US 10,504,615 B2Granted

Using cancer or pre-cancer subject sequencing data and a database of therapy biomarker distributions to determine normalized biomarker scores and generate a graphical user interface

AssigneeBostonGene Corporation

InventorsAlexander Bagaev, Feliks Frenkel, Ravshan Ataullakhanov

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Abstract

Techniques for generating therapy biomarker scores and visualizing same. The techniques include determining, using a patient's sequence data and distributions of biomarker values across one or more reference populations, a first set of normalized scores for a first set of biomarkers associated with a first therapy, and a second set of normalized scores for a second set of biomarkers associated with a second therapy, generating a graphical user interface (GUI) including a first portion associated with the first therapy and having at least one visual characteristic determined based on a normalized score of the respective biomarker in the first set of normalized scores; and a second portion associated with a second therapy and having at least one visual characteristic determined based on a normalized score of the respective biomarker in the second set of normalized scores; and displaying the generated GUI.

Claims30

Dependent claims

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 in at least a reference subset of a plurality of biomarkers across a respective group of people, 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 first distribution of values for the first biomarker;
determining, using both the sequencing data and the biomarker information:
a first set of normalized scores for a first set of biomarkers associated with a first therapy in the plurality of therapies, and
a second set of normalized scores for a second set of biomarkers associated with a second therapy in the plurality of therapies,
wherein determining the first set of normalized scores comprises determining a first normalized score for the first biomarker at least in part by determining a statistical score for the first biomarker based on the first distribution of values for the first biomarker;
determining, using the first set of normalized scores and second set of normalized scores, respective first and second therapy scores for the first and second therapies;
generating a graphical user interface (GUI) that comprises:
a first portion associated with the first therapy in the plurality of therapies, the first portion including a first plurality of GUI elements, each of the first plurality of GUI elements being associated with a respective biomarker in the first set of biomarkers and having at least one visual characteristic determined based on a normalized score of the respective biomarker in the first set of normalized scores;
a second portion associated with the second therapy in the plurality of therapies, the second portion including a second plurality of GUI elements different from the first plurality of GUI elements, each of the second plurality of GUI elements being associated with a respective biomarker in the second set of biomarkers and having at least one visual characteristic determined based on a normalized score of the respective biomarker in the second set of normalized scores;
and
displaying the generated GUI.

13 more elements

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 at least one database, biomarker information indicating a distribution of values for each biomarker in at least a reference subset of a plurality of biomarkers across a respective group of people, 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 scores for a first set of biomarkers associated with a first therapy in the plurality of therapies, and
a second set of normalized scores for a second set of biomarkers associated with a second therapy in the plurality of therapies,
wherein determining the first set of normalized scores comprises determining a first normalized score for the first biomarker at least in part by determining a statistical score for the first biomarker based on the first distribution of values for the first biomarker;
determining, using the first set of normalized scores and second set of normalized scores, respective first and second therapy scores for the first and second therapies;
generating a graphical user interface (GUI) that comprises:
a first portion associated with the first therapy in the plurality of therapies, the first portion including a first plurality of GUI elements, each of the first plurality of GUI elements being associated with a respective biomarker in the first set of biomarkers and having at least one visual characteristic determined based on a normalized score of the respective biomarker in the first set of normalized scores;
a second portion associated with the second therapy in the plurality of therapies, the second portion including a second plurality of GUI elements different from the first plurality of GUI elements, each of the second plurality of GUI elements being associated with a respective biomarker in the second set of biomarkers and having at least one visual characteristic determined based on a normalized score of the respective biomarker in the second set of normalized scores;
and
displaying the generated GUI.

9 more elements

A method, comprising:

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 at least one database, biomarker information indicating a distribution of values for each biomarker in at least a reference subset of a plurality of biomarkers across a respective group of people, 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 scores for a first set of biomarkers associated with a first therapy in the plurality of therapies, and
a second set of normalized scores for a second set of biomarkers associated with a second therapy in the plurality of therapies,
wherein determining the first set of normalized scores comprises determining a first normalized score for the first biomarker at least in part by determining a statistical score for the first biomarker based on the first distribution of values for the first biomarker;
determining, using the first set of normalized scores and second set of normalized scores, respective first and second therapy scores for the first and second therapies;
generating a graphical user interface (GUI) that comprises:
a first portion associated with the first therapy in the plurality of therapies, the first portion including a first plurality of GUI elements, each of the first plurality of GUI elements being associated with a respective biomarker in the first set of biomarkers and having at least one visual characteristic determined based on a normalized score of the respective biomarker in the first set of normalized scores;
a second portion associated with the second therapy in the plurality of therapies, the second portion including a second plurality of GUI elements different from the first plurality of GUI elements, each of the second plurality of GUI elements being associated with a respective biomarker in the second set of biomarkers and having at least one visual characteristic determined based on a normalized score of the respective biomarker in the second set of normalized scores;
and
displaying the generated GUI.

9 more elements

Dependencies are inferred from the claim text.

Facts

Application: 16/456,370Filed 28 Jun 2019 · continuation
Priority: 13 Jun 2017
Published: US 2019/0325993 A124 Oct 2019
Granted: 10 Dec 2019
Term ends: Not estimatedThe source records don’t support an estimate.

Classification29 codes

G16B 45/00
Ict specially adapted for bioinformatics-related data visualisation
C12Q 1/6886
For diseases caused by alterations of genetic material: for cancer
G06F 16/285
Relational databases: clustering or classification
G06F 17/18
Complex mathematical operations: for evaluating statistical data , e.g. average values, frequency distributions, probability functions, regression…

Family

Application62/518,787Us provisional application · filed 13 Jun 2017
Application62/598,440Us provisional application · filed 13 Dec 2017
Application16/006,279Parent of this continuation · filed 12 Jun 2018
US 2019/0325993 A1Pre-grant publication · published 24 Oct 2019
US 10,340,030 B2Parent of this continuation
US 2018/0358128 A1Published application
US 10,504,615 B2This patent

From the US filing history. Foreign family members aren’t listed.

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