Process for Measuring Tumor Response to an Initial Oncology Treatment

Abstract

There is disclosed a process for determining early patient response to an initial therapy administration, comprising a rapid determination of effectiveness of a therapy after an initial treatment for a cancer indication. More specifically, the rapid determination of effectiveness is made days following initial therapy. There is further disclosed a process for determining early patient response to an initial cancer treatment, comprising (a) conducting a baseline PET FDG or PET FLT scan of the tumor region in a patient by determining tumor tissue metabolic rate and/or apoptotic rate (for FLT), (b) providing a single potentially effective dose of a therapeutic to the patient, (c) conducting a second PET FDG or PET FLT scan by determining tumor tissue metabolic rate, and (d) comparing the results of the first PET scan to the second PET scan to determine an imaging response in the PET scan results whereby at least a 1% reduction in tumor tissue metabolic rate indicates that the patient would benefit to treat the tumor with the initial cancer treatment. Preferably, in addition to the PET scans conducted before and after an initial dose of a cancer drug, the present disclosure further provides parallel before and after measurement(s) of the level of circulating tumor DNA (ctDNA) for specific oncogene mutations/alterations to identify early patient response to drug therapy.

Claims

1. A process for determining whether a patient would benefit from cancer treatment with a particular therapeutic, comprising (a) conducting a baseline PET scan in a patient by determining tumor tissue metabolic rate, (b) providing a single potentially effective dose of a therapeutic to the patient, (c) conducting a second PET scan of the patient by determining tumor tissue metabolic rate, wherein the second PET scan is conducted 1-14 days following the dose of the therapeutic, and (d) comparing the results of the first PET scan to the second PET scan to determine a response in the PET scan results such that at least a 1% reduction in tumor tissue metabolic rate indicates that the patient would benefit to treat the tumor with the therapeutic.

2. The process for determining whether a patient would benefit for cancer treatment with a particular therapeutic of claim 1, wherein the PET scans determines lesion volume VOI ROIs to obtain maximum SUVmax and SUV SUV minimum SUVmin.

3. The process for determining whether a patient would benefit from cancer treatment with a particular therapeutic of claim 1, further comprising conducting a DNA aberration marker test to quantitate a plasma-free DNA alteration of a cancer marker selected from the list of markers in Tables 1A and 1B.

4. The process for determining whether a patient would benefit from cancer treatment with a particular therapeutic of claim 3, wherein the DNA aberration marker test conducted at substantially the same time as the first PET scan and the second PET scan.

6. The process for determining whether a patient would benefit for cancer treatment with a particular therapeutic of claim 1, wherein the second PET scan is conducted within 14 days after completion of a first dose of a therapeutic to the patient.

7. The process for determining whether a patient would benefit for cancer treatment with a particular therapeutic of claim 6, wherein the second PET scan is conducted form 1-10 days after completion of a first dose of a therapeutic to the patient.

8. A process for determining patient subgroup inclusion in a clinical trial of a targeted therapy for cancer, comprising (a) conducting a baseline PET FDG or PET FLT scan of the tumor region in a patient by determining baseline tumor tissue metabolic rate, (b) providing a single dose of a clinical trial test targeted therapeutic to the patient, (c) conducting a second PET FDG or PET FLT scan within 1-14 days following the single dose, by determining tumor tissue metabolic rate, and (d) comparing the results of the first PET scan to the second PET scan to determine an imaging response in the PET scan results, whereby at least a 1% reduction in tumor tissue metabolic rate indicates that the patient would be included in the clinical trial subgroup.

9. The process for determining patient subgroup inclusion in a clinical trial of a targeted therapy for cancer of claim 8, further comprising conducting a parallel before and after measurement or serial measurements of the level of circulating tumor DNA (ctDNA) for specific oncogene mutations/alterations from a response biomarker specific for a tumor to identify early patient response to drug therapy, wherein the response biomarker is selected from the group consisting of the response biomarkers in Tables 1A and 1B.

10. A process for determining whether a patient would benefit for cancer treatment with a particular therapeutic, comprising (a) conducting a baseline measurement of the level of circulating tumor DNA (ctDNA) for specific oncogene mutations/alterations from a response biomarker specific for a tumor to identify early patient response to drug therapy, wherein the response biomarker is selected from the group consisting of the response biomarkers in Tables 1A and 1B, (b) providing a single potentially effective dose of a therapeutic to the patient, (c) conducting a second measurement of the level of circulating tumor DNA (ctDNA) for specific oncogene mutations/alterations from a response biomarker specific for a tumor, wherein the response biomarker is selected from the group consisting of the response biomarkers in Tables 1A and 1B, wherein the second or serial measurement(s) are conducted 1-14 days following the dose of the therapeutic, and (d) comparing the results of the first measurement to the second measurement to determine if at least a 1% reduction indicates that the patient would benefit to continue to treat the tumor with the therapeutic.

11. The process for determining whether a patient would benefit for cancer treatment with a particular therapeutic of claim 10, wherein the second or serial measurement(s) are conducted from 1-10 days after completion of a first dose of a therapeutic to the patient.

Description

BRIEF DESCRIPTION OF THE FIGURE

[0023] FIG. 1 shows at PET scan of a person's tumor conducted prior to treatment (left) and two days after treatment (right) demonstrating early metabolic response.

DETAILED DESCRIPTION

[0024] The present disclosure provides using PET imaging in the first 14 days after treatment (and compare to pretreatment PET imaging) to be able to predict which patients will respond and who will not. This is applicable to patients with Ewing sarcoma or in general to patients with cancer treated with a variety of modalities. The ability of .sup.18F-FDG PET imaging to be an early indicator of response and predict survival has been recently corroborated in Ewing sarcoma (Joo Hyun O.sup.1, et al. Response to early treatment evaluated with .sup.18F-18F-FDG PET and PERCIST 1.0 predicts survival in patients with Ewing sarcoma family of tumors treated with a monoclonal antibody to the insulin-like growth factor 1 receptor. Journal of Nuclear Medicine, published on Jan. 21, 2016 as doi:10.2967/jnumed.115.162412) which is not prior art to the priority provisional patent application filed on 1 Mar. 2015.

[0025] An early marker of response, as provided herein solves several problems: (i) it permits patients who are not benefitting from therapy to be taken off that therapy and moved to another treatment after just a few days (or at most 14 days), rather than 6 weeks or months; (ii) it allows better assessment of who might be benefitting from therapy and reduces the chances that a patient with true benefit might be removed from treatment because CAT or MRI or similar imaging measuring tumor size shows pseudogrowth even while the tumor is dying; and (iii) it permits the early selection of responders for clinical trials such that a greater percentage of drugs will achieve statistical significance for efficacy and subsequent commercial approval with labeling requiring/suggesting that the presently disclosed procedure be conducted after a single treatment dose in order to determine who stays on the treatment and who gets moved to a different treatment. This is important because drugs that produce definitive responses, but in only small subsets of patients, may not be approvable in unselected patient populations. Yet these drugs can be successful once there is the ability to select the subgroup of responders within days of the first dose of drug.

[0026] The present disclosure provides a method for determining the effectiveness of a kinase inhibitor drug with a patient using a PET image, comprising the steps of: (1) obtaining three-dimensional images of different PET images at the time of or just prior to kinase drug administration of a therapeutic dose; (2) administering a single therapeutic dose to the, patient and (2) determining the lesion volume VOI ROIs to obtain maximum SUV/max and SUV SUV/minimum SUVmin; (3) in the same direction to cut the three-dimensional PET images obtained several faults, and each fault in the corresponding region of interest in the lesion volume VOI The lesion outline the region of interest based on a number of SUV and other activity values on the line ROI; (4) the three-dimensional PET image following the same line of the corresponding volume of the SUV activity as the reference value, the activity of drawing lines of different volumes and the corresponding Activityvolume curve; (5) calculating the time of administration of the specific activitythe area under the line of the curve of the volume; (6) in accordance with PET images acquired under different administration times to obtain and calculate different administration activity of time under the volume relationship line area under the curve, the effectiveness of drug is determined using T-test for statistical analysis.

[0027] The presently disclosed method uses early response to predict response. It is applicable to a wide range of tumors and agents, and would not require understanding the precise role of the biomarker portfolio in the tumor. Further, the use of early response biomarkers to predict tumor response, even if the overall response rate is 15% or even less, can find those patients who will be responders by giving them only one dose of drug. Therefore, in the context of oncology clinical drug trial designs, the present disclosed method to find responders 3-7 days following a single drug administration, significantly improves probability of running a successful clinical drug trial and improves overall drug approval rates.

[0028] As many as 85% of patients are harmed by a drug treatment, due to staying on an ineffective drug for eight weeks or longer before anyone realizes the drug is not effective for the patient's tumor, and having alternative perhaps more effective therapy delayed. The present method is able to determine treatment effectiveness at a much earlier time in order to change ineffective treatments earlier or to determine which patients should continue on a clinical study. For example, if 50% of the patients that are predicted to respond by the present early predictive method do respond (Joo Hyun O.sup.1 et al. Journal of Nuclear Medicine, published on Jan. 21, 2016 as doi:10.2967/jnumed.115.162412), and the overall response rate in an unselected patient population is 15%, using this method, only 15% of patients will continue on therapy unnecessarily until week 8, while using traditional imaging methods, 85% of patients will continue on treatment unnecessarily until week 8. This example assumes there are 100 patients and 15 will be true responders. Yet the present method will detect 30 patients to continue on study. The other 70 patients will move off trial after a day 5 assessment. Of the 30 patients who continue on study, 15 will respond and 15 will be unnecessarily treated until week 8+. But 15 of 100 unnecessarily treated is a lot better than 85 of 100. Further, a 50% response rate in oncology is considered a breakthrough therapy and no randomized trial is needed. The trade-off is that everyone will get a single dose of drug, but if the drug is relatively nontoxic (such as a targeted therapy) that should be acceptable. Accordingly, the present disclosed method is a non-traditional paradigm that will minimize side effect exposure when treatment benefit is not being well realized. This will also help to better design clinical drug trials such that better measurement criteria of treatment effectiveness can be utilized to better measure key risk/benefit criteria.

[0029] One technique that can be used for additional information is using FDG Positron Emission Tomography (PET) for treatment monitoring. An FDG PET (Positron Emission Tomography) scan is a radiological test that looks at tissue functioning, such as metabolic rates of tissues. With an FDG PET scan, a small amount of a radioactive sugar is injected into the blood. Cells that are growing, such as tumor cells, use sugar, and can be seen on 3-dimensional imaging. However, treatment monitoring, often comes at a later time during the course of treatment, after a patient has been exposed to multiple side effects of a treatment that may or may not have been effective. Efforts to determine particular drug effectiveness have been looking at personalized pharmacokinetic profiles. For example, uses of PET imaging has been done in combination with radiolabeled TM's (tyrosine kinase inhibitors such as erlotnib and gefitinib) to measure pharmacokinetics of the tyrosine kinase inhibitors. However, the dose of the radiolabeled TM's has been a microdose, not a full therapeutic dose. Pharmacokinetic analysis has been used to stratify patients. It was hypothesized that a patient's response to TKIs are dependent on achieving pharmacological active drug levels in tumor tissue and quantitative PET imaging can predict kinase inhibitor tumor concentrations. In this regard, VU Medical Center in the Netherlands is running a clinical trial to determine whether tumor concentrations of TKIs at pharmacological active doses can be predicted from PET studies using tracer amounts (micro-doses) of radiolabeled kinase inhibitors. However, the use of PET scans in this regard requires a correlation between local tumor drug concentration and specific efficacy.

[0030] As an additional measuring process, in addition to PET scans and run at the same time as the PET scans, a quantitative amount of circulating tumor DNA (ctDNA) in blood (plasma), urine, and other bodily fluids can be measured. What is measured is a relevant (to the tumor) biomarkers, which are specific oncogenes from cancer patients that have been shown to be correlated with radiographic (e.g., CAT, PET, MRI) indication of response to therapy. ctDNA or cell-free tumor DNA present in a cancer patient's blood (plasma) and subsequent urine that is derived from and the consequence of tumor cell death (apoptosis or necrosis) or shed in other ways. The relative amounts of ctDNA correlates with the tumor burden (i.e., number of tumor cells) within a cancer patient with higher amounts of ctDNA associated with greater tumor burden. The amount of ctDNA within a cancer patient's plasma and urine can be measured by quantitating the number of DNA copies present for specific oncogene aberrations derived from tumor cells. Therefore, as tumor burden increases in a patient, there is greater absolute number of tumor cell turnover (i.e., cell death) or other processes that shed tumor DNA, which equates to a larger number of copies of oncogenic tumor DNA present within plasma and subsequently urine. The relative measurement of ctDNA can be used to determine effectiveness of a cancer therapy and has been demonstrated for numerous metastatic cancers including breast, lung and colorectal cancer. For example, levels of the oncogene KRAS within metastatic cancer patients is correlated with responsiveness to chemotherapy. In histiocytic disorders, a cancer-related disease, approximately 50% of patients harbor a BRAF oncogene (i.e., BRAFV600E) and these patients responded to BRAF inhibitors. Relative measurement of BRAFV600E in urine from these patients receiving a BRAF inhibitor decreased at least 5-fold from baseline (prior to therapy) as compared to post-therapy and correlated with radiographic response. Furthermore, these changes in ctDNA levels are observed within days.

[0031] Comparative measurement of ctDNA levels from a single therapeutic dose at baseline and within days (1-14) post-therapy (and the serial pattern examined) is used as a responsive biomarker for determining which patients will respond to continued therapy. For example, for Ewing sarcoma patients, monitoring ctDNA levels of hybrid genes of 5EWSR1 fused to parts of either FL11, ERG of EVT1. For instance, in lung cancer, this technique shows that an initial rise in ctDNA and then fall within days is predictive or response. In Marchetti et al. (J. Thoracic Oncl. 10:1437-1443, October 2015, and not prior art to the priority provisional application) an early prediction of a response to tyrosine kinase inhibitors by quantifying EGFR mutations (a biomarker) was found that a PCR test and sequencing of plasma found for EGFR a progressive decrease in SQ1 decrease starting from day 4 after therapy.

[0032] In conducting a biomarker analysis, the sequence of the point mutation or deletion mutation is detected with tissue (solid tumor) or plasma, urine or other body fluid samples collected before and at multiple times after (but within 14 days) the initiation of treatment. Preferably, the after samples are collected before a second dose or a second round of treatment is initiated in order to determine the effectiveness of only the single first dose or round of treatment. The initial samples (before treatment are analyzed with PCR primer sets bracketed around the cancer marker location to determine and confirm an appropriate tumor marker. For example, for EGFR mutation analysis with 42 patients, there was an exon 19 deletion in 31 cases (74%) and an L858R point mutation in exon 21 in 11 cases (26%).

[0033] Using early response to predict true response is done by comparing PET FDG at days 1 to 14, with baseline (pretherapy) PET-FDG, or comparing ctDNA levels of the biomarker on days 1 to 14, with baseline (pretherapy) ct DNA (in blood, urine or other bodily fluids) or integrating both parameters (PET-FDG and ct DNA changes). Other forms of PET scans, such as PET-FLT, may also be used.

[0034] Other molecular markers that could be used, but will be specific to the tumor to be treated, are selected from Table 1A and 1B.

TABLE-US-00001 TABLE 1A INTEGRATED GENE LIST (includes mutations, amplifications, deletions and other changes) ABCB1 ARFRP1 AURKC BIRC3 C11orf30 CD274 CD36 CDK2 (EMSY) (PDL1) ABCC1 ARID1A AVPR2 BIRC5 C17orf39 CDX2 CD37 CDK4 (GID4) ABCC2 ARID1B AXIN1 BLM CA9 CHIC2 CD38 CDK6 ABCC6 ARID2 AXL BMI1 CAD CHN1 CD4 CDK7 ABCG2 ASMTL AR BCL11A CALCA CLP1 CD40 CDK8 ABL1 ACSL6 ARAF BCL3 CALCR CLTC CD44 CDK9 ABL2 AFF1 B2M BCL9 CALM1 CLTCL1 CD52 CDKN1A ACE AFF4 BAD BMP10 CALM2 CNTRL CD58 CDKN1B (CEP110) ACPP ARHGAP26 BAP1 BRAF CALM3 COL1A1 CD70 CDKN2A (GRAF) ACTB ARHGEF12 BARD1 BRCA1 CARD11 CREB3L1 CD74 CDKN2B ACVR1B ARNT BBC3 BRCA2 CASP3 CREB3L2 CD79A CDKN2C ACVRL1 ATF1 BCL10 BRD4 CASP7 CSF1 CD79B CDKN2D ADA ATG5 BCL11B BRIP1 CASP8 CCNG1 CDA CEACAM5 ADAM15 ATIC BCL2 BRSK1 CASP9 CCR4 CDC7 CEBPA AFP ASXL1 BCL2A1 BTG1 CBFB CCR5 CDC73 CENPE AKT1 ATM BCL2L1 BTG2 CBL CCT6B CDH1 CHD2 AKT2 ATP1A3 BCL2L2 BTK CBR3 CD109 CDH2 CHD4 AKT3 ATP7A BCL6 BTLA CCL3 CD151 CDH20 CHEK1 ALK ATR BCL7A BUB1 CCND1 CD19 CDH5 CHEK2 ALOX12 ATRX BCOR CAMTA1 CCND2 CD22 CDK1 CIAPIN1 ALOX12B AURKA BCORL1 CARS CCND3 CD248 CDK12 CIC AMER1 AURKB BCR CBFA2T3 CCNE1 CPS1 CRLF2 CSF3R (FAM123B or WTX) ANGPT1 APC BGLAP CIITA CLDN18 CREBBP CSF1R CTCF ANGPT2 APH1A BIRC2 CKS1B CLU CRKL CSF2 CTLA4 CTNNA1 DHFR EP300 FOXO4 FGFR2 GATA1 HOXD13 HOXD13 CTNNB1 DIABLO EPCAM FSTL3 FGFR3 GATA2 HBB HSPA5 CTSG DICER1 EPHA3 FUS FGFR4 GATA3 HBEGF HLF CUL3 DKK1 EPHA5 F13B FH GATA4 HDAC1 HMGA1 CUX1 DLL4 EPHA6 F2 FHIT GATA6 HDAC11 HMGA2 CXCL12 DNM2 EPHA7 F3 FLCN GDF2 HDAC2 HOXA11 CXCR1 DNMT3A EPHB1 F5 FLT1 GGH HDAC4 HOXA13 CXCR2 DOT1L EPHB4 FAF1 FLT3 GLI1 HDAC6 HOXA9 CXCR4 DPP4 EPHB6 FAM46C FLT3LG GLP2R HDAC7 HOXC11 CYBA DPYD ERBB2 FANCA FLT4 GNA11 HFE HOXC13 CYLD DTX1 ERBB3 FANCC FLYWCH1 GNA12 HGF HOXD11 CYP11B1 DUSP2 ERBB4 FANCD2 FOLH1 GNA13 HIF1A IL11RA CYP11B2 DUSP9 ERCC2 FANCE FOLR1 GNAQ HIST1H1C IGH CYP17A1 EIF4A2 ERCC5 FANCF FOXL2 GNAS HIST1H1D IGK CYP19A1 ELF4 ERG FANCG FOXO1 GNRHR HIST1H1E IGL CYP1B1 ELL ERRFI1 FANCL FOXO3 GPC3 HIST1H2AC IL3 CYP2C19 ELN ESR1 FAS FOXP1 GPR124 HIST1H2AG IFNA2 (TNFRSF6) CYP2C8 EPOR ESR2 FASLG FOXP4 GRIN2A HIST1H2AL IFNB1 CYP2C9 EPS15 ETS1 FAT1 FRS2 GRIN3B HIST1H2AM IFNG CYP2D6 E2F1 ETV1 FBXO11 FUBP1 GRM3 HIST1H2BC IGF1R CYP3A4 EBF1 ETV4 FBXO31 FYN GSK3B HIST1H2BJ IGF2 CYP4B1 ECT2L ETV5 FBXW7 FZD1 GSTO1 HIST1H2BK IGF2R DDIT3 EDNRA ETV6 FGF1 FZD10 GSTO2 HIST1H2BO IKBKE DDX10 EDNRB EWSR1 FGF10 FZD2 GSTP1 HIST1H3B IKZF1 DDX6 EED EXOSC6 FGF14 FZD5 GTSE1 HNF1A IKZF2 DEK EEF2 EZH2 FGF19 FZD7 GUCY1A2 HOXA3 IKZF3 DUSP22 EGFL7 FCGR2B FGF2 FZD8 G6PD HPSE IL13RA2 DAXX EGFR FCRL4 FGF23 GAS7 HERPUD1 HRAS IL1A DCT EIF4EBP1 FEV FGF3 GMPS HEY1 HRH2 IL2 DDR2 ELP2 FGFR1OP FGF4 GPHN HIP1 HSD3B1 IL21R DDX3X EML4 FLI1 FGF6 GABRA6 HIST1H4I HSP90AA1 IL25 DDX5 ENG FNBP1 FGFR1 GADD45B HSP90AB1 HSP90B1 IL29 ICK JUN LRP1B MED12 MLLT3 NRAS PAK3 PLA2G10 ID3 KAT6A LRP2 MEF2B MLLT4 NRP2 PALB2 PLA2G12A (MYST3) (AF6) IDH1 KDSR LRP6 MEF2C MLLT6 NSD1 PARK2 PLA2G12B IDH2 KIF5B LRRK2 MEFV MN1 NT5C2 PARP1 PLA2G1B IL2RA KMT2A LTA MEN1 MNX1 NTRK1 PARP2 PLA2G2A (MLL) IL4 KDM2B LTF MET MSI2 NTRK2 PARP8 PLA2G2D IL4R KDM4C LTK MGMT MSN NTRK3 PASK PLA2G2E IL7R KDM5A LYN MIB1 MUC1 NUP93 PAX5 PLA2G2F INHBA KDM5C LZTR1 MITF MYB NUP98 PBRM1 PLA2G3 INPP4B KDM6A LMO2 MKI67 MYH9 NACA PC PLA2G5 INPP5D KDR MAF MLH1 MYO18A NBEAP1 PCBP1 PLA2G6 (SHIP) (BCL8) INSR KEAP1 MAFB MMP2 NAE1 NCOA2 PCLO PLAU IRF1 KEL MAGEA1 MPL NAMPT NDRG1 PDCD1 PLCG1 IRF2 KIF11 MAGEA4 MRE11A NAT2 NFKB2 PDCD11 PLCG2 IRF4 KIT MAGED1 MS4A1 NCF2 NIN PDCD1LG2 PLK1 (PDL2) IRF8 KLF4 MAGI2 MSH2 NCL NUMA1 PDGFB PLK4 IRS2 KLHL6 MALT1 MSH3 NCOR2 NUP214 PDGFRA PMP22 ITGA1 KLK2 MAP2K1 MSH6 NCSTN NUTM2A PDGFRB PMS2 ITGA5 KLK3 MAP2K2 MST1R NF1 NR4A3 PDK1 PNP ITGAM KMT2C MAP2K4 MSTN NF2 OMD PDPK1 POLD1 (MLL3) ITGAV KMT2D MAP3K1 MTF1 NFE2L2 OPRD1 PGF POLE (MLL2) ITGB1 KRAS MAP3K14 MTHFR NFKB1 PAX3 PGR POT1 ITGB2 LASP1 MAP3K6 MTOR NFKBIA PAX7 PHF6 PPARA ITGB3 LCP1 MAP3K7 MTR NGF PBX1 PHLPP2 PPARD ITGB5 LPP MAPK1 MUTYH NKX2-1 PCM1 PIK3C2B PPARG ITGB6 LYL1 MAPK3 MYC NOD1 PCSK7 PIK3CA PPP2R1A ITK LAG3 MCL1 MYCL NOD2 PDE4DIP PIK3CB PRAME (MYCL1) ITPA LEF1 MDM2 MYCN NOTCH1 PER1 PIK3CD PRDM1 JAZF1 LGALS1 MDM4 MYD88 NOTCH2 PHF1 PIK3CG PREX2 JAK1 LHCGR MED1 MYH11 NOTCH3 PICALM PIK3R1 PRKAR1A JAK2 LMO1 MDS2 MLF1 NPM1 P2RX7 PIK3R2 PRKCA JAK3 LOXL2 MECOM MLLT1 NQO1 P2RY8 PGR PRKCB (ENL) JARID2 LPA MKL1 MLLT10 NR4A1 PAG1 PIM1 PAFAH1B2 (AF10) PLAG1 RAD51 S100A9 SSX2 SSTR2 TPM4 TNFRSF14 UBB PML RAD5IL3 S1PR1 SSX4 SSTR3 TRIM24 TNFRSF17 UBC POU2AF1 RAF1 S1PR2 STL SSTR4 TRIP11 TNFRSF4 UGT1A1 PPP1CB RANBP2 SDHA SLC7A11 SSTR5 TTL TNFRSF8 UGT1A7 PRDM16 RARA SDHB SLCO1B1 STAT3 TEC TNFRSF9 UMPS PRRX1 RASGEF1A SDHC SLIT2 STAT4 TEK TNFSF10 USP9X PSIP1 RB1 SDHD SMAD2 STAT5A TERC TNFSF13 VCAM1 PRKCI RBM10 SELL SMAD3 STAT5B TERT TNFSF13B VDR PRKDC RELN SELP SMAD4 STAT6 TET1 TNKS VEGFA PRLR RET SERP2 SMARCA1 STK11 TET2 TOP1 VEGFB PRSS8 RHEB SERPINA1 SMARCA4 SUFU TGFB1 TOP2A VEGFC PSMB5 RHOA SERPINE1 SMARCB1 SULTIC4 TGFBR1 TOR1A VHL PSMB8 RICTOR SETBP1 SMC1A SUZ12 TGFBR2 TP53 VKORC1 PTCH1 RNF43 SETD2 SMC3 SYK TGM2 TP63 VPS4B PTCH2 ROCK2 SF3B1 SMC4 T TH TP73 VWF PTEN ROS1 SFTPC SMO TACR1 TLL2 TPMT WHSC1 (MMSET or NSD2) PTGS2 RPE65 SGK1 SNCAIP TAF1 TLR2 TRAF2 WHSCIL1 PTH RPS27A SHH SOCS1 TBL1XR1 TLR3 TRAF3 WDR90 PTK2B RPTOR SLC10A3 SOCS2 TBX22 TLR4 TRAF5 WISP3 PTPN11 RRM2 SLC16A1 SOCS3 TBX3 TLR5 TRPM8 WT1 PTPN2 RUNX1 SLC19A1 SOD2 TAL1 TLR7 TSC1 XBP1 PTPN6 RUNX3 SLC29A1 SOX10 TAL2 TLR8 TSC2 XIAP (SHP-1) PTPRC RABEP1 SLC5A5 SOX2 TAF15 TLR9 TSHR XPC PTPRD RALGDS SLC6A2 SOX9 TCF3 TMEM30A TUSC2 XPO1 (E2A) PTPRO RAP1GDS1 SEC31A SPEN TCL1A TMPRSS2 TUSC3 XRCC1 (TCL1) PRRX1 RBM15 SET SPG7 TFE3 TMSB4XP8 TYK2 XRCC2 (TMSL3) PSIP1 RHOH SH3GL1 SPOP TFG TNC TYMS YPEL5 PTK7 RNF213 SLC1A2 SPP1 TFPT TNF TYR YES1 QKI RPL22 SNX29 SPTA1 TFRC TNFAIP3 USP6 YY1AP1 (RUNDC2A) RAC1 RPN1 SRSF3 SRC TLX1 TNFRSF10A U2AF1 ZBTB2 RAD21 RUNX1T1 SS18 SRSF2 TLX3 TNFRSF10B U2AF2 ZEB2 (ETO) RAD50 RUNX2 SSX1 SSTR1 TPM3 TNFRSF11A UBA52 ZMYM3 ZBTB16 ZMYM2 ZNF384 ZNF521 ZNF217 ZNF24 (ZSCAN3) ZNF703 ZRSR2

TABLE-US-00002 TABLE 1B Rearrangements and other Alterations ALK FGFR1 ALK FGFR1 PDGFRA BCL2 FGFR2 PDGFRB BCL6 FGFR3 RAF1 BCR IGH RARA BRAF IGK RET BRCA1 IGL ROS1 BRCA2 JAK1 SYT/SSX1 SYT/SSX2 BRD4 JAK2 TMPRSS2 CCND1 KIT TRG CRLF2 KMT2A (MLL) EGFR MSH2 EPOR MYB ETV1 MYC ETV4 NOTCH2 ETV5 NTRK1 ETV6 NTRK2 EWSR1 PAX3/FKHR PAX7/FKHR EWS-FLI EWS/FLI1, type 1 EWS/FLI1, type 2 EWS/ERG EWS/ETV1 EWS/ETV4 EWS/FEV