(12) United States Patent (10) Patent No.: US 8,148,067 B2 Lal Et Al

(12) United States Patent (10) Patent No.: US 8,148,067 B2 Lal Et Al

US008148067B2 (12) United States Patent (10) Patent No.: US 8,148,067 B2 Lal et al. (45) Date of Patent: Apr. 3, 2012 (54) METHODS FOR DIAGNOSING AND 5,219,727 A 6/1993 Wang et al. MONITORING THE STATUS OF SYSTEMC 5,264,351 A 1 1/1993 Harley 5,278,043 A 1/1994 Bannwarth et al. LUPUSERYTHEMATOSUS 5,310,652 A 5/1994 Gelfand et al. 5,314,809 A 5/1994 Erlich et al. (75) Inventors: Preeti G. Lal, Santa Clara, CA (US); 5,322,770 A 6/1994 Gelfand 5,340,720 A 8, 1994 Stetler Gavin E. Williams, Menlo Park, CA 5,346,994 A 9/1994 Chomczynski (US); Kirk E. Fry, Palo Alto, CA (US); 5,352,600 A 10, 1994 Gelfand et al. Jingtao Sun, Foster City, CA (US); 5,374,553 A 12/1994 Gelfand et al. Russel L. Dedrick, Kensington, CA 5,385,824 A 1/1995 Hoet et al. (US) 5,389,512 A 2/1995 Sninsky et al. 5,393,672 A 2f1995 Van Ness et al. 5,405,774 A 4, 1995 Abramson et al. (73) Assignee: Xdx, Inc., Brisbane, CA (US) 5,407,800 A 4/1995 Gelfand et al. 5,411,876 A 5/1995 Bloch et al. (*) Notice: Subject to any disclaimer, the term of this 5,418,149 A 5/1995 Gelfand et al. patent is extended or adjusted under 35 5,420,029 A 5/1995 Gelfand et al. U.S.C. 154(b) by 676 days. 5.426,039 A 6/1995 Wallace et al. 5,445,940 A 8, 1995 Brenner et al. 5,455,170 A 10, 1995 Abramson et al. (21) Appl. No.: 11/938,227 5,459,037 A 10, 1995 Sutcliffe et al. 5,464.937 A 11/1995 Sims et al. (22) Filed: Nov. 9, 2007 5,466,591 A 11/1995 Abramson et al. 5,468,613 A 11/1995 Erlich et al. (65) Prior Publication Data 5,476,774 A 12/1995 Wang et al. 5.487,970 A 1/1996 Rowley et al. US 2009/O298060A1 Dec. 3, 2009 5,487.972 A 1/1996 Gelfand et al. 5,491,063 A 2f1996 Fisher et al. Related U.S. Application Data (Continued) (60) Provisional application No. 60/858,147, filed on Nov. 9, 2006. FOREIGN PATENT DOCUMENTS EP O217992 A2 4f1987 (51) Int. Cl. (Continued) CI2O I/68 (2006.01) (52) U.S. Cl. ........................................ 435/6.1: 435/6.11 OTHER PUBLICATIONS (58) Field of Classification Search ........................ None See application file for complete search history. Extended European Search Report received for European Patent Application No. 0786 1283.5, mailed on Dec. 27, 2010, 17 pages. (56) References Cited Notice of Allowance received for U.S. Appl. No. 1 1/893,236, mailed on Dec. 10, 2010, 18 Pages. U.S. PATENT DOCUMENTS Non Final Office Action received for U.S. Appl. No. 12/628,168, 4,190.535 A 2f1980 Luderer et al. mailed on Dec. 10, 2010, 35 Pages. 4,215,051 A 7, 1980 Schroeder et al. Garraway et al., “Array-based approaches to cancer genome analy 4,350,593. A 9, 1982 Kessler sis'. Drug Discovery Today: Disease Mechanisms, vol. 2, No. 2, 4,358,535 A 11, 1982 Falkow et al. 2005, pp. 171-177. 4,376, 110 A 3, 1983 David Hayashi et al., “Effects of glucocorticoids on gene transcription'. 4,582,789 A 4, 1986 Sheldon, III et al. European Journal of Pharmacology, vol. 500, 2004, pp. 51-62. 4,683, 195 A 7, 1987 Mullis et al. 4,683.202 A 7, 1987 Mullis (Continued) 4,751,001 A 6, 1988 Saunders 4,762,780 A 8/1988 Spector et al. 4,789,630 A 12/1988 Bloch et al. Primary Examiner — James Martinell 4,800,159 A 1, 1989 Mullis et al. 4,818,418 A 4, 1989 Saunders (74) Attorney, Agent, or Firm — Morrison & Foerster LLP 4,843,155 A 6/1989 Chomczynski 4,889,818 A 12/1989 Gelfand et al. 4,908,318 A 3, 1990 Lerner (57) ABSTRACT 4.946,778 A 8, 1990 Ladner et al. 4.946,952 A 8, 1990 Kiefer The invention presents a method of diagnosing or monitoring 4,965,188 A 10, 1990 Mullis et al. the status of systemic lupus erythematosus (SLE) in a subject 5,053,134 A 10, 1991 Luderer et al. or patient comprising detecting the expression of all genes of 5,063,162 A 11, 1991 Kiefer 5,066,584 A 1 1/1991 Gyllensten et al. a diagnostic set in the Subject or patient wherein the diagnos 5,075.216 A 12/1991 Innis et al. tic set comprises two or more genes having expression cor 5,079,352 A 1/1992 Gelfand et al. related with the classification or status of SLE; and diagnos 5,091,310 A 2f1992 Innis ing or monitoring the status of SLE in the Subject or patient by 5, 120,525 A 6/1992 Goldenberg 5,142,033. A 8, 1992 Innis applying at least one statistical method to the expression of 5,143,854 A 9/1992 Pirrung et al. the genes of the diagnostic set. 5,210,015 A 5, 1993 Gelfand et al. 5,212,071 A 5, 1993 Fearon et al. 5,215,882 A 6, 1993 Bahl et al. 16 Claims, 3 Drawing Sheets US 8,148,067 B2 Page 2 U.S. PATENT DOCUMENTS 6,204,371 B1 3/2001 Levinson 6,214,979 B1 4/2001 Gelfand et al. 5,491,086 A 2, 1996 Gelfand et al. 6,218,122 B1 4/2001 Friend et al. 5,501,963 A 3/1996 Burckhardt 6,222,093 B1 4/2001 Marton et al. 3. A 39. puts al. 6,225,084 B1 5/2001 Falb et al. 5,514,556 A 5/1996 Shearer et al. 8534 4-w R 299; SEelfand et etal. al. 5,538,848. A 7/1996 Livak et al. 6,242,185 B1 6/2001 Kaser et al. 33.5 A 1918. it al. 6,245,334 B1 6/2001 Seilhammer et al. 5,569,583 A 10/1996 Greenberg et al. g33. R 38: Site 1 5,571,673 A 1 1/1996 Picone 5857, 58. 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