Molecular profiling of tumors
Inventors
Von Hoff, Daniel D. • Wright, Alan • McGinniss, Matthew J. • Bender, Ryan P. • Loesch, David M. • Alarcon, Arlet • Penny, Robert J. • Pawlowski, Traci
Assignees
Interested in licensing this patent?
MTEC can help explore whether this patent might be available for licensing for your application.
Publication Number
US-8768629-B2
Publication Date
2014-07-01
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 method of identifying one or more candidate treatment for a subject in need of treatment for a cancer by performing a multi-assay molecular profiling panel on a sample. The method includes immunohistochemistry (IHC) analysis on TOP1, TYMS, MGMT, PTEN, ERBB2, and SPARC; microarray analysis on TOP1, TYMS, MGMT, PTEN, ERBB2, and SPARC; fluorescent in-situ hybridization (FISH) analysis on ERBB2; and DNA sequencing analysis on PIK3CA, KRAS, and BRAF. The method is directed to identifying candidate treatments based on these measured biomarkers.
A computer accesses a rules database comprising biomarker-drug association rules and performs the rules in the database for each gene or gene product analyzed in the IHC, microarray, FISH, and DNA sequencing steps. The rules-based processing links the biomarker results to candidate therapeutic options.
After performing the rules, the method produces a computer generated report based on the rules as performed. The report identifies the one or more candidate treatment for the subject and is described together with biomarker panels and representative mapping of biomarker results to recommended versus resistant therapeutic agents using Table 1 and Table 2.
Claims Coverage
The independent claim describes one multi-assay biomarker profiling method for cancer treatment identification, with rules database interpretation and computer-generated reporting. The inventive coverage combines four assay types and biomarker-drug association rule execution to identify one or more candidate treatments.
Multi-assay biomarker profiling panel for cancer treatment identification
Performing an immunohistochemistry (IHC) analysis on a sample on at least TOP1, TYMS, MGMT, PTEN, ERBB2, and SPARC; performing a microarray analysis on the sample on at least TOP1, TYMS, MGMT, PTEN, ERBB2, and SPARC; performing a fluorescent in-situ hybridization (FISH) analysis on the sample on ERBB2; and performing DNA sequencing analysis on the sample on PIK3CA, KRAS, and BRAF.
Rules database application of biomarker-drug association rules
Using a computer to access a rules database comprising biomarker-drug association rules and perform all rules in the database for each gene or gene product analyzed in the IHC, microarray, FISH, and DNA sequencing steps.
Computer generated report identifying candidate treatments
Producing a computer generated report based on the rules as performed, wherein the report identifies the one or more candidate treatment.
The claim coverage centers on a multi-assay biomarker panel, a computer applying biomarker-drug association rules from a rules database for each analyzed gene or gene product, and a computer generated report that identifies one or more candidate treatments.
Stated Advantages
Maps biomarker states to known treatment efficacy while excluding contraindications.
Produces a computer-generated report identifying one or more candidate treatment(s).
Supports prioritizing candidate therapies and updating rules using literature and clinical evidence.
Reported expected outcomes include extended progression free survival (PFS), disease free survival (DFS), overall survival (OS), and lifespan.
Documented Applications
Cancer treatment selection for a subject in need of treatment for a cancer by identifying one or more candidate treatments using biomarker profiling and rules-based interpretation.
Interested in licensing this patent?