Comprehensive genomic profiling (cgp) of metastatic invasive lobular carcinomas reveals heterogeneity
AssigneeFoundation Medicine, Inc.
InventorEthan SOKOL
Life of this patent
Estimating the term…
Abstract
The present disclosure relates to methods of treating or delaying progression of invasive lobular carcinoma (ILC) metastasis in an individual, methods for evaluating, identifying, and/or assessing an individual having an ILC metastasis, as well as methods for genomic profiling of an ILC metastasis.
Claims37
A method of treating or delaying progression of invasive lobular carcinoma (ILC) metastasis, comprising:
- (a) acquiring knowledge of a tumor mutational burden (TMB) of at least about 10 mutations/megabase (mut/Mb) in a sample from an individual having an ILC metastasis;
- and
- (b) responsive to said knowledge, administering to the individual an effective amount of an immune checkpoint inhibitor.
2-3. (canceled)
6-10. (canceled)
A method of treating or delaying progression of invasive lobular carcinoma (ILC) metastasis, comprising:
- (a) acquiring knowledge of a PD-L1-positive ILC metastasis in a sample from an individual having an ILC metastasis;
- and
- (b) responsive to said knowledge, administering to the individual an effective amount of an immune checkpoint inhibitor.
17-21. (canceled)
23-29. (canceled)
34-36. (canceled)
A method of treating or delaying progression of invasive lobular carcinoma (ILC) metastasis, comprising:
- (a) acquiring knowledge of an alteration in one or more genes in a sample from an individual having an ILC metastasis, wherein the one or more genes comprise one or more of:
- PIK3CA, BRCA1, BRCA2, ESR1, ERBB2, ARID1A, NF1, RB1, KRAS, PTEN, FGFR2, NCOR1, SMAD4, BRAF, FOXP1, APC, SOX9, CASP8, PTPN11, TERT, ALK, and KMT2D;
- and
- (b) responsive to said knowledge, administering to the individual an effective amount of an anti-cancer agent.
38-39. (canceled)
41-158. (canceled)
160-162. (canceled)
164-177. (canceled)
A method for genomic profiling of an invasive lobular carcinoma (ILC) metastasis, comprising:
- (a) detecting one or more biomarkers in a sample from an individual having an ILC metastasis, wherein the one or more biomarkers comprise one or more of:
- (i) a tumor mutational burden (TMB) of at least about 10 mutations/megabase (mut/Mb),
- (ii) a PD-L1-positive ILC metastasis, and
- (iii) an alteration in one or more genes, wherein the one or more genes comprise one or more of:
- PIK3CA, BRCA1, BRCA2, ESR1, ERBB2, ARID1A, NF1, RB1, KRAS, PTEN, FGFR2, NCOR1, SMAD4, BRAF, FOXP1, APC, SOX9, CASP8, PTPN11, TERT, ALK, and KMT2D;
- and
- (b) providing a report to a party.
179-287. (canceled)
A system, comprising:
- a memory configured to store one or more program instructions;
- and
- one or more processors configured to execute the one or more program instructions, the one or more program instructions when executed by the one or more processors are configured to:
- (a) obtain a plurality of sequence reads of one or more nucleic acids, wherein the one or more nucleic acids are derived from a sample obtained from an individual;
- (b) analyze the plurality of sequence reads for the presence of a tumor mutational burden (TMB) of at least about 10 mutations/megabase (mut/Mb);
- and
- (c) detect, based on the analyzing, a TMB of at least about 10 mut/Mb, in the sample.
289-292. (canceled)
A non-transitory computer readable storage medium comprising one or more programs executable by one or more computer processors for performing a method, comprising:
- (a) obtaining, using the one or more processors, a plurality of sequence reads of one or more nucleic acids, wherein the one or more nucleic acids are derived from a sample obtained from an individual;
- (b) analyzing, using the one or more processors, the plurality of sequence reads for the presence of a tumor mutational burden (TMB) of at least about 10 mutations/megabase (mut/Mb);
- and
- (c) detecting, using the one or more processors and based on the analyzing, a TMB of at least about 10 mut/Mb, in the sample.
294-297. (canceled)
A system, comprising:
- a memory configured to store one or more program instructions;
- and
- one or more processors configured to execute the one or more program instructions, the one or more program instructions when executed by the one or more processors are configured to:
- (a) obtain a plurality of sequence reads of one or more nucleic acids, wherein the one or more nucleic acids are derived from a sample obtained from an individual;
- (b) analyze the plurality of sequence reads for the presence of an alteration in one or more genes, wherein the one or more genes comprise PIK3CA, BRCA1, BRCA2, ESR1, ERBB2, ARID1A, NF1, RB1, KRAS, PTEN, FGFR2, NCOR1, SMAD4, BRAF, FOXP1, APC, SOX9, CASP8, PTPN11, TERT, ALK, CDH1 or KMT2D;
- and
- (c) detect, based on the analyzing, an alteration in one or more genes, wherein the one or more genes comprise PIK3CA, BRCA1, BRCA2, ESR1, ERBB2, ARID1A, NF1, RB1, KRAS, PTEN, FGFR2, NCOR1, SMAD4, BRAF, FOXP1, APC, SOX9, CASP8, PTPN11, TERT, ALK, CDH1 or KMT2D, in the sample.
299-348. (canceled)
A non-transitory computer readable storage medium comprising one or more programs executable by one or more computer processors for performing a method, comprising:
- (a) obtaining, using the one or more processors, a plurality of sequence reads of one or more nucleic acids, wherein the one or more nucleic acids are derived from a sample obtained from an individual;
- (b) analyzing, using the one or more processors, the plurality of sequence reads for the presence of an alteration in one or more genes, wherein the one or more genes comprise PIK3CA, BRCA1, BRCA2, ESR1, ERBB2, ARID1A, NF1, RB1, KRAS, PTEN, FGFR2, NCOR1, SMAD4, BRAF, FOXP1, APC, SOX9, CASP8, PTPN11, TERT, ALK, CDH1 or KMT2D;
- and
- (c) detecting, using the one or more processors and based on the analyzing, an alteration in one or more genes, wherein the one or more genes comprise PIK3CA, BRCA1, BRCA2, ESR1, ERBB2, ARID1A, NF1, RB1, KRAS, PTEN, FGFR2, NCOR1, SMAD4, BRAF, FOXP1, APC, SOX9, CASP8, PTPN11, TERT, ALK, CDH1 or KMT2D, in the sample.
350-399. (canceled)
Dependencies are inferred from the claim text.