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Next-generation sequencing and genome analysis in dimorphic fungi and human: using genomic variation to recognize and understand disease

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dc.contributor.advisorClay, Oliver
dc.creatorGallo Bonilla, Juan Esteban
dc.creator.degreeDoctor en Ciencias Biomédicas
dc.date.accessioned2017-10-10T12:32:35Z
dc.date.available2017-10-10T12:32:35Z
dc.date.created2017-08-29
dc.date.issued2017
dc.description.abstractThe work of this thesis has a common focus on bioinformatics, comparative genomics of fungal genomes and clinical genomics of human chronic disease. We primarily focused on using genomic data of dimorphic fungal pathogens in order to obtain a better perspective and understanding of how commonly used assembly, annotation and genomic comparison bioinformatics programs dealt with genomic data. Our group re-sequenced the reference strains that had been used for the existing assemblies and annotations of Paracoccidioides spp., and used the new, higher quality reads to substantially improve the reference assemblies and annotations of these pathogenic fungi. We also sequenced de novo the species Emmonsia crescens and E. parva, which are closely related to the causal agent of blastomycosis, Blastomyces dermatitidis, but non-pathogenic or with low virulence. We performed comparative analyses of gene content and structure between various strains of B. dermatitidis, E. crescens and E. parva. Using available sequences, we then designed and analytically validated two primer pairs from regions that are unique to Histoplasma capsulatum but present across diverse strains of this species, and can therefore be utilized to detect the presence of H. capsulatum. Using the same approach, we also designed and analytically validated three primer pairs of high confidence for the amplification of sequence fragments that are unique to the genus Paracoccidioides. We designed and implemented an algorithm that takes any given sequence(s) and splits the sequence into fragments in order to query the unique percentage of the fragment against a group of sequences that are closely related to the query as well as outgroups that may be relevant in clinical settings, including human. we genotyped 67 selected SNPs within the 9p21.3 locus of the human genome, motivated by its proven association with cardiovascular disease, for a Colombian cohort of 357 healthy individuals with data collected for detailed hemodynamic and other phenotypic traits. We also sequenced the exome of a patient with familiar hypercholesterolemia.eng
dc.description.embargo2021-10-12 01:01:01: Script de automatizacion de embargos. info:eu-repo/date/embargoEnd/2021-10-11
dc.description.embargo2019-10-11 07:55:01: Script de automatizacion de embargos. 11 oct 2019 Le llego el correo automático de finalización de embargo. 11 oct 2019 Correo recibido, Por favor no abrir acceso a esta tesis ya que aun nos encontramos en proceso de publicación en revista científica de algunos de sus contenidos. Gracias Juan Esteban Gallo Scientific Director GenomaCES 11 oct 2019 se cambia el nombre del documento y se embarga nuevamente por dos años
dc.format.mimetypeapplication/pdf
dc.identifier.doihttps://doi.org/10.48713/10336_13803
dc.identifier.urihttp://repository.urosario.edu.co/handle/10336/13803
dc.language.isospa
dc.publisherUniversidad del Rosariospa
dc.publisher.departmentFacultad de Ciencias Naturales y Matemáticasspa
dc.publisher.programDoctorado en Ciencias Biomédicasspa
dc.rights.accesRightsinfo:eu-repo/semantics/openAccess
dc.rights.accesoAbierto (Texto Completo)spa
dc.rights.ccAtribución-NoComercial-SinDerivadas 2.5 Colombiaspa
dc.rights.licenciaEL AUTOR, manifiesta que la obra objeto de la presente autorización es original y la realizó sin violar o usurpar derechos de autor de terceros, por lo tanto la obra es de exclusiva autoría y tiene la titularidad sobre la misma. PARGRAFO: En caso de presentarse cualquier reclamación o acción por parte de un tercero en cuanto a los derechos de autor sobre la obra en cuestión, EL AUTOR, asumirá toda la responsabilidad, y saldrá en defensa de los derechos aquí autorizados; para todos los efectos la universidad actúa como un tercero de buena fe. EL AUTOR, autoriza a LA UNIVERSIDAD DEL ROSARIO, para que en los términos establecidos en la Ley 23 de 1982, Ley 44 de 1993, Decisión andina 351 de 1993, Decreto 460 de 1995 y demás normas generales sobre la materia, utilice y use la obra objeto de la presente autorización. -------------------------------------- POLITICA DE TRATAMIENTO DE DATOS PERSONALES. Declaro que autorizo previa y de forma informada el tratamiento de mis datos personales por parte de LA UNIVERSIDAD DEL ROSARIO para fines académicos y en aplicación de convenios con terceros o servicios conexos con actividades propias de la academia, con estricto cumplimiento de los principios de ley. Para el correcto ejercicio de mi derecho de habeas data cuento con la cuenta de correo habeasdata@urosario.edu.co, donde previa identificación podré solicitar la consulta, corrección y supresión de mis datos.spa
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/2.5/co/
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dc.source.instnameinstname:Universidad del Rosariospa
dc.source.reponamereponame:Repositorio Institucional EdocURspa
dc.subjectGenomicsspa
dc.subjectBioinformaticsspa
dc.subject.ddcEnfermedades
dc.subject.decsBiología Computacionalspa
dc.subject.decsGenoma fúngicospa
dc.subject.decsGenoma viralspa
dc.subject.decsEnfermedad crónicaspa
dc.subject.keywordGenomicseng
dc.subject.keywordBioinformaticseng
dc.titleNext-generation sequencing and genome analysis in dimorphic fungi and human: using genomic variation to recognize and understand diseasespa
dc.typedoctoralThesiseng
dc.type.hasVersioninfo:eu-repo/semantics/acceptedVersion
dc.type.spaTesis de doctoradospa
local.department.reportEscuela de Medicina y Ciencias de la Saludspa
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Doctorado en Ciencias Biomédicas