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WO 2017/050939 A2 30 March 2017 (30.03.2017) P O P C T

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WO 2017/050939 A2 30 March 2017 (30.03.2017) P O P C T (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 2017/050939 A2 30 March 2017 (30.03.2017) P O P C T (51) International Patent Classification: (74) Agents: SANDERSON, Andrew et al; Potter Clarkson G01N33/5 74 (2006.01) LLP, The Belgrave Centre, Talbot Street, Nottingham Not tinghamshire NG1 5GG (GB). (21) International Application Number: PCT/EP20 16/0726 17 (81) Designated States (unless otherwise indicated, for every kind of national protection available): AE, AG, AL, AM, (22) Date: International Filing AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, 22 September 2016 (22.09.201 6) BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, (25) Filing Language: English DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KN, KP, KR, (26) Publication Language: English KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, (30) Priority Data: MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, 15 16801 .6 22 September 2015 (22.09.2015) GB OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, (71) Applicant: IMMUNOVIA AB [SE/SE]; Medicon Village, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, SE-223 8 1 Lund (SE). ZW. (72) Inventors: BORREBAECK, Carl Arne Krister; Hel- (84) Designated States (unless otherwise indicated, for every gonavagen 21, S-223 63 Lund (SE). WINGREN, Christer kind of regional protection available): ARIPO (BW, GH, Lars Bertil; Ostakravagen 23, Sandby, SE-247 32 Sodra GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, (SE). TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, 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, [Continued on nextpage] (54) Title: METHOD, ARRAY AND USE THEREOF (57) Abstract: The present invention relates to a method for determining the locality and/or presence of pancreatic cancer in an individual comprising or consisting of the steps of: (a) providing a sample to be tested from the indi vidual, and (b) determining a biomarker signature of the test sample by measuring the expression in the test sample of one or more biomarkers se lected from the group defined in Table A, wherein the expression in the test sample of one or more biomarkers selected from the group defined in Table A is indicative of the locality and/or presence of pancreatic cancer in the in dividual. The invention also comprises arrays and kits of parts for use in the method of the invention. Smallest error < © o Condensed signatures. o w o 2017/050939 A2 1II 11 II II 11 III 11 II lll l ll llll II III II I II SM, TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, Published GW, KM, ML, MR, NE, SN, TD, TG). without international search report and to be republished upon receipt of that report (Rule 48.2(g)) METHOD. ARRAY AND USE THEREOF Field of Invention The present invention relates to methods for detecting pancreatic cancer, and biomarkers and arrays for use in the same. Background Pancreatic ductal adenocarcinoma (PDAC) is the 4th most common cancer-related cause of death (Siegel et al, 2012). Multiple factors account for its poor prognosis and early diagnosis provides today the only possibility for cure. PDAC is often detected at late stages with 80% of patients not eligible for surgery due to either locally advanced or metastatic disease (Hidalgo, 2010; Porta et al, 2005; Siegel et al, 2012). The biological diversity of tumours due to its localization in pancreatic cancer has been previously demonstrated. Tumours in the body/tail of pancreas are rarer than tumour in the head of pancreas (77% of PDAC). Because of differences in e.g., blood supply, and lymphatic and venous backflow, there are also differences in the disease presentation with body/tail tumours causing less jaundice, more pain, higher albumin and CEA levels and lower CA19-9 levels. Body/tail tumours are more often detected at a later stage than head tumours and have a higher rate of metastasis. As the biological differences can result in different treatment efficiency, biomarkers that can discriminate between tumour localization would be of clinical relevance and could pave the way for personalized treatment strategies. However, few differences have been found on a genetic level, with no significant variation in the overall number of mutations, deletions and amplifications, or in K-ras point mutations. Accordingly, there is a continuing need to provide methods for determining biomarkers that can determine the locality and/or presence of pancreatic cancer tumours. Summary of the Invention A major problem with tumours of the body/tail in comparison with pancreatic head cancer is distant metastasis, especially in the liver, and resection of the tumour does not increase postoperative survival in metastatic disease. On the other hand, patients with local-stage body/tail tumours had higher survival rates compared with local-stage pancreatic head cancer. Several antibodies identified markers that showed on differential protein expression levels between head and body/tail tumours. A condensed signatures differentiating the groups could be defined. Consequently, these results are encouraging for a future development of a blood protein biomarker signature discriminating body/tail and head tumours at an early disease stage. Taken together, we provide information that serum protein markers associated with different tumour locations in the pancreas could be identified. Serum protein markers associated with tumour localization were identified. A first aspect of the invention provides a method for determining the locality of and/or diagnosing pancreatic cancer in an individual comprising or consisting of the steps of: a) providing a sample to be tested from the individual; b) determining a biomarker signature of the test sample by measuring the expression, presence or amount in the test sample of one or more biomarkers selected from the group defined in Table A (i), (ii) or (iii); wherein the expression in the test sample of the one or more biomarker selected from the group defined in Table A (i), (ii) or (iii) is indicative of the locality and/or presence of pancreatic cancer in the individual. By "sample to be tested", "test sample" or "control sample" we include a tissue or fluid sample taken or derived from an individual. Preferably the sample to be tested is provided from a mammal. The mammal may be any domestic or farm animal. Preferably, the mammal is a rat, mouse, guinea pig, cat, dog, horse or a primate. Most preferably, the mammal is human. Preferably the sample is a cell or tissue sample (or derivative thereof) comprising or consisting of plasma, plasma cells, serum, tissue cells or equally preferred, protein or nucleic acid derived from a cell or tissue sample. Preferably test and control samples are derived from the same species. In an alternative or additional embodiment the tissue sample is pancreatic tissue. In an alternative or additional embodiment, the cell sample is a sample of pancreatic cells. By "expression" we mean the level or amount (relative and/or absolute) of a gene product such as ctDNA (circulating DNA), mRNA or protein. Expression may be used to define clusters associated with disease states of interest. Alternatively or additionally, "expression" excludes the measurement of ctDNA. Methods of detecting and/or measuring the concentration of protein and/or nucleic acid are well known to those skilled in the art, see for example Sambrook and Russell, 2001 , Cold Spring Harbor Laboratory Press. By "biomarker" we mean a naturally-occurring biological molecule, or component or fragment thereof, the measurement of which can provide information useful in determining the locality and/or presence of pancreatic cancer. For example, the biomarker may be a naturally-occurring nucleic acid, protein or carbohydrate moiety, or an antigenic component or fragment thereof. By 'determining the locality of pancreatic cancer, ' 'indicative of the pancreatic cancer locality' and the like we include determining (or providing indication of) whether the pancreatic cancer is located in and/or originated from (a) the head of the pancreas; or (b) the body and/or tail of the pancreas. The terms 'pancreas head, 'pancreas neck,' 'pancreas body' and 'pancreas tail' are well-known and understood by the skilled person. Hence, by 'the head of the pancreas,' 'the neck of the pancreas,' 'the body of the pancreas' and 'the tail of the pancreas' we include the conventional understanding of the terms by the skilled person. Alternatively or additionally, by 'the head of the pancreas' we mean or include foundational model of anatomy identification number (FMAID) 10468 (for more information on the FMA and FMAIDs, see Rosse & Cornelius, 2003, Ά reference ontology for biomedical informatics: the Foundational Model of Anatomy,' J. Biomed. Informatics, 36(6): 478-500 and the FMA browser, accessible at http://xiphoid.biostr.washington.edu/fma/index.html). Synonyms for 'the head of the pancreas' include 'right extremity of pancreas,' 'pancreatic head' and 'caput pancreatis'. Alternatively or additionally, by 'the neck of the pancreas' we mean or include FMAID 14517. Synonyms for 'the neck of the pancreas' include 'pancreatic neck' and 'collum pancreatis'. Alternatively or additionally, by 'the body of the pancreas' we mean or include FMAID 14518. Synonyms for 'the body of the pancreas' include 'pancreatic body' and 'corpus pancreatis'.
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