Implementation of Whole-Genome and Transcriptome Sequencing Into Clinical Cancer Care

Edwin Cuppen; Olivier Elemento; Richard Rosenquist; Svetlana Nikic; Maarten IJzerman; Isabelle Durand Zaleski; Geert Frederix; Lars-Åke Levin; Charles G Mullighan; Reinhard Buettner; Trevor J Pugh; Sean Grimmond; Carlos Caldas; Fabrice Andre; Ilse Custers; Elias Campo; Hans van Snellenberg; Anna Schuh; Hidewaki Nakagawa; Christof von Kalle; Torsten Haferlach; Stefan Fröhling; Vaidehi Jobanputra

doi:10.1200/PO.22.00245

Implementation of Whole-Genome and Transcriptome Sequencing Into Clinical Cancer Care

Edwin Cuppen, Olivier Elemento, Richard Rosenquist, Svetlana Nikic, Maarten IJzerman, Isabelle Durand Zaleski, Geert Frederix, Lars-Åke Levin, Charles G Mullighan, Reinhard Buettner, Trevor J Pugh, Sean Grimmond, Carlos Caldas, Fabrice Andre, Ilse Custers, Elias Campo, Hans van Snellenberg, Anna Schuh, Hidewaki Nakagawa, Christof von KalleTorsten Haferlach, Stefan Fröhling, Vaidehi Jobanputra

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

Abstract

PURPOSE: The combination of whole-genome and transcriptome sequencing (WGTS) is expected to transform diagnosis and treatment for patients with cancer. WGTS is a comprehensive precision diagnostic test that is starting to replace the standard of care for oncology molecular testing in health care systems around the world; however, the implementation and widescale adoption of this best-in-class testing is lacking.

METHODS: Here, we address the barriers in integrating WGTS for cancer diagnostics and treatment selection and answer questions regarding utility in different cancer types, cost-effectiveness and affordability, and other practical considerations for WGTS implementation.

RESULTS: We review the current studies implementing WGTS in health care systems and provide a synopsis of the clinical evidence and insights into practical considerations for WGTS implementation. We reflect on regulatory, costs, reimbursement, and incidental findings aspects of this test.

CONCLUSION: WGTS is an appropriate comprehensive clinical test for many tumor types and can replace multiple, cascade testing approaches currently performed. Decreasing sequencing cost, increasing number of clinically relevant aberrations and discovery of more complex biomarkers of treatment response, should pave the way for health care systems and laboratories in implementing WGTS into clinical practice, to transform diagnosis and treatment for patients with cancer.

Original language	English
Article number	e2200245
Journal	JCO Precision Oncology
Volume	6
DOIs	https://doi.org/10.1200/PO.22.00245
Publication status	Published - Dec 2022

Keywords

Humans
Neoplasms/diagnosis

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10.1200/PO.22.00245

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Cuppen, E., Elemento, O., Rosenquist, R., Nikic, S., IJzerman, M., Zaleski, I. D., Frederix, G., Levin, L.-Å., Mullighan, C. G., Buettner, R., Pugh, T. J., Grimmond, S., Caldas, C., Andre, F., Custers, I., Campo, E., van Snellenberg, H., Schuh, A., Nakagawa, H., ... Jobanputra, V. (2022). Implementation of Whole-Genome and Transcriptome Sequencing Into Clinical Cancer Care. JCO Precision Oncology, 6, Article e2200245. https://doi.org/10.1200/PO.22.00245

@article{2a832b20a15743dcb1cb6221c82c6b68,

title = "Implementation of Whole-Genome and Transcriptome Sequencing Into Clinical Cancer Care",

abstract = "PURPOSE: The combination of whole-genome and transcriptome sequencing (WGTS) is expected to transform diagnosis and treatment for patients with cancer. WGTS is a comprehensive precision diagnostic test that is starting to replace the standard of care for oncology molecular testing in health care systems around the world; however, the implementation and widescale adoption of this best-in-class testing is lacking.METHODS: Here, we address the barriers in integrating WGTS for cancer diagnostics and treatment selection and answer questions regarding utility in different cancer types, cost-effectiveness and affordability, and other practical considerations for WGTS implementation.RESULTS: We review the current studies implementing WGTS in health care systems and provide a synopsis of the clinical evidence and insights into practical considerations for WGTS implementation. We reflect on regulatory, costs, reimbursement, and incidental findings aspects of this test.CONCLUSION: WGTS is an appropriate comprehensive clinical test for many tumor types and can replace multiple, cascade testing approaches currently performed. Decreasing sequencing cost, increasing number of clinically relevant aberrations and discovery of more complex biomarkers of treatment response, should pave the way for health care systems and laboratories in implementing WGTS into clinical practice, to transform diagnosis and treatment for patients with cancer.",

keywords = "Humans, Neoplasms/diagnosis",

author = "Edwin Cuppen and Olivier Elemento and Richard Rosenquist and Svetlana Nikic and Maarten IJzerman and Zaleski, {Isabelle Durand} and Geert Frederix and Lars-{\AA}ke Levin and Mullighan, {Charles G} and Reinhard Buettner and Pugh, {Trevor J} and Sean Grimmond and Carlos Caldas and Fabrice Andre and Ilse Custers and Elias Campo and {van Snellenberg}, Hans and Anna Schuh and Hidewaki Nakagawa and {von Kalle}, Christof and Torsten Haferlach and Stefan Fr{\"o}hling and Vaidehi Jobanputra",

year = "2022",

month = dec,

doi = "10.1200/PO.22.00245",

language = "English",

volume = "6",

}

Cuppen, E, Elemento, O, Rosenquist, R, Nikic, S, IJzerman, M, Zaleski, ID, Frederix, G, Levin, L-Å, Mullighan, CG, Buettner, R, Pugh, TJ, Grimmond, S, Caldas, C, Andre, F, Custers, I, Campo, E, van Snellenberg, H, Schuh, A, Nakagawa, H, von Kalle, C, Haferlach, T, Fröhling, S & Jobanputra, V 2022, 'Implementation of Whole-Genome and Transcriptome Sequencing Into Clinical Cancer Care', JCO Precision Oncology, vol. 6, e2200245. https://doi.org/10.1200/PO.22.00245

TY - JOUR

T1 - Implementation of Whole-Genome and Transcriptome Sequencing Into Clinical Cancer Care

AU - Cuppen, Edwin

AU - Elemento, Olivier

AU - Rosenquist, Richard

AU - Nikic, Svetlana

AU - IJzerman, Maarten

AU - Zaleski, Isabelle Durand

AU - Frederix, Geert

AU - Levin, Lars-Åke

AU - Mullighan, Charles G

AU - Buettner, Reinhard

AU - Pugh, Trevor J

AU - Grimmond, Sean

AU - Caldas, Carlos

AU - Andre, Fabrice

AU - Custers, Ilse

AU - Campo, Elias

AU - van Snellenberg, Hans

AU - Schuh, Anna

AU - Nakagawa, Hidewaki

AU - von Kalle, Christof

AU - Haferlach, Torsten

AU - Fröhling, Stefan

AU - Jobanputra, Vaidehi

PY - 2022/12

Y1 - 2022/12

N2 - PURPOSE: The combination of whole-genome and transcriptome sequencing (WGTS) is expected to transform diagnosis and treatment for patients with cancer. WGTS is a comprehensive precision diagnostic test that is starting to replace the standard of care for oncology molecular testing in health care systems around the world; however, the implementation and widescale adoption of this best-in-class testing is lacking.METHODS: Here, we address the barriers in integrating WGTS for cancer diagnostics and treatment selection and answer questions regarding utility in different cancer types, cost-effectiveness and affordability, and other practical considerations for WGTS implementation.RESULTS: We review the current studies implementing WGTS in health care systems and provide a synopsis of the clinical evidence and insights into practical considerations for WGTS implementation. We reflect on regulatory, costs, reimbursement, and incidental findings aspects of this test.CONCLUSION: WGTS is an appropriate comprehensive clinical test for many tumor types and can replace multiple, cascade testing approaches currently performed. Decreasing sequencing cost, increasing number of clinically relevant aberrations and discovery of more complex biomarkers of treatment response, should pave the way for health care systems and laboratories in implementing WGTS into clinical practice, to transform diagnosis and treatment for patients with cancer.

AB - PURPOSE: The combination of whole-genome and transcriptome sequencing (WGTS) is expected to transform diagnosis and treatment for patients with cancer. WGTS is a comprehensive precision diagnostic test that is starting to replace the standard of care for oncology molecular testing in health care systems around the world; however, the implementation and widescale adoption of this best-in-class testing is lacking.METHODS: Here, we address the barriers in integrating WGTS for cancer diagnostics and treatment selection and answer questions regarding utility in different cancer types, cost-effectiveness and affordability, and other practical considerations for WGTS implementation.RESULTS: We review the current studies implementing WGTS in health care systems and provide a synopsis of the clinical evidence and insights into practical considerations for WGTS implementation. We reflect on regulatory, costs, reimbursement, and incidental findings aspects of this test.CONCLUSION: WGTS is an appropriate comprehensive clinical test for many tumor types and can replace multiple, cascade testing approaches currently performed. Decreasing sequencing cost, increasing number of clinically relevant aberrations and discovery of more complex biomarkers of treatment response, should pave the way for health care systems and laboratories in implementing WGTS into clinical practice, to transform diagnosis and treatment for patients with cancer.

KW - Humans

KW - Neoplasms/diagnosis

U2 - 10.1200/PO.22.00245

DO - 10.1200/PO.22.00245

M3 - Review article

C2 - 36480778

VL - 6

JO - JCO Precision Oncology

JF - JCO Precision Oncology

M1 - e2200245

ER -

Implementation of Whole-Genome and Transcriptome Sequencing Into Clinical Cancer Care

Abstract

Keywords

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