Techniques for identifying follicular lymphoma types
AssigneeBostonGene Corporation
InventorsMark Meerson, Nikita Kotlov, Olga Kudryashova, Alexander Bagaev
Life of this patent
Estimating the term…
Abstract
Aspects of the disclosure relate to methods, systems, computer-readable storage media, and graphical user interfaces (GUIs) that are useful for characterizing subjects having certain cancers, for example lymphomas. The disclosure is based, in part, on methods for determining the tumor microenvironment (TME) type of a lymphoma (e.g., follicular lymphoma) subject and identifying the subject's prognosis based upon the TME type determination.
Claims30
A method for determining a follicular lymphoma (FL) tumor microenvironment (TME) type for a subject having, suspected of having, or at risk of having a follicular lymphoma (FL), the method comprising:
- using at least one computer hardware processor to perform:
- (a) obtaining RNA expression data for the subject, the RNA expression data indicating first RNA expression levels for genes in a first plurality of gene groups and second RNA expression levels for genes in a second plurality of gene groups different from the first plurality of gene groups, wherein genes in the second plurality of gene groups are associated with B cells;
- (b) generating an FL TME signature for the subject using the RNA expression data, the FL TME signature comprising:
- a first gene expression signature comprising first gene group expression scores for respective gene groups in the first plurality of gene groups, and
- a second gene expression signature comprising second gene group expression scores for respective gene groups in the second plurality of gene groups associated with B cells, the generating comprising:
- determining the first gene expression signature by determining the first gene group expression scores using the first RNA expression levels, and
- determining the second gene expression signature by determining the second gene group expression scores using the second RNA expression levels;
- and
- (c) identifying, using the FL TME signature and from among a plurality of FL TME types, an FL TME type for the subject.
3-8. (canceled)
20-21. (canceled)
23-25. (canceled)
27-34. (canceled)
37-44. (canceled)
(canceled)
49-51. (canceled)
A system, comprising:
- at least one computer hardware processor;
- and
- at least one 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 a method for determining a follicular lymphoma (FL) tumor microenvironment (TME) type for a subject having, suspected of having, or at risk of having a follicular lymphoma (FL), the method comprising:
- (a) obtaining RNA expression data for the subject, the RNA expression data indicating first RNA expression levels for genes in a first plurality of gene groups and second RNA expression levels for genes in a second plurality of gene groups different from the first plurality of gene groups, wherein genes in the second plurality of gene groups are associated with B cells;
- (b) generating an FL TME signature for the subject using the RNA expression data, the FL TME signature comprising:
- a first gene expression signature comprising first gene group expression scores for respective gene groups in the first plurality of gene groups, and
- a second gene expression signature comprising second gene group expression scores for respective gene groups in the second plurality of gene groups associated with B cells, the generating comprising:
- determining the first gene expression signature by determining the first gene group expression scores using the first RNA expression levels, and
- determining the second gene expression signature by determining the second gene group expression scores using the second RNA expression levels;
- and
- (c) identifying, using the FL TME signature and from among a plurality of FL TME types, an FL TME type for the subject.
At least one computer-readable storage medium storing processor-executable instructions that, when executed by at least one computer hardware processor, cause the at least one computer hardware processor to perform a method for determining a follicular lymphoma (FL) tumor microenvironment (TME) type for a subject having, suspected of having, or at risk of having a follicular lymphoma (FL), the method comprising:
- (a) obtaining RNA expression data for the subject, the RNA expression data indicating first RNA expression levels for genes in a first plurality of gene groups and second RNA expression levels for genes in a second plurality of gene groups different from the first plurality of gene groups, wherein genes in the second plurality of gene groups are associated with B cells;
- (b) generating an FL TME signature for the subject using the RNA expression data, the FL TME signature comprising:
- a first gene expression signature comprising first gene group expression scores for respective gene groups in the first plurality of gene groups, and
- a second gene expression signature comprising second gene group expression scores for respective gene groups in the second plurality of gene groups associated with B cells, the generating comprising:
- determining the first gene expression signature by determining the first gene group expression scores using the first RNA expression levels, and
- determining the second gene expression signature by determining the second gene group expression scores using the second RNA expression levels;
- and
- (c) identifying, using the FL TME signature and from among a plurality of FL TME types, an FL TME type for the subject.
54-58. (canceled)
Dependencies are inferred from the claim text.