Patent SG-11201910041W-A (SG)
Title: Systems and methods for assessing drug efficacy
Inventor: ZHANG SHILE
IPC: G07D11/60
Filed: 2018-12-03
Abstract: GROUPFEATURE ANTIGEN PRESENTATION allMut ANTIGEN PRESENTATION nonSynMut ANTIGEN PRESENTATION BM ANTIGEN PRESENTATION PSMB10 ANTIGEN PRESENTATION TAP1 ANTIGEN PRESENTATION TAP2 ANTIGEN PRESENTATION HLA-A ANTIGEN PRESENTATION HLA-B ANTIGEN PRESENTATION HLA-C ANTIGEN PRESENTATION HLA-DQA1 ANTIGEN PRESENTATION HLA-DRB1 T CELL/NK SIGNATURE HLA-E T CELL/NK SIGNATURE NKG7 T CELL/NK SIGNATURE CMKLR1 CYTOLYTIC SIGNATURE cd8 dec CYTOLYTIC SIGNATURE cd4_dec CYTOLYTIC SIGNATURE cd19_dec CYTOLYTIC SIGNATURE GZMA CYTOLYTIC SIGNATURE PRF1 GROUP FEATURE CHECHPOINT CTLA4 CHECHPOINT PD1 CHECHPOINT PDL1 CHECHPOINT PDL2 CHECHPOINT LAG3 CHECHPOINT TIG IT CHECHPOINT CD276 INTERFERON Y CCL5 INTERFERON 7 CD27 INTERFERON Y CXCL9 INTERFERON Y CXCR6 INTERFERON Y ID01 INTERFERON 7 STAT1 MDSC/TREG CD15 MDSC/TREG CD25 MDSC/TREG CD33 MDSC/TREG CD39 MDSC/TREG CD11B MDSC/TREG FOXP3 TRAINING PREDICTION (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (43) International Publication Date 06 June 2019 (06.06.2019) WIPO I PCT 111111111111101111111111111111011111010111111111111111111111111111111011111011110111111 (10) International Publication Number WO 2019/109089 Al (51) International Patent Classification: G16B 40/20 (2019.01) GOON 20/00 (2019.01) (21) International Application Number: PCT/US2018/063658 (22) International Filing Date: 03 December 2018 (03.12.2018) (25) Filing Language: English (26) Publication Language: English (30) Priority Data: 62/593,802 01 December 2017 (01.12.2017) US (71) Applicant: ILLUMINA, INC. [US/US]; 5200 Illumina Way, San Diego, California 92122 (US). (72) Inventors: ZHANG, Shile; 5200 Illumina Way, San Diego, California 92122 (US). WANG, Mengchi; 9500 Gilman Dr., La Jolla, California 92093 (US). WISE, Aaron; 5200 Illumina Way, San Diego, California 92122 (US). KANG, Han; 5200 Illumina Way, San Diego, California 92122 (US). ONUCHIC, Vitor Ferreira; 5200 Illumina Way, San Diego, California 92122 (US). KRUGLYAK, Kristi- na; 5200 Illumina Way, San Diego, California 92122 (US). (74) Agent: SHEEHAN, Teige P.; Heslin Rothenberg Farley & Mesiti P.C., 5 Columbia Circle, Albany, New York 12203 (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, (54) Title: SYSTEMS AND METHODS FOR ASSESSING DRUG EFFICACY FIG. 4 (57) : Provided is a computer-implemented method, including inputting to a trained machine learning classifier genomic in- formation of a non-training subject that includes features from a tumor sample, wherein the trained machine learning classifier trained on features of tumor samples obtained from training subjects and their a responsiveness to checkpoint inhibition treatment and the machine-learning classifier is trained to predict responsiveness to the treatment, and generating a checkpoint inhibition responsiveness classification predictive of the subjects responding to the checkpoint inhibition with the trained machine-learning classifier, and re- porting the checkpoint inhibition responsiveness classification using a graphical user interface. Also provided are a computer system for performing the method and a machine learning classifier trained by the method. [Continued on next page] WO 2019/109089 Al I0111I0III11II111111011101110111I10I II 111 VIII VIII VIII01110111IIII111110I111IIII1111 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, 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))