Patent SG-11201903139S-A (SG)
Title: Methods for expression profile classification
Inventor: FAN JUE
IPC: G16B40/30
Filed: 2017-11-07
Abstract: INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (43) International Publication Date 17 May 2018 (17.05.2018) WIPO I PCT ill~~~~~~~~ 011101010VIIIOH olo oluolui lino Elio oimIE (10) International Publication Number WO 2018/089378 Al (51) International Patent Classification: GOOF 19/10 (2011.01) GOOF 19/24 (2011.01) GOOF 19/20 (2011.01) (21) International Application Number: PCT/US2017/060451 (22) International Filing Date: 07 November 2017 (07.11.2017) (25) Filing Language: English (26) Publication Language: English (30) Priority Data: 62/419,291 08 November 2016 (08.11.2016) US 62/446,227 13 January 2017 (13.01.2017) US (71) Applicant: CELLULAR RESEARCH, INC. [US/US]; 4040 Campbell Avenue, Suite 110, Menlo Park, CA 94025 (US). (72) Inventors: FAN, Jue; c/o Cellular Research, Inc., 4040 Campbell Avenue, Suite 110, Menlo Park, CA 94025 (US). ZHANG, Jesse; c/o Cellular Research, INC., 4040 Camp- bell Avenue, Suite 110, Menlo Park, CA 94025 (US). HU, Jing; c/o Cellular Research, INC., 4040 Campbell Avenue, Suite 110, Menlo Park, CA 94025 (US). (74) Agent: MALLON, Joseph, J.; 2040 Main Street, Four- teenth 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, = (54) Title: METHODS FOR EXPRESSION PROFILE CLASSIFICATION 400 Receive a molecular counts matrix 408,---d Preprocess the molecular counts matrix to generate a dista ce matrix Hierarchical 412 cluster expression profiles of cells to generate a dendrogram 416 Split and test the dendrogram to generate a set of labels Merge the first set of labels to generate a second set of labels Select features from the second set of labels to identify features for distinguishing cell types (57) : Disclosed herein are methods and systems for identifying targets for distinguishing cell types. In some embodiments, the method comprises: hierarchically clustering expression profiles of cells to generate a dendrogram with each leaf representing the expression profile of a different individual cell. The dendrogram can be pruned by eliminating invalid splits (and their children). The remaining leaves in the dendrogram can be merged, independent of their locations in the dendrogram, based on their distances to one another to generate clusters of expression profiles. The method can identify targets for distinguishing cell types based on targets that are expressed differentially in the clusters. [Continued on next page] WO 2018/089378 Al MIDEDIMOMOIDEIREEMOOMMEITOMMOVOIMIE 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))