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Systems and methods for identifying cancer treatments from normalized biomarker scores

  • US 10,340,031 B2
  • Filed: 06/12/2018
  • Issued: 07/02/2019
  • Est. Priority Date: 06/13/2017
  • Status: Active Grant
First Claim
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1. A system, comprising:

  • at least one computer hardware processor;

    at least one database that stores biomarker information; and

    at least one non-transitory computer-readable storage medium storing processor-executable instructions that, when executed by the at least one computer hardware processor, cause the at least one computer hardware processor to perform;

    obtaining sequencing data about at least one biological sample of a subject known to have or suspected of having cancerous cells or pre-cancerous cells;

    accessing, in the at least one database, biomarker information indicating a distribution of values for each biomarker, across a respective group of people, in at least a reference subset of the plurality of biomarkers, each of the plurality of biomarkers being associated with at least one therapy in a plurality of therapies, the plurality of biomarkers including a first biomarker and the biomarker information including a distribution of values for the first biomarker;

    determining, using both the sequencing data and the biomarker information;

    a first set of normalized biomarker scores for a first set of biomarkers associated with a first therapy in the plurality of therapies,a second set of normalized biomarker scores for a second set of biomarkers associated with a second therapy in the plurality of therapies, anda third set of normalized biomarker scores for a third set of biomarkers associated with a third therapy in the plurality of therapies,wherein the first set of biomarkers is different from the second set of biomarkers, and wherein determining the first set of normalized biomarker scores comprises determining a first normalized biomarker score for the first biomarker using the distribution of values for the first biomarker at least in part by;

    determining an un-normalized score for the first biomarker using the sequencing data,determining a Z-score based on the first distribution of values for the first biomarker, anddetermining a normalized score for the first biomarker based on the un-normalized score and the Z-score; and

    determining, using the first, second, and third sets of normalized biomarker scores and a statistical model, respective first, second, and third therapy scores for the first, second and third therapies;

    wherein the plurality of therapies comprise at least three therapies selected from the group consisting of;

    an anti-PD1 therapy, an anti-CTLA4 therapy, an IL-2 therapy, an IFN alpha therapy, an anti-cancer vaccine therapy, an anti-angiogenic therapy, and an anti-CD20 therapy, andwherein the first, second, and third sets of biomarkers associated with the first, second and third each comprises at least three biomarkers selected from the group of biomarkers associated with the respective therapy in Table 2.

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