Methods and systems for therapy monitoring and trial design
AssigneeScipher Medicine Corporation
InventorsSusan Ghiassian, Viatcheslav R. AKMAEV, Ivan VOITALOV
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Abstract
Described are methods and systems for identifying a disease gene expression signature determined to revert a disease gene expression signature in a subject suffering from a disease to a non-diseased expression signature (e.g., gene expression of a non-diseased subject). Also provided herein are methods of designing a study (e.g., a clinical trial) comprising identifying diseased subjects who exhibit a quantifiable change in the disease gene expression signature towards gene expression of a non-diseased subject.
Claims27
A method of treating a subject suffering from a disease, disorder, or condition, the method comprising:
- administering to a test subject a therapeutically effective amount of (i) a therapy, based at least in part on a trained machine learning classifier analyzing a disease gene expression signature to predict responsiveness of the test subject to the therapy, or (ii) a second therapy different from the therapy, based at least in part on the trained machine learning classifier analyzing the disease gene expression signature to predict non-responsiveness of the test subject to the therapy,
- wherein the disease gene expression signature is determined at least in part by:
- receiving gene expression data from a cohort of subjects suffering from the disease, disorder, or condition;
- stratifying the cohort of subjects into two or more groups based at least in part on the gene expression data;
- calculating differences in gene expression between the two or more groups of subjects and a group of non-diseased subjects;
- selecting one or more genes having significant differences in gene expression between the two or more groups of subjects and the group of non-diseased subjects (“disease candidate genes”);
- compiling a set of disease genes comprising the disease candidate genes;
- and
- selecting at least a subset of the set of disease genes to thereby determine the disease gene expression signature.
A method of monitoring therapeutic efficacy in a subject suffering from a disease, disorder, or condition, the method comprising:
- monitoring changes in a disease gene expression signature after administration of a therapy, wherein the disease gene expression signature has been determined at least in part by:
- analyzing gene expression data from a cohort of subjects suffering from the same disease, disorder, or condition as the subject;
- stratifying the cohort of subjects into two or more groups based on the gene expression data;
- determining differences in gene expression between the two or more groups of subjects and a group of non-diseased subjects;
- selecting one or more genes having significant differences in gene expression between the two or more groups of subjects and the group of non-diseased subjects (“disease candidate genes”);
- compiling a set of disease genes comprising the disease candidate genes;
- and
- selecting at least a subset of the set of disease genes to thereby determine the disease gene expression signature.
Dependencies are inferred from the claim text.