Bioinformatics for Precision Medicine in Oncology: principles and application to the SHIVA clinical trial
Precision medicine (PM) requires the delivery of individually adapted medical care based on the genetic characteristics of each patient and his/her tumor. The last decade witnessed the development of high-throughput technologies such as microarrays and next-generation sequencing which paved the way...
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Format: | Article |
Language: | English |
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Frontiers Media S.A.
2014-05-01
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Series: | Frontiers in Genetics |
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Online Access: | http://journal.frontiersin.org/Journal/10.3389/fgene.2014.00152/full |
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language |
English |
format |
Article |
sources |
DOAJ |
author |
Nicolas eServant Nicolas eServant Nicolas eServant Julien eRoméjon Julien eRoméjon Julien eRoméjon Pierre eGestraud Pierre eGestraud Pierre eGestraud Philippe eLa Rosa Philippe eLa Rosa Philippe eLa Rosa Georges eLucotte Georges eLucotte Georges eLucotte Séverine eLair Séverine eLair Séverine eLair Virginie eBernard Bruno eZeitouni Bruno eZeitouni Bruno eZeitouni Fanny eCoffin Fanny eCoffin Fanny eCoffin Gérôme eJules-Clément Gérôme eJules-Clément Gérôme eJules-Clément Gérôme eJules-Clément Florent eYvon Florent eYvon Florent eYvon Alban eLermine Alban eLermine Alban eLermine Patrick ePoullet Patrick ePoullet Patrick ePoullet Stéphane eLiva Stéphane eLiva Stéphane eLiva Stuart ePook Stuart ePook Stuart ePook Tatiana ePopova Camille eBarette Camille eBarette Camille eBarette Camille eBarette François ePrud'homme François ePrud'homme François ePrud'homme Jean-Gabriel eDick Maud eKamal Christophe eLe Tourneau Christophe eLe Tourneau Emmanuel eBarillot Emmanuel eBarillot Emmanuel eBarillot Philippe eHupé Philippe eHupé Philippe eHupé Philippe eHupé |
spellingShingle |
Nicolas eServant Nicolas eServant Nicolas eServant Julien eRoméjon Julien eRoméjon Julien eRoméjon Pierre eGestraud Pierre eGestraud Pierre eGestraud Philippe eLa Rosa Philippe eLa Rosa Philippe eLa Rosa Georges eLucotte Georges eLucotte Georges eLucotte Séverine eLair Séverine eLair Séverine eLair Virginie eBernard Bruno eZeitouni Bruno eZeitouni Bruno eZeitouni Fanny eCoffin Fanny eCoffin Fanny eCoffin Gérôme eJules-Clément Gérôme eJules-Clément Gérôme eJules-Clément Gérôme eJules-Clément Florent eYvon Florent eYvon Florent eYvon Alban eLermine Alban eLermine Alban eLermine Patrick ePoullet Patrick ePoullet Patrick ePoullet Stéphane eLiva Stéphane eLiva Stéphane eLiva Stuart ePook Stuart ePook Stuart ePook Tatiana ePopova Camille eBarette Camille eBarette Camille eBarette Camille eBarette François ePrud'homme François ePrud'homme François ePrud'homme Jean-Gabriel eDick Maud eKamal Christophe eLe Tourneau Christophe eLe Tourneau Emmanuel eBarillot Emmanuel eBarillot Emmanuel eBarillot Philippe eHupé Philippe eHupé Philippe eHupé Philippe eHupé Bioinformatics for Precision Medicine in Oncology: principles and application to the SHIVA clinical trial Frontiers in Genetics bioinformatics Sequencing Clinical Trial oncology SHIVA precision medicine |
author_facet |
Nicolas eServant Nicolas eServant Nicolas eServant Julien eRoméjon Julien eRoméjon Julien eRoméjon Pierre eGestraud Pierre eGestraud Pierre eGestraud Philippe eLa Rosa Philippe eLa Rosa Philippe eLa Rosa Georges eLucotte Georges eLucotte Georges eLucotte Séverine eLair Séverine eLair Séverine eLair Virginie eBernard Bruno eZeitouni Bruno eZeitouni Bruno eZeitouni Fanny eCoffin Fanny eCoffin Fanny eCoffin Gérôme eJules-Clément Gérôme eJules-Clément Gérôme eJules-Clément Gérôme eJules-Clément Florent eYvon Florent eYvon Florent eYvon Alban eLermine Alban eLermine Alban eLermine Patrick ePoullet Patrick ePoullet Patrick ePoullet Stéphane eLiva Stéphane eLiva Stéphane eLiva Stuart ePook Stuart ePook Stuart ePook Tatiana ePopova Camille eBarette Camille eBarette Camille eBarette Camille eBarette François ePrud'homme François ePrud'homme François ePrud'homme Jean-Gabriel eDick Maud eKamal Christophe eLe Tourneau Christophe eLe Tourneau Emmanuel eBarillot Emmanuel eBarillot Emmanuel eBarillot Philippe eHupé Philippe eHupé Philippe eHupé Philippe eHupé |
author_sort |
Nicolas eServant |
title |
Bioinformatics for Precision Medicine in Oncology: principles and application to the SHIVA clinical trial |
title_short |
Bioinformatics for Precision Medicine in Oncology: principles and application to the SHIVA clinical trial |
title_full |
Bioinformatics for Precision Medicine in Oncology: principles and application to the SHIVA clinical trial |
title_fullStr |
Bioinformatics for Precision Medicine in Oncology: principles and application to the SHIVA clinical trial |
title_full_unstemmed |
Bioinformatics for Precision Medicine in Oncology: principles and application to the SHIVA clinical trial |
title_sort |
bioinformatics for precision medicine in oncology: principles and application to the shiva clinical trial |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Genetics |
issn |
1664-8021 |
publishDate |
2014-05-01 |
description |
Precision medicine (PM) requires the delivery of individually adapted medical care based on the genetic characteristics of each patient and his/her tumor. The last decade witnessed the development of high-throughput technologies such as microarrays and next-generation sequencing which paved the way to PM in the field of oncology. While the cost of these technologies decreases, we are facing an exponential increase in the amount of data produced. Our ability to use this information in daily practice relies strongly on the availability of an efficient bioinformatics system that assists in the translation of knowledge from the bench towards molecular targeting and diagnosis. Clinical trials and routine diagnoses constitute different approaches, both requiring a strong bioinformatics environment capable of i) warranting the integration and the traceability of data, ii) ensuring the correct processing and analyses of genomic data and iii) applying well-defined and reproducible procedures for workflow management and decision-making. To address the issues, a seamless information system was developed at Institut Curie which facilitates the data integration and tracks in real-time the processing of individual samples. Moreover, computational pipelines were developed to identify reliably genomic alterations and mutations from the molecular profiles of each patient. After a rigorous quality control, a meaningful report is delivered to the clinicians and biologists for the therapeutic decision. The complete bioinformatics environment and the key points of its implementation are presented in the context of the SHIVA clinical trial, a multicentric randomized phase II trial comparing targeted therapy based on tumor molecular profiling versus conventional therapy in patients with refractory cancer. The numerous challenges faced in practice during the setting up and the conduct of this trial are discussed as an illustration of PM application. |
topic |
bioinformatics Sequencing Clinical Trial oncology SHIVA precision medicine |
url |
http://journal.frontiersin.org/Journal/10.3389/fgene.2014.00152/full |
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doaj-39bea5026b3849e0b2338d109ce7d0d32020-11-24T21:23:48ZengFrontiers Media S.A.Frontiers in Genetics1664-80212014-05-01510.3389/fgene.2014.0015276805Bioinformatics for Precision Medicine in Oncology: principles and application to the SHIVA clinical trialNicolas eServant0Nicolas eServant1Nicolas eServant2Julien eRoméjon3Julien eRoméjon4Julien eRoméjon5Pierre eGestraud6Pierre eGestraud7Pierre eGestraud8Philippe eLa Rosa9Philippe eLa Rosa10Philippe eLa Rosa11Georges eLucotte12Georges eLucotte13Georges eLucotte14Séverine eLair15Séverine eLair16Séverine eLair17Virginie eBernard18Bruno eZeitouni19Bruno eZeitouni20Bruno eZeitouni21Fanny eCoffin22Fanny eCoffin23Fanny eCoffin24Gérôme eJules-Clément25Gérôme eJules-Clément26Gérôme eJules-Clément27Gérôme eJules-Clément28Florent eYvon29Florent eYvon30Florent eYvon31Alban eLermine32Alban eLermine33Alban eLermine34Patrick ePoullet35Patrick ePoullet36Patrick ePoullet37Stéphane eLiva38Stéphane eLiva39Stéphane eLiva40Stuart ePook41Stuart ePook42Stuart ePook43Tatiana ePopova44Camille eBarette45Camille eBarette46Camille eBarette47Camille eBarette48François ePrud'homme49François ePrud'homme50François ePrud'homme51Jean-Gabriel eDick52Maud eKamal53Christophe eLe Tourneau54Christophe eLe Tourneau55Emmanuel eBarillot56Emmanuel eBarillot57Emmanuel eBarillot58Philippe eHupé59Philippe eHupé60Philippe eHupé61Philippe eHupé62Institut CurieINSERMMines ParisTechInstitut CurieINSERMMines ParisTechInstitut CurieINSERMMines ParisTechInstitut CurieINSERMMines ParisTechInstitut CurieINSERMMines ParisTechInstitut CurieINSERMMines ParisTechInstitut CurieInstitut CurieINSERMMines ParisTechInstitut CurieINSERMMines ParisTechInstitut CurieINSERMMines ParisTechINSERMInstitut CurieINSERMMines ParisTechInstitut CurieINSERMMines ParisTechInstitut CurieINSERMMines ParisTechInstitut CurieINSERMMines ParisTechInstitut CurieINSERMMines ParisTechINSERMInstitut CurieINSERMMines ParisTechInstitut CurieInstitut CurieInstitut CurieInstitut CurieInstitut CurieInstitut CurieINSERMInstitut CurieInstitut CurieINSERMMines ParisTechInstitut CurieINSERMMines ParisTechCNRSPrecision medicine (PM) requires the delivery of individually adapted medical care based on the genetic characteristics of each patient and his/her tumor. The last decade witnessed the development of high-throughput technologies such as microarrays and next-generation sequencing which paved the way to PM in the field of oncology. While the cost of these technologies decreases, we are facing an exponential increase in the amount of data produced. Our ability to use this information in daily practice relies strongly on the availability of an efficient bioinformatics system that assists in the translation of knowledge from the bench towards molecular targeting and diagnosis. Clinical trials and routine diagnoses constitute different approaches, both requiring a strong bioinformatics environment capable of i) warranting the integration and the traceability of data, ii) ensuring the correct processing and analyses of genomic data and iii) applying well-defined and reproducible procedures for workflow management and decision-making. To address the issues, a seamless information system was developed at Institut Curie which facilitates the data integration and tracks in real-time the processing of individual samples. Moreover, computational pipelines were developed to identify reliably genomic alterations and mutations from the molecular profiles of each patient. After a rigorous quality control, a meaningful report is delivered to the clinicians and biologists for the therapeutic decision. The complete bioinformatics environment and the key points of its implementation are presented in the context of the SHIVA clinical trial, a multicentric randomized phase II trial comparing targeted therapy based on tumor molecular profiling versus conventional therapy in patients with refractory cancer. The numerous challenges faced in practice during the setting up and the conduct of this trial are discussed as an illustration of PM application.http://journal.frontiersin.org/Journal/10.3389/fgene.2014.00152/fullbioinformaticsSequencingClinical TrialoncologySHIVAprecision medicine |