Methods of treating and prognosing nonhematopoietic malignant tumors

1. A method of treating mutant tumor-infiltrating leukocytes comprising:

determining that a patient having a nonhematopoietic malignant tumor comprising a breast tumor has one or more somatic gene mutations present in tumor-infiltrating leukocytes of the breast tumor, wherein the one or more somatic gene mutations are present in one or more genes selected from the group consisting of KDM5C, CDK8, MPL, ARID1A, FLT3, FGFR1, JAK1, GLI1, EZH2, EP300, BCOR, NF1, SMARCB1, EPHA10, IRF4, INSR, EPHA2, SMO, DUSP27, NOTCH2, HNF1A, MYO18A, MET, RPTOR, ATP10A, PTCH1, BRCA1, NCOR2, PASD1, NEB, MUC4, POU2F2, HLA-A, ALK, TET2, HLA-B, FGFR4, GATA2, FLT1, ATM, ITK, FREM2, INPP4B, CSF1R, PIGN, SOX17, MLL4, TTC28, TNFSF9, TRRAP, DNMT3A, TP53, IDH2, EPHA7, WT1, PNRC1, EGFR, ETV6, SMARCA4, MLL2, MAP3K1, ALOX12B, ARID2, EPHA8, ERBB2, EPHA4, PBRM1, BCL6, HDAC2, MLL, CPLD, CEBPA, JAK3, ASXL1, KIT, MEF2B, and ERG; are in a coding region, and result in an amino acid substitution or a premature stop codon; and are not identified in neoplastic cells of the breast tumor itself, said determining comprising:

obtaining a sample of tissue from the breast tumor;

isolating the tumor-infiltrating leukocytes from the tissue of the breast tumor;

extracting DNA from the tumor-infiltrating leukocytes; and

sequencing the DNA of the tumor-infiltrating leukocytes; and

administering to the patient determined to have the one or more somatic gene mutations present in the tumor-infiltrating leukocytes of the breast tumor an agent that preferentially kills or inhibits proliferation or activity of leukocytes relative to nonhematopoietic cells, wherein the agent is known or indicated to treat leukemia and is imatinib, daunorubicin, cytarabine, decitabine, azacitidine, etoposide, mercaptopurine, prednisone, idelalisib, ibrutinib, or ABT-199.

2. The method of claim 1 , wherein the tumor-infiltrating leukocytes are neutrophils, eosinophils, basophils, monocytes, macrophages, and/or lymphocytes.

3. The method of claim 1 , wherein the patient is a human patient.

4. The method of claim 1 , wherein the patient has not had neoadjuvant chemotherapy.

5. The method of claim 1 , wherein the tumor-infiltrating leukocytes are CD45+ cells.

6. The method of claim 1 , wherein the one or more somatic gene mutations are selected from the group consisting of ALK p.A892T, ALK p.H1030P, ALK p.L1145V, ALK p.R1209Q, ALOX12B p.D492N, ARID1A p.Q1365K, ASXL1 p.G792D, ATM p.A1211T, ATM p.P1564S, ATM p.R2105S, ATP10A p.P35A, BCL6 p.K558M, BCOR p.P1156L, BCOR p.P1613L, BCOR p.P1648L, BCOR p.V293I, BRCA1 p.S1613G, CDK8 p.V169I, CEBPA p.A79T, CSF1R p.R216Q, CYLD p.G173C, DNMT3A p.T260N, DNMT3A p.Y533C, DUSP27 p.Q737L, DUSP27 p.T1124N, EGFR p.A871E, EP300 p.G1777C, EP300 p.M1972T, EP300 p.Q2355L, EP300 p.R1737H, EPHA2 p.E302G, EPHA7 p.G592S, EPHA10 p.L80Q, ERG p.P299L, ETV6 p.P25S, EZH2 p.A478S, EZH2 p.A483S, FGFR1 p.G205D, FGFR1 p.M731V, FGFR4 p.S776F, FLT1 p.V1331I, FLT3 p.P439S, FLT3 p.Q394*, FREM2 p.G1608D, GATA2 p.A286P, GLI1 p.G162C, HLA-A p.A270S, HLA-A p.E176V, HLA-B p.R155S, HNF1A p.A562V, IDH2 p.K205R, IDH2 p.W164L, INPP4B p.K816E, INSR p.R162S, IRF4 p.A370V, IRF4 p.M146I, ITK p.D510N, JAK1 p.S260G, JAK3 p.Q1094*, KDM5C p.A612T, KIT p.G126E, KIT p.G93S, MAP3K1 p.S1002F, MEF2B p.P197R, MEF2B p.P279S, MET p.Q165K, MLL p.A2061T, MLL p.K3846M, MLL2 p.E4152K, MLL2 p.H4930L, MLL4 p.S214P, MPL p.E54V, MUC4 p.A2025V, MY018A p.A958V, NCOR2 p.A1706T, NEB p.Y1092C, NF1 p.A1670V, NF1 p.K1517M, NF1 p.N2775S, NF1 p.Q2434H, NOTCH2 p.A21T, NOTCH2 p.P1101T, NOTCH2 p.S1708P, PASD1 p.Q213E, PIGN p.T569N, PNRC1 p.R97Q, POU2F2 p.L459F, PTCH1 p.I685M, RPTOR p.V476M, SMARCA4 p.D694E, SMARCB1 p.N154K, SMO p.A379V, SOX17 p.G178R, TET2 p.E1874K, TET2 p.Q1702*, TNFSF9 p.A58S, TP53 p.M169I, TP53 p.R2′18L, TP53 p.R283P, TRRAP p.S1073G, TTC28 p.K2346Q, and WT1 p.T278I.