Determining genomic rearrangements in clinical lung specimens for assessment of metastatic disease, actionable targets and disease monitoring

Abstract

Introduction : Large genomic rearrangements are numerous in lung tumors, with several recurrent events commonly screened for therapeutic intent. The uniqueness of events provides tumor specific signatures useful in distinguishing independent primary tumors from intrapulmonary metastases in multifocal disease and as markers for disease monitoring in the blood. Accurate mapping of structural variations in clinical tumor biopsy and cytology specimens from a single test would hold significant clinical utility. Methods: Methodologies were developed to partner a wide range of clinical specimens, including core biopsies, tumor touch preps, bronchoscopic and cytology specimens, with sequencing protocols. A direct in situ whole genome amplification methodology was specifically developed to generate genomic DNA from limited clinical specimens. Analysis was performed on tissues obtained directly from clinical procedures on consented patients in the Mayo Clinic lung cancer practice. Results: Protocols successfully generated reproducible structural variance profiles on a wide range of clinical specimens including fresh frozen, alcohol fixed and air dried tissues. Bioinformatics algorithms efficiently distinguished independent primaries and identified related tumors. Numerous potential targetable events were observed, with the precise mapping of events enabling determination of complex rearrangements. The utility of using large genomic rearrangements for monitoring in cell-free DNA was also demonstrated. Conclusion: We describe a robust sequencing test, applicable to a wide range of clinical specimens, providing significant clinical impact.