Diagnostic to support clinical trial matching and exploratory biomarker analyses in cancer patients
AssigneeH. Lee Moffitt Cancer Center and Research Institute, Inc.
InventorsEric B. HAURA, John M. KOOMEN, Theresa A. BOYLE, Sudhir PUTTY REDDY, Aileen Y. ALONTAGA
Life of this patent
Estimating the term…
Abstract
Disclosed are novel RNA and protein expression panels and methods of using said panels for the detection of cancer and determining the suitability of a subject for a treatment regimen or clinical trial.
Claims17
A genomic assay panel for cancer diagnosis and clinical trial relevance comprising 204 genes selected from the group consisting of ABRAXAS1, ACKR2, ACKR3, ACOT12, ACTA2, ADORA2A, AKT1, AKT2, AKT3, ALK, ANPEP, APC, AR, ARID1A, ASCL1, ATM, ATR, AXL, B2M, BAG1, BARD1, BCL2, BCL2L11, BIRC5, BRAF, BRCA1, BRCA2, BRIP1, BTN2A1, BTN3A1, CCND1, CCNE1, CD14, CD274, CD33, CD3D, CD3E, CD3G, CD4, CD68, CD70, CD80, CD83, CD86, CD8A, CDH1, CDH2, CDK12, CDK2, CDK4, CDK6, CDKN2A, CHD1, CHEK1, CHEK2, CIITA, CREBBP, CSF1R, CT83, CTAG1A, CTAGE1, CTLA4, CTNNB1, DDR2, DLL3, DUSP4, E2F1, EGFR, ERBB2, ERBB3, ERBB4, ESR1, EZH2, FANCA, FGFR1, FGFR2, FGFR3, FGFR4, FLT1, FLT3, FLT4, FOLR1, FSHR, GATA6, GRB2, GSK3B, HAVCR2, HDAC1, HGF, HLA-A, HLA-B, HLA-C, HLA-DPA1, HLA-DPB1, HLA-DQA1, HLA-DQA2, HLA-DQB1, HLA-DRA, HLA-DRB1, HMMR, HRAS, IDH1, IDH2, IL11, IL13RA2, IL2RB, IRS2, JAK2, KDR, KEAP1, KIT, KLRK1, KRAS, LAG3, LCK, MAGEA1, MAGEA10, MAGEA3/6, MAGEA4, MAGEB2, MAGEC1, MAGEC2, MAP2K1, MAP2K2, MAPK1, MAPK3, MCL1, MDM2, MDM4, MET, MET_e14_skip, MICA, MICB, MKI67, MLH1, MRE11, MS4A1, MSH2, MSH6, MTOR, MUC1, MYC, NBN, NCAM1, NEUROD1, NF1, NFE2L2, NFKB1, NFKB2, NRAS, NRG1, NTRK1, NTRK2, NTRK3, OR5V1, PALB2, PARP1, PARP2, PCSK9, PDCD1, PDCD1LG2, PDGFRA, PDGFRB, PIK3CA, PMS2, POLE, POU2F3, PPP2R2A, PSCA, PTCH1, PTEN, PTK7, PTP4A1, PVR, RAD51, RAD51B, RAD51C, RAD51D, RAD54L, RAF1, RB1, RET, RICTOR, ROS1, SDC1, SETD2, SIK1, SLC34A2, SMAD4, STK11, TACSTD2, TAFAZZIN, TERT, TFF1, TIGIT, TMPRSS2, TNFRSF10A, TNFRSF10B, TP53, ULBP1, VIM, WEE1, WT1, and/or YAP1.
A proteomic assay panel for cancer diagnosis and clinical trial relevance comprising the peptide targets comprising ACTA_VAPEEHPTLLTEAPLNPK (SEQ ID NO:
- 1), ACTB_AGFAGDDAPR (SEQ ID NO:
- 2), AKT1_SLLSGLLK (SEQ ID NO:
- 3), AKT2_EGISDGATMK (SEQ ID NO:
- 4), AKT2_SLLAGLLK (SEQ ID NO:
- 5), AKT3_TDGSFIGYK (SEQ ID NO:
- 6), ALBU_LVNEVTEFAK (SEQ ID NO:
- 7), ALK_DPEGVPPLLVSQQAK (SEQ ID NO:
- 8), ALK_NCLLTCPGPGR (SEQ ID NO:
- 9), ARAF_GLNQDCCVVYR (SEQ ID NO:
- 10), ARAF_IGTGSFGTVFR (SEQ ID NO:
- 11), BCL2_FATVVEELFR (SEQ ID NO:
- 12), BRAF_GLIPECCAVYR (SEQ ID NO:
- 13), BT2A1_DPYGGVAPALK (SEQ ID NO:
- 14), BT3A1_TANPILLVSEDQR (SEQ ID NO:
- 15), CADH1_NDVAPTLMSVPR (SEQ ID NO:
- 16), CADH1_TAYFSLDTR (SEQ ID NO:
- 17), CADH2_GPFPQELVR (SEQ ID NO:
- 18), CADH2_LSDPANWLK (SEQ ID NO:
- 19), CCND1_AEETCAPSVSYFK (SEQ ID NO:
- 20), CCND1_AYPDANLLNDR (SEQ ID NO:
- 21), CD20_AHTPYINIYNCEPANPSEK (SEQ ID NO:
- 22), CD3D_LSGAADTQALLR (SEQ ID NO:
- 23), CD3E_GSKPEDANFYLYLR (SEQ ID NO:
- 24), CD4_ILGNQGSFLTK (SEQ ID NO:
- 25), CD80_ADFPTPSISDFEIPTSNIR (SEQ ID NO:
- 26), CD8A_AAEGLDTQR (SEQ ID NO:
- 27), CDK2_DLKPQNLLINTEGAIK (SEQ ID NO:
- 28), CDK2_VVPPLDEDGR (SEQ ID NO:
- 29), CDK4_DLKPENILVTSGGTVK (SEQ ID NO:
- 30), CDK4_VPNGGGGGGGLPISTVR (SEQ ID NO:
- 31), CDK6_ILDVIGLPGEEDWPR (SEQ ID NO:
- 32), CDN2A_ALLEAGALPNAPNSYGR (SEQ ID NO:
- 33), CDN2A_LPVDLAEELGHR (SEQ ID NO:
- 34), CHK1_DIKPENLLLDER (SEQ ID NO:
- 35), CTG1B_ASGPGGGAPR (SEQ ID NO:
- 36), CTNB1_AIPELTK (SEQ ID NO:
- 37), EGFR_GSTAENAEYLR (SEQ ID NO:
- 38), EGFR_IPLENLQIIR (SEQ ID NO:
- 39), ERBB2_ELVSEFSR (SEQ ID NO:
- 40), G3P_VGVNGFGR (SEQ ID NO:
- 41), GSK3B_LLEYTPTAR (SEQ ID NO:
- 42), HBA_VGAHAGEYGAEALER (SEQ ID NO:
- 43), HBB_VNVDEVGGEALGR (SEQ ID NO:
- 44), I13R2_FPYLEASDYK (SEQ ID NO:
- 45), K2C5_LAELEEALQK (SEQ ID NO:
- 46), K2C6A_SGFSSVSVSR (SEQ ID NO:
- 47), K2C7_SAYGGPVGAGIR (SEQ ID NO:
- 48), KI67_SGASEANLIVAK (SEQ ID NO:
- 49), KIT_LLCTDPGFVK (SEQ ID NO:
- 50), KKLC1_LVELEHTLLSK (SEQ ID NO:
- 51), KRAS_SFEDIHHYR (SEQ ID NO:
- 52), LMNA_SGAQASSTPLSPTR (SEQ ID NO:
- 53), LMNA_VAVEEVDEEGK (SEQ ID NO:
- 54), MAGAl_VADLVGFLLLK (SEQ ID NO:
- 55), MAGA3_LLTQHFVQENYLEYR (SEQ ID NO:
- 56), MAGA4_EHTVYGEPR (SEQ ID NO:
- 57), MAGA6_LLTQYFVQENYLEYR (SEQ ID NO:
- 58), MAGAA_VTDLVQFLLFK (SEQ ID NO:
- 59), MAGB2_SGSLVQFLLYK (SEQ ID NO:
- 60), MAGC1_YTGYFPVIFR (SEQ ID NO:
- 61), MAGC2_VAELVEFLLLK (SEQ ID NO:
- 62), MCL1_LLFFAPTR (SEQ ID NO:
- 63), MET_TEFTTALQR (SEQ ID NO:
- 64), MET_VADFGLAR (SEQ ID NO:
- 65), MICA_EGLHSLQEIR (SEQ ID NO:
- 66), MKO1_GQVFDVGPR (SEQ ID NO:
- 67), MK03_GQPFDVGPR (SEQ ID NO:
- 67), MK03_NYLQSLPSK (SEQ ID NO:
- 68), MP2K1_IPEQILGK (SEQ ID NO:
- 69), MP2K1_VSHKPSGLVMAR (SEQ ID NO:
- 70), MP2K2_ISELGAGNGGVVTK (SEQ ID NO:
- 71), MTOR_LFDAPEAPLPSR (SEQ ID NO:
- 72), MTOR_VLGLLGALDPYK (SEQ ID NO:
- 73), NTRK2_SNEIPSTDVTDK (SEQ ID NO:
- 74), NTRK3_NCLVGANLLVK (SEQ ID NO:
- 75), NTRK3_VVSLEEPELR (SEQ ID NO:
- 76), Pan-RAS_LVVVGAGGVGK (SEQ ID NO:
- 77), PARP1_VFSATLGLVDIVK (SEQ ID NO:
- 78), PARP1_VVSEDFLQDVSASTK (SEQ ID NO:
- 79), PARP2_AEGLLQGK (SEQ ID NO:
- 80), PCNA_CAGNEDIITLR (SEQ ID NO:
- 81), PD1L1_LQDAGVYR (SEQ ID NO:
- 82), PD1L2_ATLLEEQLPLGK (SEQ ID NO:
- 83), PGFRA_FQTIPFNVYALK (SEQ ID NO:
- 84), PGFRB_GFSGIFEDR (SEQ ID NO:
- 85), PK3CA_LFQPFLK (SEQ ID NO:
- 86), PK3CA_LINLTDILK (SEQ ID NO:
- 87), PSCA_AVGLLTVISK (SEQ ID NO:
- 88), PTEN_GVTIPSQR (SEQ ID NO:
- 89), PTEN_IYSSNSGPTR (SEQ ID NO:
- 90), RAF1_GLQPECCAVFR (SEQ ID NO:
- 91), RAF1_GYASPDLSK (SEQ ID NO:
- 92), RAF1_VVDPTPEQFQAFR (SEQ ID NO:
- 93), RAS Mt_LVVVGACGVGK (SEQ ID NO:
- 94), RASH_SFEDIHQYR (SEQ ID NO:
- 95), RASN_SFADINLYR (SEQ ID NO:
- 96), RET_LLEGEGLPFR (SEQ ID NO:
- 97), RET_VFLSPTSLR (SEQ ID NO:
- 98), ROS1_IQDQLQLFR (SEQ ID NO:
- 99), TACD2_AAGDVDIGDAAYYFER (SEQ ID NO:
- 100), TBBL_EVDQQLLSVQTR (SEQ ID NO:
- 101), TBB1_GASALQLER (SEQ ID NO:
- 102), TBB5_ISVYYNEATGGK (SEQ ID NO:
- 103), TENA_VATYLPAPEGLK (SEQ ID NO:
- 104), TR10A_IQDLLVDSGK (SEQ ID NO:
- 105), TR10B_LLVPANEGDPTETLR (SEQ ID NO:
- 106), UFO_APLQGTLLGYR (SEQ ID NO:
- 107), UFO_TATITVLPQQPR (SEQ ID NO:
- 108), VGFR1_AVSSFPDPALYPLGSR (SEQ ID NO:
- 109), VIME_ILLAELEQLK (SEQ ID NO:
- 110), VIME_SLYASSPGGVYATR (SEQ ID NO:
- 111), and/or WEE1_SPTEPGPER (SEQ ID NO:
- 112).
Dependencies are inferred from the claim text.