Molecular profiling of tumors
Inventors
Von Hoff, Daniel D. • Loesch, David M. • Alarcon, Arlet • Penny, Robert J. • Wright, Alan • McGinniss, Matthew J. • Bender, Ryan P. • Pawlowski, Traci
Assignees
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Publication Number
US-9292660-B2
Publication Date
2016-03-22
Expiration Date
Abstract
Provided herein are methods and systems of molecular profiling of diseases, such as cancer. In some embodiments, the molecular profiling can be used to identify treatments for a disease, such as treatments that were not initially identified as a treatment for the disease or not expected to be a treatment for a particular disease.
Core Innovation
The invention provides a system for generating a report that identifies a therapeutic agent for an individual with lung cancer. The system includes at least one device configured to assay a plurality of molecular targets in a biological sample from the individual to determine molecular profile test values for the molecular targets, including PTEN, CTNNB1, cKIT, BRAF and PIK3CA.
The system further includes at least one computer database that provides a reference value for each molecular target and a listing of available therapeutic agents for the molecular targets. Computer-readable program code receives the molecular profile test values, compares each test value with its corresponding reference value from the database, and uses the comparison to indicate a likely benefit of a therapeutic agent.
A rules database maps biomarker expression and/or mutations, including biomarker states determined from the assays, to therapeutic agents. The mapping includes positive associations indicating likely benefit and contraindicating negative mappings indicating likely lack of benefit, and the report lists the molecular targets for which comparisons indicate likely benefit and the corresponding therapeutic agents identified from the database.
Claims Coverage
One independent claim is identified. The inventive features relate to lung-cancer-specific multi-target molecular profiling, reference-value comparison, database-driven therapeutic-agent identification, and report generation listing target membership and therapeutic agents associated with likely benefit.
Multi-target molecular profiling device for lung cancer
A system for generating a report identifying a therapeutic agent for an individual with lung cancer comprising at least one device configured to assay a plurality of molecular targets in a biological sample from the individual with lung cancer to determine molecular profile test values for the plurality of molecular targets, wherein the plurality of molecular targets comprises PTEN, CTNNB1, cKIT, BRAF and PIK3CA.
Reference-value and therapeutic-agent database
At least one computer database comprising a reference value for each of the plurality of molecular targets and a listing of available therapeutic agents for the plurality of molecular targets.
Compare molecular profile test values to reference values
A computer-readable program code comprising instructions to input the molecular profile test values and to compare each of the molecular profile test values with a corresponding reference value from the at least one computer database.
Identify therapeutic agents when comparison indicates likely benefit
A computer-readable program code comprising instructions to access the at least one computer database and to identify at least one therapeutic agent if present in the at least one computer database for each of the plurality of molecular targets wherein said comparison to the reference values indicates a likely benefit of the at least one therapeutic agent.
Generate report listing targets and therapeutic agents
A computer-readable program code comprising instructions to generate a report that comprises a listing of the members of the plurality of molecular targets for which the comparison to the reference value indicated a likely benefit of the at least one therapeutic agent and the at least one therapeutic agent identified.
Across the independent claim, the core claim coverage is a computer-based workflow that assays multiple lung-cancer molecular targets in a biological sample to obtain molecular profile test values, compares each test value to stored reference values, uses the comparison to indicate likely benefit, identifies available therapeutic agents from a database accordingly, and generates a report listing the molecular targets with likely benefit and the corresponding therapeutic agents.
Stated Advantages
The patent refers to reported clinical outcome improvements such as improved PFS/DFS/OS and lifespan when treatment selection is based on profiling-based selection.
Documented Applications
Methods and systems for molecular profiling of a biological sample from an individual with lung cancer in order to select candidate anticancer treatments.
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