US 20040225449A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2004/0225449 A1 Bevilacqua et al. (43) Pub. Date: Nov. 11, 2004 (54) SYSTEMS AND METHODS FOR which is a continuation-in-part of application No. CHARACTERIZING A BIOLOGICAL 09/605,581, filed on Jun. 28, 2000, now abandoned. CONDITION OR AGENT USING SELECTED GENE EXPRESSION PROFILES (60) Provisional application No. 60/141,542, filed on Jun. 28, 1999. Provisional application No. 60/195,522, (76) Inventors: Michael P. Bevilacqua, Boulder, CO filed on Apr. 7, 2000. (US); John C. Cheronis, Conifer, CO (US); Victor Tryon, Loveland, CO Publication Classification (US); Danute M. Bankaitis-Davis, Longmont, CO (US) (51) Int. Cl." .......................... G06F 19/00; G01N 33/48; GO1N 33/50 Correspondence Address: (52) U.S. Cl. ................................................................ 702/20 Barbara J. Carter Bromberg & Sunstein LLP ABSTRACT 125 Summer Street (57) Boston, MA 02110-1618 (US) Methods are provided for evaluating a biological condition Appl. No.: 10/781,558 of a Subject using a calibrated profile data Set derived from (21) a data Set having a plurality of members, each member being (22) Filed: Feb. 17, 2004 a quantitative measure of the amount of a Subject's RNA or protein as distinct constituents in a panel of constituents. The Related U.S. Application Data biological condition may be a naturally occurring physi ological State or may be responsive to treatment of the (63) Continuation-in-part of application No. 09/821,850, Subject with one or more agents. Calibrated profile data Sets filed on Mar. 29, 2001, now Pat. No. 6,692,916, may be used as a descriptive record for an agent. Patent Application Publication Nov. 11 9 2004 Sheet 1 of 49 ? GDSEINES)00||O.1GZ[]O100||DSENESÐG?,OLSENE9009 TIT\/WSDSN\/S)(JO/STTEOETCHILTON[…]TTV/WSDSETCHW\/SOOOTESEdW\/SClOOTE PÎìÎìîì Patent Application Publication Nov. 11, 2004 Sheet 2 of 49 US 2004/0225449 A1 Patent Application Publication Nov. 11, 2004 Sheet 3 of 49 SETI-JOHd pî?ipî? KOILSIN\/HOEWNÅLIOIXOL SETI-HO-Ho] Patent Application Publication Nov. 11 9 2004 Sheet 5 of 49 US 2004/0225449 A1 Patent Application Publication Nov. 11, 2004 Sheet 6 of 49 US 2004/0225449 A1 1OEITETS _LOEITETAS „N,RHE8||WTIN Patent Application Publication Nov. 11, 2004 Sheet 7 of 49 US 2004/0225449 A1 EnTVASLISESVEJONIGNV=SvavIvaBHIJOHEMOd=ALLOIGEAJdEHISHAO&dwla?oo3,MENHOVE ·LNE|WEdÅL LTTISER-NO||LICINOO Patent Application Publication Nov. 11, 2004 Sheet 9 of 49 US 2004/0225449 A1 1101 1102 1103 LOCATION 1 TISSUE MULTIPLE OUANTIFIED SAMPLE RNA PROFILE SPECIES DATA RETRIEVE EVALUATE INFORMATION | OUANTIFIED UPDATE FROM PROFILE DATA DEMNE DATABASE DATABASE N VIEW OF CONDITION OVER OVER RETREVED NETWORK NETWORK INFORMATION 109 1109 DATABASE US 2004/0225449 A1 ?NITIJOJdCJELOBTES?NISnNºISHQTWIJLTVOINITOOMULESVHd Patent Application Publication Nov. 11, 2004 Sheet 11 of 49 US 2004/0225449 A1 2 TO N. 2. Sgdal 2 ... I - - | | | | | | || III N 2 2 s CD CN v O. O. O. O. O. O. O. O. O. 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