SG11201907738UA - Ranking system for immunogenic cancer-specific epitopes - Google Patents

Abstract

Epitopeidentification Component computation 'Mathirieleething m odel Weight assignment Peptide-level score designation Sample-level score designation Immunogenicity score designation () INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (43) International Publication Date 04 October 2018 (04.10.2018) W I PO I PCT ~~~~~~~~~~~~~ 011101010VIIIOH olo HE mil mo lio (10) International Publication Number WO 2018/183980 A3 (51) International Patent Classification: A61K 31/7052 (2006.01) A61K 39/02 (2006.01) A61K 31/7105 (2006.01) A61K 48/00 (2006.01) A61K 39/00 (2006.01) C07H 21/02 (2006.01) (21) International Application Number: PCT/US2018/025597 (22) International Filing Date: 31 March 2018 (31.03.2018) (25) Filing Language: English (26) Publication Language: English (30) Priority Data: 62/479,320 31 March 2017 (31.03.2017) US (72) Inventors; and (71) Applicants: PEI-JIA, Yang; 4f, No.208, Xinhu 2nd Rd, Neihu Dist, Taipei City, 114 (TW). CHENG, Jen-Hao; 4f, No.208, Xinhu 2nd Rd, Neihu Dist, Taipei City, 114 (TW). CHEN, Ying-Ja [US/ ]; 4f, No.208, Xinhu 2nd Rd, Nei- hu Dist, Taipei City, 114 (TW). CHEN, Shu-Jen [US/ ]; 2f.-1, No.69-1, Hejiang St., Zhongshan Dist., Taipei City, 104 (TW). CHEN, Hua-Chien; 4f., No. 17, Ln. 63, Sec. 2, Dunhua S. Rd. Daan Dist., Taipei City, 106 (TW). (74) Agent: KAO, Laurence; OPES IP CONSULTING CO., LTD, 4f. No.203, Sec. 1, Fuxing S. Rd., Daan Dist., Taipei City, 10666 (TW). (81) Designated States (unless otherwise indicated, for every kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP, KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, 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, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (84) Designated States (unless otherwise indicated, for every kind of regional protection available): ARIPO (BW, GH, (54) Title: RANKING SYSTEM FOR IMMUNOGENIC CANCER-SPECIFIC EPITOPES Tumor 8f normal tis LIES Whole exome sequencing Variant deterrnina on Ranking FIGURE 1 (57) : This disclosure relates to systems and methods that identify, predict, and rank immunogenic T-cell epitopes. In particular, this disclosure identifies epitopes that arose from disease-associated mutations, wherein the epitopes are predicted to elicit immune response from T cells. Specifically, this disclosure simultaneously considers peptide-level information, including MHC Class I and II presentation, helper and cytotoxic T cell response and sample-level information, including mutation clonality and MHC allele dosage. In some embodiment, the systems and methods are used for personalized treatment of cancers. [Continued on next page] WO 2018/183980 A3 MIDEDIMOMOIDEIREEMOMiliMOIHMOMMEfin GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, 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, SM, TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW, KM, ML, MR, NE, SN, TD, TG). Declarations under Rule 4.17: as to the identity of the inventor (Rule 4.17(i)) as to applicant's entitlement to apply for and be granted a patent (Rule 4.17(11)) as to the applicant's entitlement to claim the priority of the earlier application (Rule 4.17(iii)) of inventorship (Rule 4.17(iv)) Published: with international search report (Art. 21(3)) before the expiration of the time limit for amending the claims and to be republished in the event of receipt of amendments (Rule 48.2(h)) (88) Date of publication of the international search report: 20 December 2018 (20.12.2018)