US 11,705,220 B2
Systems and methods for identifying cancer treatments from normalized biomarker scores
Alexander Bagaev, Moscow (RU); Feliks Frenkel, Moscow (RU); and Ravshan Ataullakhanov, Moscow (RU)
Assigned to BostonGene Corporation, Waltham, MA (US)
Filed by BostonGene Corporation, Waltham, MA (US)
Filed on Apr. 22, 2021, as Appl. No. 17/237,672.
Application 17/237,672 is a continuation of application No. 16/856,566, filed on Apr. 23, 2020, granted, now 11,004,542.
Application 16/856,566 is a continuation of application No. 16/662,280, filed on Oct. 24, 2019, granted, now 10,636,513.
Application 16/662,280 is a continuation of application No. 16/456,370, filed on Jun. 28, 2019, granted, now 10,504,615.
Application 16/456,370 is a continuation of application No. 16/006,279, filed on Jun. 12, 2018, granted, now 10,340,030.
Claims priority of provisional application 62/598,440, filed on Dec. 13, 2017.
Claims priority of provisional application 62/518,787, filed on Jun. 13, 2017.
Prior Publication US 2021/0257058 A1, Aug. 19, 2021
Int. Cl. G16B 45/00 (2019.01); G16H 50/30 (2018.01); C12Q 1/6886 (2018.01); G16H 50/20 (2018.01); G16H 50/70 (2018.01); G06F 16/28 (2019.01); G16B 5/00 (2019.01); G16B 20/00 (2019.01); G16B 40/00 (2019.01); G16B 50/00 (2019.01); G16B 5/20 (2019.01); G16B 25/10 (2019.01); G16B 40/20 (2019.01); G16B 50/30 (2019.01); G16B 40/30 (2019.01); G16B 30/00 (2019.01); G06F 17/18 (2006.01); G16H 20/00 (2018.01); G16H 50/50 (2018.01); G16H 20/10 (2018.01); G16H 20/40 (2018.01); G16H 70/20 (2018.01); G16H 10/20 (2018.01)
CPC G16B 45/00 (2019.02) [C12Q 1/6886 (2013.01); G06F 16/285 (2019.01); G06F 17/18 (2013.01); G16B 5/00 (2019.02); G16B 5/20 (2019.02); G16B 20/00 (2019.02); G16B 25/10 (2019.02); G16B 30/00 (2019.02); G16B 40/00 (2019.02); G16B 40/20 (2019.02); G16B 40/30 (2019.02); G16B 50/00 (2019.02); G16B 50/30 (2019.02); G16H 10/20 (2018.01); G16H 20/00 (2018.01); G16H 20/10 (2018.01); G16H 20/40 (2018.01); G16H 50/20 (2018.01); G16H 50/30 (2018.01); G16H 50/50 (2018.01); G16H 50/70 (2018.01); G16H 70/20 (2018.01); C12Q 2600/156 (2013.01); C12Q 2600/158 (2013.01)] 16 Claims
 
1. A method comprising:
using at least one computer hardware processor to perform:
obtaining sequencing data about at least one biological sample of a subject;
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, each biomarker in the reference subset being associated with at least one candidate therapy, wherein the at least one candidate therapy is associated with a clinical trial, the reference subset of the plurality of biomarkers including a first biomarker associated with a first gene and a second biomarker associated with a second gene different from the first gene, and the biomarker information including a first distribution of values for the first biomarker and a second distribution of values for the second biomarker;
determining, using the sequencing data, un-normalized biomarker scores for at least some biomarkers in the reference subset of the plurality of biomarkers, the un-normalized biomarker scores including a first un-normalized biomarker score for the first biomarker and a second un-normalized biomarker score for the second biomarker;
determining normalized biomarker scores for the at least some biomarkers in the reference subset of the plurality of biomarkers at least in part by adjusting the un-normalized biomarker scores for the at least some biomarkers to a common scale, the adjusting comprising adjusting the first and second un-normalized biomarker scores to the common scale using the first and second distributions of values respectively;
identifying the subject as a member of one or more cohorts using the normalized biomarker scores for the subject, wherein each of the one or more cohorts is associated with a positive or negative outcome of the at least one candidate therapy; and
outputting an indication of the one or more cohorts in which the subject is identified as a member.