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(12) Patent Application Publication (10) Pub. No.: US 2014/0031308A1 Diane Et Al US 2014003 1308A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2014/0031308A1 Diane et al. (43) Pub. Date: Jan. 30, 2014 (54) BENCHMARKS FOR NORMAL CELL on Feb. 8, 2011, provisional application No. 61/469, IDENTIFICATION 812, filed on Mar. 31, 2011. (76) Inventors: Longo Diane, Foster City, CA (US); Todd M. Covey, San Carlos, CA (US); Publication Classification David M. Soper, San Francisco, CA (US); Garry P. Nolan, San Francisco, (51) Int. C. CA (US); Alessandra Cesano, Redwood GOIN33/50 (2006.01) city, CA (US) G06F 9/72 (2006.01) (52) U.S. C. (21) Appl. No.: 13/821,539 CPC ............ G0IN33/5008 (2013.01); G06F 19/12 PCT Fled: Sep. 8, 2011 (2013.01) (22) USPC ...... 514/43; 435/29: 435/7.21: 703/11: 703/2 (86) PCT NO.: PCT/US11?01565 S371 (c)(1), (57) ABSTRACT (2), (4) Date: Oct. 2, 2013 Provided herein are methods, compositions, and kits for Related U.S. Application Data determining cell signaling profiles in normal cells and com (60) Provisional application No. 61/381,067, filed on Sep. paring the cell signaling profiles of normal cells to cell sig 8, 2010, provisional application No. 61/440,523, filed naling profiles from a test sample. 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Patent Application Publication Jan. 30, 2014 Sheet 4 of 37 US 2014/0031308A1 o o N co C C d O in bu-de-Tell Patent Application Publication Jan. 30, 2014 Sheet 5 of 37 US 2014/0031308A1 FLT-WTAML that signal FLT-WTAML that signal like Healthy BMMb like FLT3-ITDAML O Healthy BMMb S FLT3 ITDAML O FLT3 WTAML -0.2 O.O 0.2 0.4 DOnOrS with low mutational load Principal Component 1 FIG. 5 Patent Application Publication Jan. 30, 2014 Sheet 6 of 37 US 2014/0031308A1 n d d H 2 X O u? O S. () 2 Z Mr. 2 D .9 t G o O Z S 9. d Patent Application Publication Jan. 30, 2014 Sheet 7 of 37 US 2014/0031308A1 Patent Application Publication Jan. 30, 2014 Sheet 8 of 37 US 2014/0031308A1 Patent Application Publication Jan. 30, 2014 Sheet 9 of 37 US 2014/003.1308A1 1. 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Ironic O NMSN ovs C. v . & cNY &S v v vam v-v- SR v- w SR v Patent Application Publication Jan. 30, 2014 Sheet 20 of 37 US 2014/0031308A1 Patent Application Publication Jan. 30, 2014 Sheet 21 of 37 US 2014/0031308A1 Patent Application Publication Jan. 30, 2014 Sheet 22 of 37 US 2014/003.1308A1 s||eoIIego96equeoued Patent Application Publication Jan. 30, 2014 Sheet 23 of 37 US 2014/003.1308A1 SIIeoIIejoe6e?ueoued 06080/090?70Z0L0 Patent Application Publication Jan. 30, 2014 Sheet 24 of 37 US 2014/003.1308A1 SII30IIego36equeoued 06080/09OGO?70Z0|| Patent Application Publication Jan. 30, 2014 Sheet 26 of 37 US 2014/003.1308A1 SII30IIegoa6e?uaouad 06080/09070£OZO?0 GIVIS-TE-TIOGG069’do_ XHE-dTTELT-Ž?GLWLS-dTc-T| Patent Application Publication Jan. 30, 2014 Sheet 27 of 37 US 2014/003.1308A1 §§9LVLS-dTOCHL XXJB-dTICIT-§§§§§ (>s||30.36e?ueouedIIego LVLS-dTOdLº-sninuu?S| 090Z0||06080107 ?âueu \uo?eIndodlleo TWVX Patent Application Publication Jan. 30, 2014 Sheet 28 of 37 US 2014/003.1308A1 auenuauu?oads Z10-016||DJ Patent Application Publication Jan. 30, 2014 Sheet 29 of 37 US 2014/003.1308A1 Patent Application Publication Jan. 30, 2014 Sheet 30 of 37 US 2014/003.1308A1 JOLUu XEW+36eudeGVNG ||"odol Patent Application Publication Jan. 30, 2014 Sheet 31 of 37 US 2014/003.1308A1 ||(odol Patent Application Publication Jan. 30, 2014 Sheet 32 of 37 US 2014/003.1308A1 0!89#7Z0 SunOH £Gd-duduuÁT.AunjeeH O N N we efueuo po 0'?7. 90E 00; 89#7Z SunoH r CN d OO Co (St CN o 9 0 w v. V. | efueuo po- zuo-d efuelo pio XVZH-d US 2014/0031308A1 9 OO CO V N O C Cd 9 o O w CN CO r CN efueuo po asuo-d efueuo pio XVZH-d Patent Application Publication Jan. 30, 2014 Sheet 34 of 37 US 2014/0031308A1 JOuOCl,CII NOOO€07 NOODI]Z0?7 :?u?odeuilqºuZq9uvuziLivqZ,u9ug?9 O v efueuopio efueuopio eue Sejoni Ouned XVZH-d Patent Application Publication Jan. 30, 2014 Sheet 35 of 37 US 2014/003.1308A1 9"| eneA 89 ayuso d pozbol Patent Application Publication Jan. 30, 2014 Sheet 36 of 37 US 2014/0031308A1 Patent Application Publication Jan. 30, 2014 Sheet 37 of 37 US 2014/0031308A1 i A. P S - v 1. , US 2014/003.1308 A1 Jan. 30, 2014 BENCHMARKS FOR NORMAL CELL elements in single cells derived from the plurality of normal IDENTIFICATION samples; e) identifying one or more cell-type markers in single cells derived from the plurality of normal samples: f) CROSS-REFERENCE gating cells in the plurality of normal samples based on the one or more cell-type markers associated with the single cells; 0001. This application claims the benefit of U.S. Patent and g) generating the statistical model that specifies the range Application Nos. 61/381,067 filed Sep. 8, 2010: 61/440,523 of activation levels associated with cells in the normal filed Feb. 8, 2011: 61/469,812 filed Mar. 31, 2011; and samples. 61/499,127 filed Jun. 20, 2011, which are incorporated by reference in their entireties. 0005. In another embodiment, the statistical model further specifies the variance of activation levels of the one or more BACKGROUND OF THE INVENTION activatable elements associated cells in the plurality of nor mal samples. In another embodiment, the one or more acti 0002 Personalized medicine seeks to provide prognoses, Vatable elements are selected from the group consisting of diagnoses and other actionable medical information for an pStat1, pStat3, pStata, pStats, pStat6 and p-p38. In another individual based on their profile of one or more biomarkers.
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