OncoTree: A Cancer Classification System for Precision Oncology

Ritika Kundra; Hongxin Zhang; Robert Sheridan; Sahussapont Joseph Sirintrapun; Avery Wang; Angelica Ochoa; Manda Wilson; Benjamin Gross; Yichao Sun; Ramyasree Madupuri; Baby A. Satravada; Dalicia Reales; Efsevia Vakiani; Hikmat A. Al-Ahmadie; Ahmet Dogan; Maria Arcila; Ahmet Zehir; Steven Maron; Michael F. Berger; Cristina Viaplana; Katherine Janeway; Matthew Ducar; Lynette Sholl; Snjezana Dogan; Philippe Bedard; Lea F. Surrey; Iker Huerga Sanchez; Aijaz Syed; Anoop Balakrishnan Rema; Debyani Chakravarty; Sarah Suehnholz; Moriah Nissan; Gopakumar V. Iyer; Rajmohan Murali; Nancy Bouvier; Robert A. Soslow; David Hyman; Anas Younes; Andrew Intlekofer; James J. Harding; Richard D. Carvajal; Paul J. Sabbatini; Ghassan K. Abou-Alfa; Luc Morris; Yelena Y. Janjigian; Meighan M. Gallagher; Tara A. Soumerai; Ingo K. Mellinghoff; Abraham A. Hakimi; Matthew Fury; Jason T. Huse; Aditya Bagrodia; Meera Hameed; Stacy Thomas; Stuart Gardos; Ethan Cerami; Tali Mazor; Priti Kumari; Pichai Raman; Priyanka Shivdasani; Suzanne MacFarland; Scott Newman; Angela Waanders; Jianjiong Gao; David Solit; Nikolaus Schultz

doi:10.1200/CCI.20.00108

OncoTree: A Cancer Classification System for Precision Oncology

Ritika Kundra, Hongxin Zhang, Robert Sheridan, Sahussapont Joseph Sirintrapun, Avery Wang, Angelica Ochoa, Manda Wilson, Benjamin Gross, Yichao Sun, Ramyasree Madupuri, Baby A. Satravada, Dalicia Reales, Efsevia Vakiani, Hikmat A. Al-Ahmadie, Ahmet Dogan, Maria Arcila, Ahmet Zehir, Steven Maron, Michael F. Berger, Cristina ViaplanaKatherine Janeway, Matthew Ducar, Lynette Sholl, Snjezana Dogan, Philippe Bedard, Lea F. Surrey, Iker Huerga Sanchez, Aijaz Syed, Anoop Balakrishnan Rema, Debyani Chakravarty, Sarah Suehnholz, Moriah Nissan, Gopakumar V. Iyer, Rajmohan Murali, Nancy Bouvier, Robert A. Soslow, David Hyman, Anas Younes, Andrew Intlekofer, James J. Harding, Richard D. Carvajal, Paul J. Sabbatini, Ghassan K. Abou-Alfa, Luc Morris, Yelena Y. Janjigian, Meighan M. Gallagher, Tara A. Soumerai, Ingo K. Mellinghoff, Abraham A. Hakimi, Matthew Fury, Jason T. Huse, Aditya Bagrodia, Meera Hameed, Stacy Thomas, Stuart Gardos, Ethan Cerami, Tali Mazor, Priti Kumari, Pichai Raman, Priyanka Shivdasani, Suzanne MacFarland, Scott Newman, Angela Waanders, Jianjiong Gao, David Solit, Nikolaus Schultz

Research output: Contribution to journal › Review article › peer-review

43 Scopus citations

Abstract

PURPOSE Cancer classification is foundational for patient care and oncology research. Systems such as International Classification of Diseases for Oncology (ICD-O), Systematized Nomenclature of Medicine Clinical Terms (SNOMED-CT), and National Cancer Institute Thesaurus (NCIt) provide large sets of cancer classification terminologies but they lack a dynamic modernized cancer classification platform that addresses the fast-evolving needs in clinical reporting of genomic sequencing results and associated oncology research. METHODS To meet these needs, we have developed OncoTree, an open-source cancer classification system. It is maintained by a cross-institutional committee of oncologists, pathologists, scientists, and engineers, accessible via an open-source Web user interface and an application programming interface. RESULTS OncoTree currently includes 868 tumor types across 32 organ sites. OncoTree has been adopted as the tumor classification system for American Association for Cancer Research (AACR) Project Genomics Evidence Neoplasia Information Exchange (GENIE), a large genomic and clinical data-sharing consortium, and for clinical molecular testing efforts at Memorial Sloan Kettering Cancer Center and Dana-Farber Cancer Institute. It is also used by precision oncology tools such as OncoKB and cBioPortal for Cancer Genomics. CONCLUSION OncoTree is a dynamic and flexible community-driven cancer classification platform encompassing rare and common cancers that provides clinically relevant and appropriately granular cancer classification for clinical decision support systems and oncology research.

Original language	English (US)
Pages (from-to)	221-230
Number of pages	10
Journal	JCO Clinical Cancer Informatics
Volume	5
DOIs	https://doi.org/10.1200/CCI.20.00108
State	Published - 2021

ASJC Scopus subject areas

General Medicine

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Kundra, R., Zhang, H., Sheridan, R., Sirintrapun, S. J., Wang, A., Ochoa, A., Wilson, M., Gross, B., Sun, Y., Madupuri, R., Satravada, B. A., Reales, D., Vakiani, E., Al-Ahmadie, H. A., Dogan, A., Arcila, M., Zehir, A., Maron, S., Berger, M. F., ... Schultz, N. (2021). OncoTree: A Cancer Classification System for Precision Oncology. JCO Clinical Cancer Informatics, 5, 221-230. https://doi.org/10.1200/CCI.20.00108

Kundra, R, Zhang, H, Sheridan, R, Sirintrapun, SJ, Wang, A, Ochoa, A, Wilson, M, Gross, B, Sun, Y, Madupuri, R, Satravada, BA, Reales, D, Vakiani, E, Al-Ahmadie, HA, Dogan, A, Arcila, M, Zehir, A, Maron, S, Berger, MF, Viaplana, C, Janeway, K, Ducar, M, Sholl, L, Dogan, S, Bedard, P, Surrey, LF, Sanchez, IH, Syed, A, Rema, AB, Chakravarty, D, Suehnholz, S, Nissan, M, Iyer, GV, Murali, R, Bouvier, N, Soslow, RA, Hyman, D, Younes, A, Intlekofer, A, Harding, JJ, Carvajal, RD, Sabbatini, PJ, Abou-Alfa, GK, Morris, L, Janjigian, YY, Gallagher, MM, Soumerai, TA, Mellinghoff, IK, Hakimi, AA, Fury, M, Huse, JT, Bagrodia, A, Hameed, M, Thomas, S, Gardos, S, Cerami, E, Mazor, T, Kumari, P, Raman, P, Shivdasani, P, MacFarland, S, Newman, S, Waanders, A, Gao, J, Solit, D & Schultz, N 2021, 'OncoTree: A Cancer Classification System for Precision Oncology', JCO Clinical Cancer Informatics, vol. 5, pp. 221-230. https://doi.org/10.1200/CCI.20.00108

@article{ac59e92188ac47238469488f619c0b31,

title = "OncoTree: A Cancer Classification System for Precision Oncology",

abstract = "PURPOSE Cancer classification is foundational for patient care and oncology research. Systems such as International Classification of Diseases for Oncology (ICD-O), Systematized Nomenclature of Medicine Clinical Terms (SNOMED-CT), and National Cancer Institute Thesaurus (NCIt) provide large sets of cancer classification terminologies but they lack a dynamic modernized cancer classification platform that addresses the fast-evolving needs in clinical reporting of genomic sequencing results and associated oncology research. METHODS To meet these needs, we have developed OncoTree, an open-source cancer classification system. It is maintained by a cross-institutional committee of oncologists, pathologists, scientists, and engineers, accessible via an open-source Web user interface and an application programming interface. RESULTS OncoTree currently includes 868 tumor types across 32 organ sites. OncoTree has been adopted as the tumor classification system for American Association for Cancer Research (AACR) Project Genomics Evidence Neoplasia Information Exchange (GENIE), a large genomic and clinical data-sharing consortium, and for clinical molecular testing efforts at Memorial Sloan Kettering Cancer Center and Dana-Farber Cancer Institute. It is also used by precision oncology tools such as OncoKB and cBioPortal for Cancer Genomics. CONCLUSION OncoTree is a dynamic and flexible community-driven cancer classification platform encompassing rare and common cancers that provides clinically relevant and appropriately granular cancer classification for clinical decision support systems and oncology research.",

author = "Ritika Kundra and Hongxin Zhang and Robert Sheridan and Sirintrapun, {Sahussapont Joseph} and Avery Wang and Angelica Ochoa and Manda Wilson and Benjamin Gross and Yichao Sun and Ramyasree Madupuri and Satravada, {Baby A.} and Dalicia Reales and Efsevia Vakiani and Al-Ahmadie, {Hikmat A.} and Ahmet Dogan and Maria Arcila and Ahmet Zehir and Steven Maron and Berger, {Michael F.} and Cristina Viaplana and Katherine Janeway and Matthew Ducar and Lynette Sholl and Snjezana Dogan and Philippe Bedard and Surrey, {Lea F.} and Sanchez, {Iker Huerga} and Aijaz Syed and Rema, {Anoop Balakrishnan} and Debyani Chakravarty and Sarah Suehnholz and Moriah Nissan and Iyer, {Gopakumar V.} and Rajmohan Murali and Nancy Bouvier and Soslow, {Robert A.} and David Hyman and Anas Younes and Andrew Intlekofer and Harding, {James J.} and Carvajal, {Richard D.} and Sabbatini, {Paul J.} and Abou-Alfa, {Ghassan K.} and Luc Morris and Janjigian, {Yelena Y.} and Gallagher, {Meighan M.} and Soumerai, {Tara A.} and Mellinghoff, {Ingo K.} and Hakimi, {Abraham A.} and Matthew Fury and Huse, {Jason T.} and Aditya Bagrodia and Meera Hameed and Stacy Thomas and Stuart Gardos and Ethan Cerami and Tali Mazor and Priti Kumari and Pichai Raman and Priyanka Shivdasani and Suzanne MacFarland and Scott Newman and Angela Waanders and Jianjiong Gao and David Solit and Nikolaus Schultz",

note = "Publisher Copyright: {\textcopyright} 2021 by American Society of Clinical Oncology.",

year = "2021",

doi = "10.1200/CCI.20.00108",

language = "English (US)",

volume = "5",

pages = "221--230",

journal = "JCO Clinical Cancer Informatics",

issn = "2473-4276",

publisher = "American Society of Clinical Oncology",

}

TY - JOUR

T1 - OncoTree

T2 - A Cancer Classification System for Precision Oncology

AU - Kundra, Ritika

AU - Zhang, Hongxin

AU - Sheridan, Robert

AU - Sirintrapun, Sahussapont Joseph

AU - Wang, Avery

AU - Ochoa, Angelica

AU - Wilson, Manda

AU - Gross, Benjamin

AU - Sun, Yichao

AU - Madupuri, Ramyasree

AU - Satravada, Baby A.

AU - Reales, Dalicia

AU - Vakiani, Efsevia

AU - Al-Ahmadie, Hikmat A.

AU - Dogan, Ahmet

AU - Arcila, Maria

AU - Zehir, Ahmet

AU - Maron, Steven

AU - Berger, Michael F.

AU - Viaplana, Cristina

AU - Janeway, Katherine

AU - Ducar, Matthew

AU - Sholl, Lynette

AU - Dogan, Snjezana

AU - Bedard, Philippe

AU - Surrey, Lea F.

AU - Sanchez, Iker Huerga

AU - Syed, Aijaz

AU - Rema, Anoop Balakrishnan

AU - Chakravarty, Debyani

AU - Suehnholz, Sarah

AU - Nissan, Moriah

AU - Iyer, Gopakumar V.

AU - Murali, Rajmohan

AU - Bouvier, Nancy

AU - Soslow, Robert A.

AU - Hyman, David

AU - Younes, Anas

AU - Intlekofer, Andrew

AU - Harding, James J.

AU - Carvajal, Richard D.

AU - Sabbatini, Paul J.

AU - Abou-Alfa, Ghassan K.

AU - Morris, Luc

AU - Janjigian, Yelena Y.

AU - Gallagher, Meighan M.

AU - Soumerai, Tara A.

AU - Mellinghoff, Ingo K.

AU - Hakimi, Abraham A.

AU - Fury, Matthew

AU - Huse, Jason T.

AU - Bagrodia, Aditya

AU - Hameed, Meera

AU - Thomas, Stacy

AU - Gardos, Stuart

AU - Cerami, Ethan

AU - Mazor, Tali

AU - Kumari, Priti

AU - Raman, Pichai

AU - Shivdasani, Priyanka

AU - MacFarland, Suzanne

AU - Newman, Scott

AU - Waanders, Angela

AU - Gao, Jianjiong

AU - Solit, David

AU - Schultz, Nikolaus

PY - 2021

Y1 - 2021

N2 - PURPOSE Cancer classification is foundational for patient care and oncology research. Systems such as International Classification of Diseases for Oncology (ICD-O), Systematized Nomenclature of Medicine Clinical Terms (SNOMED-CT), and National Cancer Institute Thesaurus (NCIt) provide large sets of cancer classification terminologies but they lack a dynamic modernized cancer classification platform that addresses the fast-evolving needs in clinical reporting of genomic sequencing results and associated oncology research. METHODS To meet these needs, we have developed OncoTree, an open-source cancer classification system. It is maintained by a cross-institutional committee of oncologists, pathologists, scientists, and engineers, accessible via an open-source Web user interface and an application programming interface. RESULTS OncoTree currently includes 868 tumor types across 32 organ sites. OncoTree has been adopted as the tumor classification system for American Association for Cancer Research (AACR) Project Genomics Evidence Neoplasia Information Exchange (GENIE), a large genomic and clinical data-sharing consortium, and for clinical molecular testing efforts at Memorial Sloan Kettering Cancer Center and Dana-Farber Cancer Institute. It is also used by precision oncology tools such as OncoKB and cBioPortal for Cancer Genomics. CONCLUSION OncoTree is a dynamic and flexible community-driven cancer classification platform encompassing rare and common cancers that provides clinically relevant and appropriately granular cancer classification for clinical decision support systems and oncology research.

AB - PURPOSE Cancer classification is foundational for patient care and oncology research. Systems such as International Classification of Diseases for Oncology (ICD-O), Systematized Nomenclature of Medicine Clinical Terms (SNOMED-CT), and National Cancer Institute Thesaurus (NCIt) provide large sets of cancer classification terminologies but they lack a dynamic modernized cancer classification platform that addresses the fast-evolving needs in clinical reporting of genomic sequencing results and associated oncology research. METHODS To meet these needs, we have developed OncoTree, an open-source cancer classification system. It is maintained by a cross-institutional committee of oncologists, pathologists, scientists, and engineers, accessible via an open-source Web user interface and an application programming interface. RESULTS OncoTree currently includes 868 tumor types across 32 organ sites. OncoTree has been adopted as the tumor classification system for American Association for Cancer Research (AACR) Project Genomics Evidence Neoplasia Information Exchange (GENIE), a large genomic and clinical data-sharing consortium, and for clinical molecular testing efforts at Memorial Sloan Kettering Cancer Center and Dana-Farber Cancer Institute. It is also used by precision oncology tools such as OncoKB and cBioPortal for Cancer Genomics. CONCLUSION OncoTree is a dynamic and flexible community-driven cancer classification platform encompassing rare and common cancers that provides clinically relevant and appropriately granular cancer classification for clinical decision support systems and oncology research.

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UR - http://www.scopus.com/inward/citedby.url?scp=85102096013&partnerID=8YFLogxK

U2 - 10.1200/CCI.20.00108

DO - 10.1200/CCI.20.00108

M3 - Review article

C2 - 33625877

AN - SCOPUS:85102096013

SN - 2473-4276

VL - 5

SP - 221

EP - 230

JO - JCO Clinical Cancer Informatics

JF - JCO Clinical Cancer Informatics

ER -

OncoTree: A Cancer Classification System for Precision Oncology

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