Computational approaches for integrative cancer genomics

Given the complexity and heterogeneity of cancer, the development of new high-throughput wide-genome technologies has open new possibilities for its study. Several projects around the globe are exploiting these technologies for generating unprecedented amount of data for cancer genomes. Its analysis...

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Detalles Bibliográficos
Autor: Pérez Llamas, Christian
Tipo de recurso: tesis doctoral
Estado:Versión publicada
Fecha de publicación:2015
País:España
Institución:CBUC, CESCA
Repositorio:TDR. Tesis Doctorales en Red
OAI Identifier:oai:www.tdx.cat:10803/328729
Acceso en línea:http://hdl.handle.net/10803/328729
Access Level:acceso abierto
Palabra clave:Cancer
Genomics
Mutations
Drivers
High-throughput
Genòmica
Mutacions
616
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spelling Computational approaches for integrative cancer genomicsPérez Llamas, ChristianCancerGenomicsMutationsDriversHigh-throughputGenòmicaMutacions616Given the complexity and heterogeneity of cancer, the development of new high-throughput wide-genome technologies has open new possibilities for its study. Several projects around the globe are exploiting these technologies for generating unprecedented amount of data for cancer genomes. Its analysis, integration and exploration are still a key challenge in the field. In this dissertation, we first present Gitools, a tool for accessing databases in biology, analysing high-throughput data, and visualising multi-dimensional results with interactive heatmaps. Then, we show IntOGen, the methodology employed for collection and organization of the data, the methods used for its analysis, and how the results and analysis were made available to other researchers. Finally, we compare several methods for impact prediction of non-synonymous mutations, showing that new tools specifically designed for cancer outperform those traditionally used for general diseases, and also the need for using other sources of information for better prediction of cancer mutations.Davant de la complexitat i heterogeneitat del cancer, el desenvolupament de noves tecnologies per l'estudi de genomes, ha obert noves posibilitats. Diversos projectes al voltant del mon les fan servir per generar quantitats de dades de genomes de cancer mai vistes abans. En aquest treball, primer presentem Gitools, una eina que permet obtenir dades de bases de dades en biologia, anal itzar dades genomiques, i visual itzar els resul tats multidimensionals mitjançant mapes de calor interactius. Després mostrem IntOGen, les metodologies per obtenir i organitzar les dades, els metodes per el seu analisi, i com es van possar a disposició d'altres investigadors. Finalment, comparem diversos metods de predicció de l'impacte de les mutacions no sinonimes, que ens mostra com nou metods desenvolupats per cancer funcionen millor que els utilitzats tradicionalment per enfermetats generals, aixis com la necesitat de recorrer a altres fonts d'informació per tenir millor prediccions per mutacions de cancer.Programa de doctorat en BiomedicinaUniversitat Pompeu FabraLópez Bigas, NúriaUniversitat Pompeu Fabra. Departament de Ciències Experimentals i de la Salut201520152015info:eu-repo/semantics/doctoralThesisinfo:eu-repo/semantics/publishedVersion154 p.application/pdfapplication/pdfhttp://hdl.handle.net/10803/328729TDX (Tesis Doctorals en Xarxa)reponame:TDR. Tesis Doctorales en Redinstname:CBUC, CESCAInglésL'accés als continguts d'aquesta tesi queda condicionat a l'acceptació de les condicions d'ús establertes per la següent llicència Creative Commons: http://creativecommons.org/licenses/by-nc-sa/3.0/es/http://creativecommons.org/licenses/by-nc-sa/3.0/es/info:eu-repo/semantics/openAccessoai:www.tdx.cat:10803/3287292026-06-14T12:46:07Z
dc.title.none.fl_str_mv Computational approaches for integrative cancer genomics
title Computational approaches for integrative cancer genomics
spellingShingle Computational approaches for integrative cancer genomics
Pérez Llamas, Christian
Cancer
Genomics
Mutations
Drivers
High-throughput
Genòmica
Mutacions
616
title_short Computational approaches for integrative cancer genomics
title_full Computational approaches for integrative cancer genomics
title_fullStr Computational approaches for integrative cancer genomics
title_full_unstemmed Computational approaches for integrative cancer genomics
title_sort Computational approaches for integrative cancer genomics
dc.creator.none.fl_str_mv Pérez Llamas, Christian
author Pérez Llamas, Christian
author_facet Pérez Llamas, Christian
author_role author
dc.contributor.none.fl_str_mv López Bigas, Núria
Universitat Pompeu Fabra. Departament de Ciències Experimentals i de la Salut
dc.subject.none.fl_str_mv Cancer
Genomics
Mutations
Drivers
High-throughput
Genòmica
Mutacions
616
topic Cancer
Genomics
Mutations
Drivers
High-throughput
Genòmica
Mutacions
616
description Given the complexity and heterogeneity of cancer, the development of new high-throughput wide-genome technologies has open new possibilities for its study. Several projects around the globe are exploiting these technologies for generating unprecedented amount of data for cancer genomes. Its analysis, integration and exploration are still a key challenge in the field. In this dissertation, we first present Gitools, a tool for accessing databases in biology, analysing high-throughput data, and visualising multi-dimensional results with interactive heatmaps. Then, we show IntOGen, the methodology employed for collection and organization of the data, the methods used for its analysis, and how the results and analysis were made available to other researchers. Finally, we compare several methods for impact prediction of non-synonymous mutations, showing that new tools specifically designed for cancer outperform those traditionally used for general diseases, and also the need for using other sources of information for better prediction of cancer mutations.
publishDate 2015
dc.date.none.fl_str_mv 2015
2015
2015
dc.type.none.fl_str_mv info:eu-repo/semantics/doctoralThesis
info:eu-repo/semantics/publishedVersion
format doctoralThesis
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10803/328729
url http://hdl.handle.net/10803/328729
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.rights.none.fl_str_mv http://creativecommons.org/licenses/by-nc-sa/3.0/es/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by-nc-sa/3.0/es/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv 154 p.
application/pdf
application/pdf
dc.publisher.none.fl_str_mv Universitat Pompeu Fabra
publisher.none.fl_str_mv Universitat Pompeu Fabra
dc.source.none.fl_str_mv TDX (Tesis Doctorals en Xarxa)
reponame:TDR. Tesis Doctorales en Red
instname:CBUC, CESCA
instname_str CBUC, CESCA
reponame_str TDR. Tesis Doctorales en Red
collection TDR. Tesis Doctorales en Red
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15,300724

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