US007790366B1

(12) United States Patent (10) Patent No.: US 7,790,366 B1 Houghton et al. (45) Date of Patent: *Sep. 7, 2010

(54) NANBV DIAGNOSTICS AND VACCINES 4,683, 195 A 7, 1987 Mullis et al...... 435/6 4,683.202 A 7, 1987 Mullis et al...... 435,912 (75) Inventors: Michael Houghton, Danville, CA (US); 4,702,909. A 10/1987 Villarejos et al...... 435/5 GeorgeQui-Lim Kuo, Choo, San El Francisco, Cerrito, CA CA (US); (US) 4,707.439 A * 1 1/1987 Seto ...... 435/5 4,722,897 A * 2/1988 Soeda et al...... 435/69.1 (73) Assignee: Novartis Vaccines and Diagnostics, 4,769,326 A * 9/1988 Rutter ...... 435.68.1 Inc., Emeryville, CA (US) 4,870,026 A * 9/1989 Wands ...... 436,538 (*) Notice: Subject to any disclaimer, the term of this 4,891.313 A 1/1990 Berger et al...... 435/7.94 patent is extended or adjusted under 35 5,077, 193 A 12, 1991 Mishiro et al...... 435/5 U.S.C. 154(b) by 0 days. 5,101,024 A * 3/1992 Kudo et al...... 536,23.53 5,106,726 A 4/1992 Wang ...... 435/5 This patent is Subject to a terminal dis- 5, 191,064 A 3/1993 Arima et al...... 530/324 claimer. 5,218,099 A 6/1993 Reyes et al...... 536,23.72 5,268,278 A * 12/1993 Canosi et al...... 435/69.7 (21) Appl. No.: 08/441,443 5,310,893 A * 5/1994 Erlich et al...... 536, 24.31 (22) Filed: May 15, 1995 5,372,928 A 12/1994 Miyamura 5,436,126 A 7/1995 Wang ...... 435/5 Related U.S. Application Data (60) Division of application No. 08/307,273, filed on Sep. 16, 1994, now Pat. No. 6,074,816, which is a division of application No. 08/103,961, filed on Aug. 9, 1993, (Continued) now Pat. No. 5,350,671, which is a continuation of FOREIGN PATENT DOCUMENTS application No. 07/456,637, filed on Dec. 21, 1989, now abandoned, which is a continuation-in-part of AU 89.10967 11, 1989 application No. 07/355,002, filed on May 18, 1989, now abandoned, which is a continuation-in-part of application No. 07/341,334, filed on Apr. 20, 1989, now abandoned, which is a continuation-in-part of (Continued) application No. PCT/US88/04125, filed on Nov. 18, 1988, and a continuation-in-part of application No. OTHER PUBLICATIONS 07/325,338, filed on Mar. 17, 1989, now abandone which is a continuation-in-part of application N Prince et al. 1984 Lancet Nov. 10. p. 1071, Nov. 10, 1984.* 07/271,450, filed on Nov. 14, 1988, now abandone which is a continuation-in-part of application N (Continued) 07/263,584, filed on Oct. 26, 1988, now abandone Primary Examiner Mary K Zeman which is a continuation-in-part of application N (74) Attorney, Agent, or Firm—Alisa Harbin; Otis Littlefield 07/191,263, filed on May 6, 1988, now abandone which is a continuation-in-part of application N (57) ABSTRACT 07/161,072, filed on Feb. 26, 1988, now abandone which is a continuation-in-part of application N 07/139,886, filed on Dec. 30, 1987, now abandone A family of cDNA sequences derived from hepatitis C virus which is a continuation-in-part of application No. (HCV) are provided. These sequences encode antigens which 07/122,714, filed on Nov. 18, 1987, now abandoned. react immunologically with antibodies present in individuals with non-A non-B hepatitis (NANBH), but which are absent (51) Int. Cl. from individuals infected with hepatitis A virus, or hepatitis B A6 IK 39/00 (2006.01) virus, and also are absent in control individuals. The HCV (52) U.S. Cl...... 435/5: 435/7.1:435/69.1; cDNA sequences lack Substantial homology to the sequences 435/320.1; 436/501:536/23.1:536/24.1 of hepatitis delta virus (HDV) and HBV. A comparison of the (58) Field of Classification Search ...... 435/5, sequences of amino acids encoded in the HCV cDNA with the 435/6, 7.1, 810,948,975; 424/89, 86; 536/24.5, sequences of Flaviviruses indicates that HCV may be related 536/23.1, 23.72, 24.3, 24.32, 24.33: 514/44; to the Flaviviruses. 436/501, 63, 94,811, 820 See application file for complete search history. The HCV cDNA sequences and the polypeptides encoded therein are useful as reagents for the detection and therapy of (56) References Cited HCV. The reagents provided in the invention are also useful U.S. PATENT DOCUMENTS for the isolation of NANBH agent(s), for the propagation of these agents in tissue culture, and for the screening of antiviral 4,395,395 A 7/1983 Tabor et al...... 435.5 4,464.474. A * 8/1984 Coursaget ...... 436,513 agents for HCV. 4,659,678 A 4, 1987 Forrest et al...... 436,512 4,673,634 A 6, 1987 Seto ...... 435/5 299 Claims, 168 Drawing Sheets US 7,790,366 B1 Page 2

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Takkinen, “Complete Nucleotide Sequence of the Nonstructural Pro Reply to Tenth Opposition to Chiron Japanese Patent Application No. tein Genes of Semliki forest Virus.” Nucl. Acids Res. 14(14):5667 O1-5.00565. 5682 (1986). Eleventh Opposition to Chiron Japanese Patent Application No. Tamashiro, et al., “Structure of the Heterogeneous L-S Junction 01-5.00565, filed by Kokusai Shiyaku (and translation) with support Region of Human Cytomegalovirus Strain AD 169 DNA. J. Virol. ing documents. 52(2):541-548 (1984). Reply to Eleventh Opposition to Chiron Japanese Patent Application “Mysterious Strain of Hepatitis Is Identified.” The Wall Street Jour No. 01-500S65. nal, Friday, Apr. 21, 1989. Twelfth Opposition to Chiron Japanese Patent Application No. Vallari, et al., “Serological Markers of Posttransfusional Hepatitis C 01-5.00565, filed by Shigeo Kimura (and translation) with supporting Viral Infection.” J. Clin. Microbiol. 30(3):552-556 (1992). documents. 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In Latently Infected Cells.” Proc. Natl. Acad. Sci. USA81:3806-3810 Reply to Fourteenth Opposition to Chiron Japanese Patent Applica (1984). tion No. 01-500.565. Young, et al., “Efficient Isolation of Genes By Using Antibody Translation of Decision on Opposition Against Patent Application Probes.” Proc. Natl. Sci. USA 80: 1194-1198 (1983). No. 01-500565, issued Dec. 22, 1995. Suzuki, et al., “Characterization of A cDNA for Human Protein C Statement of Grounds for Opposition to Australian Patent No. Inhibitor.” J. Biol. Chem. 262(2):611-616 (1987). 640,920, filed by Hoffman La Roche with supporting documents. First Opposition to Chiron Japanese Patent Application No. Australian Litigation Bundle, for Chiron Australian Patent No. 01-5.00565, filed by Steven Woodsmall (and translation) with Sup 624,105. porting documents. Murex Reply in the Litigation of Chiron Australian Patent No. Reply to First Opposition to Chiron Japanese Patent Application No. 624,105. O1-5.00565. First Opposition to Chiron European Application No. 0318216, filed Second Opposition to Chiron Japanese Patent Application No. by Akzo Pharma BV (Jan. 27, 1994) with supporting documents. 01-5.00565, filed by Akira Yamamoto (and translation) with support Second Opposition to Chiron European Application No. 0318216, ing documents. filed by Murex Diagnostics Limited(Sep. 12, 1994) with supporting Reply to Second Opposition to Chiron Japanese Patent Application documents. No. 01-500S65. Third Opposition to Chiron European Application No. 0318 216, Third Opposition to Chiron Japanese Patent Application No. filed by United Biomedical (Sep. 15, 1994) with supporting docu 01-5.00565, filed by Asako Sudo (and translation) with supporting mentS. documents. Fourth Opposition to Chiron European Application No. 0318216, Reply to Third Opposition to Chiron Japanese Patent Application No. filed by Beringwerke (Sep. 15, 1994). O1-5.00565. Fifth Opposition to Chiron European ApplicationNo. 0318216, filed Fourth Opposition to Chiron Japanese Patent Application No. by The Research Foundation for Microbial Diseases (Sep. 14, 1994) 01-5.00565, filed by Yashimi Tawara (and translation) with support with Supporting documents. ing documents. Sixth Opposition to Chiron European Application No. 0318 216, Reply to Fourth Opposition to Chiron Japanese Patent Application filed by F. Hoffman-La Roche AG(Sep. 15, 1994). J.A. Kemp & Co.(Chiron): Response By Patentee To Notices of No. 01-500S65. Opposition re EP 318 216, Jun. 1995. Fifth Opposition to Chiron Japanese Patent Application No. Miscellaneous Documentation (believed to have been supplied to 01-5.00565, filed by Tetsuo Nakamura (and translation). Prof. Donald Chisum by Dr. Bradley or the Center for Disease Con Reply to Fifth Opposition to Chiron Japanese Patent Application No. trol). O1-5.00565. Daniel W. Bradley v. Chiron Corporation, Civil Action No. 94-4342 Sixth Opposition to Chiron Japanese Patent Application No. Litigation Bundle, with Supporting documents. 01-5.00565, filed by Toren K.K. (and translation) with supporting documents. U.K. Litigation Bundle 1). Reply to Sixth Opposition to Chiron Japanese Patent Application No. U.K. Litigation Bundle 2). O1-5.00565. U.K. Litigation Bundle 5). Seventh Opposition to Chiron Japanese Patent Application No. U.K. Litigation Bundle 6). 01-5.00565, filed by Sumitomo Metal Industries, Ltd. (and transla U.K. Litigation Bundle 7. tion) with Supporting documents. U.K. Litigation Bundle 7a). Reply to Seventh Opposition to Chiron Japanese Patent Application U.K. Litigation Bundle 7b). No. 01-500S65. U.K. Litigation Bundle 7c). Eighth Opposition to Chiron Japanese Patent Application No. U.K. Litigation Bundle 8). 01-5.00565, filed by Hiroshi Iino (and translation) with supporting U.K. Litigation Bundle 9). documents. U.K. Litigation Bundle 9.a. 1. 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Non-B Board of Appeal dated: Aug. 13, 1999, re: TO188/97-3.3.4 re: Incon Hepatitis.” Viral Hepatitis. 1981 International Symposium (Szmu sistency of the argumentation of patentee concerning Articl 123 (2) ness, et al., eds. (pp. 656-657) 1985, Franklin Institute Press); (Con EPC. (pp. 6). sidered in U.S. Appl. No. 08/103.961, reference I.A.27). Letter from Lederer, Keller & Riederer to the European Patent Office Petrovskis et al., “Use of Xgt11 To Isolate Genes for Two dated Aug. 23, 1999, re: T 0188/97-3.34 (European Patent No. 0318 Pseudorabies Virus Glycoproteins with Homology to Herpes 216)—Request for early oral proceedings. (pp. 2). Simplex Virus and Varicella-Zoster Virus Glycoproteins.”.J. of Immu Letter from European Patent Office dated Sep. 7, 1999 re: Summon nology 60(1):185-193 (1986). parties to attend Oral Proceedings on Feb. 29 and Mar. 1, 2000. (pp. Purcell, “Blood-Borne Non-A. Non-B Hepatitis.” Update 2:2 (1988). 1). US 7,790,366 B1 Page 10

Letter from J. A. Kemp & Co. to The European Patent Office dated (2) Exibit marked DJK-11 refered to in the affidavit of David James Sep. 17, 1999, re: Inconvenience of dates for Oral Proceedings com Kemp on Aug. 16, 1999 In the Federal Court of Australia New South mencing week of Feb. 28, 2000. (pp. 2). Wales District Registry General Division. Case No. NG10029 of Letter from European Patent Office to J. A. Kemp & Co. Dated Oct. 1997. (pp. 69). 26, 1999 re: Annex to the summons to attend oral proceedings (3)Exibit marked DJK-12 referred to in the affidavit of David James (Appeal No.T018.8/97-334). (pp. 21—2 sets of 10 plus cover letter). Kemp on Aug. 16, 1999 or Aug. 16, 1999 In the Federal Court of Letter from European Patent Office Board of Appeals to J. A. Australia New South Wales District Registry. Case No. G102 of Kemp & Co. dated Nov. 29, 1999, re: T 0188/97-3.3.4 (European 1997. (pp. 51). Patent No. 0318216)—Requesting A exhibit XI mentioned in pat (4) Exibit marked DJK-13 referred to in the affidavit of David James entees statement. (pp. 2). Kemp on Aug. 16, 1999 In the Federal Court of Australia New South Letter from Lederer, Keller & Riederer to J.A. Kemp & Co. dated Wales District Registry Case No. G1029-of 1997. (pp. 2). Dec. 8, 1999, re: Appeal T 188/97-3.34—Possible postponement of (5) Exibit marked DJK-14 referred to in the affidavit of David James the oral proceedings. (pp. 1). Kemp on Aug. 16, 1999 In the Federal Court of Australia New South Letter from J. A. Kemp & Co. to The European Patent Office dated Wales District Registry. Case No. G1029 of 1997. (pp. 4). Dec. 10, 1999, re: Attempted Intervention under EPC Article 105 by (6) Exibit marked DJK-15 referred to in the affidavit of David James Innogenetics N.V (pp. 4). Kemp on Aug. 16, 1999 In The Federal Court of AustraliaNew South Letter from The European Patent Office to all parties dated Dec. 17. Wales District Registry. Case No. G1029-of 1997. (pp. 3). 1999 to inform of the Oral proceedings on Feb. 29 2000 and Mar. 1, (7)Exibit marked DJK-16 referred to in the affidavit of David James 2000 would continue on Jun. 27, 28 and 29, 2000. (pp. 3). Kemp on Aug. 16, 1999 In The Federal Court of AustraliaNew South Letter from J.A. Kemp & Co. to The European Patent Office acknowl Wales District Registry. Case No. G1029-of 1997. (pp. 49). edging receipt of summons dated Dec. 17, 1999.(pp. 2). (8)Exibit marked DJK-17 referred to in the affidavit of David James Letter from Brookes & Martinto Registry Board of Appeal European Kemp on Aug. 16, 1999 In The Federal Court of AustraliaNew South Patent Office dated Dec. 21, 1999. re: Appeal No. T188/37-3.3. Wales District Registry. Case No. G1029-of 1997. (pp. 15). 4—Opposition to Chiron European Patent 318 216 (pp. 2). (9)Exibit marked DJK-18 referred to in the affidavit of David James Acknowledge Copy-Letter from J.A. Kemp & Co. to The European Kemp on Aug. 16, 1999 In The Federal Court of AustraliaNew South Patent Office dated Jan. 7, 2000, re: Written submissions for the Oral Proceedings (Feb. 29th and Mar. 1, 2000). (pp. 2). Wales District Registry. Case No. G1029-of 1997. (pp. 4). Letter from European Patent Office to J. A. Kemper & Co. re: Minutes (10) Exibit marked DJK-19 referred to in the affidavit of David James from oral proceedings of Feb. 29, 2000. (pp. 4). Kemp on Aug. 16, 1999 In The Federal Court of AustraliaNew South Letter from Lederer, Keller & Riederer to European Patent Office Wales District Registry. Case No. G1029-of 1997. (pp. 31). Board of Appeal dated May 11, 2000, re: Use of German language (11)Exibit marked DJK-20 referred to in the affidavit of David James during the oral proceedings from Jun. 27-29, 2000. (pp. 2). Kemp on Aug. 16, 1999 In The Federal Court of AustraliaNew South (1) Letter from Ann De Clercq & Co, B.V.B.A. to European Patent Wales District Registry. Case No. G1029-of 1997. (pp. 146). Office dated Jul 27, 1999 r : Amended version of the Written state Acknowledgement—Letter from J. A. Kemp & Co. to The European ment setting out the grounds for Opposition/Appeal/Intervention in Patent Office dated Jun. 15, 2000, re: Appeal TO188/97-3.34 Signed accordance. (pp. 89) (2) WO/93/18054A2 published Sep. 16, 1993, versions of the Statement of Dr. Weiner and the Declaration of Dr. WIPO, (pp. 133). Lamson. (pp. 1). Letter from Lederer, Keller & Reiderer to European Patent Office Acknowledgement—Letter from J. A. Kemp & Co. to The European dated May 25, 2000, re:TO 188/97-3.34 European Patent No. 0318 Patent Office dated Jun. 16, 2000 re: missing Figure 5 (Section 3, p. 216—Response to the Communication of the Technical Board of 6 of D642).(pp. 5). Appeal 3.34. (pp. 35). Acknowledgement—Letter from J. A. Kemp & Co. to The European Letter from Ann Declerq & Co. B.V.B.A. to The European Patent Patent Office dated Jun. 16, 2000 re: Bring to the Board's attention to Office dated May 26, 2000 re: Response to the Communication of the some procedural points; which are directly from Opponenet's VI Technical Board of Appeal 3.34 dated Oct. 26, 1999. (pp. 25). Submissions.(pp. 5). Letter from Ann Declerq & Co. B.V.B.A. to The European Patent (1) Boards of Appeal of the European Patent Office-Decision dated Office dated May 26, 2000 re: articles of Weiner et al. 1990 and Jan. 21, 1999; re: Application No. 82304478.9.(pp. 13) (2) Boards of Houghton et. al., 1991. Weiner et. al. (1991) “Molecular Biology of Appeal of the EPO-Decision date Jul. 6, 1994 re: Application No. the Hepatitis C Viruses: Implications for Diagnosis, Development 82902213.6 (pp. 12) (3) Boards of Appeal of the European Patent and Control of Viral Disease.” Hepatology 14:381-388. Houghton et. Office Decision date Mar. 10, 1944 re: Application No. 84300759.2 al. (1990) “Detection of Hepatitis C Viral Sequences in Non-A. (pp. 7). Non-B Hepatitis.” The Lancet 335:1-3. (pp. 12 total). Letter from Ann DeClercq & Co. B.V.B.A. dated Jun. 16, 2000, re: Letter from J. A. Kemp & Co. to European Patent Office dated May Appeal Case T 188/97-3.3.4 European Patent 0318216/EP 88.310 26, 2000, re: Written submissions on behalf of the Patentee filed in 922.5; Dr. Peter Simmonds accompanying Dr. Ann Clerq to the Oral Preparation for Oral Proceedings commencing Tuesday, Jun. 27. Proceedings (pp. 1). 2000. (pp. 5). Letter from D.M. Goldin dated Jun. 19, 2000 re: Appeal TO188/97 Appeal No.T0188/97-334 Concerning European Patent No. 318,216 3.34 re: Original signed version of the Statement of Professor Thiel Chiron Corporation—Further Written submissions on Behalf of The (pp. 1). Patentee. dated May 2000 from J.A. & Co. (pp. 28). Letter from Lederer, Keller & Riederer to The European Patent Office (Jun. 2000) Main Request for Contracting States: AT, BE, CH, DE, Board of Appeal 3.34 dated Jun. 20, 2000 re: AppealT0188/97-3.34 FR, IT, LI, LU, NL & SE (pp. 12). Chiron Corporation European Patent No. 318 216 (Application No. (Jun. 2000) Main Request for Contracting States: ES (pp. 8). 310922.5) Typing error in the Witness Statement by Dr. Geert (Jun. 2000) Main Request for Contracting State: GR (pp. 12). Maertens. (pp. 1). (Jun. 2000) Auxiliary Request A For Contracting States: AT:BE: CH; Letter from Lederer, Keller & Riederer to The European Patent Office DE FR: IT: LI; LU: NL & SE, (pp. 13). dated Jun. 21, 2000 re: T 0188/97-3.34 European Patent No. 0318 (Jun. 2000) Auxilary Request B. For Contracting States: AT, BE, CH, 216 European Patent Application No. 88.310922.5-2105: Response DE FR, IT, LI, LU, NL & SE, (pp. 11). to patentee's submission of Jun. 16, 2000. (pp. 5). (Jun. 2000) Auxiliary Request C For Contracting States: AT, BE, CH, Authorisation of Representatives for Chiron Corp. dated Jun. 26. DE FR, IT, LI, LU, NL & SE, (pp. 14). 2000, signed by Robert P. Blackburn, VP & Chief Patent Counsel. (Jun. 2000) Auxilary Request D For Contracting States: AT, BE, CH, (pp. 5). DE FR, IT, LI, LU, NL & SE, (pp. 10). Acknowledgement—Letter from J.A. Kemp & Co. to European (1)Affidavit of David James Kemp on Aug. 16, 1999 In the Federal Patent Office dated Jun. 24, 2000 re: Appeal TO188/97-3.34 Euro Court of Australia New South Wales District Registry General Divi pean Patent No. 318216; Dr. Simmonds accompanying Dr. De Clerq sion, Case No. NG10029 of 1997. (pp. 20). to the Oral Proceedings.(pp. 4). US 7,790,366 B1 Page 11

Acknowledgement—Letter from J. A. Kemp & Co. to European Regions” Journal of Gerneral Virology vol.72:2697-2704. Okamoto Patent Office dated Jun. 26, 2000 and attachments re: AppealT01887 et al. (1992) “Full-Length Sequence of a Hepatitis C Virus Genome 97-3.34; Consolidated list of documents. (pp. 27). Having Poor Homology to Reported Isolates: Comparitive Study of Acknowledgement—Letter from J. A. Kemp & Co. to European Four Distinct Genotypes' Virology vol. 188:331-341. Kato et Patent Office and attachements dated Jun. 26, 2000; re: Appeal al.(1990)"Molecular Cloning of the Human Hepatitis C Virus TO188/97-3.34 European Patent No. 318216–Original signed ver Genome from Japanese Patients with Non-A, and Non-B Hepatitis' sions of the Statement of Professor Thiel. (pp. 16). Proc. Natl. Acad. Sci. USA, vol. 87:9524-9528. Acknowledgement; Letter from J.A. Kemp & Co. to European Patent Declaration of George Lamson dated May 25, 2000 (pp. 76 total) and Office dated Jun. 26, 2000; Bring to the Boards attention admissibil attachments, (1) Curriculum vitae of George Lamson, (pp. 2) (2) ity of Opponents VI's Opposition—Appeal. (pp. 4). Sequence Comparison-HCV Figure 14 from EP318216 vs. GBV-C, Acknowledgement—Letter from J. A. Kemp & Co. to European HGV. (pp. 2). Patent Office and attachments dated Jun. 26, 2000 re: AppealT01887 Statement of Amy J. Weiner, PhD dated May 25, 2000 (3 pages) and 97-3.34 European Patent No. 318 216; Declaration by Dr. M. attachments. (1) Curriculum Vitae of Amy J. Weiner (pp. 7); Figure of Houghton with annexes MH-1, MH-2 and MH-3.(pp. 27). 5-1-1 (pp. 1). Letter from European Patent Office to J. A. Kemp & Co. dated Jul. 18. (1)Affidavit of Murray Briggs Gardner on Jul. 20, 1996 before The 2000; re: Minutes of the oral proceedings of Jun. 27-30, 2000.(pp. 4). Federal Court of Australia New South Wales District Registry Gen Acknowledgement—Letter from J.A. Kemp & Co. to The European eral Division case No. G106 of 1994. (pp. 10) (2) Affidavit of Robert Patent Office and attachments dated Aug. 29, 2000 re: Appeal Jian on Oct. 31, 1995 before The Federal Court of Australian New No.T0188/97-3.34 concerning European Patent No. 318,216; South Wales District Registry General Division, case No. G106 of amended pages for incorporation into the specification of the granted 1994, (pp. 5). patent.(pp. 12). Chiron HCV Case 1 European Patent No. 318,216 Appeal No. (1) Affidavit of Amy Joan Weiner on Nov. 1, 1995 before The Federal TO188/97; Claims Maintained By Board of Appeal At Oral Proceed Court of Australia New South Wales District Registry General Divi ings on Jun. 27-30 2000 "Auxilary Request E”); Hand-Amended sion case No. G106 of 1994. (2) Annexure marked "AJW-5” to the Claims AS Submitted to the Board (Definitive), Plus Retyped Equiva Affidavit of Amy Joan Weiner affirmed on Nov. 1, 1995. In The lents (For Ease of Reference); Claims 1-5 For Contracting States: AT, Federal Court of Australia New South Wales District Registry Gen BE, CH, DE, FR, IT, LI, LU, NL & ES: Claims 1-9 For Contracting eral Division 1994 and attachments (a) letter from Dr. Lau to the State: ES: Claims 1-12 For Contracting State: GR (pp. 45). Deputy Editor of the The Lancet with correct results amended in Letter from the European Patent Office to J.A. Kemp & Co. dated figure 1 of article The Lancet 341:1501-1504. Feb. 23, 2001 re: Decision of the Technical Board of Appeal 3.3.4 of Affidavit of Michael Houghton on Nov. 29, 1995 In The Federal Feb. 8, 2001.(pp. 75). Court of Australia New South Wales District Registry General Divi Loose in cover—Letter from J. A. Kemp & Co. to Dr. Gladys Monroy sion case No. G 106 of 1994. (pp. 2) (Tab 1) Affidavit of Christopher (Morrison & Forester LLP) dated Aug. 13, 2001 re: Documents in John Burrell on Nov. 20, 1995 In The Federal Court of Australia New relation to case (Chiron HCV-1—NANBV Diagnostics Opposition South Wales District Registry General Division case No. G 106 of by Roche & Others to Chiron European Patent No. 0318 216 & 1994 (pp. 54).(1a) Annexure marked "CJB-1” to the Affidavit of Subsequent Appeal No.T018.8/97.(pp. 2). Christopher John Burrell Sworn on Nov. 20, 1995 and Curriculum Expert's Report of Dr. Peters Simmonds on May 25, 2000 (pp. 13). Vitae.(pp. 14).(1b) Annexure marked "CJB-2'to the Affidavit of Curriculum vitae of Dr. Peter Simmonds (pp. 25). Christopher John Burrell on Nov. 20, 1995 and attachments. In The Expert Report of Genevieve Inchauspéon May 16, 2000 (pp. 23). Federal Court of Australia New South Wales District Registry Gen Curriculum vitae of Genevieve Inchauspé.(pp. 10). eral Division case No. G 106 of 1994 (pp. 6). (Tab 2) Cross exami Revised Expert Repoprt of Dr. Geert G.H. Maertens on May 28, 2000 nation of Dr. Reyes (pp. 9) (Tab3) Aldous J. Chiron Corporation v. to the European Patent Office (pp. 40). Curriculum vitae of Dr. Geert Murex Diagnostics Ltd., Chiron Corporation v. Organon Teknkika G.H. Maertens. (pp. 6) Figures 1-4. (pp. 4). Ltd. 1996R.P.C. (pp. 3.) (Tab4) Morritt L.J., Chiron Corporation v. (1) Extract from the Examination file of EP-A-0 556292 (EP appli Murex Diagnostics Ltd., Chiron Corporation v. Organon Teknika cation No. 92900091.7) in name of Chiron (pp. 4); (2) Letter from Ltd., 1996 R.P.C. (pp. 2) (Tab 5) Affidavit of Michael Houghton on J.A. Kemp & Co.) to European Patent Office; datedMar. 24, 1997 re: Feb. 9, 1994 In The High Court of Justice Chancery Division Patents A two month extension for the Examination Report dated Nov. 19. Court case Nos. Ch 1992 C. No. 489 CH 1992 C. No. 1513. (pp. 5) 1996. (pp. 1); (3) A letter from J. A. Kemp & Co. to European Patent (Tab 6) Second affidavit of Michael Houghton (pp. 4). (Tab 7) patent Office dated May 23, 1997 re: new claims 1-24 to replace current on behind Tab 100 (listed under US patent). (Tab 8) PCT (Tab 9) Euro file and original claims 1-21 (pp. 7); (4) Communication from Euro pean Patent Application US Patent No. 5.734,019 to Miyamura et al. pean Patent Office pursuant to Article 96(2) and Rule 51 (2) EPC Mar. 3, 1998. US Patent No. 5,843,752 to Dasmahapatia et al. Dec. 1, dated Mar. 4, 1998 (pp. 4); (5) A letter from J.A. Kemp & Co. to the 1998. WO 93/1023912 May 27, 1993 WIPO (Tab 10) EPO 537856 European Patent Office dated Sep. 8, 1998 re: Response to the Com A1 Apr. 21, 1993 EPO. munication pursuant to Article 96(2) and Rule 51(2) EPC datedMar. (1) Decision of May 8, 1996 of Board of Appeal of The European 4, 1998 to replace new pp. 24 to 27 (pp. 10). Patent Officere: Patent Publication No. 0122791 (pp. 2); (2) Decision Expert's Report and Witness Statement of David James Kemp on of May 8, 1996 of Board of Appeal of The European Patent Office re: May 26, 2000 (pp. 6). Patent Publication No.: 0122791 (pp. 2); (3) Decision of the Techni Houghtonetal. (1996) “Developementofan HCV vaccine”(based on cal Board of Appeal 3.3.4 of May 8, 1996 of European Patent Office presentation at Rome Hepatitis meeting) in Apr., 1996; (pp. 17). re: Case No. T 0694/92-3.34 (pp. 3); (4) Summary of Facts and Statement of Professor Dr. Heinz-Jürgen Thiel dated May 26, 2000 Submissions re: European Patent No. 0122791 (pp. 36). (pp. 9) and attachments(1) Annexure “H-JT-1” To the Statement of Okamoto et al., (1991). "Nucleotide Sequence of the Genomic RNA Dr. Heinz-Jürgen Thiel, Curriculum Vitae, (2) Annexure “H-JT-2' To of Hepatitis CVirus Isolated from a Human Carrier: Comparison with The Statement of Professor Dr. Heinz-Jürgen Thiel, Hepacivirus Reported Isolates for Conserved and Divergent Regions.” J. Gen. Figure (3) Annexure “H-JT-3” To the Statement of Professor of Dr. Virol. 72:2697-2704. Heinz-Jürgen Thiel SequenZvergleich von HCV-1 mitanderen Geno (1) Supplementary Expert Report of Professor J.W. Almosnd in The type im Sequenzberiech Fig. 14 (Sequence), (4)Annexure “H-JT-4” High Court of Justice Chancery Division Patents Court on Jun. 1993. To The Statement of Professor Dr. Heinz-Jürgen CH 1992 C. Nos. 489 and 1513 (pp. 2); (2) Letter from Simons & Thiel—Supplementary Expert's Report of Howard Christopher Tho Simons to Messrs. Bristows Cooke & Carpmael re: The reagents used mas, dated Feb. 4, 1993 Okamoto et al.(1990) “The 5' Terminal in the experiments on Jun. 18, 1993 (pp. 3). Sequence of the Hepatitis CVirus Genome” Japan Journal Exp. Med. vander Poel, C.L. et al., (1994). “Hepatitis C Virus SixYears On.” The vol. 60:167-177. Okamoto et al. (1991) “Nucleotide sequence of the Lancet 344:1475-1479. genomic RNA of hepatitis C Virus Isolated from Human Carrier: Yanagi, M. et al. (1996). “Contamination of Commercially Available Comparison with Reported Isolated for Conserved and Divergent Fetal Bovine Sera with Bovine Diarrhea Virus Genomes: Implica US 7,790,366 B1 Page 12 tions for the Study of Hepatitis C Virus in Cell Cultures,” J. Infect. Roche's Responsive Brief re: Claim Construction, dated Mar. 24. Dis. 174:1324-1327. 2000, in the United States District Court for the Northern District of Abstract Volums of IX Triennial International Symposium on Viral California, Oakland Division, Chiron Corporation vs. F. Hoffmann Hepatitis and Liver Disease, Apr. 21-25, 1996, Rome, Italy (pp. 3). La Roche Ltd. et al., Civil Action No. C98-0315CW, pp. 1-25. Sequence Comparison HCV v. BVDV. Mar. 7, 1997 (pp. 2). Tanaka et al., (1995) “A Novel Sequence Found at the 3'Terminus of Biogen, Inc. vs. Medeva Plc. On Oct. 31, 1996 (Decision of the House Hepatitis C Virus Genome” Biochemical and Biophysical Research of Lords) (pp. 28). Communications 215(2): 744-749. Linnen, J. etal. (1996). “Molecular Cloning and Disease Association Tanaka et al., (1996) "Structure of the 3'Terminus of the Hepatitis C of Hepatitis GVirus: A TRansfusion-Transmissible Agent.” Science Virus Genome” Journal of Virology 70(5): 3307-3312. 271:505-508. Transcript of proceedings corresponding to Murex diagnostics Aus Linnen et al. (1996). “Sequence Listing of Hepatitis G Virus.” Sci tralia Pty Limited and Chiron Corp., Federation Court of Australia, ence 271:505-508. (pp. 1). New South Wales District Registry General Division, dated Jun. Jun. Meinkoth, J. etal. (1984). “Hybridization of Nucleic Acids Immobi 24, 1996, pp. 1-65. lized on Solid Supports.” Analyt. Biochem. 138:267-284. Transcript of proceedings corresponding to Murex diagnostics Aus Tribunal of Milan. First Instance Decision No. 9816 dated Nov. 11, tralia Pty Limited and Chiron Corp., federation of Australia, New 1999 Sorin Biomedica S.p.A. v. Chiron Co. et al (pp. 4). South Wales District Registry, General Division, dated Jun. 25, 1996, Honda, M. et al., (1991). “A Phylogenetically Conserved Stem-Loop pp. 66-134. Structure at the 5' Border of the Internal Ribosome Entry Site of Transcript of proceedings corresponding to Murex diagnostics Aus Hepatitis C Virus is Required for Cap-Independent Viral Transla tralia Pty Limited and Chiron Corp., Federation Court of Australia, tion.” J. Virol. 73:1165-1174. New South Wales District Registry General Division, dated Jun. Jun. Kessler, L. Ed., (2000). “Nonradioactive Analysis of 26, 1996, pp. 135-200. Biomoleculose.” Second Edition, Springer. pp. 6, 7,437-442. Transcript of proceedings corresponding to Murex diagnostics Aus Abriganani, S. et al. (1998). “Perspectives for a Hepatitis C Virus tralia Pty Limited and Chiron Corp., Federation Court of Australia, Vaccine.” Clin. and Diagnost. Virol. 10:181-185. New South Wales District Registry General Division, dated Jun. Jun. Rice et al. (1985) “Nucleotide Sequence of Yellow Fever Virus: 27, 1996, pp. 201-241. Implication for Flavivirus Gene Expression and Evolution.” Science, Transcript of proceedings corresponding to Murex diagnostics Aus vol. 229:726-32. tralia Pty Limited and Chiron Corp., Federation Court of Australia, Experimental Reportre: European Patent 0318216 European Patent New South Wales District Registry, General Division, dated Jul. 2, Application 88.310922.5 Patentee: Chiron Corp. Opponent: F. Hoff 1996, pp. 244-319. man-La Roche AG (Opp.) VI on Mar. 8, 1996 (amended Mar 18, Transcript of proceedings corresponding to Murex diagnostics Aus 1996). tralia Pty Limited and Chiron Corp., Federation Court of Australia, Bradley (1990) "Hepatitis Non-A. Non-B Viruses Become Identified New South Wales District Registry, General Division, dated Jun. Jul. as Hepatitis C and E Viruses”. Prog. Med. Virol. vol. 37: 101-135. 3, 1996, pp. 320-391. Ezzell, C., (1988) “Candidate Cause Identified of Non-a, and Non-B Transcript of proceedings corresponding to Murex diagnostics Aus Hepatitis', Nature vol. 333:19. tralia Pty Limited and Chiron Corp., Federation Court of Australia, Affidavit of Daniel Bradley, Ph.D., given on Aug. 12, 1999, in the New South Wales District Registry, General Division, dated Jul. 4. Federal Court of Australia, New South Wales District Registry, No. G 1996, pp. 392-463. 1029 of 1997, Roche Australian litigation, pp. 1-26. Transcript of proceedings corresponding to Murex diagnostics Aus Amended Answer and Counterclaims of the Roche Defendents to tralia Pty Limited and Chiron Corp., Federation Court of Australia, Chiron's Amended and Second Supplemental Complaint, filed Jan. New South Wales District Registry, General Division, dated Jun. Jul. 10, 2000, in the United States District Court for the Northern District 5, 1996, pp. 464-539. of California, Chiron Corporation vs. F. Hoffmann-La Roche Ltd. et Transcript of proceedings corresponding to Murex diagnostics Aus al., Civil Action No. C98-0315 CW, pp. 1-33. tralia Pty Limited and Chiron Corp., Federation Court of Australia, Chiron Corporation's Amended and Second Supplemental Com New South Wales District Registry, General Division, dated Jun. Jul. plaint and Demand for Jury Trial, filed Jun. 1, 1999, in the United 8, 1996, pp. 540-610. States District Court for the Northern District of California, Oakland Transcript of proceedings corresponding to Murex diagnostics Aus Division, Chiron Corporation vs. F. Hoffmann-La Roche Ltd. et al., tralia Pty Limited and Chiron Corp., Federation Court of Australia, Civil Action No. C98-0315CW, pp. 1-16. New South Wales District Registry, General Division, dated Jul. 9, Chiron Corporation's Opening Brief on Claim Construction, filed 1996, pp. 610-683. Mar. 1, 2000, in the United States District Court for the Northern Transcript of proceedings corresponding to Murex diagnostics Aus District of California, Oakland Division, Chiron Corporation vs. tralia Pty Limited and Chiron Corp., Federation Court of Australia, Hoffmann-La Roche Ltd. et al., Civil Action No. C98-0315CW, pp. New South Wales District Registry, General Division, dated Jul. 10, 1-25. 1996, pp. 684-769. Chiron's Claim Construction Reply Brief, filed Mar. 31, 2000, in the Transcript of proceedings corresponding to Murex diagnostics Aus United States District Court for the Northern District of California, tralia Pty Limited and Chiron Corp., Federation Court of Australia, Oakland Division, Chiron Corporation vs. Hoffmann-La Roche Ltd. New South Wales District Registry, General Division, dated Jul. 11, et al., Civil Action No. C98-0315CW, pp. 1-16. 1996, pp. 770-854. Decision of EPO Board of Appeals mailed Feb. 23, 2001, issued Feb. Transcript of proceedings corresponding to Murex diagnostics Aus 8, 2001 re: European Application No. 883.10922.5-2106, File No. tralia Pty Limited and Chiron Corp., Federation Court of Australia, T0188 (97-334. Applicant: Chiron Corporation, Interlocutory deci New South Wales District Registry, General Division, dated Jul. 12, sion of the Opposition Division of the European Patent Office posted 1996, pp. 855-959. Dec. 18, 1996 concerning maintenance of European patent No. 0318 Transcript of proceedings corresponding to Murex diagnostics Aus 216 in amended form. tralia Pty Limited and Chiron Corp., Federation Court of Australia, Kolykhalov et al., (1996) “Identification of a Highly Conserved New South Wales District Registry, General Division, dated Jul. 15, Sequence Element at the 3"Terminus of Hepatitis C Virus Genome 1996, pp. 960-1038. RNA” Journal of Virology, 70(6):3363-3371. Transcript of proceedings corresponding to Murex diagnostics Aus Oct. 22, 1998 Declaration of Dr. Daniel W. Bradley in connection tralia Pty Limited and Chiron Corp., Federation Court of Australia, with Roche’s Invalidation Appeal Against Japanese Patent No. New South Wales District Registry, General Division, dated Jul. 16, 2656995, pp. 1-34. 1996, pp. 1039-1134. Roche's Response Chart Pursuant to Civ. L. R. 16-9(b), filed Jan. 24. 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Transcript of proceedings corresponding to Murex diagnostics Aus Deposition of Gregory R. Reyes, vol. 1, Sep. 11, 2000, in Chiron tralia Pty Limited and Chiron Corp., Federation Court of Australia, Corp. v. Hoffman-La Roche, Ltd., et al., No. C 98-0315 CW (N.D. New South Wales District Registry, General Division, dated Jul. 18, Cal.); Deposition pp. 1-183 & Index pp. 1-17. 1996, pp. 1215-1294. Deposition of Gregory R. Reyes, vol.II, Oct. 4, 2000, in Chiron Corp. Transcript of proceedings corresponding to Murex diagnostics Aus v. Hoffman-La Roche, Ltd., et al. No. C 98-0315 CW (N.D. Cal.), tralia Pty Limited and Chiron Corp., Federation Court of Australia, Deposition pp. 201-325, Index pp. 1-10. New South Wales District Registry, General Division, dated Jul. 19. Deposition of Stephen M. Feinstone, M.D., Jun. 26, 2000. In Chiron 1996, pp. 1295-1385. Corp. v. Hoffman-La Roche, Ltd., et al., No. C 98-0315 CW (N.D. Transcript of proceedings corresponding to Murex diagnostics Aus Cal.), Deposition pp. 1-170, Index pp. 1-18. tralia Pty Limited and Chiron Corp., Federation Court of Australia, Deposition of Gordon P. Erspamer, vol. I, Jul. 18, 2000, in Chiron New South Wales District Registry, General Division, dated Jul. 29. Corp. v. Hoffman-La Roche, Ltd., et al., No. C 98-0315 CW (N.D. 1996, pp. 1386-1465. Cal), Deposition pp. 1-174. Index pp. 1-21. Transcript of proceedings corresponding to Murex diagnostics Aus Deposition of Gordon P. Erspamer, vol. II, Sep. 28, 2000, in Chiron tralia Pty Limited and Chiron Corp., Federation Court of Australia, Corp. v. Hoffman-La Roche, Ltd., et al., No. C 98-0315 CW (N.D. New South Wales District Registry, General Division, dated Jul. 30, Cal.), Deposition pp. 175-308, Index pp. 1-17. 1996, pp. 1466-1537. Deposition of Dr. Alfred Prince, Sep. 21 2000, in Chiron Corp. v. Transcript of proceedings corresponding to Murex diagnostics Aus Hoffman-La Roche, Ltd., et al., No. C 98-0315 CW (N.D. Cal.), tralia Pty Limited and Chiron Corp., Federation Court of Australia, Deposition pp. 1-80, Index pp. 1-7. New South Wales District Registry, General Division, dated Jul. 31. Deposition of Shirley S.W. Wong-Chen, Sep. 26, 2000, in Chiron 1996, pp. 1538-1603. Corp. v. Hoffman-La Roche, Ltd., et al., No. C 98-0315 CW (N.D. Transcript of proceedings corresponding to Murex diagnostics Aus Cal.), Deposition pp. 1-134, Index pp. 1-15. tralia Pty Limited and Chiron Corp., Federation Court of Australia, Deposition of Donald S. Chisum, Aug. 15, 2000, in Chiron Corp. v. New South Wales District Registry, General Division, dated Aug. 1, Hoffman-La Roche, Ltd., et al., No. C 98-0315 CW (N.D. Cal.), 1996, pp. 1604-1676. Deposition pp. 1-312, Index pp. 1-30. Transcript of proceedings corresponding to Murex diagnostics Aus Deposition (Videotaped) of Martha Ann Truett, vol. I, Jun. 6, 2000, in tralia Pty Limited and Chiron Corp., Federation Court of Australia, Chiron Corp. v. Hoffman-La Roche, Ltd., et al., No. C 98-0315 Cw New South Wales District Registry, General Division, dated Aug. 2, (N.D. Cal.), Deposition pp. 1-221. Index pp. 1-22. 1996, pp. 1677-1755. Deposition (Videotaped) of Martha Ann Truett, vol. II, Jun. 7, 2000, in Chiron Corp. v. Hoffman-La Roche, Ltd., et al., No. C 98-0315 Transcript of proceedings corresponding to Murex diagnostics Aus CW (N.D. Cal.), Deposition pp. 222-430, Index pp. 1-22. tralia Pty Limited and Chiron Corp., Federation Court of Australia, Deposition (Videotaped) of Martha Ann Truett, vol. III, Aug.9, 2000, New South Wales District Registry, General Division, dated Aug. 5, in Chiron Corp. v. Hoffman-La Roche, Ltd., et al., No. C98-0315 CW 1996, pp. 1756-1835. (N.D. Cal.), Deposition pp. 431-589, Index pp. 1-19. Transcript of proceedings corresponding to Murex diagnostics Aus Deposition of Michael S. Urdea, Ph.D., vol. I, Feb. 16, 2000, in tralia Pty Limited and Chiron Corp., Federation Court of Australia, Chiron Corp. v. Hoffman-La Roche, Ltd., et al., No. C 98-0315 CW New South Wales District Registry, General Division, dated Aug. 6, (N.D. Cal.), Deposition pp. 1-200, Index pgs. 1-22. 1996, pp. 1836-1916. Deposition of Michael S. Urdea, Ph.D., vol.II, Feb. 17, 2000, in Transcript of proceedings corresponding to Murex diagnostics Aus Chiron Corp. v. Hoffman-La Roche, Ltd., et al., No. C 98-0315 CW tralia Pty Limited and Chiron Corp., Federation Court of Australia, (N.D. Cal.), Deposition pp. 202-392, Index pp. 1-22. New South Wales District Registry, General Division, dated Aug. 7, Deposition of Michael S. Urdea, Ph.D., vol. III, Feb. 18, 2000, in 1996, pp. 1917-1994. Chiron Corp. v. Hoffman-La Roche, Ltd., et al., No. C 98-0315 CW Transcript of proceedings corresponding to Murex diagnostics Aus (N.D. Cal.), Deposition pp. 393-521, Index pp. 1-16. tralia Pty Limited and Chiron Corp., Federation Court of Australia, Deposition (Videotaped) of Amy J. Weiner, Ph.D., vol. I, Aug. 17. New South Wales District Registry, General Division, dated Aug. 8, 2000, in Chiron Corp. v. Hoffman-La Roche, Ltd., et al., No. C 1996, pp. 1995-2059. 98-0315 CW (N.D. Cal.), Deposition pp. 1-291, Index pp. 1-30. Transcript of proceedings corresponding to Murex diagnostics Aus Deposition of George Kuo, Ph.D., vol. I, Nov. 8, 1999, in Chiron tralia Pty Limited and Chiron Corp., Federation Court of Australia, Corp. v. Hoffman-La Roche, Ltd., et al., No. C 98-0315 CW (N.D. New South Wales District Registry, General Division, dated Aug.9, Cal.). Deposition pp. 1-244. Index pp. 1-23. 1996, pp. 2060-2121. Deposition of George Kuo, Ph.D., vol. II Nov. 9, 1999, in Chiron Transcript of proceedings corresponding to Murex diagnostics Aus Corp. v. Hoffman-La Roche, Ltd., et al., No. C 98-0315 CW (N.D. tralia Pty Limited and Chiron Corp., Federation Court of Australia, Cal.), Deposition pp. 245-477, Index pp. 1-23. New South Wales District Registry, General Division, dated Aug. 12, Deposition of George Kuo, Ph.D., vol. III, Nov. 11, 1999, in Chiron 1996, pp. 2122-2200. Corp. v. Hoffman-La Roche, Ltd., et al., No. C 98-0315 CW (N.D. Transcript of proceedings corresponding to Murex diagnostics Aus Cal.), Deposition pp. 478-648, Index pp. 1-19. tralia Pty Limited and Chiron Corp., Federation Court of Australia, Deposition of Qui Lim Choo, Ph.D., vol. I, Dec. 15, 1999 In Chiron New South Wales District Registry, General Division, dated Aug. 13, Corp. v. Hoffman-La Roche, Ltd., et al., No. C 98-0315 CW (N.D. 1996, pp. 220 1-2280. Cal.), Deposition pp. 1-165, Index pp. 1-15. Transcript of proceedings corresponding to Murex diagnostics Aus Deposition of Qui Lim Choo, Ph.D., vol.II, Dec. 16, 1999, in Chiron tralia Pty Limited and Chiron Corp., Federation Court of Australia, Corp. v. Hoffman-La Roche, Ltd., et al., No. C 98-0315 CW (N.D. New South Wales District Registry, General Division, dated Aug. 14. Cal.), Deposition pp. 166-359, Index pp. 1-18. 1996, pp. 2281-2368. Deposition of Qui Lim Choo, Ph.D., vol. III, Dec. 17, 1999, in Chiron Transcript of proceedings corresponding to Murex diagnostics Aus Corp. v. Hoffman-La Roche, Ltd., et al., No. C 98-0315 CW (N.D. tralia Pty Limited and Chiron Corp., Federation Court of Australia, Cal.), Deposition pp. 360-540, Index pp. 1-18. New South Wales District Registry, General Division, dated Aug. 15, Deposition of Qui Lim Choo, Ph.D., vol. IV. May 18, 2000, in Chiron 1996, pp. 2369-2455. Corp. v. Hoffman-La Roche, Ltd., et al., No. C 98-0315 CW (N.D. Yanagi et al., (1997) “Transcripts from a single full length cDNA Cal.), Deposition pp. 541-692, Index pp. 1-16. clone of hepatitis C virus are infectious when directly transfected into Deposition of Qui Lim Choo, Ph.D., vol. V. May 19, 2000, in Chiron the liver of a chimpanzee.” Proc. Natl. Acad. Sci. U.S.A. 94: 8738 Corp. v. Hoffman-La Roche, Ltd., et al., No. C 98-0315 CW (N.D. 8743. Cal.), Deposition pp. 693-885, Index pp. 1-19. Yamamdaetal. (1996) “Genetic Organization and Diversity of the 3' Deposition of Qui Lim Choo, Ph.D., vol. VI, Aug. 7, 2000, in Chiron Noncoding Region of the Hepatitis C Virus Genome.” Virology Corp. v. Hoffman-La Roche, Ltd., et al., No. C 98-0315 CW (N. D. 223:255-261. Cal.), Deposition pp. 886-990, Index pp. 1-12. US 7,790,366 B1 Page 14

Deposition of Michael Houghton, Ph.D., vol. I, Dec. 8, 1999, in c) Reply Declaration of Dr. Michael Botchan, Mar. 31, 2000. Chiron Corp. v. Hoffman-La Roche, Ltd., et al., No. C 98-0315 CW d) Declaration of Professor dr. H.J. Thiel, Feb. 14, 2000. (N.D. Cal.), Deposition pp. 1-198, Index pp. 1-19. e) Reply Declaration of Professor Dr. H.J. Thiel, Mar. 31, 2000. Deposition of Michael Houghton, Ph.D., vol. II, Dec. 9, 1999, in (f) Declaration of Dr. William Brammar, Jun. 26, 2000. Chiron Corp. v. Hoffman-La Roche, Ltd., et al., No. C 98-0315 CW g) Declaration of Lynn William Enquist, Ph.D., Jan. 18, 2000. (N.D. Cal.), Deposition pp. 199-396, Index pp. 1-22. h) Second Declaration of Lynn William Enquist, Ph.D. Mar. 23, 2000. Deposition of Michael Houghton, Ph.D., vol. III, Dec. 10, 1999, in i) Declaration of Peter Simmonds, B.M. Ph.D., Mrcpath, Jan. 20. Chiron Corp. v. Hoffman-La Roche, Ltd., et al., No. C 98-0315 CW 2000. (N.D. Cal.), Deposition pp. 397-553, Index pp. 1-18. k) Second Declaration of Peter Simmonds, B.M. Ph.D., Mrcpath, Deposition of Michael Houghton, Ph.D., vol. IV. May 24, 2000, in Mar. 23, 2000. Chiron Corp. v. Hoffman-La Roche, Ltd., et al., No. C 98-0315 CW Transcript of Proceedings before the Honorable Claudia Wilken, Jul. (N.D. Cal.), Deposition pp. 554-717. Index pp. 1-20. 11, 2000, in Chiron Corp. v. Hoffman-La Roche, Ltd., et al., No. C Deposition of Michael Houghton, Ph.D., vol. V. May 25, 2000, in 98-0315 CW (N.D. Cal.), pp. 1-174, Index pp. 1-22. Chiron Corp. v. Hoffman-La Roche, Ltd., et al., No. C 98-0315 CW Declaration of Daniel W. Bradley, Ph.D., in Support of His Motion to (N.D. Cal.), Deposition pp. 718-876, Index pp. 1-18. Dismiss for Want of Personal and Subject Matter Jurisdiction, Jul. 20. Deposition of Michael Houghton, Ph.D., vol. VI, May 26, 2000, in 1998, in Chiron Corp. v. Hoffman-La Roche, Ltd., et al., No. C Chiron Corp. v. Hoffman-La Roche, Ltd., et al., No. C 98-0315 CW 98-0315 CW (N.D. Cal.). (N.D. Cal.), Deposition pp. 877-1071, Index pp. 1-16. Declaration of Daniel W. Bradley, Ph.D. in Opposition to Chiron's Deposition of Michael Houghton, Ph.D., vol. VII, Aug. 11, 2000, in Motion for Partial Summary Judgment on Count Five of its Supple Chiron Corp. v. Hoffman-La Roche, Ltd., et al., No. C 98-0315 CW mental Complaint, Aug. 21, 1998 in Chiron Corp. v. Hoffman-La (N.D. Cal.), Deposition pp. 1072-1302, Index pp. 1-32. Roche, Ltd., et al., No. C 98-0315 CW (N.D. Cal.). Order Construing disputed terms and Phrases in Chiron Corp. v. Affidavit of Daniel W. Bradley, Ph.D., Oct. 23, 2001. Hoffman–La Roche, Ltd., et al., No. C98-0315 CW (N.D. Cal.), Aug. Affidavit of Daniel W. Bradley, Ph.D., on Aug. 12, 1999, before the 31, 2000. Federal Court of New New South Wales District Registry Case No: G The expert declarations on claim construction in Chiron Corp. v. 1029 of 1997. Hoffman-La Roche, Ltd., et al., No. C 98-0315 CW (N.D. Cal.). Affidavit of Daniel W. Bradley, Ph.D. Oct. 22, 1998. a) Declaration of Dr. Michael Botchan, Oct. 21, 1999. b) Reply Declaration of Dr. Michael Botchan, Feb. 10, 2000. * cited by examiner U.S. Patent Sep. 7, 2010 Sheet 1 of 168 US 7,790,366 B1

FIG. 1 AlaserCysLeuasncys SeralaSerleIleProAspargGluValleuTyr ArgGlu GGCCTCCTGCTTGAACTGCTCGGCGAGCATCATACCGACAGGGAAGTCCTCTACCGAGA CCGGAGGACGAACTTGACGAGCCGCTCGTAGTATGGACTGTCCCTTCAGGAGATGGCTCT PheaspCluMetGluglucys SerglinHisleuProTyrIleGluglinGlyMet Met Leu 6. GTTCGATGAGATGGAAGAGTGCTCTCAGCACTTACCGTACATCGAGCAAGGGATGATGCT CAAGCTACTCTACCTTCTCACGAGAGTCGTGAATGGCATGTAGCTCGTTCCCTACTACGA AlaGluglinPhelysGln Lys AlaleuglyLeu l2 CGCCGAGCAGTTCAVAGCAGAAGGCCCTCGGCCTCC GCGGCTCGTCAAGTTCGTCTTCCGGGAGCCGGAGG

FIG. 3 GlyCysValValleValGlyArgValValleuSerGlyLys ProAla Ile Ile ProAsp l CTGGCTGCGTGGTCATAGTGGGCAGGGTCGTCTTGTCCGGGAAGCCGGCAATCATACCTG GACCGACGCACCAGTATCACCCGTCCCAGCAGAACAGGCCCTTCGGCCGTTAGTATGGAC T ArgGluValleuTyrargGlu Pheaspolu MetGluglucys SerGln His Leu ProTyr 6 ACAGGGAAGTCCTCTACCGAGAGTTCGATGAGATGGAAGAGTGCTCTCAGCACTTACCGT TGTCCCTTCAGGAGAGGCTCCAAGCTACTCTACCTTCTCACGAGAGTCGTGAATGGCA A IleGluglinGlyMetMetLeualaGluGln PhelysGlnLys AlaleuglyLeuleuglin l2 ACATCGAGCAAGGGATGATGCTCGCCGAGCAGTTCAAGCAGAAGGCCCTCGGCCTCCTGC GAGCCGTCCCTACTACGAGCGGCTCGTCAAGTTCGTCTTCCGGGAGCCGGAGGACG ThralaSerargGlnalaGluVallealaProAlaValGlnThrasnTrpGln Lys Leu 8. AGACCGCGTCCCGTCAGGCAGAGGTTATCGCCCCTGCTGTCCAGACCAACTGGCAAAAAC TCGGCGCAGGGCAGTCCGTCTCCAATAGCGGGGACGACAGGTCTGGTTGACCGTTTTTG GluThrPheTrpAlays HismetTrpAsnPheleserGlyleGlnTyrLeual agly 24l TCGAGACCTTCTGGGCGAAGCATATGTGGAACTTCATCAGTGGGATACAATACTTGGCGG AGCTCTGGAAGACCCGCTTCGTATACACCTTGAAGTAGTCACCCTATGTTATGAACCGCC LeuSerThreu ProGlyAs nProAlaleAlaserLeuMet Ala PheThrala AlaVal GCTTGTCAACGCTGCCTGGTAACCCCGCCATTGCTTCATTGATGGCTTTTACAGCTGCTG CGAACAGTTGCGACGGACCATTGGGGCGGTAACGAAGTAACTACCGAAAATGTCGACGAC ThrSerProLeu ThrThrSerGln 36 TCACCAGCCCACTAACCACTAGCCAAA AGGGTCGGGTGATTGGTGATCGGTTT

U.S. Patent Sep. 7, 2010 Sheet 5 of 168 US 7,790,366 B1

F.G. 6 As pala His PheteuSerGlnThrily solin SerglyGlu As nLeu ProTyrLeuValAla l GATGCCCACTTTCTATCCCAGACAAAGCAGAGTGGGGAGAACCTTCCTTACCTGGTAGCG CTACGGGTGAA AGATAGGGTCTGTTTCGTCTCACCCCCTTGGAAGGAATGGACCATCGC TyrginAlaThrvalcys Ala Arg AlaGlin Ala ProProProSerTrpAspGnMetTrp 61 TACCAAGCCACCGTGTGCGCTAGGGCTCAAGCCCCTCCCCCATCGTGGGACCAGATGTGG ATGGTTCGGTGGCACACGCGATCCCGAGTTCGGGGAGGGGGTAGCACCCTGGTCTACACC LysCyseule Argeu Lys ProThrLeu HisGlyProThrProLeu LeuTyrArg Leu 2 AAGGTTTGATTCGCCTCAAGCCCACCCTCCATGGGCCAACACCCCGCTATACAGACTG TTCACAAACTAAGCGGAGTTCGGGTGGGAGGTACCCGGTTGTGGGGACGATATGTCTGAC GlyAlavalGln AsnGluleThrleu Thrh is Proval Thrys TyrIleMetThrcys 8. GGCGCTGTTCAGAATGARATCACCCTGACGCACCCAGTCACCAAATACATCATGACATGC CCGCGACAAGTCTACTTAGTGGGACTGCGTGGGTCAGTGGTTTATGTAGTACTGTACG MetSerala AspleugluVal ValThrSerThrTrpVal LeuValGlyGlyVal Leu Ala 24 ATGTCGGCCGACCTGGAGGTCGTCACGAGCACCTGGGTGCTCGTTGGCGGcGTccTGGCT TACAGCCGGCTGGACCTCCAGCAGTGCTCGGGACCCACGAGCA ACCGCCGCAGGACCGA Ala Leuala Ala TyrCysLeuSerThurglycysVal ValleValGlyArgVal Valleu Sol GCTTTGGCCGCGTATTGccTGTCA ACAGGCTGcGTGGTCATAGTGGGCAGGGTCGTCTTG CGAAACCGGCGCATAACGGACAGTGTCCGACGCACCAGATCACCCGTCCCAGCAGAAC SerGlyLysProAlaleIleProAspargCluVal LeuTyrArgGlu Phe Asp6luMet 35 TCCCGGAAGCCGGCAATCATACCTGACAGGGAAGTCCTCTACCGAGAGTTCGATGAGATG AGGCCCTTCGGCCGTTAGTANGGACTGTCCCTTCAGGAGATGGCTCTCAAGCTACTCTAC GluglucysSerGln His Leu ProTyrIleGluglinGlyMet MetLeu AlaGluglin Phe 42 GAAGAGTGCTCTCAGCACTTACCGTACATCGAGCAAGGGATGATGCTCGCCGAGCAGTTC CTCTCACGAGAGTCGTGAATGGCATGTAGCTCGTTCCCTACTACGAGCGGCTCGTCAAG LysGln Lys AlaleuglyLeuleuGlnThrAlaserArgGltalagluVallealaPro 48 AAGCAGAAGGCCCTCGGCCTCCTGCAGACCGCGTCCCGTCAGGCAGAGGTTATCGCCCCT TTCGCTCCGGGAGCCGGAGGACGTCTGGCGCAGGGCAGTCCGTCTCCAATAGCGGGGA AlavalGlnThrAs nTrpGlnLysLeugluThrPheTrpalays hisMetTrp-Asnphe 54 GCTGTCCAGACCAACTGGCAAAAACTCGAGACCTTCTGGGCGAAGCATATGTGGAACTTC CGACAGGTCTGGTTGACCGTTTTTGAGCTCTGGAAGACCCGCTCGTATACACCTTGAAG IleSerglyieGlnTyrLeuaiaGlyLeuSerThrLeuProGlyasnproalaleala 60 ATCAGTGGGATACAATACTTGGCGGGCTTGTCAACGCGCCTGGTAACCCCGCCATTGCT TAGTCACCCTATGTTATGAACCGCCCGAACAGTTGCGACGGACCATGGGGCGGTAACGA Sereuiet AlapheThrala AlaValThrSerProLeu ThrThrSerGln 66. TCATGATGGCTACAGCTGCGTCACCAGCCCACAACCACAGCCAAA AGTAACTACCGAAAAGTCGACGACAGTGGTCGGGTGATTGGGATCGGTTT U.S. Patent Sep. 7, 2010 Sheet 6 of 168 US 7,790,366 B1

FIG. 7

P 4 up Overlap with 8l------PheThrala Ala Val ThrSerProLeu ThrThrSerGlnThreueu Pheastnereu l CTTTTACAGCTGCTGTCACCAGCCCACTAACCACTAGCCAAACCCTCCTCTTCA ACATAT GAAAATGTCGACGACAGTGGTCGGGTGATTGGTGATCGGTTTGGGAGGAGAAGTTGTATA GlyGlyTrpVal Ala AlaGln Leuala Ala ProGlyalaAlaThrAla PheValGlyAla 6 TGGGGGGGTGGGTGGCTGCCCAGCTCGCCGCCCCCGGTGCCGCTACTGCCTTTGTGGGCG ACCCCCCCACCCACCGACGGGTCGAGCGGCGGGGGCCACGGCGATGACGGAAACACCCGC GlyLeualaGlyala AlaleGlySerValGlyLeuglyLysValeulle AspleLeu 2. CTGGCTTAGCTGGCGCCGCCATCGGCAGGTTGGACTGGGGAAGGTCCTCATAGACATCC GACCGAATCGACCGCGGCGGTAGCCGTCACAVACCTGACCCCTTCCAGGAGTATCTGTAGG AlaGlyTyrgly AlaGlyValAlaGlyAlaeuVal.AlaphelysleMetSerGlyGlu 18 TTGCAGGGTATGGCGCGGGCGTGGCGGGAGCTCTTGTGGCATTCAAGATCATGAGCGGTG AACGTCCCATACCGCGCCCGCACCGCCCTCGAGAACACCGTAAGTCTAGTACCGCCAC Val ProSerThrglu AspleuVal AsnleureuProAlaleleuSerProGlyAlaleu 24l AGGTCCCCTCCACGGAGGACCTGGTCAATCTACTGCCCGCCATCCTCTCGCCCGGAGCCC TCCAGGGGAGGTGCCTCCTGGACCAGTTAGATGACGGGCGGTAGGAGAGCGGGCCTCGGG ValvalGlyval ValcysAla Alaleleu ArgArg His ValGlyProGlyGluglyala 30 TCGTAGTCGGCGTGGTCTGTGCAGCAATACTGCGCCGGCACGTTGGCCCGGGCGAGGGGG AGCATCAGCCGCACCAGACACGTCGTTAGACGCGGCCGTGCMACCGGGCCCGCTCCCCC ValGlnTrpMetAsnArgeuleAlaphealaSerArgGlyAsn His ValSer 36 CAGTGCAGTGGATGAACCGGCTGATAGCCTTCGCCTCCCGGGGGAACCATGTTTCCCC GTCACGTCACCTACTTGGCCGACTATCGGAAGCGGAGGGCCCCCTTGGTACAAAGGGG

U.S. Patent Sep. 7, 2010 Sheet 9 of 168 US 7,790,366 B1

FIG. 9A SelegluThrleTheUPrOG nASpAlaVal SerArghr61 in ArgArgGyArg 1 TCCATTGAGACAATCACGCTCCCCCAGGATGCTGTCTCCCGCACTCAACGTCGGGGCAGG AGGTAACTCTGTTAGTGCGAGGGGGTCCTACGACAGAGGGCGTGAGTTGCAGCCCCGTCC Thrgy ArgGlyy SPOGly IleTyrArgPheVal AlaproGyGluArgProSerGly 6l ACTGGCAGGGGGAAGCCAGGCATCTACAGATTTGTGGCACCGGGGGAGCGCCCCTCCGGC TGACCGTCCCCCTTCGGTCCGTAGATGTCTAAACACCGTGGCCCCCTCGCGGGGAGGCCG MetPheSpSerSerWai LeuCySG uCySTyrASpAlaGlyCySAaTrpTyr(Glueu 12 ATGTTCGACTCGTCCGTCCTCTGTGAGTGCTATGACGCAGGCTGTGCTTGGTATGAGCTC TACAAGCTGAGCAGGCAGGAGACACTCACGATACTGCGTCCGACACGAACCATACTCGAG

181 ACGCCCGCCGAGACTACAGTTAGGCTACGAGCGTACATGAACACCCCGGGGCTTCCCGTGEEEEEEEEEERIAEEE AlayrMetASnThrroGlyLeuPrOVal TGCGGGCGGCTCTGATGTCAATCCGATGCTCGCATGTACTTGTGGGGCCCCGAAGGGCAC CySGln ASpH iSLeuGlupher pGluGlyVal PheThr6ly euThrHiSI leASpAla 2ll TGCCAGGACCATCTTGAATTTTGGGAGGGCGTCTTTACAGGCCTCACTCATATAGATGCC ACGGTCCTGGTAGAACTTAAAACCCTCCCGCAGAAATGTCCGGAGTGAGTATATCTACGG HSPheeuSerGlnThrily SGInSerGlyGluASnLeuPrOTyrLeuVal AlayrGln 501 CACTTTCTATCCCAGACAAAGCAGAGTGGGGAGAACCTTCCTTACCTGGTAGCGTACCAA GTGAAAGATAGGGTCTGTTTCGTCTCACCCCTCTTGGAAGGAATGGACCATCGCATGGTT Ala ThrVal CySA la ArgAlaGln AlaproProProSerTrpASpGlnMetTrpLySCyS 361 GCCACCGTGTGCGCTAGGGCTCAAGCCCCTCCCCCATCGTGGGACCAGATGTGGAAGTGT CGGTGGCACACGCGATCCCGAGTTCGGGGAGGGGGTAGCACCCTGGTCTACACCTTCACA Leule ArgeuysProThreuhi SGlyPrOThrPrOLeueuTry ArgeuGlyAla 421 TTGATTCGCCTCAAGCCCACCCTCCATGGGCCAA CACCCCTGCTATACAGACTGGGCGCT AACTAAGCGGAGTTCGGGTGGGAGGTACCCGGTTGTGGGGACGATAGTCTGACCCGCGA Val Gln ASnGlu I leThrLeuThrHiSPrOVal ThrySTyrI leMetThrCySMetSer 481 GTTCAGAATGAAATCACCCTGACGCACCCAGTCACCAAATACATCATGA CATGCATGTCG CAAGCTTACTTTAGTGGGACTGCGTGGGTCAGTGGTTTATGTAGTACTGTA CGACAGC Ala ASpLeu6luVal Val ThrSerThrTrpVal LeuVal GlyGlyVal LeuAlaAlaleu 541 GCCGACCTGGAGGTCGTCACGAGCACCTGGGTGCTCGTTGGCGGCGTCCTGGCTGCTTTG CGGCTGGACCTCCAGCAGTGCTCGTGGACCCACGAGCAACCGCCGCAGGACCGACGAAAC 601 E881:GCCGCGTATTGCCTGTCAA SAAEREAEEE CAGGCTGCGTGGTCATAGTGGGCAGGGTCGTCTTGTCCGGG CGGCGCATAACGGACAGTTGTCCGACGCACCAGTATCACCCGTCCCAGCAGAACAGGCCC LySPOAla Ile I lePro A SpArgGluValleuTyr ArgGuPhe ASpGluMetGluGlu 66l AAGCCGGCAATCATACCTGACAGGGAAGTCCTCTACCGAGAGTTCGATGAGATGGAAGAG TTCGGCCGTTAGTATGGACTGTCCCTTCAGGAGATGGCTCTCAAGCTA CTCTACCTTCTC CySSerGlnHiSLeuProTyrI leGluGlnGlyMetMetLeu Ala Guglin PheySGln 721 TGCTCTCAGCACTTACCGTACATCGAGCAAGGGATGATGCTCGCCGAGCAGTTCAAGCAG ACGAGAGTCGTGAATGGCATGTAGCTCGTCCCTACTACGAGCGGCTCGTCAAGTTCGTC ySA la LeuGlyLeueuGlnThrAlaSer ArgGln AlaGluVal Ile Ala PrOA la Val 781 AAGGCCCTCGGCCTCCTGCAGACCGCGTCCCGTCAGGCAGAGGTATCGCCCCTGCTGTC TTCCGGGAGCCGGAGGACGTCTGGCGCAGGGCAGTCCGTCTCCAATAGCGGGGA CGACAG U.S. Patent Sep. 7, 2010 Sheet 10 of 168 US 7,790,366 B1

FIG. 9B GlnThr ASnTrpGlnySLeuGluThrphe TripAlaySHSMetTrpASnPhelleSer 841 CAGACCAACTGGCAAAAACTCGAGACCTTCTGGGCGAAGCATATGTGGAACTTCATCAGT GTCTGGTTGACCGTTTTGAGCCTGGAAGACCCGCTCGTATA CACCTTGAAGTAGTCA GlyleGlnTyreu Ala GlyLeuSerThrLeuPrOGlyASnProAla I leAlaSerLeu 90 GGGATACAATACTTGGCGGGCTTGTCAACGCTGCCTGGTAACCCCGCCATTGCTTCATTG CCCTATGTTATGAACCGCCCGAACAGTTGCGACGGACCATTGGGGCGGTAACGAAGTAAC MetAla PheThra AlaWalThrSerProLeu ThrThrSerGlnThreuteuPheASn 961 ATGGCTTTTACAGCTGCTGTCACCAGCCCACTAACCACTAGCCAAACCCTCCTCTTCAAC TACCGAAAATGTCGA CGACAGGGCGGGTGATTGGTGATCGGTTTGGGAGGACAAGTTG Ile Leu6 yGlyTrpVal Ala Alagln Leula AlaproGy Ala Allahr AlapheWal 1021 ATATTGGGGGGGTGGGTGGCGCCCAGCTCGCCGCCCCCGGTGCCGCTACTGCCTTTGTG TATAACCCCCCCACCCACCGACGGGTCGAGCGGCGGGGGCCACGGCGATGACGGAAACAC GlyAlaGlyLeu AlaGlyAla Ala I leGySerWalGlyLeuGlyLySVal LeuleASp 081 GGCGCTGGCTTAGCTGGCGCCGCCATCGGCAGTGTTGGACTGGGGAAGGTCCTCATAGAC CCGCGACCGAATCGACCGCGGCGGTAGCCGTCACAACCTGACCCCTTCCAGGAGTATCTG I leLeu AlaGlyTyr Gly AlaGlyVal AlaGly AlaleuVal Ala Phely SleMetSet 1141 ATCCTTGCAGGGTATGGCGCGGGCGTGGCGGGAGCTCTTGTGGCATTCAAGATCAGAGC TAGGAACGTCCCATA CCGCGCCCGCACCGCCCTCGAGA ACACCGTAAGTTCTAGTACTCG GlyGluVal ProSerThrGUASpeuVal ASn LeueuPrOAla I leLeuSerPro Gly 1201 GGTGAGGTCCCCTCCACGGAGGACCTGGTCAATCTACTGCCCGCCATCCTCTCGCCCGGA CCA CTCCAGGGGAGGTGCCTCCTGGACCAGTTAGATGACGGGCGGTAGGAGAGCGGGCCT AlaleuVal Val GlyVal Val CySA la AlaleleuArgArghi SVal GlyPrOGlyGlu 1261 GCCCTCGAGTCGGCGTGGTCTGTGCAGCAATACTGCGCCGGCACGTTGGCCCGGGCGAG CGGGAGCATCAGCCGCACCAGACACGTCGTTATGACGCGGCCGTGCAACCGGGCCCGCTC 1521 GGGGCAGTGCAGTGGATGAACCGGCTGATAGCCTTCGCCTCCCGGGGGAACCATGTTTCCCCEli ETEEASEEEEEEEEEEEEEEEEEEASEA-6E CCCCGTCACGCACCTACTTGGCCGACTATCGGAAGCGGAGGGCCCCCTTGGTACAAAGGGG

U.S. Patent Sep. 7, 2010 Sheet 12 of 168 US 7,790,366 B1

FIG. 11

as MetASnus uro an a co - OVerlapArgeul leAlapheWith 52------laSer ArgGlyASnHiSVal SerPrOThrHSTyrVal 1 GATGAACCGGCTGATAGCCTTCGCCTCCCGGGGGAACCATGTTTCCCCCACGCA CTACGT CTACTTGGCCGACTATCGGAAGCGGAGGGCCCCCTTGGTACAAAGGGGGTGCGTGATGCA PrOGluSerASpAla AlalaArgWalThrA alleleuSerSerLeuThrVal Thr61 in 61 GCCGGAGAGCGATGCAGCTGCCCGCGTCACTGCCATA CTCAGCAGCCTCACTGTAACCCA CGGCCTCTCGCTACGTCGACGGGCGCAGTGACGGTATGAGTCGTCGGAGTGACATTGGGT LeuleuArgArgeuiSGlnTrp leSerSerGUCySThrThrPrOCySSerGlySer 21 iii.6888&AEEff CGAGGA CTCCGCTGACGTGGTCACCTATTCGAGCCTCACATGGTGAGGTACGAGGCCAAG TrpLeurgASpleTrp A SpTrpleCySGuValleuSer A SppheiySThrTrpLeu 181. CTGGCTAAGGGACATCTGGGACTGGATATGCGAGGTGTTGAGCGACTTTAAGACCTGGCT GACCGATTCCCTGTAGACCCTGACCTATACGCTCCACAA CTCGCTGAAATTCTGGACCGA LySA laySLeuMetPOG neuproGlyleProPheWal SerCySGlnArgGlyTyr 241 AAAAGCTAAGCTCATGCCACAGCTGCCTGGGATCCCCTTGTGTCCTGCCAGCGCGGGTA TTTCGATTCGAGTACGGTGTCGACGGACCCTAGGGGAAACACAGGACGGTCGCGCCCAT LySGlyVal TrpArgWal 30 TAAGGGGGTCTGGCGAGTG ATTCCCCCAGACCGCTCAC

U.S. Patent Sep. 7, 2010 Sheet 14 of 168 US 7,790,366 B1

CysSerLeuThrVal Thrgl neueuarglargeuhisGlnTrpIleSerSerGlucy's l ACTGCAGCCTCACGTAACCCAGCTCCTGAGGCGACGCACCAGTGGATAAGCTCGGAGT TGACGTCGGAGTGACATTGGGTCGAGGACTCCGCTGACGTGGTCACCTATTCGAGCCTCA ThrThrProCysSerGlySerTrpLeuargaspleTrp-AspTrpleCysGluValleu 6 GTACCACTCCATGCTCCGGTTCCTGGCTAAGGGACATCTGGGACTGGATATGCGAGGTGT CATGGTGAGGTACGAGGCCAAGGACCGATTCCCTGTAGACCCTGACCTATACGCTCCACA

8- P Serasp?helys8 - x x 4 × 8 b x a ThrrpLeuysalaled Overlap with 33b------Lys LeuMetProGln Leu ProGly leproPhe l2l TGAGCGACTTTAAGACCTGGCTAAAAGCTAAGCTCATGCCACAGCTGCCTGGGATCCCCT ACTCGCTGAAATTCTGGACCGATTTTCGATTCGAGTACGGTGTCGACGGACCCTAGGGGA

ValSerCysGlin ArgGlyTyrLysGlyVal TripArgGlyAspGly IleMetHis Thrarg l8l TTGTGTCCTGCCAGCGCGGGTATAAGGGGGTCTGGCGAGGGGACGGCATCATGCACACTC AACACAGGACGGTCGCGCCCATATTCCCCCAGACCGCTCCCCTGCCGTAGTACGTGTGAG CyshisCysGlyAlaGlu IleThrCly His Valleys As nGlyThrmet ArgleValGly 24 GCTGCCACTGTGGAGCTGAGATCACTGGACATGTCAAAAACGGGACGATGAGGATCGTCG CGACGGTGACACCTCGACTCTAGTGACCTGTACAGTTTTTGCCCTGCTACTCCTAGCAGC ProArgThroys ArgAsnMetTrpSerGlyThrphe ProleAsn AlatyrThrThrgly 30 GTCCTAGGACCTGCAGGAACATGTGGAGTGGGACCTTCCCCATTAATGCCTACACCACGG CAGGATCCGGACGTCCTTGTACACCTCACCCTGGAAGGGGTAATTACGGATGTGGTGCC ProCys Thr ProLeu ProAla ProAsnTyrThrPhealaleu TripArgValSerial aGlu 36 GCCCCTGTACCCCCCTTCCTGCGCCGAACTACACGTTCGCGCTATGGAGGGTGTCTGCAG CGGGGACATGGGGGGAAGGACGCGGCTTGATGTGCAAGCGCGATACCTCCCACAGACGTC GluTyrvalGluIleArgGlnvaiglyAsppheHis TyrValThrglyet ThrThrasp 42 AGGAATATGTGGAGATAAGGCAGGTGGGGGACTTCCACTACGGACGGGTATGACTACTG TCCTTATACACCTCTATTCCGTCCACCCCCTGAAGGTGATGCACTGCCCATACTGATGAC AsnleuysCys ProCysGln Val ProSerProGluphePheThrglu 48l. ACAATCTCAAATGCCCGTGCCAGGTCCCATCGCCCGAATTTTTCACAGAAT TGTTAGAGTTTACGGGCACGGTCCAGGGTAGCGGGCTTAAAAAGTGTCTTA U.S. Patent Sep. 7, 2010 Sheet 15 of 168 US 7,790,366 B1

FIG. 14A Alayr.NetSerLySA lahi SGly leAspproASn I leArgThr6lyVal Argh rile 1 TGCTTACATGTCCAAGGCTCATGGGATCGATCCTAACATCAGGACCGGGGTGAGAACAAT ACGAATGTACAGGTTCCGAGTACCCTAGCTAGGATTGTAGTCCTGGCCCCA CTCTTGTTA ThrThrGlySerPrOleh TyrSerThyr GlyySPheeula ASpGlyGlyCyS 61 ACCACTGGCAGCCCCATCACGTACTCCACCTACGGCAAGTTCCTTGCCGACGGCGGGTG ATGGTGACCGTCGGGGAGTGCATGAGGTGGAGCCGTTCAAGGAACGGCTGCCGCCCAC SerGlyGlyAla TyrASple Ile I leCySASpGlucySHSSerThrASpAllah rSer 12 CTCGGGGGGCGCTTATGACATAATAATTTGTGACGAGTGCCA CTCCACGGATGCCA CATC GAGCCCCCCGCGAATACTGTATTATTAAACACTGCTCACGGTGAGGTGCCTACGGGTAG I leeuGly I le GlyThrVal LeuSpGln AlaGluThr AlaGlyAlaArgeuVal Val 18 CATCTTGGGCATCGGCACTGTCCTTGACCAAGCAGAGACTGCGGGGGCGAGACTGGTTGT GTAGAACCCGTAGCCGTGACAGGAACTGGTTCGTCTCTGACGCCCCCGCTCTGACCAACA Leula ThrAla ThrprOPrOGlySerWalThrVal ProHis PrOASn I leGlu0 luVal 241 GCTCGCCACCGCCACCCCTCCGGGCTCCGTCACTGTGCCCCATCCCAACATCGAGGAGGT CGAGCGGTGGCGGTGGGGAGGCCCGAGGCAGTGACACGGGGTAGGGTTGTAGCTCCTCCA AlaleuSerThrThr61 yGlu I lePro Phetyr GlyLySA la I leProLeuGUWall le 50 TGCTCTGTCCACCACCGGAGAGATCCCTTTTTACGGCAAGGCTATCCCCCTCGAAGTAAT A CGAGACAGGTGGTGGCCTCTCTAGGGAAAAATGCCGTCCGATAGGGGGAGCTTCATTA LySGlyGyArgHiSLeu I lePheCySH is SerLySLysySCySASpGlueu Ala Ala 361 CAAGGGGGGGAGACATCTCATCTTCTGTCATTCAAAGAAGAAGTGCGACGAACTCGCCGC GTTCCCCCCCTCTGTAGAGTAGAAGACAGTA AGTTTCTTCTTCACGCTGCTTGAGCGGCG LySLeuVal AlaleuGly I leASnAlaVal AlatyrTyrArgGlyLeuASpVal SerVal 421 AAAGCTGGTCGCATTGGGCATCAATGCCGTGGCCTACTACCGCGGTCTTGACGTGTCCGT TTCGACCAGCGTAACCCGTAGTTACGGCACCGGATGATGGCGCCAGAACTGCACAGGCA IleProThrSerGlyASpVal Val Val Val Alaihr ASpAlaleuMetThr6lyTyrThr 481 CATCCCGACCAGCGGCGAGTTGTCGTCGTGGCAA CCGATGCCCTCATGACCGGCTATAC GTAGGGCTGGCGCCGCTACAACAGCAGCACCGTTGGCTACGGGAGTACTGGCCGATATG GlyASpheASpSerWalle ASpTyrASnThrCySWalThr61 in ThrWalASpheSer 54 CGGCGACTTCGACTCGGTGATAGACTACAATACGTGTGTCACCCAGACAGTCGATTTCAG GCCGCGAAGCTGAGCCACTATCTGATGTTATGCACACAGGGGTCTGTCAGCTAAAGTC LeuSpproThrPheThrIle Gluhr leThreuPrOGnASpAlaWalSer ArgThr 601 CCTTGACCCTACCTTCACCATTGAGACAATCACGCTCCCCCAGGATGCTGTCTCCCGCAC GGAACTGGGAGGAAGGGTAA CTCTGTTAGTGCGAGGGGGTCCTACGACAGAGGGCGTG Gln Arg Argely ArghrGly ArgGlyLySPrOGly IleTyrArghe Val AlaproGly 66. TCAACGTCGGGGCAGGACTGGCAGGGGGAAGCCAGGCATCTACAGATTTGTGGCACCGGG AGTTGCAGCCCCCTCCTGACCGTCCCCCTTCGGTCCGTAGATGTCTAAACACCGTGGCCC GuArgPrOSer GlyMetPheSpSerSerVal LeuCysGluCySTyrASpA aGlyCyS 721 GGAGCGCCCCTCCGGCATGTTCGACTCGTCCGTCCTCTGTGAGTGCATGACGCAGGCTG CCTCGCGGGGAGGCCGTACAAGCTGAGCAGGCAGGAGACACTCACGATACTGCGTCCGAC AlarpTyrGluteuThrPro AlaguThrThrVal Argeu ArgAlaTyrMetASnThr 781 TGCTTGGTATGAGCTCACGCCCGCC6AGACTACAG TAGGCTACGAGCGTACATGAACAC ACGAACCATACTCGAGGCGGGCGGCTCTGATGTCAATCCGATGCTCGCATGTACTTGTG PrOGlyeuPrOVal CysG nASpH SLeuGUPheTrpGlugly Val PheThrGyeu 841 CCCGGGGCTTCCCGTGTGCCAGGACCATCTTGAATTTTGGGAGGGCGTCTTTACAGGCCT GGGCCCCGAAGGGCACA CGGTCCTGGTAGAACTTAAAACCCTCCCGCAGAAATGTCCGGA U.S. Patent Sep. 7, 2010 Sheet 16 of 168 US 7,790,366 B1

FIG. 14B Thrhi SI leASpAllah SPheleuSerGlnThrySGlnSerGlyGUASpeuPrOTyr 901 CACTCATATAGATGCCCACTTTCTATCCCAGACAAAGCAGAGTGGGGAGAACCTTCCTTA GTGAGTATATCTACGGGTGAAAGATAGGGTCTGTTTCGTCTCACCCCTCTTGGAAGGAAT LeuVal Alayrol nAlaThrVal CyS AlaArgAlaGln AlaproProProSerTrpASp 961 CCTGGTAGCGTACCAAGCCACCGTGTGCGCTAGGGCTCAAGCCCCCCCCCATCGTGGGA GGACCATCGCATGGTTCGGTGGCACACGCGATCCCGAGTTCGGGGAGGGGGTAGCACCCT GlinMetTrpLySCySLeuleArgeu-ySPOThrLeuHiSGlyPrOThrPrOLeueu 1021 CCAGATGTGGAAGTGTTTGATTCGCCTCAAGCCCACCCTCCATGGGCCAA CACCCCTGC GGCTA CACCTTCACAAACTAAGCGGAGTTCGGGTGGGAGGTACCCGGTTGTGGGGA CGA Tyr ArgeuGlyAlaVal Gln ASnGlu I leThrLeuThrHis ProVal ThrLySTyrIle 1081 ATACAGACTGGGCGCTGTTCAGAATGAAATCACCCTGACGCACCCA GTCACCAAATA CAT TATGTCTGACCCGCGACAAGTCTTACTTTAGTGGGACTGCGTGGGTCAGTGGTTTATGTA MetThrCySMetSer Ala A SpleUGUVal Val ThrSerThrrpVal LeuVal GlyGly 1141 CATGACATGCATGTCGGCCGACCTGGAGGTCGTCACGAGCACCTGGGTGCTCGTTGGCGG GTACTGTACGTACAGCCGGCTGGACCTCCAGCAGTGCTCGTGGACCCA CGAGCAA CCGCC Wall Leula Alaleu Ala AlaTyrCySLeuSerThrGly CySWal Wall leVal GlyArg 1201 CGTCCTGGCTGCTTTGGCCGCGTATTGCCTGTCAA CAGGCTGCGTGGTCATAGTGGGCAG GCAGGACCGACGAAACCGGCGCATAACGGACAGTTGTCCGACGCACCAGTATCACCCGTC Wal Wall LeuSerGlyLySPrOAlale I lePro A SpArgGluVal LeuTyr ArgG UPhe 1261 GGCGTCTTGTCCGGGAAGCCGGCAATCATACCTGACAGGGAAGTCCTCTACCGAGA GT CCAGCAGAACAGGCCCTTCGGCCGTTAGTAGGACGTCCCTTCAGGAGATGGCTCTCAA ASpGluMetGluGluCySSerGln HiSLeuPrOTyr I leGluGlnGlyMetMetLeuAla 1521 CGATGAGATGGAAGAGTGCTCTCAGCACTTACCGTACATCGAGCAAGGGATGATGCTCGC GCTA CTCTACCTTCTCACGAGAGTCGTGAAGGCATGTAGCTCGTTCCCTACTACGAGCG Glu0 in Phely SGln LySA la LeuGlyLeu LeuGlnThr AlaSerArgGln AlaGluVal 1581 CGAGCAGTTCAAGCAGAAGGCCCTCGGCCTCCGCAGACCGCGTCCCGTCAGGCAGAGGT GCTCGTCAAGTTCGTCTTCCGGGAGCCGGAGGACGTCTGGCGCAGGGCAGTCCGTCTCCA Ile AlaproAla Val GlnThr ASn TrpGlnySLeuGUThrPhelpAlaySHiSMet 1441 TATCGCCCCTGCTGTCCAGACCAACTGGCAAAAACTCGAGACCTTCTGGGCGAAGCATAT ATAGCGGGGACGACAGGTCTGGTTGACCGTTTTTGAGCTCTGGAAG ACCCGCTTCGTATA TrpASnPhelleSerGly I leGlnTyrLeu AlaGlyLeuSerThrLeuPOGlyASn PrO 1501 GTGGAACTTCATCAGTGGGATACAATACTTGGCGGGCTTGTCAA CGCTGCCTGGTAACCC CACCTTGAAGTAGTCACCCTATGTTATGAACCGCCCGAACAGTTGCGACGGACCATTGGG AlaleAlaSerLeuMetAlapheThrala AlaVal ThrSerPrOLeuThrThrSerGln 1561 CGCCATTGCTTCATTGATGGCTTTTACAGCTGCTGTCACCAGCCCA CTAACCACTAGCCA GCGGTAACGAAGAACTACCGAAAATGTCGA CGACAGTGGTCGGGTGATTGGTGATCGGT ThreuleuPhe ASn I leLeuGlyGlyTrpVal Ala AlaGlnLeu AlalaPrOGlyAla 1621. AACCCTCCTCTTCAA CATATTGGGGGGGTGGGTGGCTGCCCAGCTCGCCGCCCCCGGTGC TTGGGAGGAGAAGTTGTATAACCCCCCCACCCACCGACGGGTCGAGCGGCGGGGGCCACG Ala ThrAlapheVal GlyAlaGlyLeuAlaGlyAla Ala I leGlySerVal GlyLeuGly 1681 CGCTACTGCCTTTGTGGGCGCTGGCTTAGCTGGCGCCGCCATCGGCAGTGTTGGACTGGG GCGATGACGGAAACACCCGCGACCGAATCGACCGCGGCGGTAGCCGTCACAA CCTGACCC U.S. Patent Sep. 7, 2010 Sheet 17 of 168 US 7,790,366 B1

FIG. 14C LySVal LeuleASpleLeu AlaGlyTyr(GlyAlaGlyVal AlaGlyAlaleuVal Ala 17ll GAAGGTCCTCATAGACATCCTTGCAGGGATGGCGCGGGCGTGGCGGGAGCTCTTGTGGC CTTCCAGGAGTATCTGTAGGAACGTCCCATACCGCGCCCGCACCGCCCTCGAGAACACCG PheySI leMetSerGlyGluVal PrOSerThrGluASpeuVal ASnLeueuPrOAla 1801 ATTCAAGATCATGAGCGGTGAGGTCCCCTCCACGGAGGACCTGGTCAATCTACTGCCCGC TAAGTTCTAGTACTCGCCACTCCAGGGGAGGTGCCTCCTGGACCAGTTAGATGACGGGCG I leeuSerProGly AlaleuVal Val GlyVal Val CySA laAla I leLeuArgArghis 1861 CATCCTCTCGCCCGGAGCCCTCGTAGTCGGCGTGGTCTGTGCAGCAATACTGCGCCGGCA GTAGGAGAGCGGGCCTCGGGAGCATCAGCCGCACCAGACACGTCGTTATGACGCGGCCGT Val GlyPrOGlyGluGlyAlaVal GlnTrpMetASn Argeu I leAlapheAlaSerArg 1921 CGTTGGCCCGGGCGAGGGGGCAGTGCAGTGGATGAACCGGCTGATAGCCTTCGCCTCCCG GCAACCGGGCCCGCTCCCCCGTCACGTCACCTACTTGGCCGACTATCGGAAGCGGAGGGC

1981 GGGGAA CCATGTTTCCCCCACGCACTACGTGCCGGAGAGCGATGCAGCTGCCCGCGTCAC CCCCTTGGTACAAAGGGGGTGCGTGATGCACGGCCTCTCGCTACGTCGACGGGCGCAGTG&AEEEAi EEEEEEEEASFXEEEEEEEEEEEEEEEEEEEEEE Ala I leLeuSerSerLeuThrWalThrGlneuleu Arg Argeuhi SGln TripleSer 2011 TGCCATACTCAGCAGCCTCACTGTAACCCAGCTCCTGAGGCGACTGCACCAGTGGATAAG ACGGTATGAGTCGTCGGAGTGACATTGGGTCGAGGACTCCGCTGACGTGGTCACCTATTC SerGluCySThrThrPrOCy SSerGlySerTrpLeu ArgASpI leTrpASpTrpleCyS 20 CTCGGAGTGTACCACTCCATGCTCCGGTTCCTGGCTAAGGGACATCTGGGACTGGATATG GAGCCTCACATGGTGAGGTACGAGGCCAAGGACCGATTCCCTGTAGACCCTGACCTATAC GluVal LeuSerASpphelys ThrTrpLeulySA laySLeuMetPrOGln LeuPOGly 21 61 CGAGGTGTTGAGCGACTTTAAGACCTGGCTAAAAGCTAAGCTCATGCCACAGCTGCCTGG GCTCCA CAA CTCGCTGAAATTCTGGACCGATTTTCGATTCGAGTACGGTGTCGACGGACC I leproPheVal SerCysGln ArgGlyTyrySGlyVal TripArgVal ASpGly leMet 2221 GATCCCCTTTGTGTCCTGCCAGCGCGGGTATAAGGGGGTCTGGCGAGTGGACGGCATCAT CTAGGGGAAACACAGGACGGTCGCGCCCATATTCCCCCAGACCGCTCACCTGCCGTAGTA HiSThrArgCySHiSCysGlyAlaGlueThrGlyHSVaySASnGlyThretArg 2281 GCACACTCGCTGCCACTGTGGAGCTGAGATCACTGGACATGTCAAAAACGGGACGATGAG CGTGTGAGCGACGGTGACACCTCGACTCTAGTGACCTGTACAGTTTTTGCCCTGCTACTC I leVal GlyProArgThrCySArgASnMetTrpSerGlyThrPheproleASnAlaTyr 2341 GATCGTCGGTCCTAGGACCTGCAGGAACATGTGGAGTGGGACCTTCCCCATTAATGCCTA CTAGCAGCCAGGATCCTGGACGTCCTTGTACACCTCACCCTGGAAGGGGTAATTACGGAT ThrThrGlyProCySThrProLeuPrOAlapro ASnTyrThrPhela LeuTripArgVal 2401 CACCACGGGCCCCTGTACCCCCCTTCCTGCGCCGAACTACACGTTCGCGCTATGGAGGGT GTGGTGCCCGGGGACATGGGGGGAAGGACGCGGCTTGATGTGCAAGCGCGATACCTCCCA SerAlaGluGluTyrVal Glu I leArgGlnVal GlyASphehi STyrVal Thr6lyMet 246 GTCTGCAGAGGAATATGTGGAGATAAGGCAGGTGGGGGACTTCCACTACGTGACGGGTAT CAGACGTCTCCTTATACACCTCTATTCCGTCCACCCCCTGAAGGTGATGCACTGCCCATA ThhrASpASnLeuySCySPOCySGlnVal PrOSerPro GluphephehrGlu 252 GACTACTGACAATCTCAAATGCCCGTGCCAGGTCCCATCGCCCGAATTTTTCACAGAAT CTGATGACTGTTAGAGTTTACGGGCACGGTCCAGGGTAGCGGGCTTAAAAAGTGTCTTA U.S. Patent Sep. 7, 2010 Sheet 18 of 168 US 7,790,366 B1

FIG. 15 Alayal ASPPhelePOVal GAS euglu Thh MetAgSePQWalPheThr l GGCGGTGGACTTTATCCCTGTGGAGAACCTAGAGACAACCATGAGGTCCCCGGTGTTCAC CCGCCACCTGAAATAGGGACACCTCTTGGATCTCTGTTGGTACTCCAGGGGCCACAAGTG ASDASnSerSerPrOPrOVal Val PrOGlnSerPheGnWall Alai SLeuHiSA larO 61 GGATAACTCCTCTCCACCAGTAGTGCCCCAGAGCTTCCAGGTGGCTCACCTCCATGCTCC CCTATTGAGGAGAGGTGGTCATCACGGGGTCTCGAAGGTCCACCGAGTGGAGGTACGAGG Thr6 ySerGlyLySSerThrLySVal PrOAla Alayr Ala AlaGlnGlyTyrLySVal 121 CACAGGCAGCGGCAAAAGCACCAAGGTCCCGGCTGCATATGCAGCTCAGGGCTATAAGGT GTGTCCGTCGCCGTTTTCGTGGTTCCAGGGCCGACGTATACGTCGAGTCCCGATATTCCA LeuVal Leu ASnPrOSerVal Ala Allah reu6lyPheGlyAlaTyrMetSerLySA la 18 GCTAGTACTCAA CCCCTCTGTTGCTGCAACACTGGGCTTTGGTGCTTACATGTCCAAGGC CGATCATGAGTTGGGGAGACAA CGACGTTGTGACCCGAAACCACGAATGTACAGGTTCCG so HiSGyleASprOASneArgThr6sees as a as OVerlap With 40b------yVal ArgThr I leThrThrGlySerProle 24l TCATGGGATCGATCCTAACATCAGGACCGGGGTGAGAACAATTACCACTGGCAGCCCCAT AGTACCCTAGCTAGGATTGTAGTCCTGGCCCCA CTCTTGTTAATGGTGACCGTCGGGGTA Th Ty SerThrTyrGly-ySPheeuAla Asp6lyGlyCySSerGlyGlyAlaTyrASp 30 CACGTA CTCCACCTACGGCAAGTTCCTTGCCGACGGCGGGTGCTCGGGGGGCGCTTATGA GTGCATGAGGTGGAGCCGTTCAAGGAACGGCTGCCGCCCACGAGCCCCCCGCGAATACT Ile Ile I leCySASpGluCySHiSSerThrASpAlaThrSeri leLeuGly leGlyThr 361 CATAATAATTTGTGACGAGTGCCACTCCACGGATGCCA CATCCATCTTGGGCATTGGCAC GTATTATTAAACACTGCTCACGGTGAGGTGCCTACGGTGTAGGTAGAACCCGTAACCGTG WalleuASpGln AlaGluThrAlaGlyAlaArgeuVal Val Leu AlathrAlaThrPro l2 TGTCCTTGACCAAGCAGAGACTGCGGGGGCGAGACTGGTTGTGCTCGCCACCGCCACCCC ACAGGAACTGGTTCGTCTCTGACGCCCCCGCTCGACCAA CACGAGCGGTGGCGGTGGGG PrOGlySerVal ThrVal ProHiSPrOASnI leGluGluVal Ala LeuSerThrThrGly l8. TCCGGGCTCCGTCACTGTGCCCCATCCCAA CATCGAGGAGGTTGCTCTGTCCACCACCGG AGGCCCGAGGCAGTGACACGGGGTAGGGTTGTAGCTCCTCCAA CGAGACAGGTGGTGGCC GUI leProPhey rGlyLySA la I leProLeuGluValleysGlyGlyArgHiSLeu AGAGATCCCTTTTTACGGCAAGGCTATCCCCCTCGAAGTAATCAAGGGGGGGAGACATCT TCTCTAGGGAAAAATGCCGTTCCGATAGGGGGAGCTTCATTAGTTCCCCCCCTCTGTAGA IlePheCySHiSSerLySLySLySCySASpGlueuAla AlaySLeuVal Alaleu6ly 601 CATCTTCTGTCATTCAAAGAAGAAGTGCGACGAACTCGCCGCAAAGCTGGTCGCATTGGG GTAGAAGACAGTAAGTTTCTTCTTCACGCTGCTTGAGCGGCGTTTCGACCAGCGTAACCC IleASn AlaVal AlayrTyrArgGlyLeuASpVal SerVal I leProThrSerGlyASp 661 CATCAATGCCGTGGCCTACTACCGCGGTCTTGACGTGTCCGTCATCCCGACCAGCGGCGA GTAGTACGGCACCGGATGATGGCGCCAGAACTGCACAGGCAGTAGGGCTGGTCGCCGCT WaWa Wal Wal Ala ThrSpAlaleuMetThrGlyTyrThrGlyASppheASpSerVal 721 TGTTGTCGTCGTGGCAACCGATGCCCTCATGACCGGCTATACCGGCGACTTCGA CTCGGT ACAACAGCAGCACCGTGGCTACGGGAGTACTGGCCGATATGGCCGCTGAAGCTGAGCCA leASpCySASnThrCyS 78. GATAGACTGCAATACGTGTG CTATCTGACGTTATGCACAC U.S. Patent Sep. 7, 2010 Sheet 19 of 168 US 7,790,366 B1

FIG. 16 ySerSer ASpe UTyreuVal I leP O GCTCCTCGGACCT TTACCTGGTC AEEEEEA?ACGAGGCACGC aiCGATGTC ATTC CGAGGAGCCTGGA AATGGACCAGTGCTCCGTGCG GCTACAG TAAG Pr OIeSerTyrLeu CC CATTTCCTACT GG GTAAAGGATGA Ly ySPrOAla GlyHiSA laVal Gly lePhe Arg 121. TGAA GCCCCGCGGGGCACG CCGTGGGCATATTTA ACTT CGGGGCGCCCCGTGC GGCACCCGTATAAAT ------OV al ySA laVal ASphelePro TA AGGCGGTGGACTTTATCCC ATTCCGCCACCTGAAATAGGG 53C------GUThrThrMetArgser PrOVal Phelihr ASpASnSer 241 TAGAGA CAA CCATGAGGTCCCCGGTGTTCACGGATAA CTCCTC ATCTCTGTGGTACTCCAGGGGCCACAAGTGCCTATTGAGGAG FIG. 17 GlyTrp Argeuteu Ala Pr Ole Thr 1 GGGTGGAGGTTGCTG GCGCC CATCACGGC CCCACCTCCAA CGAC CGCGG GTAGTGCCG

Tyrhi SGly AlaGlyThrArgThr I leAlaSerProLySGlyPrOValleGlinMetTyr 81 CTACCACGGGGCCGGAA CGAGGACCATCGCGTCACCCAAGGGTCCTGTCATCCAGATGTA GATGGTGCCCCGGCCTTGCTCCTGGTAGCGCAGTGGGTTCCCAGGACAGTAGGTCTACAT ThrSnVal ASpGln ASpleUV al GlyTrpproAlapro GnGl rArgSer LeuThr 2 TACCAATGTAGACCAAGACCTTG TGGGCTGGCCCGCTCCG CAAGG Yi CCGCTCA TTGAC ATGGTTACATCTGGTTCTGGAAC ACCCGACCGGGCGAGGC GTTCCATC GGCGAGT AACTG ------0Verlap With 8h------PrOCySThrCySGlySerSer ASpeuTyrLeuVal ThrArgh iS 50l ACCCTGCACTTGCGGCTCCCGGACCTTACCTGGTCACGAGGCACG TGGGACGTGAACGCCGAGGAGCCTGGAAATGGACCAGTGCTCCGTGC U.S. Patent Sep. 7, 2010 Sheet 20 of 168 US 7,790,366 B1

FIG. 18 ASnMetTrpSerGlyThrPhePrOI leASn AlatyrThrThrGlyPrOCySThrPrOLeu 1 GAA CATGTGGAGTGGGACCTTCCCCATTAATGCCTACACCACGGGCCCCTGTACCCCCCT CTTGTACACCTCACCCTGGAAGGGGTAATTACGGATGTGGTGCCCGGGGACATGGGGGGA ------0Verlap With 25C------PrOAlaPrOASnTyrThrPhe Alaleu Trp ArgVal Ser AlaGluGluTyrVal Glue 61 TCCTGCGCCGAACTACACGTTCGCGCTATGGAGGGTGTCTGCAGAGGAATACGTGGAGAT AGGACGCGGCTTGATGTGCAAGCGCGATACCTCCCACAGACGTCTCCTTATGCACCTCTA ArgGlnVal GlyASpphei STyrVal Thr6lyMetThrThrASpASnLeuys CyS PrO 121 AAGGCAGGTGGGGGACTTCCACTACGTGACGGGTATGACTACTGACAATCTTAAATGCCC TTCCGTCCACCCCCTGAAGGTGATGCACTGCCCATACTGATGACTGTTAGAATTTACGGG CySG nWall PrOSerPrOGuPhePheThr61 UL 18 GTGCCAGGTCCCATCGCCCGAATTTTTCACAGAA T CACGGTCCAGGGTAGCGGGCTTAAAAAGTGTCTT A Val Se rPheArgVa 241. T GTATC ATTCAGAGT A CATAG TAAGTCTCA TyrPrOVa Gl ySerGln euPrOCySG1 uproGluP rOASpVal Ala Waleu ThrSer 301 ATACCCGGT AGG GTCGCAAT TACCTTGCGAGCCCGAAC CGGA CGTGGCCGTGTTGACGTC TATGGGCCA TCC CAGCGTTAAATGGAA CGCTCGGGCTTG GCCTGCACCGGCACAACTGCAG PrOSerHiSI leThrAla CCCTCCCATA TAACAGCA GGGAGGGTAT ATTGTCGT SerPro PrOSerVal AlaSer Ser Ser AlaserGlneuSe rAlaproS erLeuySA la l21 ATCACCCCCCTCTGTGGCCAGCTCCTCGGCTAGCCAGCTATC CGCTCCAT CTCTCAAGGC TAGTGGGGGGAGACACCGGTCGAGGAGCCGATCGGTCGATAG GCGAGGTA GAGAGTTCCG ThrCySThrAlaAS 8 AACTTGCACCGCTAA TTGAACGTGGCGATT U.S. Patent Sep. 7, 2010 Sheet 21 of 168 US 7,790,366 B1

FIG. 19 OVerlap With 14C------SerSerSer AlaserGlneuSer AlaproSerleutySAaThrCySThrAlaASpH is 1 AGCTCCTCGGCTAGCCAGCTATCCGCTCCATCTCTCAAGGCAACTTGCACCGCTAACCAT TCGAGGAGCCGATCGGTCGATAGGCGAGGTAGAGAGTTCCGTTGAACGTGGCGATTGGTA ASpSerPrOASpAlaGlueuleGUAla ASnLeuleu TripArgGlnGluMetGlyGlu 61 GACTCCCCTGATGCTGAGCTCATAGAGGCCAA CCTCCTATGGAGGCAGGAGATGGGCGGC CTGAGGGGACTACGA CTCGAGTATCTCCGGTTGGAGGATACCTCCGTCCTCTACCCGCCG 121 AACATCACCAGGGTTGAGTCAGAAAACAAAASCIEEEEEEEEEEASEKilisi.ESPEEEE GTGGTGATTCTGGA CTCCTTCGATCCGCTT TTGTAGTGGTCCCAA CTCAGTCTTTTGTTTCACCACTAAG ACCTGAGGAAGCTAGGCGAA Val AlaGluGlu ASpGlu ArgGlu leSerVal PrOAla Glu I leLeuArgySSerArg 18 GTGGCGGAGGAGGACGAGCGGGAGATCTCCGTACCCGCAGAAATCCTGCGGAAGTCTCGG CACCGCCTCCTCCTGCTCGCCCTCTAGAGGCATGGGCGTCTTTAGGACGCCTTCAGAGCC Arghe laGln Alaleu PrOVal TrpAla ArgPrOASpTyrASnPrOProLeuVal Glu 24 AGATTCGCCCAGGCCCTGCCCGTTGGGCGCGGCCGGACTATAACCCCCCGCTAGTGGAG TCTAAGCGGGTCCGGGACGGGCAAACCCGCGCCGGCCTGATATTGGGGGGCGATCA CCTC ThrTrpLySLySPrOASpTyrGluProProVal Val HiSGly CyS ProLeuProProPro 301 ACGTGGAAAAAGCCCGACTACGAACCACCTGTGGTCCATGGCTGTCCGCTTCCACCTCCA TGCACCTTTTTCGGGCTGATGCTTGGTGGACACCAGGTACCGACAGGCGAAGGTGGAGGT LySSerPro PrOVal Pro 56 AAGTCCCCTCCTGGCCG TTCAGGGGAGGACACGGC

FIG. 20 WalTrpAla ArgPrOASpTyr ASn PrOPrOLeuVal GluThrrp ySLySPOASpTyr 1 CGTTTGGGCGCGGCCGGACTATAACCCCCCGCTAGTGGAGACGTGGAAAAAACCCGACTA GCAAACCCGCGCCGGCCTGATATTGGGGGGCGATCACCTCTGCACCTTTTTTGGGCTGAT GluproProVala a a s a Vals is as Hisa OVerlap Gly CyS WithProLeu 8f------ProProProLySSerProProVal PrOPO 6. CGAACCACCTGTGGTCCATGGCTGCCCGCTTCCACCTCCAAAGTCCCCTCCTGTGCCTCC GCTTGGGGACACCAGGTACCGACGGGCGAAGGTGGAGGTTTCAGGGGAGGACACGGAGG PrOArgLySLySArgThrVal Val LeuThrGluSerThrLeuSerThrAlaleulaGlu 12 GCCTCGGAAGAAGCGGACGGTGGTCCTCACTGAATCAA CCCTATCTACTGCCTTGGCCGA CGGAGCCTTCTTCGCCTGCCACCAGGAGTGACTTAGTTGGGATAGATGACGGAACCGGCT 18 GCTCGCCACCAGAAGCTTTGGCAGCTCCTCAAEaEEAEEEEEEEEEEEEEEEEEEEEEASE" CTCCGGCATTACGGGCGACAATACGAC CGAGCGGTGGTCTTCGAAACCGTCGAGGAGTTGAAGGCCGTAATGCCCGCTGTTATGCTG ThrSerSerG UPrOAlaProSerGyCySProProASpSerASpAlaGuSerPhe 24 AACATCCTCTGAGCCCGCCCCTTCTGGCTGCCCCCCCGACTCCGACGCTGAGTCCTTTGC TTGTAGGAGA CTCGGGCGGGGAAGACCGACGGGGGGGCTGAGGCTGCGA CTCAGGAAACG U.S. Patent Sep. 7, 2010 Sheet 22 of 168 US 7,790,366 B1

Alaser ArgSerPheGlySerSerSerhrSerGlyeThr6ly ASpASnThrihrThr 1 GCCTCCAGAAGCTTTGGCAGCTCCTCAACTTCCGGCATTACGGGCGACAATA CGACAACA CGGAGGTCTTCGAAA CCGTCGAGGAGTTGAAGGCCGTAATGCCCGCTGTAGCTGTTGT SerSerGluPrOAlaproSerGly- - - -a as a - - - - - OVerlap With CySPrOPrOASpSer 53f------ASpAlaGluSerTyrSer Ser 61 TCCTCTGAGCCCGCCCCTTCTGGCTGCCCCCCCGA CTCCGACGCTGAGTCCTATTCCTCC AGGAGACTCGGGCGGGGAAGACCGACGGGGGGGCTGAGGCTGCGACTCAGGATAAGGAGG MetProProLeuGluGlyGluPrOGlyASpproASpeuSerASpGlySerTrpSerThr 12 ATGCCCCCCCTGGAGGGGGAGCCTGGGGATCCGGATCTTAGCGACGGGTCATGGTCAA CG TACGGGGGGGACCTCCCCCTCGGACCCCTAGGCCTAGAATCGCTGCCCAGTACCAGTTGC 181 GTCAGTAGTGAGGCCAACGCGGAGGATGTCGTGTGCTGCTCAATGTCTTACTCTTGGACASi38,385.83.35.&R.S.EXETEEA CAGTCATCA CTCCGGTTGCGCCTCCTACAGCACACGACGAGTTACAGAATGAGAA CCTGT GlyAlaleuVal ThrPrOCySA la Ala Glug luGlnySLeuPrOI leASn AlaleuSer 24, GGCGCACTCGTCACCCCGTGCGCCGCGGAAGAACAGAAACTGCCCATCAATGCACTAAGC CCGCGTGAGCAGTGGGGCACGCGGCGCCTTCTTGTCTTTGACGGGTAGTTACGTGATTCG ASnSerLeuleu ArgHiSHSASnLeuVal TyrSerThrThrSer ArgSer 301 AACTCGTTGCTACGTCACCACAATTTGGTGTATTCCACCACCTCACGCAGTG TTGAGCAA CGAGCAGTGGGTTAAACCACATAAGGTGGTGGAGTGCGTCAC FIG. 22 GlyThrTyrWalTyr ASnHiSLeuThrPrOLeuArgASpTrpAlaHiSASnGlyLeuArg GGCACCTATGTTTATAACCATCTGA CTCCTCTCGGGACTGGGCGCACAACGGCTTGCGA CCGTGGATA CAAATATTGGTAGAGTGAGGAGAAGCCCTGACCCGCGTGTTGCCGAA CGCT ASpeu?AaVal AlaVal GuPrOVal Val PheSerGinMetGluThrLySLeUI leThr 61 GATCTGGCCGTGGCTGTAGAGCCAGTCGTCTTCTCCCAAATGGAGACCAAGCTCATCACG CTAGACCGGCACCGACATCTCGGTCAGCAGAAGAGGGTTTACCTCTGGTTCGAGTAGTGC TrpGlyAlaASpThr Alala CysGlyASpI le leASnGlyLeuPrOVal Ser Ala Arg 121 TGGGGGGCAGATACCGCCGCGTGCGGTGACATCATCAACGGCTTGCCTGTTTCCGCCCGC ACCCCCCGTCTATGGCGGCGCACGCCACTGTAGTAGTTGCCGAACGGACAAAGGCGGGCG 181 AGGGGCCGGGAGATACTGCTCGGGCCAGCCGATGGAATGGTCTCCAAGGGTTGGAGGTTG TCCCCGGCCCTCTATGACGAGCCCGGTCGGCTACCTTACCAGAGGTTCCCAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAES; CCTCCAAC LeuAlaPrOI leThr Alatyr AlaGlnGlnThrArgGlyLeuleu6ly CySI leILeThr 241 CTGGCGCCCATCACGGCGTACGCCCAGCAGACAAGGGGCCTCCTAGGGTGCAAATCACCGACCGCGGGTAGTGCCGCATGCGGGTCGTCTGTTCCCCGGAGGATCCCACGTATTAGTGG SerLeuCo is meThrGlyArgASpLySASnGlnVal up to um up a OVerlap With 7e------GuglyGluVal Gln I leVal SerThrAla 301 AGCCTAACTGGCCGGGACAAAAACCAAGTGGAGGGTGAGGTCCAGATTGTGTCAA CTGCT TCGGATTGACCGGCCCTGTTTTTGGTTCACCCCCACTCCAGGTCTAACACAGTTGACGA AlaGlnThrPhee UAlaThrCySIle ASnGlyVal CySTrp 361 GCCCAAACCTTCCTGGCAA CGTGCATCAATGGGGTGTGCTG CGGGTTTGGAAGGACCGTTGCACGTAGTTACCCCACA CGAC U.S. Patent Sep. 7, 2010 Sheet 23 of 168 US 7,790,366 B1

FIG. 23 GlyGlyValValleuValGlyLeuMetalaleuThreuser ProTyrtyr Lys Arg Tyr l GGCGGTGTTGTTCTCGTCGGGTTGATGGCGCTGACTCTGTCACCATATTACAAGCGCTAT CCGCCACAACAAGAGCAGCCCAACTACCGCGACTGAGACAGTGGTATAATGTTCGCGATA IleSerTrpCysLeuTrpTrpLeuglnTyr PheleuThrArgValGlualaGlineu his 6l ATCAGCTGGTGCTTGTGGTGGCTTCAGTATTTTCTGACCAGAGTGGAAGCGCAACTGOAC TAGTCGACCACGAACACCACCGAAGTCATAAAAGACTGGTCTCACCTTCGCGTTGACGTG Val Trp IleProProLeu As nValargGlyGlyArgas palaValleleu LeuMetCys 2. GTGTGGATTCCCCCCCTCAVACGTCCGAGGGGGGCGCGACGCCGTCATCTTACTCATGTGT CACACCTAAGGGGGGGAGTGCAGGCTCCCCCCGCGCGCGGCAGTAGAATGAGTACACA AlaValhis ProThrLeuVal PheaspIleThrLysLeuleuleualaVal PheGlyPro 8 GCTGTACACCCGACTCTGGTATTTGACATCACCAAATTGCTGCTGGCCGTCTTCGGACCC CGACATGTGGGCTGAGACCATAAACTGTAGTGGTTTAACGACGACCGGCAGAAGCCTGGG LeuTripleLeuGlin AlaserLeuleu LysValProTyrpheValArgValGlnGlyLeu 24 CTTTGGATTCTTCAAGCCAGTTTGCTTAAAGTACCCTACTTTGTGCGCGTCCAAGGCCTT GAAACCTAAGAAGTTCGGTCAAACGAATTCATGGGATGAAACACGCGCAGGTTCCGGAA Leurg PheCysalaleuala ArgeysMetIleGlyGlyHisTyrValGlinMetValle 3 O CTCCGGTTCTGCGCGTTAGCGCGGAAGAGATCGGAGGCCATACGTGCAAATGGTCATC GAGGCCAAGACGCGCAATCGCGCCTTCTACTAGCCTCCGGTAATGCACGTTTACCAGTAG Illeys LeuglyAlaleu ThrglyThrTyrValTyrasnhis Leu ThrProLeu argasp 36 ATAAGTTAGGGGCGCTTACTGGCACCTATGTTTATAACCATCTCACTCCTCTCGGGAC TAATTCAATCCCCGCGAATGACCGTGGATACAAATATTGGTAGAGTGAGGAGAAGCCCTG TrpAllahis.Aso do es up eas ob do do no enGlyLeuArgAspLeualaValAlaValGluProValValPheSergin peo up so a to be overlap with 7 f ------42. TGGGCGCACAACGGCTTGCGAGATCTGGCCGTGGCTGTAGAGCCAGTCGTCTTCTCCCAA ACCCGCGTGTTGCCGAACGCTCTAGACCGGCACCGACATCTCGGTCAGCAGAAGAGGGTT MetGluThrLysLeulleThrTrpGly 48 ATGGAGACCAAGCTCATCACGTGGGGGGC TACCTTGGTTCGAGTAGTGCACCCCCCG U.S. Patent Sep. 7, 2010 Sheet 24 of 168 US 7,790,366 B1

FIG. 24 GluTyrWalWaleu euPhe euleuleuL Alasp largVal CySSerCySLeuTrp l GGGAGTACGTCGTTCTCC TGTTCC TCTGCTGCAGACGCGCGCGTCTGCTCCTGCTTGTC CCCTCATGCAGCAAGAGG ACAAGG AAG ACGAACGTCTGCGCGCGCAGACGAGGACGAACA MetMetLeueulleS erGln A la6 luAla Alaleu6 UASnLeuVal. I leLeuASn Ala 6 GGATGATGCTA CTCATAT CCCAAG CGG AGGCGGCTTTGGAGAACCTCGTAATACTTAATG CCTACTACGAGAGTATA GGGTTC GCCTCCGCCGAAACCTCTTGGAGCATTATGAATTAC AlaserLeu AlaGlyThrhi SG ly euVal SerPheeuVal PhepheCySPhela Trp 21 CAGCATCCCTGGCCGGGACGCACG TGTATCCTTCCTCGTGTTCTTCTGCTTGCAT GTCGTAGGGACCGGCCCTGCGGC CAGAA CATAGGAAGGAGCACAAGAAGACGAAACGTA TyreutySGly ySTrpWalPT rOGlyA laWalTyrThrPheTyrGlyMetTrpproLeu 181 GGTATTTGAAGGGTAAGT GGGTGC CCGGAG C GGTCTACACCTTCTACGGGATGT GGCC TC CCATAAACTTCCCATTCA CCCACG GGCCTC GC CAGATGGGAAGATGCCCTAC ACCGG AG Leuleuleueuleu A lateuP rOGln A rg A laTyr AlaleuASpThr6luVal Al aA la 241 TCCTCCTGCTCCTGTTGG CCCAGC GG GCGTACGCGCTGGACACGGAG GTGGC CG AGGAGGA CGAGGACAACC GCAACG GGGTCG CC CGCATGCGCGACCTGTGCCTC CACCG GC V er la p With llb------SerCySGlyGlyVal Val LeuVal GlyLeuMetAlaleuMe ThreuSerPrOTyrTyryS 30 CGTCGTGTGGCGGGTTGTTCTCGTCGGGTTGATGGCGCTGA CTCTGTCACCATATTACA GCAGCACA CCGCCACAACAAGAGCAGCCCAACTACCGCGACTGAGACAGTGGTATAATGT rpCySLeuTrpTrpeuGln 36. GGTGCTTGTGGTGGCTTCAGAA CCACGAA CACCACCGAAGTCTT

pAlaGluSerTyrSerSerMetPOPO CGCTGAGTCCTATTCCTCCATGCCCCCC GCGACTC luGlyG e A S D G lySerTrpSerThrWalSerSer 6. GAGGGGGAGC TTAGCGACGGGTCATGGTCAA CAGTCAGTAGT AATCGCTGCCCAGACCAGTTGTCAGTCATCA P. UAlae. e. de ASno no AlaGluASpValap oppo o a OWe Val CySCySSerMetSerTyrSerTrpThrGlyAlaleuWith 35g------121 GGCCAACGCGGAGGATGTCGTGTGCTGCTCAATGTCCTACTCTTGGACAGGCGCACTC CCGGTTGCGCCTCCTACAGCACACGACGAGTTACAGGATGAGAACCTGTCCGCGTGAG ySAlala Gluglu GlnySLeuPrOI leASn AlaleuSer ASnSerLeu 181 GCGCCGCGGAAGAACAGAAACTGCCCATCAATGCACTGAGCAA CTCGTTG CGCGGCGCCTTCTTGTCTTTGACGGGTAGTTACGTGACTCGTTGAGCAAC eAgSSASnLeyla TyrSeThrThSerAgSerAacySgnAggyS 241. CTACGTCACCACAATTTGGTGTATTCCACCACCTCACGCAGTGCTTGCCAAAGGCAGAAG GATGCAGTGGTGTAAACCACATAAGGTGGTGGAGTGCGTCACGAACGGTTTCCGTCTTC LySValThrpheSpArgeuGlnValleuASpSerHiSTyrGlnASpVal LeuySGly 30 AAAGTCACATTGACAGACTGCAAGTTCTGGACAGCCATTACCAGGACGTACTCAAGGAG TTTCAGTGTAAACTGTCTGACGTTCAAGACCTGTCGGTAATGGTCCTGCATGAGTTCCTC Wall LySA la Alaa laSerLySWall LySA laSnPhe 36 GTTAAAGCAGCGGCGCAAAAGTGAAGGCTAACTTC CAATTTCGTCGCCGCAGTTTTCACTCCGATTGAAG

U.S. Patent Sep. 7, 2010 Sheet 26 of 168 US 7,790,366 B1

AgSlyeue GlyCySeleh Set LeuhrGlyArgASpySASRG) nVal Glu 96 CAAGGGGCCTCCAGGGGCATAACACCAGCCTAACGGCCGGGACAAAAACCAAGTGG GTTCCCCGGAGGATCCCACGTATTAGTGGTCGGATTGACCGGCCCTGTTTTGGTTCACC GlyGUVal Gln I leValSerThrA fallanthrPheleuAla ThrCySIleASnGly 1021 AGGGTGAGGTCCAGATTGTGTCAACTGCTGCCCAAACCTTCCTGGCAACGTGCATCAATG CCCACTCCAGGTCTAACACAGTGACGACGGGTTGGAAGGACCGTTGCACGTAGTAC WalCySpThrWay HiSGyAlaGlyThrrg ThrileAlaSerProLySGlyPrO 1081. GGGTGGCTGGACTGTCTACCACGGGGCCGGAACGAGGACCACGCGTCACCCAAGGGTC CCCACA CGACCTGACAGATGGTGCCCCGGCCTTGCTCCTGGAGCGCAGTGGGTTCCCAG WaleGlnMety ThrASnValA S D GlnASpeuVal GlyTrpproAlaproGlnGly 1. CTGTCATCCAGATGTATACCAATGTAG A C AAGACCTTGTGGGCTGGCCCGCCCGCAAG GACAGTAGGTCTA CATAGGACATC T G TTCTGGAACACCCGACCGGGCGAGGCGTC SeArgSerleuthPOCySThrCy S lySerSer ASpeuyreuVal Thrghis 120 GTAGCCGCTCATTGACACCCTGCACTTG C GCTCCTCGGACCTTACCGGTCACGAGGC CATCGGCGAGTAACTGTGGGA CGTGAAC G C GAGGAGCCTGGAAATGGACCAGTGCTCCG AlaSpValleProWalArgArgAr g l yASpSerArggySeleue SerPrOArg 1261 ACGCCGATGTCATTCCCGTGCGCCGGCGGGGTg G GATAGCAGGGGCAGCCTGCTGTCGCCCC TGCGGCTACAGTAAGGGCACGCGGCCGCCCCACTACGTCCCCGTCGGACGACAGCGGGGC ProleSerTyreuySGySerSerGyGlyProeuleucy'sy PrOAlaGlyHiSA a 132 GGCCCATTCCTACTTGAAAGGCTCCTCGGGGGGTCCGCTGTTGTGCCCCGCGGGGCACG CCGGGTAAAGGATGAACTTTCCGAGGAGCCCCCCAGGCGACAACACGGGGCGCCCCGTGC Wall Glyepherg AlalaVal CyShr ArgGlyVal AlaySA laWa ASp?helle 381 CCGG G GCATATTTAGGGCCGCGGTGTGCACCCGTGGAGGGCTAAGGCGGTGGACTTA GGCAC C CGATAAATCCCGGCGCCA CACGTGGGCACCTCACCGATTCCGCCACCTGAAAT Pro Val GluASnLeuGluThrThrMetArgserProVal Phehr ASpASnSerSerPro ill TCCCT GTGGAGAACCTAGAGACAACCATGAGGTCCCCGGGTTCACGGATAA CTCCTCTC AGGGA CACCCTTGGATCCTGTTGGTACTCCAGGGGCCACAAGGCCTATTGAGGAGAG PrO Wal Wa PrOGInSerPheGlnVal Alahi SeuiSA aprohrGySerGyyS 501 CACCAGTAGTGCCCCAGAGCTTCCAGGTGGCTCACCTCCATGCTCCCACAGGCAGCGGCA GTGGCATCACGGGGTCTCGAAGGTCCA CCG AGGGAGGTACGAGGGGTCCGTCGCCGT SerThrySVal PrOAlaAlayr AlallaGlnGlyTyrLySVal LeuVal LeuASnPro 561 ASSESSAASSESSSSSSSSIALSSSSSSSSSAASSESSAASSAASSTTCGGGTCCAGGGCCGACGTATAC GTCCCGAATTCCACGATCAGAGGG SerVal Ala Ala Threu6lyPheGlyAlaTyretSerySAy Al lahi SGlye ASDPrO 62. CCTCTGGCTGCAA CACTGGGCTTGGGCTTACATGTCCAAGGCTCATGGGACGATC GGAGACAACGACGTTGTGACCCGAAACCACGAATGTACAGGTTCCGAGTACCCTAGCTAG ASnleArghr6 yWaArghr leThrThrGySerPro leThrlyrSerThrTyr 1681 CTA ACACAGGACCGGGGTGAGAACAATTACCACGGCAGCCCCATCACGTACTCCACCT GATTGAGTCCTGGCCCCACCTTGTTAATGGTGACCGTCGGGGTAGTGCATGAGGTGGA Gly-ySPheteu AlaaSp0 yGlyCySSerGlyGlyAlaTyrASple Ile I leCySASp 1741 ACGGCAAGTTCCTTGCCGACGGCGGGTGCTCGGGGGGCGCTTATGACATAATAATTTGTG TGCCGTTCAAGGAACGGCTGCCGCCCACGAGCCCCCCGCGAATACTGTATTATTAAACAC GlucySHiSSerThrASpAllah Ser I leeugly IleGlyThrWalteu ASpGln Ala 1801 ACGAGTGCCACTCCACGGATGCCACATCCATCTTGGGCATCGGCACTGTCCTTGACCAAG TGCTCACGGTGAGGTGCCTACGGTGTAGGTAGAACCCGTAGCCGTGACAGGAACTGGTTC GluThrAlaGlyAlaArgeuVal ValleUAlaThrAlaThrProProGlySerVal Thr 861 CAGAGACTGCGGGGGCGAGACTGGTTGTGCTCGCCACCGCCACCCCCCGGGCTCCGTCA GTCTCTGACGCCCCCGCCTGACCAACACGAGCGGTGGCGGTGGGGAGGCCCGAGGCAGT Val ProHisProASneGluGuVal AlaleuSerThrThr6 yGUI ePrOPheyr 1921. CTGTGCCCCATCCCAACACGAGGAGGGCTCTGTCCACCACCGGAGAGATCCCTTTTT GACACGGGGTAGGGTTGTAGCTCCTCCAACGAGACAGGTGGTGGCCTCTCTAGGGAAAAA U.S. Patent Sep. 7, 2010 Sheet 27 of 168 US 7,790,366 B1

FIG. 26C GyySA la leproLeu6 uValleySGlyGly Argh SLeu epheCyshi SSer 1981 ACGGCAAGGCTATCCCCCTCGAAGTAATCAAGGGGGGGAGACATCTCATCTTCTGTCATT TGCCGTTCCGATAGGGGGAGCTTCATAGTCCCCCCCCTGTAGAGTAGAAGACAGTAA LysySLySCySASpglueuAlaAlatySLeuVal AlaleuGlyleASn AlaVal Ala 2041 CAAAGAAGAAGTGCGACGAACTCGCCGCA AAGCTGGCGCATTGGGCATCAATGCCGTGG GTTTCTTCTTCACGCTGCTTGAGCGGCGTTTCGACCAGCGTAACCCGTAGTTACGGCACC TyrTyrArgGlyeuSpVal SerVal IlePro ThrSerGlyASpVal Val Val Val Ala 210 CCTACTACCGCGGCTTGACGTGTCCGTCATCCCGACCAGCGGCGATGTTGTCGTCGTGG GGATGATGGCGCCAGAACTGCACAGGCAGTAGGGCTGGTCGCCGCTACAA CAGCAGCACC ThrSpAlaleuMetThr61 yTyrThrGlyASphe SpSerWall I leASpCySASnThr 2161 CAACCGATGCCCTCATGACCGGCTATACCGGCGACTTCGA CTCGGTGATAGACTGCAATA GTTGGCTACGGGAGTACTGGCCGATATGGCCGCTGAAGCTGAGCCA CTATCTGACGTTAT CySWalThrGlnThrWalASppheSerLeuASpproThrPheThrI leGluThrilehr 2221. CGTGTGTCACCCAGACAGTCGATTTCAGCCTTGACCCTACCTTCACCATTGAGACAATCA GCACACA GTGGGTCTGTCAGC AAAGTCGGAACTGGGATGGAAGTGGTAACTCGTTAGT 228. CGCTCCCCCAGGATGCTGTCTCCCGCACTCAACGTCGGGGCAGGACTGGCAGGGGGAAGCEEEEEEEEEEEE Thr61 in ArgArgGlyArgThrGlyArgGlyLySPrO GCGAGGGGGTCCTACGACAGAGGGCGTGAGTGCAGCCCCGTCCTGACCGTCCCCCTTCG Gly leTyrArgheVal AlaproGlyGluArgPrOSerGlyMetPheSpSerSerWal 231 CAGGCATCTACAGATTGTGGCACCGGGGGAGCGCCCCTCCGGCATGTTCGACCGTCCG GTCCGTAGATGTCTAAACACCGTGGCCCCCTCGCGGGGAGGCCGTACAAGCTGAGCAGGC Leucy SG UCySyrASpAlagy CySAaTrpTyrClueuThrPrOAlaGuThrThr 240 TCCCTGTGAGTGCTATGACGCAGGCTGTGCTTGGTATGAGCTCACGCCCGCCGAGACTA AGGAGACACTCACGATACTGCGTCCGACA CGAACCATA CTCGAGTGCGGGCGGCTCTGAT WalArgeu ArgAlayrMetASnThrprOGlyLeuPrOVal CysGlnASpHiSeuGlu 246 CAGTTAGGCTA CGAGCGTACATGAACACCCCGGGGCTTCCCGGTGCCAGGACCATCTTG GT CAATCCGATGCTCGCATGTACTTGTGGGGCCCCGAAGGGCACACGGTCCTGGTAGAAC PheTrpGlu-GlyWalPheThrGlyLeuThrHiSI leASpAllahi SPheLeuSerGlnThr 252 AATTTTGGGAGGGCGTCTTTACAGGCCTCACTCATATAGATGCCCA CTTTCTATCCCAGA TTAAAACCCTCCCGCAGAAATGTCCGGAGTGAGTATATCTACGGGTGAAAGATAGGGTCT ySGlnSerGlyGluASnLeuPrOTyrLeuVal AlatyrGln AlathrWalCySA laArg 2581 CAAAGCAGAGTGGGGAGAA CCTTCCTTACCTGGTAGCGTACCAAGCCACCGTGTGCGCTA GTTTCGTCTCACCCCTCTTGGAAGGAAGGACCACGCAGGCGGTGGCACACGCGAT AaGlin AlaproProProSerTrpASpGlnMetTrp-ySCySLeule ArgeuysPro 264 GGGCCAAGCCCCTCCCCCACGTGGGACCAGATGTGGAAGTGTTGATTCGCCTCAAGC CCCGAGTCGGGGAGGGGGTAGCACCCGGTCTACACCT CACAAACTAAGCGGAGTTCG Thrleuhi SGlyPrOThrProLeuleuTyrArgeu6ly AlaVal Gln ASnGlu I lehr 2701 CCACCCTCCATGGGCCAA CACCCCTGCTATACAGACTGGGCGCTGTTCAGAATGAAATCA GGTGGGAGGTACCCGGTTGTGGGGACGATATGTCTGACCCGCGACAAGTCTTACTTAGT LeuThrHisProWai ThrySTyrI leMetThrCySMetSer AlaaSpeu6luVal Val 2761 CCCGACGCACCCAGTCACCAAATACATCATGACATGCATGTCGGCCGACCTGGAGGTCG GGGACTGCGTGGGTCA GTGGTTTATGTAGTACTGTACGTACAGCCGGCTGGACCTCCAGC ThrSeThrrpVal LeuVal GlyGlyVal Leula Alaleula Ala TyrCySLeuSer 2821 TCACGAGCACCTGGGTGCTCGTTGGCGGCGTCCTGGCTGCTTTGGCCGCGTATTGCCTGT AGTGCTCGTGGACCCACGAGCAA CCGCCGCAGGACCGACGAAACCGGCGCATAACGGACA Thr61 yCyS Val ValleVal GlyArgVal Val LeuSerGlyLySPrOAlale I lePro 2881 CAACAGGCTGCGTGGTCATAGTGGGCAGGGTCGTCTTGTCCGGGAAGCCGGCAATCATAC GTTGTCCGACGCACCAGTATCACCCGTCCCAGCAGAACAGGCCCTTCGGCCGTTAGTATG U.S. Patent Sep. 7, 2010 Sheet 28 of 168 US 7,790,366 B1

FIG. 26D TyreGuglinglyMetMeteu AlaGUGlnPheySGnySAlaleugyLeulieu 500 CGTACATCGAGCAAGGGATGATGCTCGCCGAGCAGTTCAAGCAGAAGGCCCTCGGCCTCC GCATGTAGCTCGTCCCTACTACGAGCGGCCGTCAAGTTCGTCTTCCGGGAGCCGGAGG Gln Thr AlaSerArgG nAlaGluValleAltaPrOAlaVal GlnThrASnTrpGlnLyS 306 TGCAGACCGCGTCCCGTCAGGCAGAGGTTATCGCCCCTGCTGTCCAGACCAACTGGCAAA ACGTCTGGCGCAGGGCAGTCCGTCTCCAATAGCGGGGACGACAGGTCTGGTTGACCGTTT Leu6 UThrPheTrpAlaySHSMetTrpASnPhelleSerGly leGlnTyreu Ala 512 AACTCGAGA CCTTCTGGGCGAAGCATATGTGGAACTTCATCAGTGGGATACAATACTTGG TTGAGCTCTGGAAGACCCGCTTCGTATACACCTTGAAGTAGTCACCCTATGTTATGAACC GlyLeuSerThreuPrOGlyASnPrOAlaleAlaSereuMetAlapheThrAla Ala 5181 CGGGCTTGTCAA CGCTGCCTGGTAACCCCGCCATTGCTTCATTGATGGCTTTTACAGCTG GCCCGAACAGTTGCGACGGACCATTGGGGCGGTAACGAAGTAACTACCGAAAATGTCGAC Val ThrSerPrOLeuThrThrSerGlnThreueuPheSn leLeuGlyGlyTrpVal 5241 CTGTCACCAGCCCACTAACCACAGCCAAACCCTCCTCTTCAA CATATTGGGGGGGTGGG GACAGTGGTCGGGTGATTGGTGATCGGTTTGGGAGGAGAAGTTGTATAACCCCCCCACCC 330 TGGCTGCCCAGCTCGCCGCCCCCGGGCCGCTACTGCCTTGTGGGCGCTGGCTTAGCTG38.338EEEEEEEEEEEEEEEgy ACCGACGGGTCGAGCGGCGGGGGCCACGGCGATGACGGAAACACCCGCGACCGAATCGAC Alala IleGlySerVal GlyLeuGlyLySWall LeuleASpI leLeuAlaGlyTyrGly 3561 GCGCCGCCATCGGCAGTGTTGGACTGGGGAAGGTCCTCATAGACATCCTTGCAGGGTATG CGCGGCGGTAGCCGTCACAACCTGACCCCTTCCAGGAGTATCTGTAGGAACGTCCCATAC AlaGlyVal AlaGlyAlaleuVal AlapheySIleMetSerGlyGluVal PrOSerThr 342. GCGCGGGCGTGGCGGGAGCTCTTGTGGCATTCAAGATCATGAGCGGTGAGGTCCCCTCCA CGCGCCCGCACCGCCCTCGAGAA CACCGTAAGTTCTAGTACTCGCCACTCCAGGGGAGGT GuASpeuVal ASneuleu PrOAlaleLeuSerProGlyAlaleuVal Val GlyVal 3,481 CGGAGGACCTGGTCAATCTACTGCCCGCCATCCTCTCGCCCGGAGCCCCGTAGTCGGCG GCCTCCTGGACCAGTTAGATGACGGGCGGTAGGAGAGCGGGCCTCGGGAGCATCAGCCGC 3541 TGGTCTGTGCAGCAATACTGCGCCGGCACGTTGGCCCGGGCGAGGGGGCAGTGCAGTGGAfiétiéiliigEEEEEEEEEEEEEEEEEEEEE ACCAGACACGTCGTTATGACGCGGCCGTGCAACCGGGCCCGCTCCCCCGTCACGTCACCT ASn Argeu I leAlapheAlaserArgGlyASnHiSWal SerProThrHiSTyrVal Pro 3601. TGAACCGGCTGATAGCCTTCGCCTCCCGGGGGAACCATGTTTCCCCCACGCACTACGTGC A CTTGGCCGACTATCGGAAGCGGAGGGCCCCCTTGGTACAAAGGGGGTGCGTGATGCACG GluSer ASpAla Ala Ala ArgVal ThrAla I leLeuSerSerLeuThrWalThrGlneu 3661 CGGAGAGCGATGCAGCTGCCCGCGTCACTGCCATACTCAGCAGCCTCACTGTAACCCAGC GCCTCTCGCTACGTCGACGGGCGCAGTGACGGTATGAGTCGTCGGAGTGACATTGGGTCG Leu ArgArgeuhi SG nTripleSerSerGluCySThrThrPrOCySSerGlySerTrp 3721. TCCTGAGGCGACTGCACCAGTGGATAAGCTCGGAGTGTACCACTCCATGCTCCGGTTCCTAGGACTCCGCTGACGTGGTCACCTATTCGAGCCTCACATGGTGAGGTACGAGGCCAAGGA LeurgASpleTrpASpTripleCySGuVal LeuSerASpphelys ThrTrpLeuyS 3781 GGCTAAGGGACATCTGGGACTGGATATGCGAGGGTTGAGCGACTTTAAGACCTGGCTAA CCGATTCCCTGTAGACCCTGACCTATACGCTCCACAACTCGCTGAAATTCTGGACCGATT AlaySLeuMetProGlneuPrOGlyleProPheVal SerCySGln ArgGlyTyrLyS 38.41 AA GCTAAGCTCATGCCACAGCTGCCTGGGATCCCCTTTGTGTCCTGCCAGCGCGGGTATA TT GATTCGAGTACGGTGTCGACGGACCCTAGGGGAAACACAGGACGGTCGCGCCCATATG A lyVal TrpArgWalASpGlyG IleMethi SThrArgCySHiSCySGlyAlaGlulleThr 390 AG GGGTCTGGCGAGTGGACGGCATCATGCACACTCGCTGCCACTGTGGAGCTGAGATCAG TC CCCAGACCGCTCACCTGCCGTAGTACGTGTGAGCGACGGTGACACCTCGAC CTCTAGT

U.S. Patent Sep. 7, 2010 Sheet 30 of 168 US 7,790,366 B1 FIG. 26F ASpproASpeuSer ASpGlySerTrpSerThrWalSerSerGluAlasnAlaGluASp 5041 GGGATCCGGATCTTAGCGACGGGTCATGGTCAACGGTCAGTAGTGAGGCCAACGCGGAG G CCCTAGGCCTAGAATCGCTGCCCAGTACCAGTTGCCAGCACACTCCGGTTGCGCCTCC Val Val CySCySSerMetSerTyrSerTrpThr6ly AlaleuVal ThrprOCyS Ala Ala 510 ATGTCGTGTGCTGCTCAATGTCTTACTCTGGACAGGCGCACTCGTCACCCCGTGCGCCG TACAGCACACGAC6AGTTACAGAATGAGAACCTGTCCGCGTGAGCAGTGGGGCACGCGGC Gluglu GlnySLeuPrOI leASn AlaleuSer ASnSerLeuleu ArgiSHSASnLeu 516 CGGAAGAACAGAAACTGCCCATCAATGCACAAGCAA CTCGTTGCTACGTCACCACAATT GCCTTCTTGTCTTTGACGGGTAGTTACGTGATTCGTTGAGCAA CGATGCAGTGGTGTTAA WalTyrSeThrThSer ArgSer AlaySGln ArgGlnySLySWalThrPheSpArg 522 TGGTGTATTCCACCACCTCACGCAGTGCGCCAAAGGCAGAAGAAAGTCACATTTGACA ACCACATAAGGTGGTGGAGTGCGTCACGAACGGTTTCCGTCTTCTTTCAGTGTAAACTGT Leu6l nWall Leu ASpSerHSTyrGln ASpValeully SGluVal LySAlala Alaser 528 GACTGCAAGTTCTGGACAGCCATTACCAGGACGACTCAAGGAGGTTAAAGCAGCGGCGT CTGACGTCAAGACCTGTCGGTAATGGTCCTGCATGAGTTCCTCCAATTTCGTCGCCGCA ySWall LySAla ASnLeu 534 CAAAAGTGAAGGCTAACTTG GTTTTCACTTCCGATTGAAC

FIG. 3O GyGlyGuAsnCysGlyTyrArgrgCysArgalaserGlyvale ThrThrSercys GGGGGGGAGAACTGCGGCTATCGCAGGGCCGCGCAAGCGGCGTACTGACAACTAGCTGT CCCCCCCTCTTGACGCCGATAGCGTCCACGGCGCGTTCGCCGCATGACTGTTGATCGACA GlyASn ThreuThrCySTyrley SA la ArgAla AlaCySArgAlaAlaGlyLeuGln 61 GGTAACACCCTCACTTGTTACATCAAGGCCCGAGCAGCCTGTCGAGCCGCAGGGCTCCAG CCATTGTGGGAGTGAACAATGTAGTTCCGGGCTCGTCGGACAGCTCGGCGTCCCGAGGTC AsocysthrMet------OVerlapSvay With iSAEspleuvaivailecysGiuserAiaGlyval 19q------121 GACTGCACCATGCTCGTGTGTGGCGACGACTTAGTCGTTATCTGTGAAAGCGCGGGGGTC CTGACGGGTACGAGCACA CACCGCTGCTGAATCAGCAATAGACACTCGCGCCCCCAG GlnGluSpAlalaSerLeuArgAlapheThr61 UAlaMethrArgyrSer Alapro 181 CAGGAGGACGCGGCGAGCCTGAGAGCCTTCACGGAGGCTATGACCAGGTACTCCGCCCCC GTCCTCCTGCGCCGCTCGGACTCTCGGAAGTGCCCCGATACTGGTCCATGAGGCGGGGG POGlyASpproProGinProGluTyrASpeuGlueulleThrSerCySSerSerASn 241 CCTGGGGACCCCCCACAACCAGAATACGACTTGGAGCTCATAACATCATGCTCCTCCAAC GGACCCCTGGGGGGTGTGGCTTAGCTGAACCTCGAGTATTGAGTACGAGGAGGTTG Ya Seryal Allah SASpGlyAlagylySA rgyalTyrTyreuth ArgASpROThr 301 GTGTCAGTCGCCCACGACGGCGCTGGAAAGAGGGTCTACTACCTCACCCGTGACCCTACA CACAGTCAGCGGGTGCTGCCGCGACCTTTCTCCCAGATGATGGAGGGGCACTGGGATGT ThrProLeu AlaArgAlaAlaTrpGUThr Ala Argh SThrProWall ASnSerTrpleu 361 ACCCCCCTCGCGAGAGCTGCGTGGGAGACAGCAAGACACACTCCAGCAATTCCTGGCTA TGGGGGGAGCGCCTCGACGCACCCTCTGTCGTTCTGTGTGAGGTCAGTAAGGACCGAT GlyASnIle I leMetPheAlaproThreuTripAla 42 GGCAACAAATCATGTTTGCCCCCACACTGTGGGCG CCGTTGTATTAGACAAACGGGGGTGTGACACCCGC

U.S. Patent Sep. 7, 2010 Sheet 32 of 168 US 7,790,366 B1

FIG. 28 so in asLeuysGluVal or p up us as Pro Overlap Lys AlaalaAlaSerLysValleyswith 39c.------Alaas nLeu LeuServalGluglu TGCTCAAGGAGGTTAAAGCAGCGGCGTCAAAAGTGAAGGCTAACTTGCTATCCGTAGAGG ACGAGTTCCTCCAATTTCGTCGCCGCAGTTTTCACTTCCGATTGAACGATAGGCATCTCC AlaCysSerleu ThrProProHis SerAlalysSerLys PheglyTyrglyAlays Asp 6. AAGCTTGCAGCCTGACGCCCCCACACTCAGCCAAATCCAAGTTTGGTTATGGGGCAAAAG TTCGAACGTCGGACTGCGGGGGTGTGAGTCGGTTTAGGTTCAAACCAATACCCCGTTTTC ValArgCys His Alaarg Lys Alaval Thrhis IleAs nServal TrpLys AspLeuLeu l2 ACGTCCGGCCATGCCAGAAAGGCCGTAACCCACATCAACTCCGTGTGGAAAGACCTTC TGCAGGCAACGGTACGGTCTTTCCGGCATTGGGTGTAGTTGAGGCACACCTTTCTGGAAG Glus pasnvalThrproIleAs pThrthrIleMetAla LysAs nGluVal PheCysVal 8. TGGAAGACAATGTAACACCAATAGACACTACCATCATGGCAAGAACGAGGTTTCTGCG ACCTTCTGTTACATTGTGGTTACTGTGATGGTAGTACCGATTCGCTCCAAAAGACGC Gln ProGlulysGlyGlyArgys ProAlaarg LeuleValPheproAspleugly Val 24l TTCAGCCTGAGAAGGGGGGTCGTAAGCCAGCTCGTCTCATCGTGTTCCCCGATCTGGGCG AAGTCGGACTCTCCCCCCAGCATTCGGTCGAGCAGAGTAGCACAAGGGGCTAGACCCGC ArgValCysGluLysMet AlaleuTyrAspValValThrys Leu ProLeu Alaval Met TGCGCGTGTGCGAAAAGATGGCTTTGTACGACGTGGTTACAAAGCTCCCCTTGGCCGTGA ACGCGCACACGCTTTCTACCGAAACATGCTGCACCAATGTTTCGAGGGGAACCGGCACT GlySerSerTyrglyPheglnTyrSerProGlyGlnArgValGlu PheleuVal Glin Ala 36 TGGGAAGCTCCTACGGATTCCAATACTCACCAGGACAGCGGGTTGAATTCCTCGTGCAAG ACCCTTCGAGGATGCCTAAGGTTAGAGTGGTCCTGTCGCCCAVACTTAAGGAGCACGTTC FrpLysserLysLys ThrproMetGlyPheSerTyrAspThrargCys PheaspSerThr 2 CGTGGAAGTCCAAGAAAACCCCAATGGGGTTCTCGTAGATACCCGCTGCTTGACCCA GCACCTTCAGGTTCTTTTGGGGTTACCCCAAGAGCATACTATGGGCGACGAAACTGAGGT ValThrCluser Asple Arg Thrgluglu Ala A 81 CAGTCACTGAGAGCGACATCCGTACGGAGGAGGCA GTCAGTGACTCTCGCTGTAGGCATGCCTCCTCCGT U.S. Patent Sep. 7, 2010 Sheet 33 of 168 US 7,790,366 B1

Glu PheleuValGlinalaTrpLysserLys LysThrProMetGlyPheserTyrAspThr GAATTCCTCGGCAAGCGTGGAAGTCCAAGAAAACCCCAANGGGGTTCTCGTATGAACC CTTAAGGAGCACGTTCGCACCTTCAGGTTCTTTTGGGGTTACCCCAAGAGCATACTATGC ArgCysas a sess spPheaspSerThrValThrgluSerAspIle see Overlap with 35 f------ArgThrgluglu AlaleTyrclin 6l CGCTGCTTTGACTCCACAGTCACTGAGAGCGACATCCGTACGGAGGAGGCAATCTACCAA GCGACGAAACTGAGGTGTCAGTGACTCTCGCTGTAGGCATGCCTCCTCCGTTAGATGGTT CysCys AspleuaspproGlnRalaArgValAla Ileys SerLeuThrCluarg LeuTyr 2 TGTTGTGACCTCGACCCCCAAGCCCGCGTGGCCATCAAGTCCCTCACCGAGAGGCTTTAT ACAACACTGGAGCTGGGGGTTCGGGCGCACCGGTAGTTCAGGGAGTGGCTCTCCGAAATA ValGlyGlyProLeu ThrAsnSerArgGlyGlu AsnCysGlyTyrargargcysArgAla l8l GTTGGGGGCCCTCTTACCAATTCAAGGGGGGAGAACTGCGGCTATCGCAGGTGCCGCGCG CAACCCCCGGGAGAATGGTTAAGTTCCCCCCTCTTGACGCCGATAGCGTCCACGGCGCGC SerGlyValleuThrThrSerCysGlyAsnThreu ThrCysTyrIleLysAla Arg Ala 24 AGCGGCGTACTGACAACTAGCTGTGGTAACACCCTCACGCTACACAAGGCCCGGGCA TCGCCGCAGACTGTTGATCGACACCATTGTGGGAGTGAACGATGTAGTCCGGGCCCGT AlaCysargalaAlaGlyLeuglinAspCys ThrMetLeuValCysGlyAspas pleuVal 30 GCCTGTCGAGCCGCAGGGCTCCAGGACTGCACCATGCTCGTGTGTGGCGACGACTTAGTC CGGACAGCTCGGCGTCCCGAGGTCCTGACGTGGTACGAGCACACACCGCTGCTGAATCAG VallecysGluSerAlaGlyValGlnGlulaspala Ala 36l GTTATCTGTGAAAGCGCGGGGGTCCAGGAGGACGCGGCGAG CAATAGACACTTTCGCGCCCCCAGGTCCTCCTGCGCCGCC

U.S. Patent Sep. 7, 2010 Sheet 35 of 168 US 7,790,366 B1

FIG. 32A Il ephelys Ile ArgMetTyrVal GlyGlyVal Gluhi S.Argeu61 UAlaAlaCySASn l CCATATTTAAAATCAGGATGTACGTGGGAGGGGTCGAACACAGGCTGGAAGCTGCCTGCA GGTATAAATTTTAGTCCTACATGCACCCTCCCCAGCTTGTGTCCGACCTTCGACGGACGT TrpThrArgGlyGlu ArgCySAS pleuGluASpArgASpArgSerGluleUSerProLeu 61 ACTGGACGCGGGGCGAA CGTTGCGATCTGGAAGACAGGGACAGGTCCGAGCTCAGCCCGT TGACCTGCGCCCCGCTTGCA ACGCTAGACCTTCTGTCCCTGTCCAGGCTCGAGTCGGGCA LeuleuThrThrThrGnTrpGlnVal LeuPrOCySSerPheThrThrLeuPrOAlaleu 121 TACTGCTGACCACTACACAGTGGCAGGTCCTCCCGTGTTCCTTCACAA CCCTACCAGCCT ATGACGA CTGGTGATGTGTCACCGTCCAGGAGGGCACAAGGAAGGTTGGGATGGTCGGA SerThrGlyLeuleHiSLeuhi SGlnASnleWalASpVal GlnTyrLeuTyr GlyVal 18 TGTCCACCGGCCTCATCCACCTCCACCAGAA CATTGTGGACGTGCAGTACTTGTACGGGG ACAGGGGCCGGAGTAGGTGGAGGTGGTCTTGTAACACCTGCACGTCATGAACATGCCCC GlySerSer I leAlaSerTrpAlaley STrpGluTyrVal Val Leuleupheleuleu 241. TGGGGTCAAGCATCGCGTCCTGGGCCATTAAGTGGGAGTACGTCGTTCTCCTGTTCCTTC ACCCCAGTTCGTAGCGCAGGACCCGGTAATTCACCCTCATGCAGCAAGAGGACAAGGAAG 301 TGCTTGCAGACGCGCGCGTCGCTCCTGCTTGTGGATGATGCTACTCATATCCCAAGCGG ACGAACGTCTGCGCGCGCAGAiii.6.32 CGAGGACGAACACCTACTACGATGAS&ESETEEEEEEEEEEEAS33 GTATAGGGTTCGCC Ala Ala Leu6 UASnLeuVal Ile Leu ASn Ala AlaserLeUAlaGlyThriSGlyLeu 36 AGGCGGCTTTGGAGAACCTCGTAATACTTAATGCAGCATCCCTGGCCGGGACGCACGGTC TCCGCCGAAACCTCTTGGAGCATATGAATTACGTCGTAGGGACCGGCCCTGCGTGCCAG Val SerPheteuVal PhepheCySPheAla TrpTyrLeuySGlyLySTrpVal PrOGly l2 TTGTATCCTTCCTCGTGTTCTTCTGCTTTGCATGGTATTTGAAGGGTAAGTGGGTGCCCG AACATAGGAAGGAGCACAAGAAGACGAAACGTACCATAAACTTCCCATTCACCCACGGGC AlaWalTyrThrPheTyrGlyMetTrpproLeueueueueue UAlaleuPrOGln GAGCGGCTA CACCTTCACGGGATGTGGCCTCTCCTCCTGCTCCTGTTGGCGTTGCCCC CTCGCCAGATGTGGAAGATGCCCTA CACCGGAGAGGAGGACGAGGACAACCGCAA CGGGG ArgAla Tyr Alaleu ASpThrGuVal Ala AlaSerCySGlyGlyVal Val LeuVal Gly 54 AGCGGGCGTACGCGCTGGACACGGAGGTGGCCGCGTCGTGTGGCGGGTTGTTCTCGTCG TCGCCCGCATGCGCGACCTGTGCCTCCACCGGCGCAGCACACCGCCACAACAAGAGCAGC LeuMetAlaleu ThreuSerProTyrTyrySArgTyrIleSerTrpCySLeuTrpTrp 60 GGTTGATGGCGCTGA CTCTGTCACCATATTACAAGCGCTATATCAGCTGGTGCTTGTGGT CCAACTACCGCGACTGAGACAGTGGTATAATGTTCGCGATATAGTCGACCACGAA CACCA eugny PheleuThAgyal GuAlagneuSValTipleRTOPQLeuSn 66 GGCTTCAGTATTTTCTGACCAGAGTGGAAGCGCAACTGCACGTGTGGATTCCCCCCCTCA CCGAA GTCATAAAAGACTGGTCTCACCTTCGCGTTGACGTGCACACCTAAGGGGGGGAGT Val ArgGlyGlyArgASpAlaWall I leLeueuMetCySA laVal His PrOThrLeuVal 721 ACGTCCGAGGGGGGCGCGACGCCGTCATCTTACTCATGTGTGCTGTACACCCGA CTCTGG TGCAGGCTCCCCCCGCGCTGCGGCAGTAGAATGAGTACACACGACATGTGGGCTGAGACC Phe-SpleThrySLeueuleu AlaVal PheGlyPOLeuTrpI leLeuGln AlaSer 781 TATTTGACATCACCAAATGCTGCTGGCCGTCTTCGGACCCCTTTGGATTCTTCAAGCCA ATAAACTGTAGTGGTTTAACGACGACCGGCAGAAGCCTGGGGAAACCTAAGAAGTTCGGT LeueuySVal PrOTyrPheVal ArgVal Gln Glyeuleu Arghe CyS Alaleu Ala GTTTGCTTAAAGTACCCTACTTTGTGCGCGTCCAAGGCCTTCTCCGGTTCTGCGCGTTAG CAAA CGAATTTCATGGGATGAAACACGCGCAGGTTCCGGAAGAGGCCAAGACGCGCAATC

U.S. Patent Sep. 7, 2010 Sheet 40 of 168 US 7,790,366 B1

FIG. 32F euleGuA l801 AGCTCATAGAGG CGAGTATCTCC SerGluASn ySWalValleleuSpSerP 486 AGTCAGAAAACA AAGTGGTGATTCTGGACTCCT TCGATCCGCTTGRE3 TCAGTCTTTTGT TTCACCACTA AGACCTGAGGA AGCTAGGCGAAC

SPOL euPrOPrOPrO SerPOPOVal PrO 50ll ACTACTKE TCCGCTTCCACCTCCAA 6 TCCCCTCCTGTGC TGATG AGGCG AAGGTGGAGGTTTC AGGGGAGGACACG

Glueu Alahr ArgSerPhe 56 CCGAGCTCGCCACCAGAAGCT GGCTCGAGCGGTGGTCTTCGAAA

522

5281 ATA T A SerThrWal SerSerGlu Ala ASn AlaGluASpVal Val CySCySSerMetSerTyrSer 53. GGCAACGGTCAGTAGTGAGGCCAACGCGGAGGATGTCGTGTGCTGCCAAGTCTTACT CCAGTTGCCA GTCATCA CTCCGGGCGCCTCCTACAGCACA CGACGAGTACAGAATGA

SHS A S neuVal T CCAC i GGTG AAACCACAT

552.

SG1 UVa L 5581 AGGACGTACTCA58: GGAGGTTA {5,338AGCAGCGGCG CAAAAGTGAAkiki TCCTGCATGAGTTCCCCTCCA AT CGTCGCCGC AGTTTCACTTCC Glu0 UAlaCySSerLeuThrProProHSSerA 561 TASSESSEESA ATCTCCTTCGAACGTCGGACTGCGGGGGTGTGAGTC

LeuleuGluASpASnWa Thrp rOI leASpThrT 576 ACCTTCTGGAAGACAATG T AACAC CAATAGACACTA TGGAAGACCTCTGTTAC A TTGTG GTTATCTGTGAT

U.S. Patent Sep. 7, 2010 Sheet 42 of 168 US 7,790,366 B1

FIG. 33 Sample Chimp date (dayS) ALT (alanine) Lane Reference Infection (Os in0Culation aminotransferase NUInber Number Type day) level in Sera) mL/ml) l l NANB O O 2 NANB 76 7. 3 l NANB 118 19 l l NANB 15l. N/A 5 2 NANB O O 6 2 NANB 21 52 7 2 NANB 73 13 8 2 NANB 158 N/A 9 3 NANB O 8 10 3 NANB 43 205 ll. 3 NANB 53 14 12 3 NANB 59 6 13 l NANB -3 1. 14 l NANB 55 132 15 l NANB 83 N/A 16 4 NANB 140 N/A 17 5 HAV O l 18 5 HAV 25 147 19 5 HAV O 18 20 5 HAV 268 5 21 6 HAV -8 N/A 22 6 HAV 15 100 23 6 HAV 41 O 24 6 HAV 129 N/A 26 7 HAV O 7 27 7 HAV 22 83 28 7 HAV 15 5 29 7 HAV 39 N/A 30 8 HAV O 15 31 8 HAV 26 130 32 8 HAV 74 8 33 8 HAV 205 5 34 9 HBW -290 N/A 35 9 HBV 379 9 36 9 HBV l35 6 37 O HBV O 8 38 10 HBV 111-118 (pool) 96-156 (pOOl) 39 10 HBW 205 9 40 10 HBV 240 13 41 11 HBV O ll 42 11 HBV 28-56 (pool) 8-100 (pOO) l3 11 HBV 169 9 44 11 HBV 223 10 U.S. Patent Sep. 7, 2010 Sheet 43 of 168 US 7,790,366 B1

FIG. 33A CHMPS ALT on N 9

CHMPS

HAV HAV HBV HBV U.S. Patent Sep. 7, 2010 Sheet 44 of 168 US 7,790,366 B1

Patient Lane Reference Number Number Diagnosis ALT Level ( ml) l ll NANB 1354 2 l NANB 31 3 21 NANB 14 4 21 NANB 79 5 21 NANB 26 6 31 NANB 78 7 31 NANB 87 8 31 NANB 25 9 l NANB 60 10 41 NANB 13 l 51 NANB 298 12 51 NANB 10. 13 6 NANB 474 l4 61 NANB 318 15 71 NANB 20 16 71 NANB 63 17 81 NANB 44 18 81 NANB 50 19 9 NANB N/A 20 10 NANB N/A 2. 11 NANB N/A 22 12 Normal N/A 23 13 Normal N/A 24 14 Normal N/A 26 3.074 Normal N/A 27 301.05 Normal N/A 28 300 72 Normal N/A 29 300 26 Normal N/A 30 3O46 Normal N/A 3. 30250 Normal N/A 32 30 (1 Normal N/A 33 5 AcuteHAW N/A 34 6 AcuteHAW N/A 35 17 AcuteHAW N/A 36 18 AcuteHAV N/A 37 48088 AcuteHAW N/A 38 47288 AcuteHAW N/A 39 47050 AcuteHAW N/A 40 46997 AcuteHAV N/A 41 19 Convalescent HBW N/A 42 20 (anti-HBSagh-ve; N/A 43 2. anti-HBCagtve) N/A 44 22 (anti-HBSagi-ve; N/A 45 23 anti-HBCagive) N/A 46 24 (anti-HBSagit-ve; N/A 47 25 anti-HBCagive) NAA 48 26 (anti-HBSagtive; NAA 49 27 anti-HBSagh-ve) N/A

Sequential serum samples were assayed from these patients U.S. Patent Sep. 7, 2010 Sheet 45 of 168 US 7,790,366 B1

U.S. Patent Sep. 7, 2010 Sheet 46 of 168 US 7,790,366 B1

Hind 373 Born 59

Sph I7O6 So 95

PSI 4753 ECOr 8260 PWI 4879

Pyl 7483 Ecor. 55.65 Hpo 7248 Hinds 5669 U.S. Patent Sep. 7, 2010 Sheet 47 of 168 US 7,790,366 B1

FIG. 36A

we a no SOD----COOH)--adaptor--- (NANBHpolypeptidex AlacySGGCTTGGGTGTAATGGGACGCCCAGAATTTGGGAATCGGGATGCCCACTTTCTATCC ; SEAE8ASSEEKE, Allahi SPheleuSer CGAACACCACATTAACCCTAGCGGGTCTTAAACCCTTAAGCCCTACGGGTGAAAGATAGG XXX XXXXXXXX XXX XXX XXXX GlnThrySGlnSerGlyGluASnLeuPrOTyreuVal Alayrgl nAlaThrVal CyS 6. CAGA CAAAGCAGAGTGGGGAGAA CCTCCTTACCTGGTAGCGTACCAAGCCACCGTGTGC GTCTGTTTCGTCTCACCCCTCTTGGAAGGAATGGACCATCGCATGGTTCGGTGGCACACG Ala ArgAlaGlin AlaproProProSerTrpASp0 nMetTrpLySCySLeuleArgeu 12 GCTAGGGCTCAAGCCCCTCCCCCACGTGGGACCAGATGTGGAAGTGTTTGATTCGCCTC CGATCCCGAGTTCGGGGAGGGGGTAGCACCCTGGTCTACACCTTCACAAACTAAGCGGAG LySPOThreuSGlyPOThrPrOLeueuTyrArgeu6ly AlaVal Glin ASnGlu 18 AAGCCCACCCTCCATGGGCCAA CACCCCGCTATACAGACTGGGCGCTGTTCAGAATGAA TTCGGGTGGGAGGTACCCGGTTGTGGGGACGATATGTCTGACCCGCGACAAGTCTTACTT IleThreuThrHis ProVal ThrySTyr I leMetThrCySMetSer Ala AspleuGlu 2ll ATCACCCTGACGCACCCAGTCACCAAATACATCATGACATGCATGTCGGCCGACCTGGAG TAGTGGGACTGCGTGGGTCAGTGGTTTATGTAGTACTGTACGTACAGCCGGCTGGACCTC Wal Wa ThrSerThrTrpValeuVal GlyGyWaleUAla Alaleula Ala TyrCyS 301 GTCGTCACGAGCACCTGGGGCTCGTTGGCGGCGTCCTGGCTGCTTTGGCCGCGTATTGC CAGCAGTGCTCGGGACCCA CGAGCAACCGCCGCAGGACCGA CGAA ACCGGCGCATAACG LeuSerThrGly CySWal WalleWalGlyArgVal Val LeuSerGlyLySPOAlale 361 CTGTCAA CAGGCTGCGTGGTCATAGGGGCAGGGTCGTCTTGTCCGGGAAGCCGGCAATC GACAGTTGTCCGA CGCACCAGTATCACCCGTCCCAGCAGAA CAGGCCCTTCGGCCGTTAG IlePro ASDArgGluVal LeuTyrArg(GUPheASpG UMetGluGUCySSerGin His l2 ATACCTGACAGGGAAGTCCTCTACCGAGAGTCGATGAGATGGAAGAGTGCTCTCAGCAC TATGGACTGTCCCTTCAGGAGATGGCTCCAAGCACTCTACCTCTCACGAGAGCGTG 8 TTACCGTACATCGAGCAAGGGATGATGCTCGCCGAGCAGTCAAGCAGAAGGCCCTCGGCKEETXEEEEEEEEEEEEEEEEEEEEKSEE. SAlaleugly AATGGCATGTAGCTCGTTCCCTACTACGAGCGGCTCGTCAAGTTCGTCTTCCGGGAGCCG Leue Gin Thr Ala Ser Argen Ala6 UVa I leAaPrOAlaVal GlnThrASnTrp 541. CTCCTGCAGACCGCGTCCCGTCAGGCAGAGGTTACGCCCCTGCTGTCCAGACCAACTGG GAGGACGTCTGGCGCAGGGCAGCCGTCCCAATAGCGGGGA CGACAGGTCTGGTTGACC GlnySLeuGUThrPherpAlaySHiSMetTrpASnPhelleSerGlyleGny 60 CAAAAACTCGAGA CCTTCTGGGCGAAGCAATGTGGAACTTCATCAGTGGGATACAATAC GTTTTTGAGCTCTGGAAGACCCGCTCGATACACCTTGAAGTAGTCACCCTATGTTATG Leu AlaGlyLeuSerThrLeuPrOGlyASnPro AlaleAlaSerLeuMetAlapheThr 66 TTGGCGGGCTTGTCAA CGCTGCCTGGTAACCCCGCCATTGCTCATTGATGGCTTTTACA AACCGCCCGAACA GTTGCGACGGACCAGGGGCGGTAACGAAGTAACTACCGAAAATGT Ala AlaWalThrSerProLeu ThrThrSerGlnThreuleuPheASn I leLeuGlyGy 721 GCTGCTGTCACCAGCCCACTAACCACTAGCCAAACCCTCCTCTCAA CATATTGGGGGGG CGA CGACAGTGGTCGGGTGATTGGTGACGGTTTGGGAGGAGAAGTTGTATAACCCCCCC TrpVal Ala AlaGlnLeula.AlaproGlyAlaAlaThr AlapheVal GlyAlaGlyeu 781 TGGGTGGCTGCCCAGCTCGCCGCCCCCGGTGCCGCTACTGCCTTTGTGGGCGCTGGCTTA ACCCACCGACGGGTCGAGCGGCGGGGGCCACGGCGATGACGGAAACACCCGCGACCGAAT U.S. Patent Sep. 7, 2010 Sheet 48 of 168 US 7,790,366 B1

FIG. 36B AlaGlyAla AlaleGySerWalGlyleu6ly ySWalleul leASpleLeuAlaGly 841 GCGGCGCCGCCATCGGCAGTGTTGGACTGGGGAAGGTCCCATAGACATCCTTGCAGGG CGACCGCGGCGGTAGCCGTCACAACCTGACCCCTTCCAGGAGTATCTGTAGGAACGTCCC TyrGlyAlaGlyVal AlaGly AlaleuVal AlapheySI leMetSerGlyGluVal Pro 90. TATGGCGCGGGCGTGGCGGGAGCCTTGTGGCATCAAGATCATGAGCGGTGAGGTCCCC ATACCGCGCCCGCACCGCCCTCGAGAACACCGTAAGTTCTAGTACTCGCCACCCAGGGG SerThrGluASpeuVal ASnLeuleuPrOAla I leLeuSerPrOGlyAlaleuVal Val 961 CCACGGAGGACCTGGTCAATCTACTGCCCGCCATCCTCTCGCCCGGAGCCCTCGTAGTC AGGGCCCCTGGACCAGTTAGATGACGGGCGGTAGGAGAGCGGGCCTCGGGAGCATCAG GlyVal Val CySA la Ala I leLeuArgArgHis Val GlyPOGlyGluGlyAaVal Gln 1021 GGCGTGGTCTGTGCAGCAATACTGCGCCGGCACGTGGCCCGGGCGAGGGGGCAGTGCAG CCGCACCAGACACGTCGTTATGACGCGGCCGTGCAA CCGGGCCCGCTCCCCCGTCACGC ggggggggggggggggggggNANBH) ---extra pMetASn Argeu leAla PheA aSerArgGlyASn HiSWal SerPro Wal HiSHS 1081 TGGATGAACCGGCTGATAGCCTTCGCCTCCCGGGGGAACCATGTTTCCCCAGCCATCAT ACCTACTTGGCCGACTATCGGAAGCGGAGGGCCCCCTTGGTACAAAGGGGTCAGGTA GTA

taal to 1141 RiefftySArgOP ACGCTCCCTACGGGTGGACTGTGGAGAGACAGGGCACTGCTAAGGCCCAAAT TTCGCAACTGCGAGGGATGCCCACCTGACACCTCTCTGCCCGTGACGATTCCGGGTTTA 120 CTCAGCCATGCATCGAGGGGTACAATCCGTATGGCCAACAACTAGCGCGTACGTAAAGTC GAGTCGGTACGTAGCTCCCCATGTTAGGCATACCGGTTGTTGATCGCGCATGCATTTCAG 1261 TCCTTCTCGATGGTCCATACCTTAGATGCGTTAGCATTAATCCGAATTC AGGAAAGAGCACCAGGTATGGAATCTACGCAATCGTAATTAGGCTTAAG U.S. Patent Sep. 7, 2010 Sheet 49 of 168 US 7,790,366 B1

U.S. Patent Sep. 7, 2010 Sheet 50 of 168 US 7,790,366 B1

FG. 38

U.S. Patent Sep. 7, 2010 Sheet 51 of 168 US 7,790,366 B1

FIG 39

U.S. Patent Sep. 7, 2010 Sheet 52 of 168 US 7,790,366 B1 FG. 4. A

U.S. Patent Sep. 7, 2010 Sheet 55 of 168 US 7,790,366 B1

FIG. 43

2OO

O 2 3 4 5 6 789 .O .5 X3.O OD G 492nm.

F.G. 44 637 OMOAB = O56 Poly = O77 3OO 3 25O 2 n 15 O

O In , O 1 2 3 4 5 ,6 7 8 9 .O X3,O OD Q 492nm. U.S. Patent Sep. 7, 2010 Sheet 56 of 168 US 7,790,366 B1

FIG. 45 Name Common Sequence Variable Sequence 5'-3- AAGCTTGATCGAATTC CGATCTTGC -2 CGATCCTGC -3 CGATCATGC - 4 CGATCGTGC -5 CGAAGTTGC -6 CGAAGCTGC - 7 AGATCTTGC -8 AGATCCTGC -9 AGATCATGC - 10 AGATCGTGC -l AGAAGTTGC - 2 AGAAGCTGC -3 CGATCTTGT -14 CGATCCTGT - 5 CGATCATGT -16 CGATCGTGT - 7 CGAAGTTGT - 8 CGAAGCTGT - 9 AGATCTTGT -20 AGATCCTGT -2 AGATCATG -22 AGATCGTGT -23 AGAAGGT -24 AGAAGCTGT -25 CGCTCTIGC -26 CGCTCCTGC -27 CGCTCATGC -28 CGCTCGTGC -29 CGCAGTTGC -30 CGCAGCTGC -3 CGCTCTTG -32 CGCTCCTGT -33 CGCTCATGT -34 CGCTCGTGT -35 CGCAGTTGT -36 CGCAGCTGT

U.S. Patent Sep. 7, 2010 Sheet 62 of 168 US 7,790,366 B1

FIG. 47B PhepheCySPhela TrpT 6. ISS 9 ACAAGAAGACGAAACGTACCA U

r

InMetTyrThrASnVrThrASnWall ASpGlnASp& LeuVal Gly 1921 TCGC EH ACCAATGCCAAT i88. ACCTTGTGG

U.S. Patent Sep. 7, 2010 Sheet 64 of 168 US 7,790,366 B1

FIG. 47D Wall 3001 CGGTGA T GCCAC A

U.S. Patent Sep. 7, 2010 Sheet 68 of 168 US 7,790,366 B1

D c m ut CDocs al-e eco (U CCH CU) DCDU GHe OHe r-cod --99 LHe Udos CUU) H ed -UCD Loud cris Caac H-Hoc CUCD H-HaC led D UCD CDUp CC) Utd pree care e HaH -acces CHC ---> Cod SUCO Me de H is re-cH- c)H- c. etc. each- UOCod luso misco CoC) MDC). OCH H He at Duos -99 C-Udd Uco UHe ever OcCH- Oc- YH. c. CeCH lucid r-Head (McCH - c AL) - are eco) cousco He --Udd do co-ed H Coas set did Had Mosco OUDU) s CDUP re- UDU r- Up -- st ge se- teco) den OCH cuts CDX OcCH could r- U - CH -9 ce ed) could also ce OUPU) DeCH 0-cC ra) could re- -Up co) H-He coco U Do - CH CUU He loss H CUUP CJHe CDH a ce Hech- Ugo UCD duo O le CDU ?-pa r-cCH. CUU - e H. (Voc coded rare could as Udu) OUd CU) Co DH-e DUP -UP Mean c)He (c) ClsoAS 292 SS2S2Codd -CaCH 2p risco ridco DU L-99 acco) CCC) acCH Udo (See CH-ed custo succH ridd (p OHe r-cdco r-e- ecos ?acred edus cools OsCar -- d be ces UDU Glored re-c r-He as He sea- - eHe p-a- co) (9) Hoe --> r-Up re-He co-ed cloudco eccio U b-ders ()o CMH at CUD CUs. He r-Udd UUP CHC re-Hee CSH e DeHe N UUd HCCH- DOU) -- C O)o CU) ls usco V Quo eccetag Oscheis UseS5ts o U Hne to CD Up (PC) He UCO H H re CO Sir O Ud O ym CN CN N N N N U.S. Patent Sep. 7, 2010 Sheet 69 of 168 US 7,790,366 B1

U.S. Patent Sep. 7, 2010 Sheet 75 of 168 US 7,790,366 B1

F.G. 54A ArgSer ArgASnLeuGlyLySWall I leASpThreuth CySGlyPhela ASpeuMet AGGTCGCGCAATTTGGGTAAGGTCATCGATACCCTTACGTGCGGCTTCGCCGACCTCATG CCAGCGCGTTAAACCCATTCCAGTAGCTATGGGAATGCACGCCGAAGCGGCTGGAGTAC GlyTyr I leProLeuVal Gly AlaproLeu6 yGlyAla Ala Arg Alaleu Alahi SGly 6. GGGTACATACCGCTCGTCGGCGCCCCTCTTGGAGGCGCTGCCAGGGCCCTGGCGCATGGC CCCATGTATGGCGAGCAGCCGCGGGGAGAA CCTCCGCGACGGTCCCGGGACCGCGTACCG Val ArgWall Leu6 UASpGlyVal ASny Alafhr6ly ASneuPrOGlyCy SSerPhe 12 GTCCGGGTTCTGGAAGACGGCGTGAACTATGCA ACAGGGAACCTTCCTGGTTGCTCTTC CAGGCCCAAGACCTTCTGCCGCACTTGATACGTTGTCCCTTGGAAGGACCAA CGAGAAAG Serle Pheleuleu AlaleuleuSerCySLeuThrVal PrOAlaSerAlaTyrGlnWall 181 TCTATCTTCCTTCTGGCCCTGCTCTCTTGCTTGACTGGCCCGCTCGGCCTACCAAGG AGAAGAAGGAAGACCGGGA CGAGAGAA CGAACTGACACGGGCGAAGCCGGATGGTTCAC 241 (EEASEEEEEEEEEEEEEEAS35&ECASEESTKECGCAA CTCCACGGGGCTTACCACGTCACCAATGATTGCCCAA CTCGAGTATTGTGTAC GCGTTGAGGTGCCCCGAAAGGGCAGTGGTTACTAACGGGATTGAGCTCATAACACATG Glu Ala Ala ASpAlaleleuhi SThrPrOGlyCySVal PrOCyS Val ArgG1 UGlyASn 301 GAggggg.TGCCATCCGCACACCCGGGGGCGTCCCTTGCGTCGTGAGGGCAA CTCCGCCGGCTACGGTAGGACGTGTGAGGCCCCACGCAGGGAACGCAAGCACTCCCGTTG AlaSerArgCySTrpVal AlaMetThrPrOThrVal Alahr ArgASpGlyLySLeuPro 36 GCCTCGAGGTGTTGGGTGGCGATGACCCCTACGGTGGCCACCAGGGATGGCAAACTCCCC CGGAGCTCCACAACCCACCGCTACTGGGGATGCCACCGGTGGCCCTACCGTTTGAGGGG Ala Thr61 in LeurgArgHiSI leASpLeueuVal GlySer Alathrieucy SSer Ala 421. GCGACGCAGCTTCGACGTCACATCGATCTGCTTGTCGGGAGCGCCACCCTCTGTTCGGCC CGCTGCGTCGAAGCTGCAGTGTAGCTAGACGAA CAGCCCTCGCGGTGGGAGACAAGCCGG euTyrWalGlyASpeucy SGlySerWalPheleuVal GlyG neuPheh PheSer 81 CTCTACGTGGGGGACCTATGCGGGTCTGTCTCTTGTCGGCCAA CTGTTCACCTTCCT GAGATGCACCCCCTGGATACGCCCAGACAGAAAGAACAGCCGGTTGACAAGTGGAAGAGACC PrOArgArgHSTrphrThr61 nGlyCySASnCySSereyr PrOGlyhis eThr 541 CCCAGGCGCCACTGGACGACGCAAGGTTGCAATTGCCTATCTATCCCGGCCATATAACGTGG GGGTCCGCGGTGG ACC T GCTCCGTCCAA CGTTAACGAGATAGATAGGGCCGGTATATTGC Met Ala T r 601 GGGyi CA CCGCATGGCATA GCA SSSI855. ATGATGATGAACTGGTCCCCTACGA EASTEEEEEEEEEEEa. CGGCGTGGTAATG CCAGT GGCGTACCGTAT CGTACCCTATACTACTACTTGACCAGGGGATGCTGCCGCAACCATTAC

U.S. Patent Sep. 7, 2010 Sheet 83 of 168 US 7,790,366 B1

FIG. 54 GlyTyr ArgA rg Cy y e U ThrThrSer Cy SG l y SnThreuThr 774. GGCTATCGCAGG TG C T G ACAACTAGCTG TG G T ACACCCTCACT CCGATAGCGT CC AC G A C TGTTGATCGAC AC C A TGTGGGAGTGA CySTyr Iley S Al S l 3. A laGlyLeuGl nA S D ySThrMetL 7801 TGCTA CATCAAG GC T C C G CAGGGCTCCA GG A C GCACCATG ACGATGTAGTTC CG A G G C GTCCCGAGGT CC T G CGTGGTA Val CySGlyASp AS e l U S er AlaGlyW 8.G l luASpA 786l GTGTGGGCGAC GA C A A A GCGCGGGG G TCCAGCC A GGAC CACACACCGCTG CT G TT T C C AGGTCGG T C C T Ph t C T y r P rOPrOOP r 7921 TT G G T A C C CCCCTCC C AA C C A T G G GGGGAGG G AS e C y S A S nV 8 l 7981 GA AACATCAT G C C TCCAA CG T G CAG CT TTGTAGTA C G G AGGTTGCACAGTCA Ly r Leuhr A r O 80l. AA CCTCACCC G T EEEEEEEEEECCTACAACCCCCCT GGAGGGG C A G GGATGTTGGGGGGAG li pGluThr Al r rOVal ASnSerTrpLeu6lyn ASnIle I 8101 GC i GGGAGACAGCAAG T CAGTCAATTCCTGGCTAGGCAACATAAT CGA CCCTCTGTCGTTCTGT A GGTCAGTTAAGGACCGATCCGTTGTATTAG Phe rOThreuTripAlaArgM t I eleuMetThrHisPhepheServal Leul 8161 TTT CCACA CTGTGGGCGAGGATGATACTGATGACCCATTTCTTTAGCGTCCTTATAA AAA GGTGTGACACCCGCTCCTACTATGACTACTGGGTAAAGAAATCGCAGGAATAT Ala SpGinleuGluGln Alaleu ASpCysGlu I leTyrGlyAlaCySTyrSer I lee:Rs 8221 GCC CCAGCTTGAACAGGCCCTCGATTGCGAGATCTACGGGGCCTGCTA CTCCATA CGG GGTCGAACTTGTCCGGGAGCTAACGCTCTAGATGCCCCGGACGATGAGGTATAG Glu UASpeuPrOPrOIle I le ln Argeu 8281 GAA TGATCTACCTCCAATCA TT AAAGA CTC CTT : ACTAGATGGAGGTTAGT AA TTTCTGAG U.S. Patent Sep. 7, 2010 Sheet 84 of 168 US 7,790,366 B1 Hvri----- FIG. 55A (I-5OO) WN ------rm re- ns ( - 5OO) -->

FIG. 55B (5Ot-IOOO) WN tri-ro-- nS2 --> (5O-OOO)

FIG. 55C (iOO-5OO) WN ------nS3 (OO-5OO) ---- Tri------F.G. 55D ------(5O-2OOO) nS4 she (5O-2OOO)

F.G. 55E (2OC - 25OO) ------ns5 (2OO-25OO)E.