A process to reanalyze clinical DNA sequencing data for biomarker matching in the Lung-MAP Master Protocol

Joel W Neal; Katherine Minichiello; Ryan Brennick; Richard S P Huang; Matthew C Hiemenz; Cornel Amler; Jyoti Patel; Roy Herbst; Karen L Reckamp; Hossein Borghaei; Louise Highleyman; Mary W Redman; Lincoln W Pasquina; David E Kozono

doi:10.1093/oncolo/oyae062

A process to reanalyze clinical DNA sequencing data for biomarker matching in the Lung-MAP Master Protocol

Joel W Neal, Katherine Minichiello, Ryan Brennick, Richard S P Huang, Matthew C Hiemenz, Cornel Amler, Jyoti Patel, Roy Herbst, Karen L Reckamp, Hossein Borghaei, Louise Highleyman, Mary W Redman, Lincoln W Pasquina, David E Kozono

Research output: Contribution to journal › Article › peer-review

Abstract

For cancer clinical trials that require central confirmation of tumor genomic profiling, exhaustion of tissue from standard-of-care testing may prevent enrollment. For Lung-MAP, a master protocol that requires results from a defined centralized clinical trial assay to assign patients to a therapeutic substudy, we developed a process to repurpose existing commercial vendor raw genomic data for eligibility: genomic data reanalysis (GDR). Molecular results for substudy assignment were successfully generated for 369 of the first 374 patients (98.7%) using GDR for Lung-MAP, with a median time from request to result of 9 days. During the same period, 691 of 791 (87.4%) tissue samples received successfully yielded results, in a median of 14 days beyond sample acquisition. GDR is a scalable bioinformatic pipeline that expedites reanalysis of existing data for clinical trials in which validated integral biomarker testing is required for participation.

Original language	English
Pages (from-to)	e843-e847
Journal	Oncologist
Volume	29
Issue number	6
Early online date	Mar 10 2024
DOIs	https://doi.org/10.1093/oncolo/oyae062
State	Published - Jun 2024

Keywords

Biomarkers, Tumor/genetics
Genomics/methods
Humans
Lung Neoplasms/genetics
Sequence Analysis, DNA/methods
clinical trial
genomic profiling
eligibility
Lung-MAP
biomarker

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1093/oncolo/oyae062

Cite this

Neal, J. W., Minichiello, K., Brennick, R., Huang, R. S. P., Hiemenz, M. C., Amler, C., Patel, J., Herbst, R., Reckamp, K. L., Borghaei, H., Highleyman, L., Redman, M. W., Pasquina, L. W., & Kozono, D. E. (2024). A process to reanalyze clinical DNA sequencing data for biomarker matching in the Lung-MAP Master Protocol. Oncologist, 29(6), e843-e847. https://doi.org/10.1093/oncolo/oyae062

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title = "A process to reanalyze clinical DNA sequencing data for biomarker matching in the Lung-MAP Master Protocol",

abstract = "For cancer clinical trials that require central confirmation of tumor genomic profiling, exhaustion of tissue from standard-of-care testing may prevent enrollment. For Lung-MAP, a master protocol that requires results from a defined centralized clinical trial assay to assign patients to a therapeutic substudy, we developed a process to repurpose existing commercial vendor raw genomic data for eligibility: genomic data reanalysis (GDR). Molecular results for substudy assignment were successfully generated for 369 of the first 374 patients (98.7%) using GDR for Lung-MAP, with a median time from request to result of 9 days. During the same period, 691 of 791 (87.4%) tissue samples received successfully yielded results, in a median of 14 days beyond sample acquisition. GDR is a scalable bioinformatic pipeline that expedites reanalysis of existing data for clinical trials in which validated integral biomarker testing is required for participation.",

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Neal, JW, Minichiello, K, Brennick, R, Huang, RSP, Hiemenz, MC, Amler, C, Patel, J, Herbst, R, Reckamp, KL, Borghaei, H, Highleyman, L, Redman, MW, Pasquina, LW & Kozono, DE 2024, 'A process to reanalyze clinical DNA sequencing data for biomarker matching in the Lung-MAP Master Protocol', Oncologist, vol. 29, no. 6, pp. e843-e847. https://doi.org/10.1093/oncolo/oyae062

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AU - Neal, Joel W

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AU - Brennick, Ryan

AU - Huang, Richard S P

AU - Hiemenz, Matthew C

AU - Amler, Cornel

AU - Patel, Jyoti

AU - Herbst, Roy

AU - Reckamp, Karen L

AU - Borghaei, Hossein

AU - Highleyman, Louise

AU - Redman, Mary W

AU - Pasquina, Lincoln W

AU - Kozono, David E

N1 - © The Author(s) 2024. Published by Oxford University Press.

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N2 - For cancer clinical trials that require central confirmation of tumor genomic profiling, exhaustion of tissue from standard-of-care testing may prevent enrollment. For Lung-MAP, a master protocol that requires results from a defined centralized clinical trial assay to assign patients to a therapeutic substudy, we developed a process to repurpose existing commercial vendor raw genomic data for eligibility: genomic data reanalysis (GDR). Molecular results for substudy assignment were successfully generated for 369 of the first 374 patients (98.7%) using GDR for Lung-MAP, with a median time from request to result of 9 days. During the same period, 691 of 791 (87.4%) tissue samples received successfully yielded results, in a median of 14 days beyond sample acquisition. GDR is a scalable bioinformatic pipeline that expedites reanalysis of existing data for clinical trials in which validated integral biomarker testing is required for participation.

AB - For cancer clinical trials that require central confirmation of tumor genomic profiling, exhaustion of tissue from standard-of-care testing may prevent enrollment. For Lung-MAP, a master protocol that requires results from a defined centralized clinical trial assay to assign patients to a therapeutic substudy, we developed a process to repurpose existing commercial vendor raw genomic data for eligibility: genomic data reanalysis (GDR). Molecular results for substudy assignment were successfully generated for 369 of the first 374 patients (98.7%) using GDR for Lung-MAP, with a median time from request to result of 9 days. During the same period, 691 of 791 (87.4%) tissue samples received successfully yielded results, in a median of 14 days beyond sample acquisition. GDR is a scalable bioinformatic pipeline that expedites reanalysis of existing data for clinical trials in which validated integral biomarker testing is required for participation.

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KW - Genomics/methods

KW - Humans

KW - Lung Neoplasms/genetics

KW - Sequence Analysis, DNA/methods

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KW - eligibility

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KW - biomarker

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JO - Oncologist

JF - Oncologist

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ER -

A process to reanalyze clinical DNA sequencing data for biomarker matching in the Lung-MAP Master Protocol

Abstract

Keywords

UN SDGs

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