Cargando…

The cancer precision medicine knowledge base for structured clinical-grade mutations and interpretations

Objective: This paper describes the Precision Medicine Knowledge Base (PMKB; https://pmkb.weill.cornell.edu), an interactive online application for collaborative editing, maintenance, and sharing of structured clinical-grade cancer mutation interpretations. Materials and Methods: PMKB was built usin...

Descripción completa

Detalles Bibliográficos
Autores principales: Huang, Linda, Fernandes, Helen, Zia, Hamid, Tavassoli, Peyman, Rennert, Hanna, Pisapia, David, Imielinski, Marcin, Sboner, Andrea, Rubin, Mark A, Kluk, Michael, Elemento, Olivier
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5391733/
https://www.ncbi.nlm.nih.gov/pubmed/27789569
http://dx.doi.org/10.1093/jamia/ocw148
_version_ 1783229331377487872
author Huang, Linda
Fernandes, Helen
Zia, Hamid
Tavassoli, Peyman
Rennert, Hanna
Pisapia, David
Imielinski, Marcin
Sboner, Andrea
Rubin, Mark A
Kluk, Michael
Elemento, Olivier
author_facet Huang, Linda
Fernandes, Helen
Zia, Hamid
Tavassoli, Peyman
Rennert, Hanna
Pisapia, David
Imielinski, Marcin
Sboner, Andrea
Rubin, Mark A
Kluk, Michael
Elemento, Olivier
author_sort Huang, Linda
collection PubMed
description Objective: This paper describes the Precision Medicine Knowledge Base (PMKB; https://pmkb.weill.cornell.edu), an interactive online application for collaborative editing, maintenance, and sharing of structured clinical-grade cancer mutation interpretations. Materials and Methods: PMKB was built using the Ruby on Rails Web application framework. Leveraging existing standards such as the Human Genome Variation Society variant description format, we implemented a data model that links variants to tumor-specific and tissue-specific interpretations. Key features of PMKB include support for all major variant types, standardized authentication, distinct user roles including high-level approvers, and detailed activity history. A REpresentational State Transfer (REST) application-programming interface (API) was implemented to query the PMKB programmatically. Results: At the time of writing, PMKB contains 457 variant descriptions with 281 clinical-grade interpretations. The EGFR, BRAF, KRAS, and KIT genes are associated with the largest numbers of interpretable variants. PMKB’s interpretations have been used in over 1500 AmpliSeq tests and 750 whole-exome sequencing tests. The interpretations are accessed either directly via the Web interface or programmatically via the existing API. Discussion: An accurate and up-to-date knowledge base of genomic alterations of clinical significance is critical to the success of precision medicine programs. The open-access, programmatically accessible PMKB represents an important attempt at creating such a resource in the field of oncology. Conclusion: The PMKB was designed to help collect and maintain clinical-grade mutation interpretations and facilitate reporting for clinical cancer genomic testing. The PMKB was also designed to enable the creation of clinical cancer genomics automated reporting pipelines via an API.
format Online
Article
Text
id pubmed-5391733
institution National Center for Biotechnology Information
language English
publishDate 2017
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-53917332017-04-21 The cancer precision medicine knowledge base for structured clinical-grade mutations and interpretations Huang, Linda Fernandes, Helen Zia, Hamid Tavassoli, Peyman Rennert, Hanna Pisapia, David Imielinski, Marcin Sboner, Andrea Rubin, Mark A Kluk, Michael Elemento, Olivier J Am Med Inform Assoc Research and Applications Objective: This paper describes the Precision Medicine Knowledge Base (PMKB; https://pmkb.weill.cornell.edu), an interactive online application for collaborative editing, maintenance, and sharing of structured clinical-grade cancer mutation interpretations. Materials and Methods: PMKB was built using the Ruby on Rails Web application framework. Leveraging existing standards such as the Human Genome Variation Society variant description format, we implemented a data model that links variants to tumor-specific and tissue-specific interpretations. Key features of PMKB include support for all major variant types, standardized authentication, distinct user roles including high-level approvers, and detailed activity history. A REpresentational State Transfer (REST) application-programming interface (API) was implemented to query the PMKB programmatically. Results: At the time of writing, PMKB contains 457 variant descriptions with 281 clinical-grade interpretations. The EGFR, BRAF, KRAS, and KIT genes are associated with the largest numbers of interpretable variants. PMKB’s interpretations have been used in over 1500 AmpliSeq tests and 750 whole-exome sequencing tests. The interpretations are accessed either directly via the Web interface or programmatically via the existing API. Discussion: An accurate and up-to-date knowledge base of genomic alterations of clinical significance is critical to the success of precision medicine programs. The open-access, programmatically accessible PMKB represents an important attempt at creating such a resource in the field of oncology. Conclusion: The PMKB was designed to help collect and maintain clinical-grade mutation interpretations and facilitate reporting for clinical cancer genomic testing. The PMKB was also designed to enable the creation of clinical cancer genomics automated reporting pipelines via an API. Oxford University Press 2017-05 2016-10-27 /pmc/articles/PMC5391733/ /pubmed/27789569 http://dx.doi.org/10.1093/jamia/ocw148 Text en © The Author 2016. Published by Oxford University Press on behalf of the American Medical Informatics Association. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Research and Applications
Huang, Linda
Fernandes, Helen
Zia, Hamid
Tavassoli, Peyman
Rennert, Hanna
Pisapia, David
Imielinski, Marcin
Sboner, Andrea
Rubin, Mark A
Kluk, Michael
Elemento, Olivier
The cancer precision medicine knowledge base for structured clinical-grade mutations and interpretations
title The cancer precision medicine knowledge base for structured clinical-grade mutations and interpretations
title_full The cancer precision medicine knowledge base for structured clinical-grade mutations and interpretations
title_fullStr The cancer precision medicine knowledge base for structured clinical-grade mutations and interpretations
title_full_unstemmed The cancer precision medicine knowledge base for structured clinical-grade mutations and interpretations
title_short The cancer precision medicine knowledge base for structured clinical-grade mutations and interpretations
title_sort cancer precision medicine knowledge base for structured clinical-grade mutations and interpretations
topic Research and Applications
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5391733/
https://www.ncbi.nlm.nih.gov/pubmed/27789569
http://dx.doi.org/10.1093/jamia/ocw148
work_keys_str_mv AT huanglinda thecancerprecisionmedicineknowledgebaseforstructuredclinicalgrademutationsandinterpretations
AT fernandeshelen thecancerprecisionmedicineknowledgebaseforstructuredclinicalgrademutationsandinterpretations
AT ziahamid thecancerprecisionmedicineknowledgebaseforstructuredclinicalgrademutationsandinterpretations
AT tavassolipeyman thecancerprecisionmedicineknowledgebaseforstructuredclinicalgrademutationsandinterpretations
AT rennerthanna thecancerprecisionmedicineknowledgebaseforstructuredclinicalgrademutationsandinterpretations
AT pisapiadavid thecancerprecisionmedicineknowledgebaseforstructuredclinicalgrademutationsandinterpretations
AT imielinskimarcin thecancerprecisionmedicineknowledgebaseforstructuredclinicalgrademutationsandinterpretations
AT sbonerandrea thecancerprecisionmedicineknowledgebaseforstructuredclinicalgrademutationsandinterpretations
AT rubinmarka thecancerprecisionmedicineknowledgebaseforstructuredclinicalgrademutationsandinterpretations
AT klukmichael thecancerprecisionmedicineknowledgebaseforstructuredclinicalgrademutationsandinterpretations
AT elementoolivier thecancerprecisionmedicineknowledgebaseforstructuredclinicalgrademutationsandinterpretations
AT huanglinda cancerprecisionmedicineknowledgebaseforstructuredclinicalgrademutationsandinterpretations
AT fernandeshelen cancerprecisionmedicineknowledgebaseforstructuredclinicalgrademutationsandinterpretations
AT ziahamid cancerprecisionmedicineknowledgebaseforstructuredclinicalgrademutationsandinterpretations
AT tavassolipeyman cancerprecisionmedicineknowledgebaseforstructuredclinicalgrademutationsandinterpretations
AT rennerthanna cancerprecisionmedicineknowledgebaseforstructuredclinicalgrademutationsandinterpretations
AT pisapiadavid cancerprecisionmedicineknowledgebaseforstructuredclinicalgrademutationsandinterpretations
AT imielinskimarcin cancerprecisionmedicineknowledgebaseforstructuredclinicalgrademutationsandinterpretations
AT sbonerandrea cancerprecisionmedicineknowledgebaseforstructuredclinicalgrademutationsandinterpretations
AT rubinmarka cancerprecisionmedicineknowledgebaseforstructuredclinicalgrademutationsandinterpretations
AT klukmichael cancerprecisionmedicineknowledgebaseforstructuredclinicalgrademutationsandinterpretations
AT elementoolivier cancerprecisionmedicineknowledgebaseforstructuredclinicalgrademutationsandinterpretations