Patent SG-11201903158R-A (SG)
Title: Methods for cell label classification
Inventor: HU JING
IPC: C12Q1/6869
Filed: 2017-11-07
Abstract: INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property :::` , 111111101111011101 HIM 011010101111111111111111111111111111111111111111111111 Organization International Bureau (10) International Publication Number 03 (43) International Publication Date .....•\"\" WO 2018/089377 Al 17 May 2018 (17.05.2018) WIPO I PCT _ (51) (21) (22) (25) Filing Language: (26) (30) (71) (72) International Patent Classification: Elisabeth, Marie; c/o Cellular Research, Inc., 4040 Camp- C12Q 1/6869 (2018.01) bell Avenue, Suite 110, Menlo Park, CA 94025 (US). International Application Number: (74) Agent: MALLON, Joseph, J.; 2040 Main Street, Four- PCT/US2017/060447 teenth Floor, Irvine, CA 92614 (US). International Filing Date: (81) Designated States (unless otherwise indicated, for every 07 November 2017 (07.11.2017) kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, English CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, Publication Language: English DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, Priority Data: 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, 62/419,194 08 November 2016 (08.11.2016) US MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, 62/445,546 12 January 2017 (12.01.2017) US OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, Applicant: CELLULAR RESEARCH, INC. [US/US]; SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, 4040 Campbell Avenue, Suite 110, Menlo Park, CA 94025 TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (US). (84) Designated States (unless otherwise indicated, for every Inventors: HU, Jing; c/o Cellular Research, Inc., 4040 kind of regional protection available): ARIPO (BW, GH, Campbell Avenue, Suite 110, Menlo Park, CA 94025 (US). GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, TZ, FAN, Christina; c/o Cellular Research, Inc., 4040 Camp- UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, bell Avenue, Suite 110, Menlo Park, CA 94025 (US). TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, ROSENFELD, David; c/o Cellular Research, Inc., 4040 EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, LV, Campbell Avenue, Suite 110, Menlo Park, CA 94025 (US). MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM, FAN, Jue; c/o Cellular Research, Inc., 4040 Campbell Av- TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW, enue, Suite 110, Menlo Park, CA 94025 (US). WALCZAK, KM, ML, MR, NE, SN, TD, TG). = =_ (54) Title: METHODS l FOR CELL LABEL CLASSIFICATION (57) : Disclosed herein are methods and systems for classify- ing cell labels, for example identifying a signal cell label. In some em- bodiments, the method comprises: obtaining sequencing data of bar- - 1 All cell labels 1 - cos. \ Refined coded targets created using targets in cells barcoded using barcodes, 1 13esic rug = - • through algnN hm FI d m bedeng wherein a barcode comprises a cell label and a molecular label. At- ' 1 ' ' ------' ter ranking the cell labels, a minimum of a second derivative plot of ....._, Find most variable genes a run through algorithm a cumulative sum plot can be determined. Using the methods, a cell = 612 Filtered cell label (A) = 1 label can be classified as a signal cell label or a noise cell label based Refined 16 Filtered cell labels (0) on the number of molecular labels with distinct sequences associated i = with the cell label and a cell label threshold. Find genes enddled nnolse cell labels by empadng total read labels as well as from r Remove noise moots from all cell update filtered cells from A, 4 cell labels setdiff(A B)) = - filtered cell labels C C. setdiff(A, = 1 0 (128 Use genes enriched In nurse cell labels to nm through algorithm - = Filtered cell l labels iCombine filtered cell labels ) — Ir ... ' IN M C:7 GC © \,. GC 1-1 0 r'l 1 1than FIG. I (632 Remove cell labels with Iess the minimum number of molewles Final set of filtered cell labels 6B O [Continued on next page] WO 2018/089377 Al MIDEDIMOMMIDEFIEHMEHEMBHINVOIMIE Published: — with international search report (Art. 21(3))