Patent SG-11201901432Y-A (SG)
Title: Immunotherapy markers and uses therefor
Inventor: NGUYEN ANDREW
IPC: G16B25/10
Filed: 2017-08-25
Abstract: APOBECPOLE Mutation Signature of 3 Significant POLE/APOBEC Signatures found. Yes Mutation Rate 3.71 per Megabase coding DNA Yes Immune Checkpoint Expression 5 of 9 immune checkpoint related genes over-expressed Yes Checkpoint Gene IDO1 HAVCR2 Common Name IDO TIM3 Immunotherapy Related Gene Expression Function Immune Escape Signal Immune Checkpoint Immune Checkpoint Immune Checkpoint Ligand Immune Checkpoint Ligand Status TPM Normal 55.05 Normal 27.57 24.82 Over-expressed 22.58 Over-expressed 20.18 Over-expressed 16.42 LAG3 LAG3 PDCD1LG2 PDL2 CD274 PDL1 CD40 CD40 Immune Escape Signal Normal CTLA4 CTLA4 Immune Checkpoint Over-expressed 8.39 PDCD1 PD1 Immune Checkpoint Over-expressed 5.61 I L2 IL2 Immune Stimulatory Normal 0.21 Signal FIG. 1 N O cc O O (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (43) International Publication Date 01 March 2018 (01.03.2018) W I PO I PCT omit VIII °nolo III i oiloo Imo oimIE (10) International Publication Number WO 2018/039567 Al (51) International Patent Classification: G06F 19/18 (2011.01) G06F 19/22 (2011.01) G06F 19/00 (2011.01) (21) International Application Number: PCT/US2017/048629 (22) International Filing Date: 25 August 2017 (25.08.2017) (25) Filing Language: English (26) Publication Language: English (30) Priority Data: 62/379,700 25 August 2016 (25.08.2016) US (71) Applicant: NANTOMICS, LLC [US/US]; 9920 Jefferson Boulevard, Culver City, California 90232 (US). (72) Inventors: NGUYEN, Andrew; 9920 Jefferson Boule- vard, Culver City, California 90232 (US). SANBORN, John Zachary; 9920 Jefferson Boulevard, Culver City, California 90232 (US). RABIZADEH, Shahrooz; 9920 Jefferson Boulevard, Culver City, California 90232 (US). (74) Agent: FESSENMAIER, Martin et al.; UMBERG ZIPSER LLP, 1920 Main Street, Suite 750, Irvine, Califor- nia 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, 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, (54) Title: IMMUNOTHERAPY MARKERS AND USES THEREFOR Immunotherapy Markers This analysis examines the contribution of MSI status, POLE/APOBEC, mutation rate and mutational signatures and immune checkpoint expression for sensitivity towards an immunotherapy approach. This sample contains 3 of 4 indicators that suggests sensitivity to immunotherapy. Immunotherapy Sensitivity Markers Marker Status Immunotherapy Permissive MSI Status Microsatellite Stable. No (57) : Systems and methods for prediction of the treatment outcome for immune therapy are presented in which omics data of a patient tumor sample are used. Most typically, the omics data are processed to identify mutational signatures (especially APOBEC/POLE signatures), immune checkpoint expression, and MSI status as leading indicators to predict the treatment outcome for immune therapy. Such prediction advantageously integrates various parameters that would otherwise, when individually considered, skew prediction outcome. [Continued on next page] WO 2018/039567 Al MIDEDIMOMMIDIREIHNIMIINIMEHOHMEMON TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW, KM, ML, MR, NE, SN, TD, TG). 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))