES INTERACTIVOS CON PROPIEDADES INTERFEROMETRICAS PARA APLICACIONES CLINICAS. DEMOSTRACION EN FARMACOGENETICA Y ALERGIAS MEDICAMENTOSASopen accesshttp://purl.org/coar/access_right/c_abf2Reconocimiento - No comercial - Sin obra derivada (by-nc-nd) http://creativecommons.org/licenses/by-nc-nd/4.0/info:eu-repo/semantics/openAccessoai:riunet.upv.es:10251/1425182026-06-13T07:49:27Z
dc.title.none.fl_str_mv Polymorphism genotyping based on loop-mediated isothermal amplification and smartphone detection
title Polymorphism genotyping based on loop-mediated isothermal amplification and smartphone detection
spellingShingle Polymorphism genotyping based on loop-mediated isothermal amplification and smartphone detection
YAMANAKA, ERIC-SEITI
Single-nucleotide polymorphism
Loop-mediated isothermal amplification
Point-of-care optical testing
Smartphone
Phannacogenomics
QUIMICA ANALITICA
title_short Polymorphism genotyping based on loop-mediated isothermal amplification and smartphone detection
title_full Polymorphism genotyping based on loop-mediated isothermal amplification and smartphone detection
title_fullStr Polymorphism genotyping based on loop-mediated isothermal amplification and smartphone detection
title_full_unstemmed Polymorphism genotyping based on loop-mediated isothermal amplification and smartphone detection
title_sort Polymorphism genotyping based on loop-mediated isothermal amplification and smartphone detection
dc.creator.none.fl_str_mv YAMANAKA, ERIC-SEITI
Tortajada-Genaro, Luis Antonio|||0000-0003-4021-5607
Pastor Navarro, Nuria
Maquieira, Angel|||0000-0003-4641-4957
author YAMANAKA, ERIC-SEITI
author_facet YAMANAKA, ERIC-SEITI
Tortajada-Genaro, Luis Antonio|||0000-0003-4021-5607
Pastor Navarro, Nuria
Maquieira, Angel|||0000-0003-4641-4957
author_role author
author2 Tortajada-Genaro, Luis Antonio|||0000-0003-4021-5607
Pastor Navarro, Nuria
Maquieira, Angel|||0000-0003-4641-4957
author2_role author
author
author
dc.contributor.none.fl_str_mv Departamento de Química
Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico
Escuela Técnica Superior de Ingeniería Agronómica y del Medio Natural
Generalitat Valenciana
Ministerio de Economía, Industria y Competitividad
Repositorio Institucional de la Universitat Politècnica de València Riunet
dc.subject.none.fl_str_mv Single-nucleotide polymorphism
Loop-mediated isothermal amplification
Point-of-care optical testing
Smartphone
Phannacogenomics
QUIMICA ANALITICA
topic Single-nucleotide polymorphism
Loop-mediated isothermal amplification
Point-of-care optical testing
Smartphone
Phannacogenomics
QUIMICA ANALITICA
description [EN] The genotyping of a single-nucleotide polymorphism (SNP) is addressed through methods based on loop-mediated isothermal amplification (LAMP) combined with user-friendly optical read-outs to cover the current demand for point-of-care DNA biomarker detection. The modification of primer design and reaction composition improved the assay selectivity yielding allele-specific results and reducing false-positive frequency. Furthermore, the reduced cost, ease of use and effectiveness of calorimetric detection (solution and hybridisation chip formats) were availed for the image capture by a smartphone, reching high sensitivity. In order to evaluate their discriminating capacities, LAMP-based methods were applied to human samples to genotype a SNP biomarker (rs1954787) located in the GRIK4 gene and related to the treatment response to anti-depressants drugs. Sensitive (limit of detection: 100 genomic DNA copies), reproducible ( < 15% error), fast (around 70 min) and low-cost assays were accomplished. Patient subgroups were correctly discriminated, agreeing with reference sequencing techniques. The achieved analytical performances using the developed amplification-detection principles confirmed the approach potential for point-of-care optical DNA testing.
publishDate 2018
dc.date.none.fl_str_mv 2018
2018-06-01
dc.type.none.fl_str_mv journal article
http://purl.org/coar/resource_type/c_6501
VoR
http://purl.org/coar/version/c_970fb48d4fbd8a85
dc.type.openaire.fl_str_mv info:eu-repo/semantics/article
format article
dc.identifier.none.fl_str_mv https://riunet.upv.es/handle/10251/142518
url https://riunet.upv.es/handle/10251/142518
dc.language.none.fl_str_mv Inglés
eng
language_invalid_str_mv Inglés
language eng
dc.relation.none.fl_str_mv Generalitat Valenciana https://doi.org/10.13039/501100003359 GRISOLIA%2F2014%2F024
Generalitat Valenciana https://doi.org/10.13039/501100003359 PROMETEOII%2F2014%2F040 Estudio de estrategias fisico-químicas para el desarrollo de biosensores interferométricos en soportes interactivos de aplicación en clínica
Ministerio de Economía y Competitividad http://dx.doi.org/10.13039/501100003329 CTQ2013-45875-R BIOSENSADO EN SOPORTES INTERACTIVOS CON PROPIEDADES INTERFEROMETRICAS PARA APLICACIONES CLINICAS. DEMOSTRACION EN FARMACOGENETICA Y ALERGIAS MEDICAMENTOSAS
dc.rights.none.fl_str_mv open access
http://purl.org/coar/access_right/c_abf2
Reconocimiento - No comercial - Sin obra derivada (by-nc-nd)
http://creativecommons.org/licenses/by-nc-nd/4.0/
dc.rights.openaire.fl_str_mv info:eu-repo/semantics/openAccess
rights_invalid_str_mv open access
http://purl.org/coar/access_right/c_abf2
Reconocimiento - No comercial - Sin obra derivada (by-nc-nd)
http://creativecommons.org/licenses/by-nc-nd/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Elsevier
publisher.none.fl_str_mv Elsevier
dc.source.none.fl_str_mv reponame:RiuNet. Repositorio Institucional de la Universitat Politécnica de Valéncia
instname:Universitat Politècnica de València (UPV)
instname_str Universitat Politècnica de València (UPV)
reponame_str RiuNet. Repositorio Institucional de la Universitat Politécnica de Valéncia
collection RiuNet. Repositorio Institucional de la Universitat Politécnica de Valéncia
repository.name.fl_str_mv
repository.mail.fl_str_mv
_version_ 1869405798257393664
score 15,301603

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