SG11201905640XA - Oncogenic splice variant determination - Google Patents

Abstract

Retrievethe sample junctions [ Retrieve the baseline junctions DIA Remove sample junctions with baseline junction overlap o the sample junctions overlap with the baseline junctions? RIR ..1 Yes Collect as filtered sample junctions Rid Collect as overlap sample junctions 1122 (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (43) International Publication Date 26 July 2018 (26.07.2018) WIP0 I PCT Iiiimmomiolollmonolomoilloolloomomomovoimill (10) International Publication Number WO 2018/136416 Al (51) International Patent Classification: GOOF 19/18 (2011.01) GOOF 19/22 (2011.01) (21) International Application Number: PCT/US2018/013864 (22) International Filing Date: 16 January 2018 (16.01.2018) (25) Filing Language: English (26) Publication Language: English (30) Priority Data: 62/447,382 17 January 2017 (17.01.2017) US (71) Applicant: ILLUMINA, INC. [US/US]; 5200 Illumina Way, San Diego, CA 92122 (US). (72) Inventors: SNEDECOR, June; C/o Illumina, Inc., 5200 Il- lumina Way, San Diego, CA 92122 (US). CHUANG, Han- yu; C/o Illumina, Inc., 5200 Illumina Way, San Diego, CA 92122 (US). BERRY, Gwenn; C/o Illumina, Inc., 5200 Il- lumina Way, San Diego, CA 92122 (US). CHEN, Xiao; C/ o Illumina, Inc., 5200 Illumina Way, San Diego, CA 92122 (US). (74) Agent: FULLER, Michael, L.; Knobbe, Martens, Olson & Bear LLP, 2040 Main Street, Fourteenth Floor, Irvine, CA 92614 (US). (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, GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, TZ, (54) Title: ONCOGENIC SPLICE VARIANT DETERMINATION FIG. 8 Verify unctions I Store filtered sample junctions R_0 00 O O (57) : Presented herein are systems and methods for identifying splice variants. The techniques include determining one or more sample splice junctions from a plurality of RNA sequence reads from a single biological sample, retrieving a set of baseline splice junctions determined from a plurality of healthy RNA samples and comparing the one or more sample splice junctions to the set of baseline splice junctions to identify one or more filtered sample splice junctions comprising sample splice junctions that do not overlap with the baseline splice junctions, wherein the one or more filtered sample splice junctions are candidate oncogenic events. [Continued on next page] WO 2018/136416 Al MIDEDIMOMOIDEIREEMOMMIMINHEMEOMEHOIMI 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 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)) Published: — with international search report (Art. 21(3))