(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2016/166269 Al 20 October 2016 (20.10.2016) P O P C T (51) International Patent Classification: (74) Agents: POREDDA, Andreas et al; Patent Department, C12Q 1/68 (2006.01) Sandhofer Strasse 116, 68305 Mannheim (DE). (21) International Application Number: (81) Designated States (unless otherwise indicated, for every PCT/EP2016/058324 kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, (22) International Filing Date: BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, 15 April 2016 (15.04.2016) DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, (25) Filing Language: English HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KN, KP, KR, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, (26) Publication Language: English MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, (30) Priority Data: PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, 62/149,381 17 April 2015 (17.04.2015) US SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (71) Applicant (for DE only): ROCHE DIAGNOSTICS GMBH [DE/DE]; Sandhofer StraBe 116, 68305 Man (84) Designated States (unless otherwise indicated, for every nheim (DE). kind of regional protection available): ARIPO (BW, GH, GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, (71) Applicant (for all designated States except DE, US) : F. TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, HOFFMANN-LA ROCHE AG [CH/CH]; Grenzacher- TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, strasse 124, 4070 Basel (CH). DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, (71) Applicant (for US only): ROCHE MOLECULAR SYS¬ SM, TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, TEMS, INC. [US/US]; 4300 Hacienda Drive, Pleasanton, GW, KM, ML, MR, NE, SN, TD, TG). California 94588 (US). Declarations under Rule 4.17 : (72) Inventors: BEGOVICH, Ann; 7306 Rockway Avenue, El Cerrito, California 94530 (US). DUA, Rajiv; 2084 — as to the applicant's entitlement to claim the priority of the Plumeria Lane, Manteca, California 95337 (US). KUO, earlier application (Rule 4.1 7(in)) Dwight; 325 1 Magdalena Place, Castro Valley, California Published: 94546 (US). MA, Xiaoju Max; 416 Portofino Drive #201, San Carlos, California 94070 (US). ORDINARIO, Ellen; — with international search report (Art. 21(3)) 810 York Street, Oakland, California 94610 (US). — with sequence listing part of description (Rule 5.2(a)) (54) Title: MULTIPLEX PCR TO DETECT GENE FUSIONS EML4-ALK Variantl: RNA Blend (57) Abstract: Provided herein are methods and compositions for detecting gene fusions, e.g., relevant to cancer. The present meth- © ods and compositions can be used to detect gene fusions with very high sensitivity and specificity. The present methods and compos - itions can detect gene fusions, e.g., in free circulating tumor RNA from a plasma sample. MULTIPLEX PCR TO DETECT GENE FUSIONS BACKGROUND OF THE INVENTION A number of cancers are associated with gene fusions. Perhaps the earliest reported example is the association of BCR-ABL with chronic myelogenous leukemia (CML) in the '60s (Nowell and Hungerford (1960), /. Natl. Cancer Inst. 25:85). Since then, hundreds more gene fusions have been reported for cancers in many different tissues (Presner and Chinnaiyan (2009), Curr. Opin Genet. Dev. 19:82). Another example is the tyrosine receptor kinase ALK. EML4-ALK (echinoderm microtubule-associated protein-like 4-anaplastic lymphoma kinase) fusions are associated with non-small cell lung cancer (NSCLC). In this case, the N terminal, extracellular portion of ALK is replaced by EML4 (KIF5B, HIP1, KLC1, TFG can also fuse with ALK in a similar manner). The expression of the resulting fusion gene is driven by the strong EML4 promoter, resulting in higher expression of the intracellular tyrosine kinase domain of ALK. In addition, EML4 forms a coiled-coil that results in ligand-independent dimerization, and constitutive activation of the ALK tyrosine kinase domain. Detection of a gene fusion is important for directing therapy. Most current methods of detection require biopsy of tumor tissue, which is not feasible for many cancer patients, especially in later stages. Detection in biopsied tissue sections is typically carried out by fluorescence in situ hybridization (FISH) or immunohistochemistry (IHC). The tests have high false positive rates and background, in part because of shearing during the sectioning process. Skilled cytologists are thus required to observe multiple tissue sections, which necessitates a sizable biopsy from a weakened patient. Detection of fusions has also been attempted using RT-PCR, but this has not been successful because of the highly variable nature of gene fusions. In the case of EML4-ALK4, at least 20 different fusions result in the activated tyrosine kinase. Another difficulty with RT-PCR is the amount and quality of genetic material from tumor tissue, e.g., in formalin fixed paraffin embedded (FFPE) form. See, e.g., Liu et al. (2015), PLoSOne 10: eOl 17032. Because detection is time and resource intensive, the testing rate is relatively low. Cancers associated with ALK fusions are very sensitive to ALK inhibitors such as crizotinib and ceretinib. Gene fusions with Rearranged during Transcription (RET), such as with KIF5B or CCDC6, are also sensitive to therapy, e.g., with vandetanib see Matsubara et al. (2007), /. Thorac. Oncol. 7:1872). The low rate of testing for gene fusions thus represents a great lost opportunity for treatment. SUMMARY OF THE INVENTION Provided herein are methods and compositions for detecting genetic fusions, e.g., fusion genes. Provided is a composition comprising (1) at least one first primer pair that is specific for a fusion site between a first genetic region and a second genetic region, wherein the first and second genetic regions are not adjacent in a wild type genome, and wherein the at least one primer pair comprises at least one forward primer beginning on the 5' side of the fusion site and at least one reverse primer beginning on the 3' side of the fusion site; (2) a second primer pair specific for a portion of the first genetic region that is 5' of the fusion site; and (3) a third primer pair specific for a portion of the first genetic region that is 3' of the fusion site. Alternatively, the second and third primer pairs can be specific for the second genetic region. In some embodiments, the first genetic region is in gene (e.g., gene 1). In some embodiments, the second genetic region is in a gene (e.g., gene 2). In some embodiments, the first and second genetic regions are in genes, where the fusion point between the genes in not found in a wild type genome. In some embodiments, the at least one first primer pair (1) comprises at least one forward primer that begins in gene 2, 5' of the fusion site, and optionally includes the fusion site. In some embodiments, the at least one first primer pair (1) comprises at least one reverse primer that begins in gene 1, 3' of the fusion site, and optionally includes the fusion site. In some embodiments, the at least one first primer pair comprises at least 2, 3, 4, 5, 6, 7, 8, 9, 10, or more primer pairs. In some embodiments, the composition further comprises at least one primer pair specific for a control sequence, e.g., an internal control. Examples of controls that can be used for the presently disclosed assays include, but are not limited to SDH (succinate dehydrogenase), LDHA (lactate dehydrogenase A), NONO, PGK (phosphoglycerate kinase 1), PPIH, HPRT1, beta-actin, GADPH, ACTB, and 16S rRNA. In some embodiments, each primer set ((1), (2), (3), and the optional at least one control primer pair) is associated with a different label (e.g., dye) that emits a signal distinct from the other labels. The label can be attached directly or indirectly to either the forward primer or reverse primer of each primer pair. In some embodiments, the labels are retained so that the amplification products resulting from each primer set ((1), (2), (3), and the optional at least one primer pair) are labeled. In some embodiments, the composition comprises at least one labeled probe specific for each of the amplification products resulting from each primer set ((1), (2), (3), and the optional at least one primer pair). In some embodiments, the composition further comprises a DNA polymerase, e.g., a thermostable DNA polymerase such as Taq or a Taq derivative. In some embodiments, the composition further comprises reverse transcriptase. In some embodiments, the composition further comprises dNTPs. In some embodiments, the composition further comprises buffer amenable to polymerization by the DNA polymerase and reverse transcriptase. In some embodiments, the composition further comprises a biological sample from an individual or group of individuals. In some embodiments, the individual has been diagnosed with cancer, e.g., lung cancer (e.g., non-small cell lung cancer (NSCLC), lung squamous cell carcinoma, lung adenocarcinoma), bladder carcinoma, glioblastoma, head and neck cancer, glioma, thyroid carcinoma, ovarian cancer, leukemia, lymphoma, prostate cancer, pancreatic cancer, renal cancer, or breast cancer. In some embodiments, the sample is isolated nucleic acid, e.g., DNA or RNA. In some embodiments, the sample is RNA, e.g., isolated from blood (serum or plasma), bronchoalveolar lavage, or tissue biopsy.