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US 2010/0304989 A1Published application
Molecular profiling of tumors
AssigneeCaris MPI, Inc.
InventorsDaniel D. Von Hoff, Alan Wright, Matthew J. McGinniss, Ryan P. Bender, David M. Loesch, Arlet Alarcon, Robert J. Penny, Traci Pawlowski
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Abstract
Provided herein are methods and systems of molecular profiling of diseases, such as cancer. In some embodiments, the molecular profiling can be used to identify treatments for a disease, such as treatments that were not initially identified as a treatment for the disease or not expected to be a treatment for a particular disease.
Claims49
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A method of identifying a candidate treatment for a subject in need of treatment for a cancer, comprising:
- (a) performing an immunohistochemistry (IHC) analysis on a sample from the subject to determine an IHC expression profile on at least five of:
- SPARC, PGP, Her2/neu, ER, PR, c-kit, AR, CD52, PDGFR, TOP2A, TS, ERCC1, RRM1, BCRP, TOPO1, PTEN, MGMT, and MRP1;
- (b) performing a microarray analysis on the sample to determine a microarray expression profile on at least five of ABCC1, ABCG2, ADA, AR, ASNS, BCL2, BIRC5, BRCA1, BRCA2, CD33, CD52, CDA, CES2, DCK, DHFR, DNMT1, DNMT3A, DNMT3B, ECGF1, EGFR, EPHA2, ERBB2, ERCC1, ERCC3, ESR1, FLT1, FOLR2, FYN, GART, GNRH1, GSTP1, HCK, HDAC1, HIF1A, HSP90AA1, IL2RA, HSP90AA1, KDR, KIT, LCK, LYN, MGMT, MLH1, MS4A1, MSH2, NFKB1, NFKB2, OGFR, PDGFC, PDGFRA, PDGFRB, PGR, POLA1, PTEN, PTGS2, RAF1, RARA, RRM1, RRM2, RRM2B, RXRB, RXRG, SPARC, SRC, SSTR1, SSTR2, SSTR3, SSTR4, SSTR5, TK1, TNF, TOP1, TOP2A, TOP2B, TXNRD1, TYMS, VDR, VEGFA, VHL, YES1, and ZAP70;
- (c) performing a fluorescent in-situ hybridization (FISH) analysis on the sample to determine a FISH mutation profile on EGFR and/or HER2;
- (d) performing DNA sequencing on the sample to determine a sequencing mutation profile on at least one of KRAS, BRAF, c-KIT and EGFR;
- and
- (e) comparing the IHC expression profile, microarray expression profile, FISH mutation profile and sequencing mutation profile against a rules database, wherein the rules database comprises a mapping of treatments whose biological activity is known against cancer cells that:
- i. overexpress or underexpress one or more proteins included in the IHC expression profile;
- ii. overexpress or underexpress one or more genes included in the microarray expression profile;
- iii. have no mutations, or one or more mutations in one or more genes included in the FISH mutation profile;
- and/or
- iv. have no mutations, or one or more mutations in one or more genes included in the sequencing mutation profile;
- and
- (f) identifying the candidate treatment if:
- i. the comparison in step (e) indicates that the treatment should have biological activity against the cancer;
- and
- ii. the comparison in step (e) does not contraindicate the treatment for treating the cancer.
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Dependencies are inferred from the claim text.