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

Joel W Neal ¹, Katherine Minichiello ^2,3, Ryan Brennick ⁴

¹Department of Medicine, Stanford Cancer Institute, Division of Oncology, Stanford University, Palo Alto, CA, United States.
²SWOG Statistics and Data Management Center, Seattle, WA, United States.
³Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, United States.
⁴Clinical Operations, Foundation Medicine, Inc., Cambridge, MA, United States.
⁵Clinical Development, Foundation Medicine, Inc., Cambridge, MA, United State.
⁶Pathology, Foundation Medicine, Inc., Cambridge, MA, United States.
⁷Northwestern University-Feinberg School of Medicine, Chicago, IL, United States.
⁸Yale Comprehensive Cancer Center, New Haven, CT, United States.
⁹Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, United States.
¹⁰Department of Hematology/Oncology, Fox Chase Cancer Center, Philadelphia, PA, United States.
¹¹Clinical Research Division, Fred Hutchison Cancer Center Seattle WA, United States.
¹²Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, United States.

⁰Department of Medicine, Stanford Cancer Institute, Division of Oncology, Stanford University, Palo Alto, CA, United States.

The Oncologist +

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April 10, 2024

View abstract on PubMed

Summary

Genomic data reanalysis (GDR) successfully repurposed existing commercial genomic data for cancer clinical trial eligibility, overcoming tissue limitations. This bioinformatics pipeline expedited patient assignment to therapeutic substudies, improving trial enrollment rates.

Area Of Science

Oncology
Bioinformatics
Clinical Trials

Background

Cancer clinical trials often require central confirmation of tumor genomic profiling.
Tissue exhaustion from standard-of-care testing can limit patient enrollment in these trials.
Master protocols like Lung-MAP necessitate specific genomic assay results for patient assignment.

Purpose Of The Study

To develop and implement a Genomic Data Reanalysis (GDR) process for repurposing existing commercial vendor raw genomic data.
To enable patient eligibility and assignment to therapeutic substudies within the Lung-MAP master protocol.
To overcome challenges associated with tissue sample limitations in clinical trials.

Main Methods

Developed a scalable bioinformatic pipeline for Genomic Data Reanalysis (GDR).
Applied GDR to repurpose existing commercial vendor raw genomic data for patient eligibility in the Lung-MAP trial.
Compared GDR results and turnaround time with traditional tissue-based testing.

Main Results

Successfully generated molecular results for 369 of 374 patients (98.7%) using GDR for Lung-MAP.
Achieved a median time of 9 days from request to result for GDR.
In comparison, tissue samples yielded results for 87.4% of patients (691/791) in a median of 14 days post-acquisition.

Conclusions

Genomic Data Reanalysis (GDR) is an effective and scalable method for clinical trial eligibility.
GDR significantly expedites the generation of molecular results compared to traditional tissue testing.
This approach enhances patient enrollment by overcoming tissue limitations in biomarker-driven cancer trials.

Keywords:

Lung-MAP biomarker clinical trial eligibility genomic profiling