Techniques for identifying her2-low breast cancer tumors
AssigneeBostonGene Corporation
InventorsPolina Turova, Vladimir Kushnarev, Oleg Baranov, Anna Butusova, Sofiia Menshikova, Konstantin Chernyshov, Nikita Kotlov
Life of this patent
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Abstract
Aspects of the disclosure relate to methods, systems, and computer-readable storage media, which are useful for characterizing subjects having certain cancers, for example breast cancer. The disclosure is based, in part, on methods for determining the molecular breast cancer (BC) type of a subject and identifying the subject's prognosis and/or one or more therapeutic agents for treating the subject based upon the molecular BC type determination.
Claims30
A method for identifying HER2-low breast cancer from RNA expression data of a tumor sample from a subject having breast cancer using a plurality of trained machine learning classifiers including first, second, and third trained machine learning classifiers associated with respective first, second, and third sets of genes, the method comprising:
- using at least one computer hardware processor to perform:
- obtaining the RNA expression data, the RNA expression data specifying RNA expression levels at least for genes in the first, second, and third sets of genes, the RNA expression data having been previously obtained from the tumor sample;
- determining, using the RNA expression levels for the first set of genes and the first trained machine learning classifier, whether the tumor sample has a Basal molecular subtype;
- when it is determined that the tumor sample does not have the Basal molecular subtype, determining, using the RNA expression levels for the second set of genes and the second trained machine learning classifier, whether the tumor sample has a HER2-high molecular subtype;
- and
- when it is determined that the tumor sample does not have the HER2-high molecular subtype, determining, using the RNA expression levels for the third set of genes and the third trained machine learning classifier, that the tumor sample has a HER2-low molecular subtype.
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A method for identifying a molecular subtype of breast cancer for a subject, the method comprising:
- using at least one computer hardware processor to perform:
- obtaining RNA expression data, the RNA expression data having been previously obtained from a tumor sample from a subject having breast cancer;
- and
- identifying, from among multiple breast cancer molecular subtypes and using the RNA expression data and a plurality trained machine learning classifiers, a molecular subtype for the tumor sample, the multiple breast cancer molecular subtypes comprising:
- a Basal subtype, a HER2-high subtype, a HER2-low subtype, Luminal subtype A, and Luminal subtype B.
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Dependencies are inferred from the claim text.