WO1999045954A1 - Hla-binding peptides and their uses - Google Patents

Hla-binding peptides and their uses Download PDF

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WO1999045954A1
WO1999045954A1 PCT/US1998/005039 US9805039W WO9945954A1 WO 1999045954 A1 WO1999045954 A1 WO 1999045954A1 US 9805039 W US9805039 W US 9805039W WO 9945954 A1 WO9945954 A1 WO 9945954A1
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hbv
peptide
pol
hiv
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PCT/US1998/005039
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Alessandro Sette
Ralph T. Kubo
John Sidney
Esteban Celis
Howard M. Grey
Scott Southwood
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Epimmune, Inc.
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    • CCHEMISTRY; METALLURGY
    • C07ORGANIC CHEMISTRY
    • C07KPEPTIDES
    • C07K14/00Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/195Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria
    • C07K14/36Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria from Actinomyces; from Streptomyces (G)
    • CCHEMISTRY; METALLURGY
    • C07ORGANIC CHEMISTRY
    • C07KPEPTIDES
    • C07K2317/00Immunoglobulins specific features
    • C07K2317/10Immunoglobulins specific features characterized by their source of isolation or production
    • CCHEMISTRY; METALLURGY
    • C07ORGANIC CHEMISTRY
    • C07KPEPTIDES
    • C07K2319/00Fusion polypeptide

Abstract

The present invention provides the means and methods for selecting immunogenic peptides and the immunogenic peptide compositions capable of specifically binding glycoproteins encoded by HLA allele and inducing T cell activation in T cells restricted by the allele. The peptides are useful to elicit an immune response against a desired antigen.

Description

HLA BINDING PEPTIDES AND THEIR USES

BACKGROUND OF THE INVENTION

The present invention relates to compositions and methods for preventing, treating or diagnosing a number of pathological states such as viral diseases and cancers. In particular, it provides novel peptides capable of binding selected major histocompatibility complex (MHC) molecules and inducing an immune response.

MHC molecules are classified as either Class I or Class II molecules. Class II MHC molecules are expressed primarily on cells involved in initiating and sustaining immune responses, such as T lymphocytes, B lymphocytes, macrophages, etc. Class II MHC molecules are recognized by helper T lymphocytes and induce proliferation of helper T lymphocytes and amplification of the immune response to the particular immunogenic peptide that is displayed. Class I MHC molecules are expressed on almost all nucleated cells and are recognized by cytotoxic T lymphocytes (CTLs), which then destroy the antigen-bearing cells. CTLs are particularly important in tumor rejection and in fighting viral infections.

The CTL recognizes the antigen in the form of a peptide fragment bound to the MHC class I molecules rather than the intact foreign antigen itself. The antigen must normally be endogenously synthesized by the cell, and a portion of the protein antigen is degraded into small peptide fragments in the cytoplasm. Some of these small peptides translocate into a pre-Golgi compartment and interact with class I heavy chains to facilitate proper folding and association with the subunit β2 microglobulin. The peptide-MHC class I complex is then routed to the cell surface for expression and potential recognition by specific CTLs.

Investigations of the crystal structure of the human MHC class I molecule, HLA-A2.1 , indicate that a peptide binding groove is created by the folding of the αl and α2 domains of the class I heavy chain (Bjorkman et al. , Nature 329:506 ( 1987). In these investigations, however, the identity of peptides bound to the groove was not determined.

Buus et al. , Science 242: 1065 (1988) first described a method for acid elution of bound peptides from MHC. Subsequently, Rammensee and his coworkers (Falk 2 et al. , Nature 351 :290 (1991) have developed an approach to characterize naturally processed peptides bound to class I molecules. Other investigators have successfully achieved direct amino acid sequencing of the more abundant peptides in various HPLC fractions by conventional automated sequencing of peptides eluted from class I molecules of the B type (Jardetzky, et al. , Nature 353:326 (1991) and of the A2.1 type by mass spectrometry (Hunt, et al., Science 225: 1261 (1992). A review of the characterization of naturally processed peptides in MHC Class I has been presented by Rδtzschke and Falk (Rόtzschke and Falk, Immunol. Today 12:447 (1991).

Sette et al. , Proc. Natl. Acad. Sci. USA 86:3296 (1989) showed that MHC allele specific motifs could be used to predict MHC binding capacity. Schaeffer et al. ,

Proc. Natl. Acad. Sci. USA 86:4649 (1989) showed that MHC binding was related to immunogenicity . Several authors (De Bruijn et al. , Eur. J. Immunol.. 21:2963-2970 (1991); Pamer et al. , 991 Nature 353:852-955 (1991)) have provided preliminary evidence that class I binding motifs can be applied to the identification of potential immunogenic peptides in animal models. Class I motifs specific for a number of human alleles of a given class I isotype have yet to be described. It is desirable that the combined frequencies of these different alleles should be high enough to cover a large fraction or perhaps the majority of the human outbred population.

Despite the developments in the art, the prior art has yet to provide a useful human peptide-based vaccine or therapeutic agent based on this work. The present invention provides these and other advantages.

SUMMARY OF THE INVENTION The present invention provides compositions comprising immunogenic peptides having binding motifs for HLA molecules. The immunogenic peptides, which bind to the appropriate MHC allele, comprise conserved residues at certain positions which allow the peptides to bind desired HLA molecules.

Epitopes on a number of immunogenic target proteins can be identified using the peptides of the invention. Examples of suitable antigens include prostate cancer specific antigen (PSA), hepatitis B core and surface antigens (HBVc, HBVs) hepatitis C antigens, Epstein-Barr virus antigens, human immunodeficiency type-1 virus (HIV1),

Kaposi's sarcoma herpes virus (KSHV), human papilloma virus (HPV) antigens, Lassa virus, mycobacterium tuberculosis (MT), p53, CEA, trypanosome surface antigen (TSA) and Her2/neu. The peptides are thus useful in pharmaceutical compositions for both therapeutic and diagnostic applications.

In particular, the invention provides compositions comprising an immunogenic peptide having an HLA binding motif, which immunogenic peptide is a peptide shown in Tables 3-14. Also provided are peptides comprising a conservative substitution of a residue in a peptide shown in Table 3-14. The immunogenic peptide of the invention can be further linked to a second oligopeptide. In some embodiments, the second oligopeptide is a peptide that induces a helper T response. The invention further provides nucleic acid molecules encoding immunogenic peptides as shown in Tables 3-14, or peptides comprising a conservative substitution of a residue of a peptide shown in Table 3-14. The nucleic acid may further comprise a sequence encoding a second immunogenic peptide or peptide that induces a helper T response. The peptides provided here can be used to induce a cytotoxic T cell response either in vivo or in vitro. The methods comprise contacting a cytotoxic T cell with a peptide of the invention.

Definitions The term "peptide" is used interchangeably with "oligopeptide" in the present specification to designate a series of residues, typically L- amino acids, connected one to the other typically by peptide bonds between the alpha-amino and carbonyl groups of adjacent amino acids. The oligopeptides of the invention are less than about 15 residues in length and usually consist of between about 8 and about 11 residues, preferably 9 or 10 residues. An "immunogenic peptide" is a peptide which comprises an allele-specific motif such that the peptide will bind an MHC molecule and induce a CTL response. Immunogenic peptides of the invention are capable of binding to an appropriate HLA molecule and inducing a cytotoxic T cell response against the antigen from which the immunogenic peptide is derived. Immunogenic peptides are conveniently identified using the algorithms of the invention. The algorithms are mathematical procedures that produce a score which 4 enables the selection of immunogenic peptides. Typically one uses the algorithmic score with a "binding threshold" to enable selection of peptides that have a high probability of binding at a certain affinity and will in turn be immunogenic. The algorithm is based upon either the effects on MHC binding of a particular amino acid at a particular position of a peptide or the effects on binding of a particular substitution in a motif containing peptide.

A "conserved residue" is an amino acid which occurs in a significantly higher frequency than would be expected by random distribution at a particular position in a peptide. Typically a conserved residue is one where the MHC structure may provide a contact point with the immunogenic peptide. At least one to three or more, preferably two, conserved residues within a peptide of defined length defines a motif for an immunogenic peptide. These residues are typically in close contact with the peptide binding groove, with their side chains buried in specific pockets of the groove itself. Typically, an immunogenic peptide will comprise up to three conserved residues, more usually two conserved residues. As used herein, "negative binding residues" are amino acids which if present at certain positions will result in a peptide being a nonbinder or poor binder and in turn fail to be immunogenic i.e. induce a CTL response.

The term "motif" refers to the pattern of residues in a peptide of defined length, usually about 8 to about 11 amino acids, which is recognized by a particular MHC allele. The peptide motifs are typically different for each human MHC allele and differ in the pattern of the highly conserved residues and negative residues.

The binding motif for an allele can be defined with increasing degrees of precision. In one case, all of the conserved residues are present in the correct positions in a peptide and there are no negative residues in positions 1,3 and/or 7. The phrases "isolated" or "biologically pure" refer to material which is substantially or essentially free from components which normally accompany it as found in its native state. Thus, the peptides of this invention do not contain materials normally associated with their in situ environment, e.g. , MHC I molecules on antigen presenting cells. Even where a protein has been isolated to a homogenous or dominant band, there are trace contaminants in the range of 5-10% of native protein which co-purify with the desired protein. Isolated peptides of this invention do not contain such endogenous co- purified protein. 5

The term "residue" refers to an amino acid or amino acid mimetic incorporated in an oligopeptide by an amide bond or amide bond mimetic.

DESCRIPTION OF THE PREFERRED EMBODIMENTS The present invention relates to the determination of allele-specific peptide motifs for human Class I MHC (sometimes referred to as HLA) allele subtypes, in particular, peptide motifs recognized by HLA alleles.

For HLA-A2.1 alleles a peptide of 9 amino acids preferrably has the following motif: a first conserved residue at the second position from the N-terminus selected from the group consisting of I, V, A and T and a second conserved residue at the C-terminal position selected from the group consisting of V, L, I, A and M. An alternate motif is one in which the first conserved residue at the second position from the N- terminus selected is from the group consisting of L, M, I, V, A and T and the second conserved residue at the C-terminal position selected from the group consisting of A and M . The amino acid at position 1 is preferrably not an amino acid selected from the group consisting of D, and P. The amino acid at position 3 from the N-terminus is not an amino acid selected from the group consisting of D, E, R, K and H. The amino acid at position 6 from the N-terminus is not an amino acid selected from the group consisting of R, K and H . The amino acid at at position 7 from the N-terminus is not an amino acid selected from the group consisting of R, K, H, D and E. The HLA-A2.1 binding motif for peptide of 10 residues is as follows: a first conserved residue at the second position from the N-terminus selected from the group consisting of L, M, I, V, A, and T, and a second conserved residue at the C-terminal position selected from the group consisting of V, I, L, A and M. The first and second conserved residues are separated by 7 residues. Preferrably, the amino acid at position 1 is not an amino acid selected from the group consisting of D, E and P. The N-terminal residue is not an amino acid selected from the group consisting of D and E. The residue at position 4 from the N-terminus is not an amino acid selected from the group consisting of A, K, R and H. The amino acid at positon 5 from the N-terminus is not P. The amino acid at position 7 from the N-terminus is not an amino acid selected from the group consisting of R, K .and H. The amino acid at position 8 from the N-terminus is not amino acid selected from the group consisting of D, E, R, K and H. The amino acid at position 6

9 from the N-terminus is not an amino acid selected from the group consisting of R, K and

H.

Te motif for HLA-A3.2 comprises from the N-terminus to C-terminus a first conserved residue of L, M, I, V, S, A, T and F at position 2 and a second conserved residue of K, R or Y at the C-terminal end. Other first conserved residues are C, G or D and alternatively E. Other second conserved residues are H or F. The first and second conserved residues are preferably separated by 6 to 7 residues.

The motif for HLA-A1 comprises from the N-terminus to the C-terminus a first conserved residue of T, S or M, a second conserved residue of D or E, and a third conserved residue of Y. Other second conserved residues are A, S or T. The first and second conserved residues are adjacent and are preferably separated from the third conserved residue by 6 to 7 residues. A second motif consists of a first conserved residue of E or D and a second conserved residue of Y where the first and second conserved residues are separated by 5 to 6 residues. The motif for HLA-A11 comprises from the N-terminus to the C-terminus a first conserved residue of T, V, M, L, I, S, A, G, N, C D, or F at position 2 and a C- terminal conserved residue of K, R, Y or H. The first and second conserved residues are preferably separated by 6 or 7 residues.

The motif for HLA-A24.1 comprises from the N-terminus to the C-terminus a first conserved residue of Y, F or W at position 2 and a C terminal conserved residue of

F, I, W, M or L. The first and second conserved residues are preferably separated by 6 to

7 residues.

These motifs are then used to define T cell epitopes from any desired antigen, particularly those associated with human viral diseases, cancers or autoiummune diseases, for which the amino acid sequence of the potential antigen or autoantigen targets is known.

Epitopes on a number of potential target proteins can be identified in this manner. Examples of suitable antigens include prostate specific antigen (PSA), hepatitis B core and surface antigens (HBVc, HBVs) hepatitis C antigens, Epstein-Barr virus antigens, melanoma antigens (e.g., MAGE-1), human immunodeficiency virus (HIV) antigens, human papilloma virus (HPV) antigens, Lassa virus, mycobacterium tuberculosis (MT), p53, CEA, trypanosome surface antigen (TSA) and Her2/neu. 7

Peptides comprising the epitopes from these antigens are synthesized and then tested for their ability to bind to the appropriate MHC molecules in assays using, for example, purified class I molecules and radioiodonated peptides and/or cells expressing empty class I molecules by, for instance, immunofluorescent staining and flow microfluorometry, peptide-dependent class I assembly assays, and inhibition of CTL recognition by peptide competition. Those peptides that bind to the class I molecule are further evaluated for their ability to serve as targets for CTLs derived from infected or immunized individuals, as well as for their capacity to induce primary in vitro or in vivo CTL responses that can give rise to CTL populations capable of reacting with virally infected target cells or tumor cells as potential therapeutic agents.

The MHC class I antigens are encoded by the HLA-A, B, and C loci. HLA-A and B antigens are expressed at the cell surface at approximately equal densities, whereas the expression of HLA-C is significantly lower (perhaps as much as 10-fold lower). Each of these loci have a number of alleles. The peptide binding motifs of the invention are relatively specific for each allelic subtype.

For peptide-based vaccines, the peptides of the present invention preferably comprise a motif recognized by an MHC I molecule having a wide distribution in the human population. Since the MHC alleles occur at different frequencies within different ethnic groups and races, the choice of target MHC allele may depend upon the target population. Table 1 shows the frequency of various alleles at the HLA-A locus products among different races. For instance, the majority of the Caucasoid population can be covered by peptides which bind to four HLA-A allele subtypes, specifically HLA-A2.1 , Al, A3.2, and A24.1. Similarly, the majority of the Asian population is encompassed with the addition of peptides binding to a fifth allele HLA- A 11.2.

TABLE 1

A Allele/Subtvpe N(69)* A(54) C(502)

Al 10.1(7) 1.8(1) 27.4(138)

A2.1 11.5(8) 37.0(20) 39.8(199)

A2.2 10.1(7) 0 3.3(17)

A2.3 1.4(1) 5.5(3) 0.8(4)

A2.4 - - -

A2.5 - - -

A3.1 1.4(1) 0 0.2(0)

A3.2 5.7(4) 5.5(3) 21.5(108)

Al l . l 0 5.5(3) 0

A11.2 5.7(4) 31.4(17) 8.7(44)

Al l .3 0 3.7(2) 0

A23 4.3(3) - 3.9(20)

A24 2.9(2) 27.7(15) 15.3(77)

A24.2 - - -

A24.3 - - -

A25 1.4(1) - 6.9(35)

A26.1 4.3(3) 9.2(5) 5.9(30)

A26.2 7.2(5) - 1.0(5)

A26V - 3.7(2) -

A28.1 10.1(7) - 1.6(8)

A28.2 1.4(1) - 7.5(38)

A29.1 1.4(1) - 1.4(7)

A29.2 10.1(7) 1.8(1) 5.3(27)

A30.1 8.6(6) - 4.9(25)

A30.2 1.4(1) - 0.2(1)

A30.3 7.2(5) - 3.9(20)

A31 4.3(3) 7.4(4) 6.9(35)

A32 2.8(2) - 7.1(36)

Aw33.1 8.6(6) - 2.5(13)

Aw33.2 2.8(2) 16.6(9) 1.2(6)

Aw34.1 1.4(1) - -

Aw34.2 14.5(10) - 0.8(4)

Aw36 5.9(4) - -

Figure imgf000010_0001
Table compiled from B. DuPont, Jmi nunobiologv of HLA. Vol. I, Histocompatibilil

Testing 1987, Springer-Verlag, New York 1989.

N - negroid; A = Asian; C = caucasoid. Numbers in parenthesis represent the number of individuals included in the analysis.

The nomenclature used to describe peptide compounds follows the conventional practice wherein the amino group is presented to the left (the N-terminus) 9 and the carboxyl group to the right (the C-terminus) of each amino acid residue. In the formulae representing selected specific embodiments of the present invention, the amino- and carboxyl-terminal groups, although not specifically shown, are in the form they would assume at physiologic pH values, unless otherwise specified. In the amino acid structure formulae, each residue is generally represented by standard three letter or single letter designations. The L-form of an amino acid residue is represented by a capital single letter or a capital first letter of a three-letter symbol, and the D-form for those amino acids having D-forms is represented by a lower case single letter or a lower case three letter symbol. Gly cine has no asymmetric carbon atom and is simply referred to as "Gly" or G. The procedures used to identify peptides of the present invention generally follow the methods disclosed in Falk et al. , Nature 351:290 (1991), which is incorporated herein by reference. Briefly, the methods involve large-scale isolation of MHC class I molecules, typically by immunoprecipitation or affinity chromatography, from the appropriate cell or cell line. Examples of other methods for isolation of the desired MHC molecule equally well known to the artisan include ion exchange chromatography, lectin chromatography, size exclusion, high performance ligand chromatography, and a combination of all of the above techniques.

In the typical case, immunoprecipitation is used to isolate the desired allele. A number of protocols can be used, depending upon the specificity of the antibodies used. For example, allele-specific mAb reagents can be used for the affinity purification of the

HLA-A, HLA-B,, and HLA-C molecules. Several mAb reagents for the isolation of HLA-A molecules are available. The monoclonal BB7.2 is suitable for isolating HLA-A2 molecules. Affinity columns prepared with these mAbs using standard techniques are successfully used to purify the respective HLA-A allele products. In addition to allele-specific mAbs, broadly reactive anti-HLA-A, B, C mAbs, such as W6/32 and B9.12.1, and one anti-HLA-B, C mAb, B 1.23.2, could be used in alternative affinity purification protocols as described in previous applications.

The peptides bound to the peptide binding groove of the isolated MHC molecules are eluted typically using acid treatment. Peptides can also be dissociated from class I molecules by a variety of standard denaturing means, such as heat, pH, detergents, salts, chaotropic agents, or a combination thereof. 10

Peptide fractions are further separated from the MHC molecules by reversed-phase high performance liquid chromatography (HPLC) and sequenced. Peptides can be separated by a variety of other standard means well known to the artisan, including filtration, ultrafiltration, electrophoresis, size chromatography, precipitation with specific antibodies, ion exchange chromatography, isoelectrofocusing, and the like.

Sequencing of the isolated peptides can be performed according to standard techniques such as Edman degradation (Hunkapiller, M.W. , et al.. Methods Enzymol. 91, 399 [1983]). Other methods suitable for sequencing include mass spectrometry sequencing of individual peptides as previously described (Hunt, et al., Science 225: 1261 (1992), which is incorporated herein by reference). Amino acid sequencing of bulk heterogenous peptides (e.g.. pooled HPLC fractions) from different class I molecules typically reveals a characteristic sequence motif for each class I allele.

Definition of motifs specific for different class I alleles allows the identification of potential peptide epitopes from an antigenic protein whose amino acid sequence is known. Typically, identification of potential peptide epitopes is initially carried out using a computer to scan the amino acid sequence of a desired antigen for the presence of motifs. The epitopic sequences are then synthesized. The capacity to bind MHC Class molecules is measured in a variety of different ways. One means is a Class I molecule binding assay as described in the related applications, noted above. Other alternatives described in the literature include inhibition of antigen presentation (Sette, et al. , J. Immunol. 141:3893 (1991), in vitro assembly assays (Townsend, et al., £eϋ 62:285 (1990), and FACS based assays using mutated ells, such as RMA.S (Melief, et al. , Eur. J. Immunol. 21:2963 (1991)).

Next, peptides that test positive in the MHC class I binding assay are assayed for the ability of the peptides to induce specific CTL responses in vitro. For instance, Antigen-presenting cells that have been incubated with a peptide can be assayed for the ability to induce CTL responses in responder cell populations. Antigen-presenting cells can be normal cells such as peripheral blood mononuclear cells or dendritic cells (Inaba, et al. , J. Exp. Med. 166: 182 (1987); Boog, Eur. J. Immunol. 18:219 [1988]). Alternatively, mutant mammalian cell lines that are deficient in their ability to load class I molecules with internally processed peptides, such as the mouse cell lines RMA-S (Karre, et al.. Nature. 319:675 (1986); Ljunggren, et al., Fur. J. Immunol. 11

21:2963-2970 (1991)), and the human somatic T cell hybrid, T-2 (Cerundolo, et al. , Nature 345:449-452 (1990)) and which have been transfected with the appropriate human class I genes are conveniently used, when peptide is added to them, to test for the capacity of the peptide to induce in vitro primary CTL responses. Other eukaryotic cell lines which could be used include various insect cell lines such as mosquito larvae (ATCC cell lines

CCL 125, 126, 1660, 1591, 6585, 6586), silkworm (ATTC CRL 8851), armyworm (ATCC CRL 1711), moth (ATCC CCL 80) and Drosophila cell lines such as a Schneider cell line (see Schneider J. Embryol. Exp. Morphol. 27:353-365 [1927]).

Peripheral blood lymphocytes are conveniently isolated following simple venipuncture or leukapheresis of normal donors or patients and used as the responder cell sources of CTL precursors. In one embodiment, the appropriate antigen-presenting cells are incubated with 10-100 μM of peptide in serum-free media for 4 hours under appropriate culture conditions. The peptide-loaded antigen-presenting cells are then incubated with the responder cell populations in vitro for 7 to 10 days under optimized culture conditions. Positive CTL activation can be determined by assaying the cultures for the presence of CTLs that kill radiolabeled target cells, both specific peptide-pulsed targets as well as target cells expressing endogenously processed form of the relevant virus or tumor antigen from which the peptide sequence was derived.

Specificity and MHC restriction of the CTL is determined by testing against different peptide target cells expressing appropriate or inappropriate human MHC class I.

The peptides that test positive in the MHC binding assays and give rise to specific CTL responses are referred to herein as immunogenic peptides.

The immunogenic peptides can be prepared synthetically, or by recombinant DNA technology or from natural sources such as whole viruses or tumors. Although the peptide will preferably be substantially free of other naturally occurring host cell proteins and fragments thereof, in some embodiments the peptides can be synthetically conjugated to native fragments or particles.

The polypeptides or peptides can be a variety of lengths, either in their neutral (uncharged) forms or in forms which are salts, and either free of modifications such as glycosylation, side chain oxidation, or phosphorylation or containing these modifications, subject to the condition that the modification not destroy the biological activity of the polypeptides as herein described. 12

Desirably, the peptide will be as small as possible while still maintaining substantially all of the biological activity of the large peptide. When possible, it may be desirable to optimize peptides of the invention to a length of 9 or 10 amino acid residues, commensurate in size with endogenously processed viral peptides or tumor cell peptides that are bound to MHC class I molecules on the cell surface.

Peptides having the desired activity may be modified as necessary to provide certain desired attributes, e.g. , improved pharmacological characteristics, while increasing or at least retaining substantially all of the biological activity of the unmodified peptide to bind the desired MHC molecule and activate the appropriate T cell. For instance, the peptides may be subject to various changes, such as substitutions, either conservative or non-conservative, where such changes might provide for certain advantages in their use, such as improved MHC binding. By conservative substitutions is meant replacing an amino acid residue with another which is biologically and/or chemically similar, e.g., one hydrophobic residue for another, or one polar residue for another. The substitutions include combinations such as Gly, Ala; Val, He, Leu, Met;

Asp, Glu; Asn, Gin; Ser, Thr; Lys, Arg; and Phe, Tyr. The effect of single amino acid substitutions may also be probed using D-amino acids. Such modifications may be made using well known peptide synthesis procedures, as described in e.g. , Merrifield, Science 232:341-347 (1986), Barany and Merrifield, The Peptides. Gross and Meienhofer, eds. (N.Y. , Academic Press), pp. 1-284 (1979); and Stewart and Young, Solid Phase Peptide

Synthesis. (Rockford, 111. , Pierce), 2d Ed. (1984), incorporated by reference herein.

The peptides can also be modified by extending or decreasing the compound's amino acid sequence, e.g. , by the addition or deletion of amino acids. The peptides or analogs of the invention can also be modified by altering the order or composition of certain residues, it being readily appreciated that certain amino acid residues essential for biological activity, e.g., those at critical contact sites or conserved residues, may generally not be altered without an adverse effect on biological activity. The non-critical amino acids need not be limited to those naturally occurring in proteins, such as L-α-amino acids, or their D-isomers, but may include non-natural amino acids as well, such as β-γ-δ-amino acids, as well as many derivatives of L-α-amino acids.

Typically, a series of peptides with single amino acid substitutions are employed to determine the effect of electrostatic charge, hydrophobicity, etc. on binding. 13

For instance, a series of positively charged (e.g. , Lys or Arg) or negatively charged (e.g. , Glu) amino acid substitutions are made along the length of the peptide revealing different patterns of sensitivity towards various MHC molecules and T cell receptors. In addition, multiple substitutions using small, relatively neutral moieties such as Ala, Gly, Pro, or similar residues may be employed. The substitutions may be homo-oligomers or hetero- oligomers. The number and types of residues which are substituted or added depend on the spacing necessary between essential contact points and certain functional attributes which are sought (e.g., hydrophobicity versus hydrophilicity). Increased binding affinity for an MHC molecule or T cell receptor may also be achieved by such substitutions, compared to the affinity of the parent peptide. In any event, such substitutions should employ amino acid residues or other molecular fragments chosen to avoid, for example, steric and charge interference which might disrupt binding.

Amino acid substitutions are typically of single residues. Substitutions, deletions, insertions or any combination thereof may be combined to arrive at a final peptide. Substitutional variants are those in which at least one residue of a peptide has been removed and a different residue inserted in its place. Such substitutions generally are made in accordance with the following Table 2 when it is desired to finely modulate the characteristics of the peptide.

TABLE 2

Original Residue Exemplarv Substitution

Ala Ser

Arg Lys, His

Asn Gin

Asp Glu

Cys Ser

Gin Asn

Glu Asp

Gly Pro

His Lys; Arg

He Leu; Val

Leu He; Val

Lys Arg; His

Met Leu; He

Phe Tyr; Trp

Ser Thr

Thr Ser

Trp Tyr; Phe

Tyr Trp; Phe

Val He; Leu

Figure imgf000016_0001
Pro Gly 15

Substantial changes in function (e.g., affinity for MHC molecules or T cell receptors) are made by selecting substitutions that are less conservative than those in Table 2, i.e. , selecting residues that differ more significantly in their effect on maintaining (a) the structure of the peptide backbone in the area of the substitution, for example as a sheet or helical conformation, (b) the charge or hydrophobicity of the molecule at the target site or (c) the bulk of the side chain. The substimtions which in general are expected to produce the greatest changes in peptide properties will be those in which (a) hydrophilic residue, e.g. seryl, is substituted for (or by) a hydrophobic residue, e.g. leucyl, isoleucyl, phenylalanyl, valyl or alanyl; (b) a residue having an electropositive side chain, e.g., lysl, arginyl, or histidyl, is substituted for (or by) an electronegative residue, e.g. glutamyl or aspartyl; or (c) a residue having a bulky side chain, e.g. phenylalanine, is substituted for (or by) one not having a side chain, e.g., glycine.

The peptides may also comprise isosteres of two or more residues in the immunogenic peptide. An isostere as defined here is a sequence of two or more residues that can be substituted for a second sequence because the steric conformation of the first sequence fits a binding site specific for the second sequence. The term specifically includes peptide backbone modifications well known to those skilled in the art. Such modifications include modifications of the amide nitrogen, the α-carbon, amide carbonyl, complete replacement of the amide bond, extensions, deletions or backbone crosslinks. See, generally. Spatola, Chemistry and Biochemistry of Amino Acids, peptides and Proteins. Vol. VII (Weinstein ed. , 1983).

Modifications of peptides with various amino acid mimetics or unnatural amino acids are particularly useful in increasing the stability of the peptide in vivo. Stability can be assayed in a number of ways. For instance, peptidases and various biological media, such as human plasma and serum, have been used to test stability. See, e.g.. Verhoef et al., Eur. J. Drug Metab. Pharmacokin. 11:291-302 (1986). Half life of the peptides of the present invention is conveniently determined using a 25 % human serum (v/v) assay. The protocol is generally as follows. Pooled human serum (Type AB, non-heat inactivated) is delipidated by centrifugation before use. The serum is then diluted to 25% with RPMI tissue culture media and used to test peptide stability. At predetermined time intervals a small amount of reaction solution is removed and added to either 6% aqueous trichloracetic acid or ethanol. The cloudy reaction sample is cooled 16

(4°C) for 15 minutes and then spun to pellet the precipitated serum proteins. The presence of the peptides is then determined by reversed-phase HPLC using stability-specific chromatography conditions.

The peptides of the present invention or analogs thereof which have CTL stimulating activity may be modified to provide desired attributes other than improved serum half life. For instance, the ability of the peptides to induce CTL activity can be enhanced by linkage to a sequence which contains at least one epitope that is capable of inducing a T helper cell response. Particularly preferred immunogenic peptides/T helper conjugates are linked by a spacer molecule. The spacer is typically comprised of relatively small, neutral molecules, such as amino acids or amino acid mimetics, which are substantially uncharged under physiological conditions. The spacers are typically selected from, e.g. , Ala, Gly, or other neutral spacers of nonpolar amino acids or neutral polar amino acids. It will be understood that the optionally present spacer need not be comprised of the same residues and thus may be a hetero- or homo-oligomer. When present, the spacer will usually be at least one or two residues, more usually three to six residues. Alternatively, the CTL peptide may be linked to the T helper peptide without a spacer.

The immunogenic peptide may be linked to the T helper peptide either directly or via a spacer either at the amino or carboxy terminus of the CTL peptide. The amino terminus of either the immunogenic peptide or the T helper peptide may be acylated.

Exemplary T helper peptides include tetanus toxoid 830-843, influenza 307-319, malaria circumsporozoite 382-398 and 378-389.

In some embodiments it may be desirable to include in the pharmaceutical compositions of the invention at least one component which primes CTL. Lipids have been identified as agents capable of priming CTL in vivo against viral antigens. For example, palmitic acid residues can be attached to the alpha and epsilon amino groups of a Lys residue and then linked, e.g., via one or more linking residues such as Gly, Gly-Gly-, Ser, Ser-Ser, or the like, to an immunogenic peptide. The lipidated peptide can then be injected directly in a micellar form, incorporated into a liposome or emulsified in an adjuvant, e.g. , incomplete Freund's adjuvant. In a preferred embodiment a particularly effective immunogen comprises palmitic acid attached to alpha and epsilon amino groups 17 of Lys, which is attached via linkage, e.g. , Ser-Ser, to the amino terminus of the immunogenic peptide.

As another example of lipid priming of CTL responses, E. coli lipoproteins, such as tripalmitoyl-S-glycerylcysteinlyseryl-serine (P3CSS) can be used to prime virus specific CTL when covalently attached to an appropriate peptide. See, Deres et al. ,

Nature 342:561-564 (1989), incorporated herein by reference. Peptides of the invention can be coupled to P3CSS, for example, and the lipopeptide administered to an individual to specifically prime a CTL response to the target antigen. Further, as the induction of neutralizing antibodies can also be primed with P3CSS conjugated to a peptide which displays an appropriate epitope, the two compositions can be combined to more effectively elicit both humoral and cell-mediated responses to infection.

In addition, additional amino acids can be added to the termini of a peptide to provide for ease of linking peptides one to another, for coupling to a carrier support, or larger peptide, for modifying the physical or chemical properties of the peptide or oligopeptide, or the like. Amino acids such as tyrosine, cysteine, lysine, glutamic or aspartic acid, or the like, can be introduced at the C- or N-terminus of the peptide or oligopeptide. Modification at the C terminus in some cases may alter binding characteristics of the peptide. In addition, the peptide or oligopeptide sequences can differ from the natural sequence by being modified by terminal-NH2 acylation, e.g. , by alkanoyl (C,-C2o) or thioglycolyl acetylation, terminal-carboxyl amidation, e.g. , ammonia, methylamine, etc. In some instances these modifications may provide sites for linking to a support or other molecule.

The peptides of the invention can be prepared in a wide variety of ways. Because of their relatively short size, the peptides can be synthesized in solution or on a solid support in accordance with conventional techniques. Various automatic synthesizers are commercially available and can be used in accordance with known protocols. See, for example, Stewart and Young, Solid Phase Peptide Synthesis. 2d. ed. , Pierce Chemical Co. (1984), supra.

Alternatively, recombinant DNA technology may be employed wherein a nucleotide sequence which encodes an immunogenic peptide of interest is inserted into an expression vector, transformed or transfected into an appropriate host cell and cultivated under conditions suitable for expression. These procedures are generally known in the art, 18 as described generally in Sambrook et al. , Molecular Cloning. A Laboratory Manual. Cold Spring Harbor Press, Cold Spring Harbor, New York (1982), which is incorporated herein by reference. Thus, fusion proteins which comprise one or more peptide sequences of the invention can be used to present the appropriate T cell epitope. As the coding sequence for peptides of the length contemplated herein can be synthesized by chemical techniques, for example, the phosphotriester method of Matteucci et al. , J. Am. Chem. Soc. 103:3185 (1981), modification can be made simply by substituting the appropriate base(s) for those encoding the native peptide sequence. The coding sequence can then be provided with appropriate linkers and ligated into expression vectors commonly available in the art, and the vectors used to transform suitable hosts to produce the desired fusion protein. A number of such vectors and suitable host systems are now available. For expression of the fusion proteins, the coding sequence will be provided with operably linked start and stop codons, promoter and terminator regions and usually a replication system to provide an expression vector for expression in the desired cellular host. For example, promoter sequences compatible with bacterial hosts are provided in plasmids containing convenient restriction sites for insertion of the desired coding sequence. The resulting expression vectors are transformed into suitable bacterial hosts. Of course, yeast or mammalian cell hosts may also be used, employing suitable vectors and control sequences. The peptides of the present invention and pharmaceutical and vaccine compositions thereof are useful for administration to mammals, particularly humans, to treat and/or prevent viral infection and cancer. Examples of diseases which can be treated using the immunogenic peptides of the invention include prostate cancer, hepatitis B, hepatitis C, AIDS, renal carcinoma, cervical carcinoma, lymphoma, CMV and condlyloma acuminatum.

For pharmaceutical compositions, the immunogenic peptides of the invention are administered to an individual already suffering from cancer or infected with the virus of interest. Those in the incubation phase or the acute phase of infection can be treated with the immunogenic peptides separately or in conjunction with other treatments, as appropriate. In therapeutic applications, compositions are administered to a patient in an amount sufficient to elicit an effective CTL response to the virus or tumor antigen and to cure or at least partially arrest symptoms and/or complications. An amount adequate to 19 accomplish this is defined as " therapeutical ly effective dose. " Amounts effective for this use will depend on, e.g. , the peptide composition, the manner of administration, the stage and severity of the disease being treated, the weight and general state of health of the patient, and the judgment of the prescribing physician, but generally range for the initial immunization (that is for therapeutic or prophylactic administration) from about 1.0 μg to about 5000 μg of peptide for a 70 kg patient, followed by boosting dosages of from about 1.0 μg to about 1000 μg of peptide pursuant to a boosting regimen over weeks to months depending upon the patient's response and condition by measuring specific CTL activity in the patient's blood. It must be kept in mind that the peptides and compositions of the present invention may generally be employed in serious disease states, that is, life- threatening or potentially life threatening situations. In such cases, in view of the minimization of extraneous substances and the relative nontoxic nature of the peptides, it is possible and may be felt desirable by the treating physician to administer substantial excesses of these peptide compositions. For therapeutic use, administration should begin at the first sign of viral infection or the detection or surgical removal of tumors or shortly after diagnosis in the case of acute infection. This is followed by boosting doses until at least symptoms are substantially abated and for a period thereafter. In chronic infection, loading doses followed by boosting doses may be required. Treatment of an infected individual with the compositions of the invention may hasten resolution of the infection in acutely infected individuals. For those individuals susceptible (or predisposed) to developing chronic infection the compositions are particularly useful in methods for preventing the evolution from acute to chronic infection. Where the susceptible individuals are identified prior to or during infection, for instance, as described herein, the composition can be targeted to them, minimizing need for administration to a larger population.

The peptide compositions can also be used for the treatment of chronic infection and to stimulate the immune system to eliminate virus-infected cells in carriers. It is important to provide an amount of immuno-potentiating peptide in a formulation and mode of administration sufficient to effectively stimulate a cytotoxic T cell response.

Thus, for treatment of chronic infection, a representative dose is in the range of about 1.0 μg to about 5000 μg, preferably about 5 μg to 1000 μg for a 70 kg patient per dose. 20

Immunizing doses followed by boosting doses at established intervals, e.g. , from one to four weeks, may be required, possibly for a prolonged period of time to effectively immunize an individual. In the case of chronic infection, administration should continue until at least clinical symptoms or laboratory tests indicate that the viral infection has been eliminated or substantially abated and for a period thereafter.

The pharmaceutical compositions for therapeutic treatment are intended for parenteral, topical, oral or local administration. Preferably, the pharmaceutical compositions are administered parenterally, e.g. , intravenously, subcutaneously, intradermally, or intramuscularly. Thus, the invention provides compositions for parenteral administration which comprise a solution of the immunogenic peptides dissolved or suspended in an acceptable carrier, preferably an aqueous carrier. A variety of aqueous carriers may be used, e.g., water, buffered water, 0.8% saline, 0.3% glycine, hyaluronic acid and the like. These compositions may be sterilized by conventional, well known sterilization techniques, or may be sterile filtered. The resulting aqueous solutions may be packaged for use as is, or lyophilized, the lyophilized preparation being combined with a sterile solution prior to administration. The compositions may contain pharmaceutically acceptable auxiliary substances as required to approximate physiological conditions, such as pH adjusting and buffering agents, tonicity adjusting agents, wetting agents and the like, for example, sodium acetate, sodium lactate, sodium chloride, potassium chloride, calcium chloride, sorbitan monolaurate, triethanolamine oleate, etc.

The concentration of CTL stimulatory peptides of the invention in the pharmaceutical formulations can vary widely, i.e. , from less than about 0.1 %, usually at or at least about 2% to as much as 20% to 50% or more by weight, and will be selected primarily by fluid volumes, viscosities, etc., in accordance with the particular mode of administration selected.

The peptides of the invention may also be administered via liposomes, which serve to target the peptides to a particular tissue, such as lymphoid tissue, or targeted selectively to infected cells, as well as increase the half-life of the peptide composition. Liposomes include emulsions, foams, micelles, insoluble monolayers, liquid crystals, phospholipid dispersions, lamellar layers and the like. In these preparations the peptide to be delivered is incorporated as part of a liposome, alone or in conjunction with a molecule which binds to, e.g. , a receptor prevalent among lymphoid cells, such as monoclonal 21 antibodies which bind to the CD45 antigen, or with other therapeutic or immunogenic compositions. Thus, liposomes either filled or decorated with a desired peptide of the invention can be directed to the site of lymphoid cells, where the liposomes then deliver the selected therapeutic/immunogenic peptide compositions. Liposomes for use in the invention are formed from standard vesicle-forming lipids, which generally include neutral and negatively charged phospholipids and a sterol, such as cholesterol. The selection of lipids is generally guided by consideration of, e.g. , liposome size, acid lability and stability of the liposomes in the blood stream. A variety of methods are available for preparing liposomes, as described in, e.g. , Szoka et al. , Ann. Rev. Biophys. Bioeng. 9:467 (1980), U.S. Patent Nos. 4,235,871 , 4,501 ,728, 4,837,028, and 5,019,369, incorporated herein by reference.

For targeting to the immune cells, a ligand to be incorporated into the liposome can include, e.g. , antibodies or fragments thereof specific for cell surface determinants of the desired immune system cells. A liposome suspension containing a peptide may be administered intravenously, locally, topically, etc. in a dose which varies according to, inter alia, the manner of administration, the peptide being delivered, and the stage of the disease being treated.

For solid compositions, conventional nontoxic solid carriers may be used which include, for example, pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharin, talcum, cellulose, glucose, sucrose, magnesium carbonate, and the like. For oral administration, a pharmaceutically acceptable nontoxic composition is formed by incorporating any of the normally employed excipients, such as those carriers previously listed, and generally 10-95% of active ingredient, that is, one or more peptides of the invention, and more preferably at a concentration of 25% -75 % . For aerosol administration, the immunogenic peptides are preferably supplied in finely divided form along with a surfactant and propellant. Typical percentages of peptides are 0.01 %-20% by weight, preferably 1 %-10%. The surfactant must, of course, be nontoxic, and preferably soluble in the propellant. Representative of such agents are the esters or partial esters of fatty acids containing from 6 to 22 carbon atoms, such as caproic, octanoic, lauric, palmitic, stearic, linoleic, linolenic, olesteric and oleic acids with an aliphatic polyhydric alcohol or its cyclic anhydride. Mixed esters, such as mixed or natural glycerides may be employed. The surfactant may constitute 0.1 % -20% by weight 22 of the composition, preferably 0.25-5%. The balance of the composition is ordinarily propellant. A carrier can also be included, as desired, as with, e.g. , lecithin for intranasal delivery.

In another aspect the present invention is directed to vaccines which contain as an active ingredient an immunogenically effective amount of an immunogenic peptide as described herein. The peptide(s) may be introduced into a host, including humans, linked to its own carrier or as a homopolymer or heteropolymer of active peptide units. Such a polymer has the advantage of increased immunological reaction and, where different peptides are used to make up the polymer, the additional ability to induce antibodies and/or CTLs that react with different antigenic determinants of the virus or tumor cells. Useful carriers are well known in the art, and include, e.g. , thyroglobulin, albumins such as human serum albumin, tetanus toxoid, polyamino acids such as poly(lysine:glutamic acid), influenza, hepatitis B virus core protein, hepatitis B virus recombinant vaccine and the like. The vaccines can also contain a physiologically tolerable (acceptable) diluent such as water, phosphate buffered saline, or saline, and further typically include an adjuvant. Adjuvants such as incomplete Freund's adjuvant, aluminum phosphate, aluminum hydroxide, or alum are materials well known in the art. And, as mentioned above, CTL responses can be primed by conjugating peptides of the invention to lipids, such as P3CSS. Upon immunization with a peptide composition as described herein, via injection, aerosol, oral, transdermal or other route, the immune system of the host responds to the vaccine by producing large amounts of CTLs specific for the desired antigen, and the host becomes at least partially immune to later infection, or resistant to developing chronic infection.

Vaccine compositions containing the peptides of the invention are administered to a patient susceptible to or otherwise at risk of viral infection or cancer to elicit an immune response against the antigen and thus enhance the patient's own immune response capabilities. Such an amount is defined to be an "immunogenically effective dose. " In this use, the precise amounts again depend on the patient's state of health and weight, the mode of administration, the nature of the formulation, etc. , but generally range from about 1.0 μg to about 5000 μg per 70 kilogram patient, more commonly from about 10 μg to about 500 μg mg per 70 kg of body weight. 23

In some instances it may be desirable to combine the peptide vaccines of the invention with vaccines which induce neutralizing antibody responses to the virus of interest, particularly to viral envelope antigens.

For therapeutic or immunization purposes, nucleic acids encoding one or more of the peptides of the invention can also be admisitered to the patient. A number of methods are conveniently used to deliver the nucleic acids to the patient. For instance, the nulceic acid can be delivered directly, as "naked DNA". This approach is described, for instance, in Wolff et. al. , Science 247: 1465-1468 (1990) as well as U.S. Patent Nos. 5,580,859 and 5,589,466. The nucleic acids can also be administered using ballistic delivery as described, for instance, in U.S. Patent No. 5,204,253. Particles comprised solely of DNA can be administered. Alternatively, DNA can be adhered to particles, such as gold particles. The nucleci acids can also be delivered complexed to cationic compounds, such as cationic lipids. Lipid-mediated gene delivery methods are described, for instance, in WO 96/18372; WO 93/24640; Mannino and Gould-Fogerite (1988) BioTechniques 6(7): 682-691; Rose U.S. Pat No. 5,279,833; WO 91/06309; and Feigner et al. (1987) Proc. Natl. Acad. Sci. USA 84: 7413-7414. The peptides of the invention can also be expressed by attenuated viral hosts, such as vaccinia or fowlpox. This approach involves the use of vaccinia virus as a vector to express nucleotide sequences that encode the peptides of the invention. Upon introduction into an acutely or chronically infected host or into a noninfected host, the recombinant vaccinia virus expresses the immunogenic peptide, and thereby elicits a host CTL response. Vaccinia vectors and methods useful in immunization protocols are described in, e.g. , U.S. Patent No. 4,722,848, incorporated herein by reference. Another vector is BCG (Bacille Calmette Guerin). BCG vectors are described in Stover et al. (Nature 351 :456-460 (1991)) which is incorporated herein by reference. A wide variety of other vectors useful for therapeutic administration or immunization of the peptides of the invention, e.g., Salmonella typhi vectors and the like, will be apparent to those skilled in the art from the description herein. A preferred means of administering nucleic acids encoding the peptides of the invention uses minigene constructs encoding multiple epitopes of the invention. To create a DNA sequence encoding the selected CTL epitopes (minigene) for expression in human cells, the amino acid sequences of the epitopes are reverse translated. A human codon usage table is used to guide the codon choice for each amino acid. These epitope-encoding 24

DNA sequences are directly adjoined, creating a continuous polypeptide sequence. To optimize expression and/or immunogenicity, additional elements can be incorporated into the minigene design. Examples of amino acid sequence that could be reverse translated and included in the minigene sequence include: helper T lymphocyte epitopes, a leader (signal) sequence, and an endoplasmic reticulum retention signal. In addition, MHC presentation of CTL epitopes may be improved by including synthetic (e.g. poly-alanine) or naturally-occurring flanking sequences adjacent to the CTL epitopes.

The minigene sequence is converted to DNA by assembling oligonucleotides that encode the plus and minus strands of the minigene. Overlapping oligonucleotides (30- 100 bases long) are synthesized, phosphorylated, purified and annealed under appropriate conditions using well known techniques, he ends of the oligonucleotides are joined using T4 DNA ligase. This synthetic minigene, encoding the CTL epitope polypeptide, can then cloned into a desired expression vector.

Standard regulatory sequences well known to those of skill in the art are included in the vector to ensure expression in the target cells. Several vector elements are required: a promoter with a down-stream cloning site for minigene insertion; a polyadenylation signal for efficient transcription termination; an E. coli origin of replication; and an E. coli selectable marker (e.g. ampicillin or kanamycin resistance). Numerous promoters can be used for this purpose, e.g., the human cytomegalovirus (hCMV) promoter. See, U.S. Patent Nos. 5,580,859 and 5,589,466 for other suitable promoter sequences.

Additional vector modifications may be desired to optimize minigene expression and immunogenicity. In some cases, introns are required for efficient gene expression, and one or more synthetic or naturally-occurring introns could be incorporated into the transcribed region of the minigene. The inclusion of mRNA stabilization sequences can also be considered for increasing minigene expression. It has recently been proposed that immunostimulatory sequences (ISSs or CpGs) play a role in the immunogenicity of DNA vaccines. These sequences could be included in the vector, outside the minigene coding sequence, if found to enhance immunogenicity. In some embodiments, a bicistronic expression vector, to allow production of the minigene-encoded epitopes and a second protein included to enhance or decrease immunogenicity can be used. Examples of proteins or polypeptides that could beneficially 25 enhance the immune response if co-expressed include cytokines (e.g. , IL2, IL12, GM- CSF), cytokine-inducing molecules (e.g. LeIF) or costimulatory molecules. Helper (HTL) epitopes could be joined to intracellular targeting signals and expressed separately from the CTL epitopes. This would allow direction of the HTL epitopes to a cell compartment different than the CTL epitopes. If required, this could facilitate more efficient entry of HTL epitopes into the MHC class II pathway, thereby improving CTL induction. In contrast to CTL induction, specifically decreasing the immune response by co-expression of immunosuppressive molecules (e.g. TGF-β) may be beneficial in certain diseases. Once an expression vector is selected, the minigene is cloned into the polylinker region downstream of the promoter. This plasmid is transformed into an appropriate E. coli strain, and DNA is prepared using standard techniques. The orientation and DNA sequence of the minigene, as well as all other elements included in the vector, are confirmed using restriction mapping and DNA sequence analysis. Bacterial cells harboring the correct plasmid can be stored as a master cell bank and a working cell bank.

Therapeutic quantities of plasmid DNA are produced by fermentation in E. coli, followed by purification. Aliquots from the working cell bank are used to inoculate fermentation medium (such as Terrific Broth), and grown to saturation in shaker flasks or a bioreactor according to well known techniques. Plasmid DNA can be purified using standard bioseparation technologies such as solid phase anion-exchange resins supplied by Quiagen. If required, supercoiled DNA can be isolated from the open circular and linear forms using gel electrophoresis or other methods.

Purified plasmid DNA can be prepared for injection using a variety of formulations. The simplest of these is reconstitution of lyophilized DNA in sterile phosphate -buffer saline (PBS). A variety of methods have been described, and new techniques may become available. As noted above, nucleic acids are conveniently formulated with cationic lipids. In addition, glycolipids, fusogenic liposomes, peptides and compounds referred to collectively as protective, interactive, non-condensing (PINC) could also be complexed to purified plasmid DNA to influence variables such as stability, intramuscular dispersion, or trafficking to specific organs or cell types.

Target cell sensitization can be used as a functional assay for expression and MHC class I presentation of minigene-encoded CTL epitopes. The plasmid DNA is 26 introduced into a mammalian cell line that is suitable as a target for standard CTL chromium release assays. The transfection method used will be dependent on the final formulation. Electroporation can be used for "naked" DNA, whereas cationic lipids allow direct in vitro transfection. A plasmid expressing green fluorescent protein (GFP) can be co-transfected to allow enrichment of transfected cells using fluorescence activated cell sorting (FACS). These cells are then chromium-51 labeled and used as target cells for epitope-specific CTL lines. Cytolysis, detected by 51Cr release, indicates production of MHC presentation of minigene-encoded CTL epitopes.

In vivo immunogenicity is a second approach for functional testing of minigene DNA formulations. Transgenic mice expressing appropriate human MHC molecules are immunized with the DNA product. The dose and route of administration are formulation dependent (e.g. IM for DNA in PBS, IP for lipid-complexed DNA). Twenty-one days after immunization, splenocytes are harvested and restimulated for 1 week in the presence of peptides encoding each epitope being tested. These effector cells (CTLs) are assayed for cytolysis of peptide-loaded, chromium-51 labeled target cells using standard techniques. Lysis of target cells sensitized by MHC loading of peptides corresponding to minigene-encoded epitopes demonstrates DNA vaccine function for in vivo induction of CTLs.

Antigenic peptides may be used to elicit CTL ex vivo, as well. The resulting CTL, can be used to treat chronic infections (viral or bacterial) or tumors in patients that do not respond to other conventional forms of therapy, or will not respond to a peptide vaccine approach of therapy. Ex vivo CTL responses to a particular pathogen (infectious agent or tumor antigen) are induced by incubating in tissue culture the patient's CTL precursor cells (CTLp) together with a source of antigen-presenting cells (APC) and the appropriate immunogenic peptide. After an appropriate incubation time (typically 1-4 weeks), in which the CTLp are activated and mature and expand into effector CTL, the cells are infused back into the patient, where they will destroy their specific target cell (an infected cell or a tumor cell).

The peptides may also find use as diagnostic reagents. For example, a peptide of the invention may be used to determine the susceptibility of a particular individual to a treatment regimen which employs the peptide or related peptides, and thus may be helpful in modifying an existing treatment protocol or in determining a prognosis for an affected 27 individual. In addition, the peptides may also be used to predict which individuals will be at substantial risk for developing chronic infection.

The following example is offered by way of illustration, not by way of limitation.

Example 1

Class I antigen isolation was carried out as described in the related applications, noted above. Namrally processed peptides were then isolated and sequenced as described there. An allele-specific motif and algorithms were determined and quantitative binding assays were carried out.

Using the motifs identified above for various HLA alleles, amino acid sequences from a number of antigens were analyzed for the presence of these motifs. Tables 3- ** provide the results of these searches.

The above examples are provided to illustrate the invention but not to limit its scope. Other variants of the invention will be readily apparent to one of ordinary skill in the art and are encompassed by the appended claims. All publications, patents, and patent applications cited herein are hereby incorporated by reference.

Table 3

Sequence Antigen Molecule

FTFSPTYKAFLSK HBV POL

GT PQEHIV KLK HBV POL

FTFSPTYKAFLCK HBV POL

GTLPQEHIV KIK HBV POL

LWSYVNTNMGLK HBV POL

STTD EAYFKDCLFK HBV X

LWSYVNVNMGLK HBV NUC

GTLPQDHIVQKIK HBV POL

STSSC HQSAVRK HBV POL

TTVNAHQILPKVLHK HBV X

Figure imgf000029_0001
RTPARVTGGVFLVDK HBV POL 28

Sequence Antigen Molecule

HTTNFASK HBV ay

FTFSPTYK HBV ayw

PTYKAFLCKQY HBVayw

CTTPAQGTSMY HBVayw

PTSCPPTCPGY HBVayw

FSQFSRGNY HBVayw

LMPLYACIQSK HBVayw

RVTGGVFLVDK HBVayw POL

HTLWKAGILYK HBVayw

10 QTRHYLHTLWK HBVayw

GTDNSWLSRK HBVayw

SYVNTNMGLKF HBVayw

LYSILSPF HBVayw YWGPSLYSIL HBVayw

15 LYSILSPFLPL HBVayw

PYKEFGATVEL HBVayw

CTWMNSTGFTK HCV

MYVGDLCGSVF HCV

VYLLPRRGPRL HCV

20 ITKIQNFRVYY HIV

KVYLA VPAHK HIV

KMIGGIGGFIK HIV

IVASCDKCQLK HIV

KVKQWPLTEEK HIV

25 TVNDIQKLVGK HIV

DVKQLTEAVQK HIV

AWIQDNSDIK HIV TYQIYQEPFK HIV

VTVYYGVPV K HIV

30 LTEDRWNKPQK HIV

ATDIQTKELQK HIV

Figure imgf000030_0001
QTKELQKQITK HIV 29

Sequence Antigen Molecule

WTVQPIVLPEK HIV

QVPLRPMTYK HIV nef 73-82

QVPLYPMTFK HIV nef 73-82

VPLRPMTYK HIV nef 74-82

AVDLYHFLK HIV nef 84-94

AVDLSHFLK HIV nef 84-94

ATLYCVHQR HIV, pl7, 82-90

RLRDLLLIV HIV-1 NL43 768-776

RLRDLLLIVTR HIV-1 NL43 768-778

10 RLRDYLLIVTR HIV-1 NL43 768-778

LRDLLLI TR HIV-1 NL43 769-778

QIYQEPFKNLK HIV-1 RT 507-517

AVFIHNFK HIVcon

RTLNAWVK HIVcon

15 ETAYF1LK HIVcon

RLRPGGKKK HIVgag P17/2

KIRLRPGGKK HIVgag P17/2

KIRLRPGGK HIVgag P17/2

ETTDLYCY HPV16 E7

20

Figure imgf000031_0001
GTLGIVCPICSQK HPV16 E7 30

Sequence Antigen Molecule

LMGTLGIVCPICSQK HPV16 E7

AVCDKCLK HPV16 E6

PYAVCDKCLKF HPV16 E6

HYCYSLYGTTL HPV16 E6

FYSRIREL HPV16 E6

TLEKLTNTGLY HPV18 E6

KTVLELTEVFEFAFK HPV18 E6

TMLCMCCK HPV18 E7

NTSLQDIEITCVYCK HPV18 E6

10 EVFEFAFK HPVI8 E6

KQSSKALQR Leukemia £3A2 CMI

ATGFKQSSK Leukemia t>3A2 CMI

HSATGFKQSSK Leukemia fc>3A2 CMI

FKQSSKALQR Leukemia £3A2 CMI

15 VTCLGLSY MAGE1

ITKKVADLVGFLLLK MAGE1

LVGFLLLK MAGE1

VTKAEMLESVIKNYK MAGE1

TSCILESLFR MAGE1

20 NYKHCFPEI MAGE1

SYVLVTCL MAGE1

ETDPISHTY MAGEl(a)

ETDPTSHLY MAGEl(a)

ETDPTSNTY MAGEl(a)

25 ETDPTSHVY MAGEl(a)

ETDPTSHSY MAGEl(a)

ETDPASHTY MAGEl(a)

EVDPTSHTY MAGEl(a)

ETDPTGHTY MAGEl(a)

30 ETDRTSHTY MAGEl(a)

EADPTSHTY MAGEl(a)

Figure imgf000032_0001
ETVPTSHTY MAGEl(a) 31

Sequence Antigen Molecule

ETDPTSHTY MAGE1 consensus

ETDPTGHSY MAGE1 T(a)

MFPDLESEF MAGE2

TTINYTLWR MAGE2

VIFSKASEY MAGE2

LVHFLLLKY MAGE2

LVHFLLLKY MAGE2

LVHFLLLKYR MAGE2

PVIFSKASEY MAGE2

10 STTINYTLWR MAGE2

WEWPISH MAGE2

EYLQLVFGI MAGE2

IFSKASEYL MAGE2

SFSTTINYTL MAGE2

15 LYILVTCLGL MAGE2

FATCLGLSY MAGE3

WGNWQYFFPVIFSK MAGE3

LIIVLAIIAR MAGE3

YFFPVIFSK MAGE3

20 NWQYFFPVI MAGE3

NWQYFFPVIF MAGE3

IFSKASSSL MAGE3

EVDPTSNTY MAGE41

RYPLTFGWCY nef/182

25 RYPLTFGWC nef/182

ATQIPSYK PAP

LTELYFEK PAP

HSFPHPLY PSA

TQEPALGTTCY PSA

30 VTKFMLCAGRWTGGK PSA

Figure imgf000033_0001
HVISNDVCAQVHPQK PSA 32

Sequence Antigen Molecule

LYDMSLLKNRF PSA

ETDPTGHSY T2 analog of MAGE-3

Figure imgf000034_0001

33

3 8 g S 8 8 g § 8 8

3IE CΛ

Q i

I I ! H

£ - w5 £ = 2 « y ^ ' M

» M Il e*? alt; «•* o *si

*8 5 a 2 s- & S 2 δ'3 3 *l-'sl*ι*. S SιiiϊιϊιN . j J t I w i ω I * I u I ω j ω [ » ' w j 11*» I I > | ω M i .

! I I

I — |Mlθi = lC = I

8 |w ιSι*.3 5 s- -

I I

I ! o lol e lβιβ o — _, o o C'ΣiSIS -l« *5 1*3 » S g o 8 S •fir o = lβ|0, o o — — 1°' SIM o o o I ° o S C s =18

I I O . o o •^ 00 O . CΛ υ Peptide Sequence AA Virus Strain Molecule Pos. Motif Al A2.1 A3.2 All A24

1 0731 RIL ETELRK 10 C-ERH2 713 3,11 0057 0.11

1 0745 VLV SPNI IVK 10 c EKH2 8.1 3,11 0082~ 0.0072

- 1 1131 SVFQNLQVIR ϊo C-ERB2 423 3,11 0017 0075

1 1133 HTVPWDQLFR 10 c ERB2 478 3.11 oάnT 0072

- - - 1 1127 ILKCGVLIQR 10 c ERB2 14H 3,1 i 0.040 0.0U)5

1.1143 LVSEFSRMAR 10 c ERB2 ~972 3,ϊi 0.0072 003T"

1 1136 GWFCILIKR 10 c ERB2 668 3.11 0018 0.033

1 0726 CVARCPSCVK 10 c ERB2 596 3,11 0.022 0.0O12

1.1137 WPCILIKRR 10 c ERB2 669 3.Ϊ1 0.0030 0.016

1.0728 GILIKRRQQK 10 C-ERB2 672 3,11 0.015 0.0014

1.1129 RTVCAGGCAR 10 < C-ERB2 217 3,11 0.0068 0013

1.1134 GLACHQLCAR 10 C-ERB2 508 3.11 0.011 0

Figure imgf000036_0001
1.1139 KIPVAIKVLR 10 C-ERB2 747 3,11 00009 00099

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0, Peptide Sequence AA Virus Strain Molecule Pos. Motif Al A2.1 A3.2 All A24

10291 VCEΛDYFEY 9 EBNΛ1 409 1 0016

— — 10295 PLRESIVCY 9 EBNΛ1 553 1 "o i "

10681 PVCEADYFEY 10 EBNAl 408 1 0015

10683 CT VΛGVFVY 10 EBNΛ1 50Ϊ" 0014

1.0293 CVFVYGGSK 9 EBNAl 506 3,11 030 0 1

1.1016 KT5LYNLRR 9 EBNΛ1 514 3,11 031 0.12

10297 AIKDLVMTK 9 EBNAl 578 3,11 0048 0034

10687 QTHIFAEVLK 10 EBNAl 567 3,11 0010 021

Figure imgf000037_0001
11124 GTALAIPQCR 10 EBNAl 523 3,11 00028 0056

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CΛ υ Peptide Sequence AA Virus Strain Molecule Pos Motif Al A2.1 A3.2 All A24

C

50005 CTELKLSDY 9 FLU Λ NP 44 1 3 6

50006 STLELRSRY 9 FLU Λ NP 377 1 0020

50044 ILRGSVAHK 9 FLU Λ NP 265 3 1 5 00037

50051 RMCNILKGK 9 FLU Λ NP 221 3 027 0062

50046 MQGSTLPR 9 FLU Λ NP 166 3 0031 0 10

50048 MIDCICRFY 9 FLU A NP 32 3 0059 00010

50049 MVLSAFDER 9 FLU A NP 66 3 00016 0041

50054 YIQMCTELK 9 FLU A NP 40 3 00031 0030

50042 CINDRNF R 9 FLU A NP 200 3 00028 0.024

50104 SLMQGSTLPR 10 FLU A NP 165 3 0 12 084

50095 KMIDCtCRFY 10 ' FLU A NP 31 3 050 00079

50096 LILRGSVAHK 10 FLU A NP 264 3 036 0037

50102 RSGAACAAVK 10 FLU A NP 175 3 0019 00046

10

CO 50105 SSTLELRSRY 10 FLU A NP 376 3 00018 0016

50103 RSRYWAIRTR 10 FLU A NP 382 3 0012 0

5.0101 RMVLSAFDER 10 FLU A NP 65 3 00014 0010

50061 FYIQMCΓEL 9 FLU A NP 39 24 2.9

5.0060 AYERMCNIL 9 FLU A NP 218 24 0031

Figure imgf000038_0001
50112 RFYIQMCΓEL 10 FLU A NP 38 24 0 15

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Peptide Sequence AA Virus Strain Molecule Pos. Motif Al A2.1 A3.2 All A24

H υ 1 0155 LLDTASALY 9 HBV adr CORE 420 25 00007 0

1 0186 SLDVSAAFY 9 HBV adr I'OL 10)1 1 172 00037 00006

20125 ΓTTGRTSLY 9 HBV ALL 1.382 1 3 00008 0

20126 MSTTDLEAY 9 HBV adr 1.521 085 <00008 0

— —

1 0208 PTTCRT5LY 9 HBV adr POL 1382 077 0 0

1 0387 LTKQYLNLY 9 HBV adw IΌL 1280 ~0 50 000O3 00075

1 0166 KVCNFTGLY 9 HBV adr POL 629 0068 030 0014

20127 MSPTDLEAY 9 HBV adw 1,550 0067

2-0120 FSQFSRGNY 9 HBV ayw 984 0057

~

20112 PSSWAFAKY 9 HBV adw 316 0054

10119 QSAVRKEAY 9 ' HBV adw 881 ~~0 O25~

1 0174 PLDKGIKPY 9 HBV adr POL 698 0019 <O00O2 <000O2

1 0378 SLMLLYKTY 9 HBV adw POL 1092 0017

10115 ASRDLVYSY 9 HBV ayw 499 0013

2.0124 PSRGRLGLY 9 HBV adr/adw 1,364 0011

2.0121 SSTCRNΪNY 9 HBV adr 1,036 00097

1 0519 DLLDTΛSΛLY 10 HBV adr CORE 419 11 1 0 0

1 0513 LLDPRVRGLY 10 HBV adr ENV 120 63 017 0

2.0239 LSLDVSAAFY 10 HBV ALL 1,000 4 2 <00009 00037

1 0911 FLCQQYLHLY 10 HBV adr POL 1250 1 1 00025 0014 00048 00017

20216 QTFGRKLHLY 10 HBV ayw POL 1087 1 1 00056 0012

10244 KTYCRKLHLY 10 HBV adw 1,098 069 00003 059 022 0

1 0791 KTYCRKLHLY 10 HBV adw POL 1098 0 57 00020 053 035 00001

20242 QTFGRKLHLY 10 HBV ayw 1,087 037 00097 0011

1 0556 KTFGRKLHLY 10 HBV adx POL 1069 ~ 034 00023 0094 0090 0

- -

20241 KTFGRKLHLY 10 HBV adx 1,069 00002 0 15 0095 0

1 0766 QDPRVRALY 10 HBV adw ENV 120 021 0014 0

1 0806 TTPAQGTSMY 10 HBV adw ENV 288 020 0 0

* IΛ*

2.0240 LSδTSRNINY 10 HBV adr 1,035 020 <00009 0 IΛ ** 1 0541 PLDKGIKPYY 10 HBV adr POL 698 — t — ~ 0 16~ 0 0

10238 HSASFCGSIΎ 10 HBV ayw 767 0 15 0 0019 0017 0

O 1 0795 FLTKQYLNLY 10 HBV adw POL 1279 0 12 0 0

20237 RSASPCCSPY 10 HBV adr/adw 718 0 11 0 0033 0020 0

1 0774 WLWGMDIDPY 10 HBV adw CORE 416 0081 <00002 <00002

- _ _

20233 TTPAQCTSMY 10 HBV ayw 288 0066

1 0542 HTLWKAGILY 10 HBV adr ~ θL ~~ 721 0030

Figure imgf000039_0001
20231 T5CPPICPGY 10 HBV adr 226 0018

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Peptide Sequence AA Virus Strain Molecule Pos. Motif Al A2.1 A3.2 All A24

H υ 20176 YYPEHLVNHY 10 I IUV ayw 735 24 0040 2 0172 AYRPPNAP1L 10 " ΪJBV ALL 521 24 — — 0022

20171 GYRWMCLRRF 10 HBV AI L 234 24 0011

50115 NFLISLCIHL 10 HBV POL 572 24 — - 00099

1 0377 YVSL LLYK 9 HBV adw POL 10W 3,1 i 031 74

1.0189 LLYKTFCRK 9 HBV adr POL 1066 3~iϊ 5.0 0.30

1.0379 LLYKTYGRK 9 HBV adw POL 1095 3,ii 2.5 0.40

1.0370 VTKYLPLDK 9 HBV adw POL 722 3,1 ϊ 0.014 1.3

1.0176 RHYLHTLWK 9 HBV adr POL 719 3,11 1.2 0.010

1.0367 STVPSFNPK 9 HBV adw POL 668 3,11 0.021 093

1 0215 TTDLEAYFK 9 HBV adr X" 1523 3,11 0.0006 0.92

1.0848 YVSLLLLYK 9 HBV adr POL 1061 3,11 0.39 0.92

1.0383 PTYKAFLTK 9 HBV adw POL 1274 3,11 0.17 0.71

1.0987 HLYPVARQR 9 HBV adr POL 1257 3,11 0.54 0.0020

1.0358 STMRQLGRK 9 HBV adw ENV 85 3,11 0.51 0.34

ON 1.0991 ALRFTSARR 9 HBV adr "X" 1488 3,11 0.44 <0.0005

1.0197 PVNRPIDWK 9 HBV adr POL 1197 3,11 0.080 041

1.0369 TVNENRRLK 9 HBV adw POL 703 3,11 0.016 0.40

1.1041 WNHYFQTR 9 HBV adw POL 740 3,11 0030 033

1.0152 STTSTGPCK 9 HBV adr ENV 277 3,11 0.011 0.29

1 0213 QVLPKLLHK 9 HBV adr "X" 1505 3,11 0.10 0.28

1.0172 LTKYLPLDK 9 HBV adr POL 693 3,11 0.0039 0.23

1.0374 CLHQSAVRK 9 HBV adw POL 878 3,11 0.22 0.017

1 0980 WDFSQFSR 9 HBV adr POL 963 3.11 0.011 0.20

1 0382 PLYAC1QAK 9 HBV adw POL 1259 3,11 0.18 0.034

2.0074 YVNTNMGLK 9 HBV ayw CORE 507 3.11 0 16 0048

1 0199 PLYACIQSK 9 HBV adr POL 1230 3.11 0 11 0018

* 1.0972 RLADEGLNR 9 HBV adr POL 601 3,11 0.10 0025 IΛ*

1.0976 AVNHYFKTR ON 9 HBV adr POL 711 3 Ϊ 00071 0098 IΛ 1.0975 RLKUMPAR 9 HBV adr POL 680 3,U 0.095 00002

ON 1.0977 ILYKR.ΩTR ON 9 HBV adr POL 730 3,ii 0095 <00005 o 1.0993 KVFVLGGCR 9 HBV adr "X- 1548 3,ii " 0042 0082

1.0165 NVSIPWTHK 9 HBV adr POL 621 3.11 0072 0076

1.0982 LLLYKTFCR 9 HBV adr POL IOf.5 3.1 1 --- 0072 00045

1 0978 RLVFQTSTR 9 HBV adr POL 757 3,11 0068 0.0032

1.0219 FVLCGCRHK 9 HBV adr "X" 1550 3.11 0065 0019

Figure imgf000041_0001
1 1042 RLVLQTSTR 9 HBV adw POL ~ 78 3,ii 0064 0 (102

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00

Peptide Sequence AA Virus Strain Molecule Pos. Motif Al A2.1 A3.2 All A24

H υ 1.1043 MLLYKTYGR 9 HBV adw POL 1094 3.11 0061 0.0032 a. 1.0170 TVNEKRRLK 9 HBV adr POL 674 3,i i 0048 0.037

1 1045 NLYPVARQR 9 HBV adw POL 128β ~ 3~l i 0042 00011

1 1046 LPYRPTTCR 9 HBV adw POL 1407" 3,11 0021 0

1.0845 LVSPGVWIR 9 HBV adr CORE 509 3,ii 00033 0020

1.0981 LVGSSGLPR 9 HBV adr POL 1022 3,11 00008 0015

1.0967 HISCLTFGR 9 HBV adr CORE 494 3,11 0.013 0.011

1.1047 SVPSRLPDR 9 HBV adw POL 1424 3,11 00007 0.010

1.0989 SVPSHLPDR 9 HBV adr POL 1395 3,11 0.0004 0.010

1.0564 TLPQEHIVLK 10 HBV adr POL 1179 3,11 0.092 5.6

2.0205 TVPVFNPHWK 10 ' HBV ayw POL 669 3,11 00067 4 2

1.0543 TLWKΛCILYK 10 HBV adr POL 724 3,11 3 5 1 0

1.0807 SMYPSCCCTK 10 HBV ayw ENV 295 3,11 I S 34 o 1.1153 RLPYRPTTGR 10 HBV adw POL 1406 3,11 2.8 0.030 -a- 1 0584 STTDLEAYFK 10 HBV adr X 1522 3,11 0.0066 2.7

1.0554 LLLYKTPCRK 10 HBV adr POL 1065 3,11 2.5 0.012

1.0799 TVNAHRNLPK 10 HBV adw "X" 1529 3.11 0.82 0.65

1.0586 EAYFKDCLFK 10 HBV adr X 1527 3,11 0.037 0.74

1.1081 LWDFSQFSR 10 HBV adr POL 962 3,11 0.0009 0.63

1.0789 MLLYKTYGRK 10 HBV adw POL 1094 3,11 0.61 0.O20

1 0546 TAYSHLSTSK 10 HBV adr POL 858 3,11 026 0.092

1.0562 SLGIHLNPNK 10 HBV adr POL 1150 3,11 0.20 0.078

1.1152 RLGLYRPLLR 10 HBV adw POL 1397 3.11 0.19 0.0049

1.0547 VTCGVFLVDK 10 HBV adr POL 943 3 I 0.035 0.17

1.1150 R1RTPRTPAR 10 HBV adw POL 962 3,11 0.17 0.0002

1.0581 TVNGHQVLPK 10 HBV adr X 1500 3,11 0.O73 0.092

1.1091 SLPFQFTTGR 10 HBV adr POL 1377 3,11 0.077 0043

1 1072 TLPETTWRR 10 HBV adr CORE 532 3,11 <00003 0075

IΛ 1.1089 GTDNSWLSR 10 HBV adr POL 1320^ 3,Ϊ 1 0.025 0072 IΛ

** 1.1071 STLP.EITWR 10 HBV adr CORE 531 3,11 0.0005 0.068

20210 KVTKYLPLDK 10 HBV ayw POL 721 3,11 0.027 0053

O 1 1148 STRHCDKSFR 10 HBV adw OL 792 3,1 1 0.0057 0038

1.0935 VLSCWWLQFR 10 HBV adw POL 923 3.U 0029 0.0087

1 0781 NVTKYLPLDK 10 HBV adw " i'OL 721 3,1 1 <00004 0023

1.1092 RVCCQLDPΛR 10 HBV adr X 1422 3,1 1 — - 0019 0023

1 0793 SLGIHLNPQK 10 HBV adw poi. M7 » 3.1 1 001 0.114"

Figure imgf000042_0001
1 0909 YLVSFGVWIR 10 I IBV adr CORE 3.1 1 001 0(XC7 ~Ξ

ON roo

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Hυ Peptide Sequence AA Virus Strain Molecule Pos. Motif Al A2.1 A3.2 All A24 ft.

20207 FVGPLTVNEK 10 HBV ayw OL 698 3,11 00057 0015

1 0535 YVCPLTVNEK 10 HBV adr OL 669 " 3,M 00069 0014 1 1075 RLADECLNRR 10 HBV adr POL 601 3,11 0013 00004

1 1086 IVLKLKQCFR 10 HBV adr POL 118.T 3,11 0013 00024

1 0773 PIPSSWAFAK 10 HBV adw ENV 314 3,11 <00003 0010

Figure imgf000043_0001
1 0778 LTVNENRRLK 10 HBV adw OL 702 3,11 00025 00095

* IΛ*

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Peptide Sequence AA Virus Strain Molecule Pos. Motif Al A2.1 A3.2 All A24 υ 1 0118 CTCGSSDLY 9 HCV LORF 1123 3 0 0 0010 ft. —

1 0112 NIVDVQYLY 9 HCV NSI /ENV2 47 060 0 0010 20034 VQDCNCSIY 9 HCV 302 0 54 00005 00003

20035 LTPRCMVDY 9 HCV 605 _ 0 7

1 0145 RVCEKMΛLY 9 HCV I ORF 25*88 ~ 0053

1 0140 DWCCSMSY 9 HCV LORF 2416 0039

2.0036 FΠFKIRMY 9 HCV 626 0012

1.0509 CLSAFSLHSY 10 HCV LORF 2888 ~ 041 00002 0.013 00034 00002

1.0489 TLHGPTPLLY 10 HCV LORF 1617 ~~030 0.11 0.0024

2.0037 .EYVLLLFLL 9 HCV 719 24 1.4

20169 MYVGGVEHRL 10 ' HCV 633 24 0026

2.0170 EYVLLLFLLL 10 HCV 719 24 0.010

1 0139 SVPAEILRK 9 HCV LORF 2269 3,11 0.016 0.87

1 0955 QLFTP5PRR 9 HCV ENV1 290 3,11 075 0.033

1.0090 RLGVRATRK 9 HCV CORE 43 3,11 0.74 016

1.0123 LIFCHSKKK 9 HCV LORF 1391 3,11 054 0.19

1.0122 HUPCHSKK 9 HCV LORF 1390 3,11 0.25 0.010

1 0952 KTSERSQPR 9 HCV CORE 51 3,11 0.16 0064

1.0120 AVCTRGVAK 9 HCV LORF 1183 3,11 0.016 0038

1.0143 EVPCVQPEK 9 HCV LORF 2563 3,11 00019 0033

1 0137 ΓΓRVESENK 9 HCV LORF 2241 3,11 0015 0.0079

1 0957 cirrsLTGR 9 HCV LORF 1042 3,ΪI 00095 0011

1.0496 GVAGALVAFK 10 HCV LORF 1858 3,11 087 1.1

1.0480 HLHAPTGSGK 10 HCV LORF 1227 3,11 057 00051

1.1062 RMYVGGVEHR 10 HCV NS1/ENV2 632 3,11 027 0012

1.0485 HUFCHSKKK 10 HCV LORF 1390 3,11 0.27 0.025

1.0484

IΛ TLCFGAYMSK 10 HCV LORF 1261 3,11 0 17 0.13

ON IΛ 1.1067 GVGIYLLPNR 10 HCV LORF 3002 3.11 00029 0032

**

ON 1.1063 LLFLLLADAR 10 HCV NS1/ENV2 723 3,11 0015 0 ON

Figure imgf000044_0001
o

ON ro o

I Peptide Sequence AA Virus Strain Molecule Pos. Motif Al A2.1 A3.2 All A24 oΛ

00 1 0014 FRDYVDRFY 9 HIV GAG 298 0090 ON

CΛ 20129 IYQYMDDLY 9 HIV 875" 0064

1 0028 TVLDVGDAY 9 HIV POL 802 0.018 <0.0002 0.0056 υ 1.0412 VTVLDVCDAY 10 HIV POL 801 028 0 00004 a. 1.0415 VIYQYMDDLY 10 HIV POL 874 i — 025 00007 00090

20252 VTVLDVCDAY 10 HIV 801 0088

1.0431 EVNIVTDSQY 10 HIV POL 1187 0053

1.0441 LVΛVHVΛSCY 10 HIV POL 1329 0039

1.0442 PAETGQEΓAY 10 HIV POL 1345 0013

20251 ISKIGPENPY 10 HIV 742 0.013

20255 QMAVF1HNFK 10 ' HIV 1,432 3 0.61 0.64

20064 RYLKDQQLL 9 HIV 2,778 24 0.76

20134 RYLKDQQLL 9 HIV 2,778 24 032

20065 TYQIYQEPP 9 HIV 1,033 24 030 en 20131 TYQIYQEPF 9 HIV 1,033 24 0.20

20063 IYQEPFKNL 9 HIV 1,036 24 0.052

20132 IYQEPFKNL 9 HIV 1,036 24 0033

20066 IYQYMDDLY 9 HIV 875 24 0013

10247 IYKRWIILCL 10 HIV 266 24 0.017

20190 IYKRWIILGL 10 HIV 266 24 0.014

2.0249 LYPLASLRSL 10 HIV 506 24 0014

1.0069 KLAGRWPVK 9 HIV POL 1358 3,11 2.7 0069

1.0944 ΛVFIHNFKR 9 HIV POL 1434 3,11 0.17 1.8

1.0092 AIFQSSMTK 9 HIV POL 853 3,11 1.1 0.96

1.0046 IVIWGKTPK 9 HIV POL 1075 3,11 0.085 0.37

1.0079 KLTEDRWNK 9 HIV VIF 1712 3,11 0.013 0.27

1.0027 GIPHPAGLK 9 HIV POL 788 3,11 0.23 0.065

1 0059 QIIEQLIKK 9 HIV POL 1215 3,11 00091 0.16

1.0939 KIWPSYKCR 9 HIV CAG 443 3,11 0.12 0.0005

1.0072 IIATDK3TK 9 HIV POL 1458

** 3,11 0.025 0098

ON 1.0036 MGYELHPDK 9 HIV POL 925 3,11 0064 0096 IΛ 1.0062 YLAWVPAHK 9 HIV POL 1227 3,11 0077 0057

ON ON 1.0938 KIWPSHKCR 9 HIV GAG 443 3,11 0077 <00005

1 0047 FVNTPPLVK 9 HIV POL 1111 3.11 0012 0066

1.0024 NTPVFAIKK 9 HIV i'OL ~7. 2 3,i l 0033 0060

1.0080 TVQCTHGIK 9 HIV ENV 2420 3.11 00021 0.046

1.0013 ILDIRQCPK 9 HIV GAG 287 3.ΪT 0042 00048

Figure imgf000045_0001

ON ro o

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CΛ Peptide Sequence AA Virus Strain Molecule Pos. Motif Al A2.1 A3.2 All A24

1 0015 RDYVDRFYK 9 HIV GAG 2<>Q 3.11 00007 0040 υa. i θQ58 GIIQAQPDK 9 HIV POL Tl99 3,ii <00009 0040

1 0064 VLFLDCIDK 9 HIV POL 1254 3,1 1 0.038 0032

1 0026 LVDFRELNK 9 HIV POL 769 3~ϊl 0011 0.030

1 0078 KWPRRKAK 9 HIV POL 1513 3 1 0029 O.O039

1 0942 MTKILEPFR 9 HIV POL 859 3,11 <0.0008 0016

1.0463 TVYYCVPVWK 10 HIV ENV 2185 3,11 3.8 7.8

1.0418 TVQPIVLPEK 10 HIV POL 935 3,11 0.16 5.6

1.0447 AVFIHNFKRK 10 HIV POL 1434 3,11 066 085

1.0437 KVLFLDCIDK 10 HIV POL 1253 3,11 036 078

1.0408 KLVDFRELNK 10 HIV POL 768 3,11 051 0090

1.0403 KLKPGMDGPK 10 HIV POL 706 3.ΪΪ 0.39 0.076

1.0395 FLGKIWPSYK 10 HIV GAG 440 3,11 0.32 0.024

1 1056 KIQNFRVYYR 10 HIV POL 1474 3,11 0.032 0.21

1.0410 GIPHPAGLKK 10 HIV POL 788 3,11 0011 0.17

1.0426 LVKLWYQLEK 10 HIV POL 1117 3,11 0.056 0.082

1.0398 MIGGICGFIK 10 HIV POL 642 3,11 0.0099 0.055

1.0413 MTKIL.EPFRK 10 HIV POL 859 3,11 0.015 0038

1 0453 WIQDNSDIK 10 HIV POL 1504 3,11 <00005 0.021

1.0394 FLGKIWPSHK 10 HIV GAG 440 3,11 0.020 0.0013

1.1059 IVQQQNNLLR 10 HIV ENV 2741 3,11 00024 0019

1.0417 FTTPDKKHQK 10 HIV POL 909 3,11 <0.0002 0015

1.0405 LVEICTEMEK 10 HIV POL 729 3,11 0.0002 0012

Figure imgf000046_0001
1.0392 LVQNANPDCK 10 HΓV GAG 327 3,11 <0.0002 0011

ON IΛ

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Peptide Sequence AA Virus Strain Molecule Pos. Motif Al A2.1 A3.2 All A24

H 1 0281 GSDCTΠHY 9 P53 226 1 29 5 00010 0029 U a. 1 0667 CTΛKsvTcn. 10 P53 117 1 033 0 0023 0049 0

1 0672 RVEGNLRVEY 10 p53 196 1 0022 00014 0.0020

1 0278 RVRAMAΓYK 9 p53 J56 3.11 1 5 073

1 0276 CTYSPALNK 9 P53 124 3,11 046 1 1

1 0285 NTSSSPQPK 9 P53 311 3,11 0.0009 0095

1 0284 RTEEENLRK 9 p53 283 3,11 00015 0.091

1 0287 ELNEALELK 9 P53 343 3,11 0020 00052

1 0678 RTEEENLRKK 10 p53 283 3,11 3.3 0.0080

1 1113 KTYQGSYGFR 10 P53 101 3,11 2 6 088

1 1115 WRRCPHHER 10 P53 172 3,11 0.099 0.0017

1 0679 NTSSSPQPKK 10 p53 311 3,11 00035 0054

1.1121 RVCACPGRDR 10 p53 273 3,11 0.014 0011

Figure imgf000049_0001
1.1116 GLAPPQHLIR 10 p53 187 3,11 0.013 0.0006

* IΛ* I *Λ* o

ON ro o

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Peptide Sequence AA Virus Strain Molecule Pos. Motif Al A2.1 A3.2 All A24

U 30175 KGEYFVEMY 9 PAP 322 34 <00002 0.0002 0 ft,

30174 LGEYIRKRY 9 PAP 81 1 078 <00002 0.0002 0

30166 ASCHLTELY 9 PAP 311 1 0.77 <0 002 <00002 0.055 0

30163 ESYKHEQVY 9 PAP 95 1 0098 <00002 0.0002 0

3 237 LSELSLLSLY 10 PAP 238 1 14 00026 00004 0

30235 LSELSLLSLY 10 PAP 238 1 12 00005 0.0004 0

30236 LTQLGMEQHY 10 PAP 70 1 0.62 00005 0.015 0.0024 0.0022

3.0238 KGEYFVEMYY 10 PAP 322 1 0.018 0.0057 0089

30230 LVNEILNHMK 10 PAP 263 3 0.056 0.12

30158 ΛTQIPSYKK 9 PAP 274 11 0.10 1.2

30231 ETLKSEEFQK 10 PAP 170 11 <0.0004 0.014

30161 LYFEKGEYF 9 PAP 318 24 2.5

3.0160 LYCESVHNF 9 PAP 213 24 044

3.0159 FYKDFIΛTL 9 PAP 183 24 0.11

CO 3.0162 VYNCLLPPY 9 PAP 302 24 0032

Figure imgf000050_0001
3.0232 PYASCHLTEL 10 PAP 309 24 0024

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Table 5

NO

Sequence Sise Antigen Strain Molecule Frβq Pos. Motif A01 A03 All A24 NO

WI

Bind. Bind. Bind. Bind. NO n

EDTPIGHLY 9 MAGE3a 3 analog 161 A01 12.5000

AVDPIGHLY 9 MAGE3a 3 analog 161 A01 8.0000

EVDPIAHLY 9 MAGE3a 3 analog 161 A01 5.5000

FSPAFDNLYY 10 HER-2/neu 1213 A01 5.5000 0.0005 0.0010

EVDAIGHLY 9 MAGE3a 3 analog 161 A01 5.3500

EVDPIGALY 9 - MAGE3a 3 analog 161 A01 5.0000

EVDPIGHAY 9 MAGE3a 3 analog 161 A01 4.6500 o

EADPIGHLY 9 MAGE3a 3 analog 161 A01 3.4500 *

EVDPTGHLY 9 MAGE3a 3 analog 161 A01 2.9500

EVDPIGHSY 9 MAGE3a 3 analog 161 A01 2.6667

EVDPAGHLY 9 MAGE3a 3 analog 161 A01 2.4000

EVDPASNTY 9 MAGE 4 161 A01 1.5000

PLSEDQLLY 9 PAP 147 A01 1.2000 0.0005 0.0001

LSAFSLHSY 9 HCV 2889 A01 0.8100 0.0002 0.0002

IPSYKKLIMY 10 PAP 277 A01 0.5650

YASCHLTELY 10 PAP 310 A01 0.5467 0.0003 0.0002

EVDP1GHLA 9 MAGE3a 3 analog 161 A01 0.3300 o H

CMQIAKGMSY 10 HER-2/neu 826 A01 0.2967 0.0003 0.0001 CΛ NO 00

VGSDCTTIHY 10 P53 225 A01 0.2600 0.0003 0.0003 © in

©

Figure imgf000052_0001
EVAPIGHLY 9 MAGE3a 3 analog 161 A01 0.1800 NO

Table 5

Sequence Sise Antigen Strain Molecule rrβq Pos. Motif A01 A03 All A24

NO

Bind. Biod. Bind. Bind. NO

■ in

ESHPNPECRy 10 HER-2/heu 280 A01 0.180(3 0.0003 0.0003 VO n

*.

ASCVTACPY 9 HER-2/nβu 293 A01 0.0552 0.0074

0.0008

FSPAFDH Y 9 HER-2/nβu 1213 A01 0.0425 0.0002 0.0002

ASPLDSTFY 9 HER-2/nβu 997 A01 0.0290 0.0002 0.0004

RGTQ FENDY 10 HER-2/nβu 103 A01 0.0205 0.0003 0.0015

PASPLDSTFY 10 HER-2/neu 996 A01 0.0148 0.0003 0.0001

PSQKTYQGSY 10 p53 98 A01 0.0140 0.0003 0.0003

KSTKVPAAY 9 HCV 1236 A01 0.0134 0.0009 0.0001

DSSVLCECY 9 HCV 1513 A01 0.0110 0.0002 0.0003

KISEYRHYCY 10 HPV 16 E6 79 A01 0.0090 0.0043 0.0038

NLYVS M LY 10 HBV adw POL 20 1088 A01 0.0090

GTRVRAMAIY 10 p53 154 A01/03 0.0027 0.0365 0.0002

LTCGFADLMGY 11 HCV 126 AOl/11 2.4500 0.0003 0.0120 0.0001

VMAGVGSPY 9 HER-2/neu 773 A01/A03 0.0400 0.0575 0.0079

TLWKAG1LY 9 HBV adr POL 100 724 A03 0.0017 0.2667 0.0016

KLN ASQIY 9 HIV POL 958 A03 0.0070 0.1160 0.0006 o0

LVGFLLLKY 9 MAGE1 1 109 A03 0.0033 0.0563 0.0012 CΛ

NO

00

ILRGTSFVY 9 HBV adr POL 80 1345 A03 0.0017 0.0440 0.0002 o o IΛ

RVLOGLPREY 10 HER-2/neu 545 A03 0.0015 0.0350 0.0050 w

Figure imgf000053_0001
VO

Table 5

Sequence Sise Antigen . Strain Molecule Prβq Pos. Motif A01 A03 All A24

NO NO

Bind. Bind. Bind. Bind. n vo

QLVTQLMPY 9 HER-2/neu 795 A03 0.0024 0.0112 0.0039 in i-

GLNKIVRMY 9 HIV GAG 274 A03 0.0017 0.0103 0.0002

LLGDNQVMPK 10 MAGE2 2 182 A03 0.0093 0.0014

QVRDQAEHLK 10 HIV POL 1419 A03 0.0089 0.0093

LVSAGI K 8 HIV con 1246 A03 0.0091 0.0054

VTDRGRQK 8 HIV con 1153 A03 0.0090 0.0065

TVFDAKRLIGR 11 BLA-A 68 endogenous peptide sequences A03/11 0.1050 1.3000

KTGGPIYKR 9 HLA-Aw68 endogenous peptide sequences A03/11 0.0340 0.8200

SLYTKWHY 9 PSA 237 A03/11 0.0017 0.6750 0.0140 NJ

AVAAVAARR 9 HLA-Aw68 endogenous peptide βequenceβ A03/11 0.1600 0.0825

KIQNFRVYY 9 HIV POL 1474 A03/11 0.0056 0.1190 0.1350

EMLESVIKNYK 11 MAGE1 127 A03/11 0.0087 0.0099

EVAPPEYHRK 10 HLA-Aw68 endogenous peptide βequences All 0.0008 0.0575

ETAYFLLK 8 HIV consensus 1351 All 0.0037 0.0425

RWGLLLALL 9 HER-2 neu 8 A2 1.2567

PYVSRLLGI 9 HER-2/neu 780 A24 0.1650

VYMIMVKCW 9 HER-2/neu 951 A24 0.1640 o

AYSLTLQGL 9 HER-2/neu 440 A24 0.1250

SYGVTVWEL 9 HER-2/neu 907 A24 0.1200 CΛ

NO

0 —0

L ISAWPDSL 10 HER-2/neu 410 A24 0.0835 © uoi

VWSYGVTVW 9 HER-2/neu 905 A24 0.0800 NO

Figure imgf000054_0001

Table 5

Sequence Sise Antigen Strain Molecule rrβq Pos. Motif A01 A03 All A24

Bind. Bind. Bind. Bind. in n

SYGVTVWELM 10 HER-2/neu 907 A24 0.0630

QYLAGLSTL 9 HCV 1777 A24 0.0475

TYLPTNASL 9 HER-2/neu 63 A24 0.0375

EYLVSFGVWI 10 HBV NUC 90 117 A24 0.0335

KFMLCAGRH 9 PSA 190 A24 0.0305

WFHISCLTF 9 HBV NUC 90 102 A24 0.0300

TYSTYGKFL 9 HCV 1296 A24 0.0225

VYMIMVKCWM 10 HER-2/neu 951 A24 0.0218

RFRELVSEF 9 HER-2/neu 968 A24 0.0180

CYGLGMEHL 9 HER-2/neu 342 A24 0.0176

QYSPGQRVEF 10 HCV 2614 A24 0.0175

K HALESIL 9 HER-2/neu 887 A24 0.0149

EYLVPQQGFF 10 HER-2/neu 1022 A24 0.0120

RYSEDPTVPL 10 HER-2/neu 1111 A24 0.0117

Figure imgf000055_0001
RFTHQSDVW 9 HER-2/neu 898 A24 0.0107

-0 o

H

CΛ 00

© o UI t*)

Table 5

Mage vo

Sequence AA Strain Mol. Pos. Motif Al A2.1 A3.2 All A24 NO in

DLVGFLLLK 9 108 3,11 0.0040 0.0014 NO UI

QLVFGIDVK 9 152 3,U 0.0019 0.0051

SLEQRSLHCK 10 2 3,11 0.015 0.015

SLFRAVITKK 10 96 3,11 1.2 0.98

DLVGFLLLKY 10 108 1 0.0068 0.0069 0.0009

MLESVIKNYK 10 128 3,11 0.14 0.027

WEELSVMEVY 10 1 215 1 <0.0009 <0.0002 <0.0002

VYDGREHSAY 10 223 1 <0.0009

LVGFLLLKY 9 109 1 0.0033 0.056 0.0012

LVTCLGLSY 9 171 1 0.0084 0.0014 <0.0002

VLVTCLGLSY 10 170 1 0.0048 0 0.0013 0.0007

FLLLKYRAR 9 1/2/3 112 3,11 0.0007 <0.0005

PTTINFTRQR 10 65 3,11 <0.0002 0.0033

LVGFLLLKYR 10 109 3,11 0.0034 0.0023

EKYLEYGRCR 10 246 3,11 <0.0002 0

ELVHFLLLK 9 2/3 108 3 0.0045 0.0011

AYGEPRKLL 9 231 24 0.0007

SYVLVTCLGL 10 168 24 0.0006 0.0051 n "0

EWPISHLY 9 161 1 0.0028 <0.0002 <0.0002

CΛ NO

EWRIGHLY 9 161 1 0.0002 00

© UI

EVDPASNTY 9 161 1 0.0005 © I

NO

Figure imgf000056_0001
EADPTSNTY 9 5/51 161 1 9.9 0.0006 0.0006 0

Table 5

Mage

Sequence AA Strain Mol. Pos. Motif Al A2.1 A3.2 All A24

EVDPIGHVY 9 6 161 1 1.9 <0.0002 <0.0002 0 - 4i». UI

EMLESVIK 8 1 127 3 <0.0003 0 Ui

LVFGIDVK 8 1 153 3 0.0035 0.0037

GVQGPSLK 8 1 266 3 <0.0003 0.0063

VMEVYDGR 8 1 220 3 <0.0003 0.0007

VQEKYLEY 8 1 244 1 0.0018

AYGEPRKL 8 1 231 24 0.0017

VKEADPTGHSY 11 - 1 159 1 <0.0003

IWEELSVMEVY 11 1 214 1 <0.0003 Xjx

EMLESVIKNYK 11 1 127 3 0.0087 0.0099

EADPTSHTY 9 analog 161 1 0.68

EVDPTSNTY 9 analog 161 1 1.8

EALEAQQEA 9 1 14 2.1 0 <0.0002 0

MSLEQRSLH 9 1 1 3 0.0025 0.0003

QSPQGASAF 9 1 56 3 0.0004 0

SAFPTTINF 9 1 62 3 <0.0003 0 0.0003

TSCILESLF 9 1 90 3 <0.0003 0

SCILESLFR 9 1 91 3 <0.0003 0.0026 l-0

LFRAVITKK 9 1 97 3 0.011 0.0005 o

VGFLLLKYR 9 1 110 3 0.0044 0.0051 00

ESVIKNYKH 9 1 130 3 <0.0003 0 o Ui

O

VIKNYIHCF 9 1 132 3 <0.0003 0 w

Figure imgf000057_0001

Table 5

Mag*

Sequence AA Strain Mol. Pos. Motif Al A2.1 A3.2 All A24

NO

ASESLQLVF 9 1.2 147 3 <0.0003 0 NO in

LGDNQIMPK 9 183 3 0.0007 0.0048 NO I

VMIAMEGGH 9 200 3 <0.0003 0

YDGREHSAY 9 224 3 <0.0003 0

LTQDLVQEK 9 239 3 <0.0003 0.14

CGVQGPSLK 9 265 3 <0.0003 0.0037

EMLESVIKNY 10 127 1 0.0006 <0.0002 <0.0002 0

KEADPTGHSY 10 *- J 160 1 <0.0005 <0.0002 <0.0002

ASAFPTTINF 10 61 3 <0.0003 <0.0002

AFPTTINFTR 10 63 3 <0.0003 0.0003 ON

PTTINFTRQR 10 65 3 <0.0003 0.0002

STSCILESLF 10 89 3 <0.0003 <0.0002

GFLLLKYRAR 10 111 3 0.0019 0.0008

KAEMLESVIK 10 125 3 <0.0003 0.0097

SVIKNYKHCF 10 131 3 <0.0003 <0.0002

KASESLQLVF 10 146 3 <0.0003 <0.0002 0.0012

DVKEADPTGH 10 158 3 <0.0003 <0.0002

LVMIAMEGGH 10 199 3 0.0008 0.0005

LSVMEVYDGR 10 218 3 <0.0003 0.012 o -0

H

VMEVYDGREH 10 220 3 <0.0003 0.0002 0

CΛ NO

YGRCRTVIPH 10 251 3 <0.0003 <0.0002 00

©"

U

SCGVQGPSLK 10 264 3 0.0005 0.0089 oI

Figure imgf000058_0001
>

NO

Table 5

Mag*

Sequence AA Strain Mol. Pos. Motif Al A2.1 A3.2 All A 4

VPDSDPARY 9 new 254 1 0.0038

QVPDSDPAR 9 new 254 3 <0.0003 0.0002 Ui

.fe.

VIKVSARVR 9 new 284 3 0.0016 0

PSLREAALR 9 new 296 3 <0.0003 0

EFLWGPRAL 9 new 264 24 0.0006

ETSYVKVLEY 10 new 274 1 0.56

LVQEKYLEYR 10 new 243 3 0.0008 0.0043

QVPDSDPARY 10 new 254 3 0.0014 0.0003

YVKVLEYVIK 10 new 277 3 0.0029 0.0015

YVIKVSARVR 10 new 283 3 0.019 0.0009

RALAETSYVK 10 new 270 11 0.18 0.24

SYVKVLEYVI 10 new 276 24 0.036

FFPSLREAAL 10 new 294 24 0.0044

SVIKNYK 7 1 N POL 131 3,11 0.0006 0.0028

PVTKAEMLESVIK 13 1 n E6 122 3,11 <0.0003 0

ETSYVKVLEYVIK 13 1 n E6 273 3,11 0.0044 0.0003

ITKKVADLVGFLLLK 15 1 n POL 102 3,11 0.40 1.0

VTKAEMLESVIKNYK 15 1 n POL 123 3,11 0.024 0.053

WGNWQYFFPVIFSK 15 3 POL 79 3,11 1.6 0.34 •V

O

PRALAETSY 9 1 new 268 1 <0.0018 <0.0003 <0.0002

FATCLGLSY 9 3 171 1 0.038 <0.0003 0.0004 00

©

UI

LEQRSLHCK 9 1 new 3 3 <0.0002 0 o

Figure imgf000059_0001

Table 5

Maga

Sequence AA Strain Mol. Pos. Motif Al A2.1 A3.2 All A 4

NO

AEMLESVIK 9 new 126 3 <0.0002 0.0011 NO U *»I.

LESVIKNYK 9 new 129 3 <0.0002 0.0018 NO UI

EELSVMEVY 9 new 216 3 <0.0002 0

MEVYDGREH 9 new 221 3 <0.0002 0

DSDPARYEF 9 new 256 3 •θ.0002 0

KVSARVRFF 9 new 285 3 0.0005 0

VSARVRFFF 9 new 286 3 0.0003 0.0026

HSPQGASSF 9 - 2 56 3 <0.0002 0

TTINYTLWR 9 2 66 3 0.089 1.1

00

QEEEGPRMF 9 2 83 3 <0.0002 0

MFPDLESEF 9 2 90 3 <0.0002 0 0.014

SEFQAAISR 9 2 96 3 <0.0002 0.0001

EFQAAISRK 9 2 97 3 <0.0002 0.0002

LVHFLLLKY 9 2,3 109 3 0.043 0.010

AEMLESVLR 9 2 126 3 <0.0002 0

SVLRNCQDF 9 2 131 3 <0.0002 0

VLRNCQDFF 9 2 132 3 <0.0002 0

DFFPVIFSK 9 2 138 3 <0.0002 0.0022

VIFSKASEY 9 d

2 142 3 0.081 0.033 O H

WE PISH 9 2 159 3 0.0007 0.010

CΛ NO

LGDNQVMPK 9 2 183 3 <0.0002 0.0061 00

©

UI

EGDCAPEEK 9 2,3 205 3 <0.0002 0 ©

Figure imgf000060_0001
UI NO

Table 5

Mage

Sequence AA Strain Mol. Pos. Motif Al A2.1 A3.2 All A24

QEEEGPSTF 9 3 83 3 <0.0002 0

UI

TFPDLESEF 9 3 90 3 <0.0002 0 0.0049

SEFQAALSR 9 3 96 3 <0.0002 0

EFQAALSRK 9 3 97 3 <0.0002 0.0001

SWGNWQYF 9 3 131 3 <0.0002 0

WGNWQYFF 9 3 132 3 0.0022 0.0021

YFFPVIFSK 9 3 138 3 0.0020 0.027

ASSSLQLVF 9 , 3 147 3 0.0011 0.0089

LMEVDPIGH 9 3 159 3 <0.0002 0

IIVLAIIAR 9 3 196 3 0.0069 0.0011

VQEKYLEYR 9 1 244 11 <0.0002 0 vo

SNQEEEGPR 9 2 81 11 <0.0002 0

NYKHCFPEI 9 1 new 135 24 4.8

IFGKASESL 9 1 new 143 24 0.0013

GFLIIVLVM 9 1 new 193 24 <0.0002

IFSKASEYL 9 2 143 24 0.023

EYLQLVFGI 9 2 149 24 3.5

NWQYFFPVI 9 3 135 24 0.53

IFSKASSSL 9 3 143 24 0.016 *0 o

LGSWGNHQY 10 3 129 1 <0.0020 <0.0003 0.0012

IFATCLGLSY 10 3 170 1 <0.0002 0.0005 0.0004 00

©

Ui

TSCILESLPR 10 1 new 90 3 <0.0002 0.015 o

Figure imgf000061_0001
UI

Table 5

Mage

Sequence AA Strain Mol. Pos. Motif Al A2.1 A3.2 All A24

LESVIKNYKH 10 new 129 3 <0.0002 <0.0002

U ϋl o

REHSAYGEPR 10 new 227 3 <0.0002 <0.0002 Ul

4-.

PDSDPARYEF 10 new 255 3 <0.0002 <0.0002

LEYVIKVSAR 10 new 280 3 <0.0002 <0.0002

VIKVSARVRF 10 new 283 3 <0.0002 <0.0002

KVSARVRFFF 10 new 285 3 0.0013 0.0020

STTINYTLWR 10 2 65 3 0.0014 0.091

SSNQEEEGPR 10 - 2 80 3 <0.0002 <0.0002

RMFPDLESEF 10 2 89 3 <0.0002 <0.0002 0.0016

ESEFQJVAISR 10 2 95 3 <0.0002 <0.0002

SEFQAAISRK 10 2 96 3 0.0012 0.0028 o

ISRKMVELVH 10 2 102 3 <0.0002 <0.0002

VELVHFLLLK 10 2 107 3 0.0009 0.0003

ELVHFLLLKY 10 2,3 108 3 0.0066 0.0003

LVHFLLLKYR 10 2 109 3 0.026 0.0022

HFLLLKYRAR 10 2,3 111 3 0.0014 0.0002

KAEMLESVLR 10 2 125 3 <0.0002 0.0009

ESVLRNCQDF 10 2 130 3 <0.0002 <0.0002

SVLRNCQDFF 10 2 131 3 <0.0002 <0.0002 n

H

NCQDFFPVIF 10 2 135 3 <0.0002 <0.0002 00

QDFFPVIFSK 10 2 137 3 <0.0002 0.0083 © Ui

©

PVIFSKASEY 10 2 141 3 0.016 0.0033 U)

Figure imgf000062_0001

Table 5

Hag*

Sequence AA Strain Mol. Pos. Motif Al A2.1 A3.2 All A2

KASEYLQLVF 10 2 146 3 <0.0002 <0.0002 0.0030

158 3 <0.0002 <0.0002 i~

E E PISH 10 2

VEWPISHLY 10 2 160 3 <0.0002 <0.0002

ILVTCLGLSY 10 2 170 3 0.0036 0.0002

LLGDNQVMPK 10 2 182 3 0.0093 0.0014

IEGDCAPEEK 10 2 204 3 <0.0002 <0.0002

STFPDLESEF 10 3 89 3 <0.0002 <0.0002

ESEFQAALSR 10 - 3 95 3 <0.0002 <0.0002

SEFQAALSRK 10 3 96 3 0.0010 0.0010

LSRKVAELVH 10 3 102 3 <0.0002 <0.0002 O

AELVHFLLLK 10 3 107 3 0.0008 <0.0002

LVHFLLLKYR 10 3 109 3 0.040 0.0014

GSWGNWQYF 10 3 130 3 0.0020 0.0008

SWGNWQYFF 10 3 131 3 0.0085 0.0067

KASSSLQLVF 10 3 146 3 0.0003 0.0008 0.0021

ELMEVDPIGH 10 3 158 3 <0.0003 <0.0002

MEVDPIGHLY 10 3 160 3 0.0004 0.0004

VDPIGHLYIF 10 3 162 3 <0.0003 <0.0002 o

LIIVLAIIAR 10 3 195 3 0.028 0.0021 H

REGDCAPEEK 10 3 204 3 <0.0003 <0.0002 00

RQPSEGSSSR 10 ©

1 new 74 11 0.0009 0.0009 Ul

Figure imgf000063_0001
LQLVFGIDVK 10 1 new 151 11 0.0050 0.0018

Table 5

Mage

Sequence AA Strain Mol. Pos. Motif Al A2.1 A3.2 All A24

NO

NO

RQVPDSDPAR 10 1 new 252 11 <0.0003 <0.0002 USl

NO

MNYPLWSQSY 10 3 new 68 11 <0.0003 <0.0002 uι

GFLIIVLVMI 10 1 new 193 24 0.0008

SFSTTINYTL 10 2 63 24 0.015

EFQAAISRKM 10 2 97 24 <0.0002

LYILVTCLGL 10 2 168 24 0.014

NWQYFFPVIF 10 3 135 24 0.017

AVDPIGHLY 9 , 3 analog 161 1 8.0

EADPIGHLY 9 3 analog 161 1 3.5

EVDPASNTY 9 4 161 1 1.5 3

EDTPIGHLY 9 3 analog 161 1 13

EVDPTGHLY 9 3 analog 161 1 3.0

AADSPSPPH 9 2 55 All

VPISHLYIL 9 2 170 PI

MPKTGLLII 9 2 196 PI

SMLEVFEGR 9 2 226 All

DSVFAHPRK 9 2 236 All

VFAHPRKLL 9 2 238 A24

MQDLVQENY 9 2 247 A01 O H

DPACYEFLW 9 2 265 P2 CΛ

NO 00

FLWGPRALI 9 2 271 A02 © o Ul

ALIETSYVK 9 2 277 A03/A11 Ul

Figure imgf000064_0001
VO

Table 5

Mage

Sequence AA Strain Mol. Pos. Motif Al A2.1 A3.2 All A NO NO S

TSYVKVLHH 9 2 281 All Ul

VO

Ul

EPHISYPPL 9 2 296 PI

ISYPPLHER 9 2 299 A03/A11

YPPLHERAL 9 2 301 PI

EPVTKAEML 9 2/3 128 PI

VPGSDPACY 9 2/3 261 P2

EGLEARGEA 9 3 14 A03

GLEARGEAL 9 - 3 15 A02

EARGEALGL 9 3 17 A02

ALGLVGAQA 9 3 22 A02/A03 u>

GLVGAQAPλ 9 3 24 A02/A03

LVGAQAPAT 9 3 25 A02

PATEEQEAA 9 3 31 A02/A03

EAASSSSTL 9 3 37 A02

AASSSSTLV 9 3 38 A02

LVEVTLGEV 9 3 45 A02

EVTLGEVPA 9 3 47 A02/A03

VTLGEVPAA 9 3 48 A02/A03 *n0

LPTTMNYPL 9 3 71 PI

PDLESEFQA 9 3 99 A03 CΛ vo 00

©

HFLLLKYRA 9 3 118 A03 Ul

©

Ul

Figure imgf000065_0001
FFPVIFSKA 9 3 146 A03

Table 5

Mage

Sequence AA Strain Mol. Pos. Motif Al A2.1 A3.2 All A24

NO NO

DPIGHLYIF 9 3 170 P2 Ul

NO

GDNQIMPKA 9 3 191 A03 Ul

MPKAGLLII 9 3 1 6 PI

AGLLIIVLA 9 3 199 A03

KIWEELSVL 9 3 220 A02

SVLEVFEGR 9 3 226 A03/A11

EDSILGDPK 9 3 235 A03/A11

SILGDPKKL 9 , 3 237 A02

ILGDPKKLL 9 3 238 A02

FLWGPRALV 9 3 271 A02

O

PRALVETSY 9 3 275 A01

RALVETSYV 9 3 276 A02

ALVETSYVK 9 3 277 A03/A11

LVETSYVKV 9 3 278 A02

YVKVLHHMV 9 3 283 A02

KVLHHMVKI 9 3 285 A02

MVKISGGPH 9 3 290 A03/A11

ISGGPHISY 9 3 293 A01/A03/A11

GPHISYPPL 9 3 296 PI o H

YPPLHEWVL 9 3 301 PI CΛ NO 00

VPISHLYILV 10 2 170 PI © Ui

©

MPKTGLLIIV 10 2 196 PI Ul

Figure imgf000066_0001
NO

Table 5

Mage

Sequence AA Strain Mol. Pos. Motif Al A2.1 A3.2 All A24

S;

VFEGREDSVF 10 2 230 A24

HPRKLLMQDL 10 2 241 PI

LMQDLVQENY 10 2 246 A01

EFLWGPRA I 10 2 270 A24

GPRALIETSY 10 2 274 P2

RALIETSYVK 10 2 276 All

SYVKVLHHTL 10 2 282 A24

SYPPLHERAL 10 * 2 300 A24

APEEKIWEEL 10 2/3 216 PI

PLEQRSQHCK 10 3 2 A03/A11

HCKPEEGLBA 10 3 9 A03

EARGEALGLV 10 3 17 A02

RGEALGLVGA 10 3 19 A03

EALGLVGAQA 10 3 21 A02/A03

LGLVGAQAPA 10 3 23 A03

GLVGAQAPAT 10 3 24 A02

QAPATEEQEA 10 3 29 A02/A03

EAASSSSTLV 10 3 37 A02 *3 O

TLVEVTLGEV 10 3 44 A02 H

EVTLGEVPAA 10 3 47 A02/A03 CΛ 00

PDPPQSPQGA 10 3 59 A03 ©

Ul o

Figure imgf000067_0001
LPTTMNYPLW 10 3 71 P2

Table 5

Mage

Sequence AA Strain Mol. Pos. Motif Al A2.1 A3.2 All A24 NO VO

PDLESEFQAA 10 3 99 A03 Ul

VO Ul

YFFPVIFSKA 10 3 145 A03

LGDNQIMPKA 10 3 190 A03

MPKAGLLIIV 10 3 196 PI

EVFEGREDSI 10 3 229 A02

EDSILGDPKK 10 3 235 A03/A11

SILGDPKKLL 10 3 237 A02

ILGDPKKLLT 10 - 3 238 A02

GDPKKLLTQH 10 3 240 A03/A11 ON O

DPKKLLTQHF 10 3 241 P2

LTQHFVQENY 10 3 246 A01/A03/A11

FVQENYLEYR 10 3 250 A03/A11

ACYEFLWGPR 10 3 267 A03/A11

GPRALVETSY 10 3 274 P2

RALVETSYVK 10 3 276 A03/A11

ALVETSYVKV 10 3 277 A02

LVETSYVKVL 10 3 278 A02

YVKVLHHMVK 10 3 283 A03/A11

MVKISGGPHI 10 3 290 A02 O

H

KISGGPHISY 10 3 292 A01 CΛ

NO 00

SPPHSPQGA 9 2 60 P2A ©

Ul

©

Ul

APATEEQEA 9 3 30 P2A NO

Figure imgf000068_0001

Table 5

Mage

Sequence AA Strain Mol. Pos. Motif Al A2.1 A3.2 All A24

VO NO

DPPQSPQGA 9 3 60 P2A i USl

NO

APATEEQQTA 10 2 30 P2A Ul

J-

FPDLESEFQA 10 2/3 98 P2A

APATEEQEAA 10 3 30 P2A

DPIGHLYIFA 10 3 170 P2A

EADPTGHSY 9 1 161 1 0.56 0 0 0.0002 <0.0002

KVADLVGFLL 10 1 105 0.0005 0.041 0.0039 0.0030 0.0070

ASSLPTTMNY 10 , 3 8 1 2.3 0.043

TQDLVQEKY 9 1 240 1 0.57 0.0001 0 0 0

LVQEKYLEY 9 1 243 3 016 0 0.0016 0.0098 0 σv

ILLWQPIPV 9 3 <0.0007 1.4 0.0048 0.0048 0

EVDPIGHLY 9 3 3.7 0.0022

ASSFSTTINY 10 2 8 1 0.016 0 0.0016 0.0054 0

VTCLGLSY 8 1 172 1 0.022 0 0.0001 0.0007 0

SSLPTTMNY 9 3 9 1 0.037 0 0.013 0.12 0

GSWGNWQY 9 3 77 1 0.0059 0 0.0009 0.025 0

DLVQEKYLEY 10 1 new 242 3 0 0 0.0010 0 0

SSFSTTINY 9 2 9 1 0.016 0 0.0095 0.056 0

*

MLESVIKNY 9 1 128 1 0.0016 0.0002 0.0006 0 0 n0

KHVELVHFL 9 2 <0.0007 0.13 0.0007 0 0.0043 CΛ NO 0

KMVELVHFLL 10 2 105 <0.0008 0.071 0.0004 0.0001 0.0008 -—0

©

Ui β

LVFGIBLMBV 10 3 0.0030 0.065 0.0007 0 0 Ul

Figure imgf000069_0001
NO

Table 5

Mage

Sequence AA Strain Mol. Pos. Motif Al Λ2.1 A3.2 All A24

NO NO

SLFRAVITK 9 96 3,11 <0.0007 0.0001 3.9 2.6 0

Ul

NO

ADLVGFLLLK 10 107 3 0.0012 0.0003 0.0081 0.022 0 Ul

ESLFRAVITK 10 95 3 <0.0008 0 0.0090 0.0052 0

MLESVIKNYK 10 0 0 0.034 0.0045 0

LVGFLLLK 8 109 3 0.0029 0.0002 0.027 0.034 0

TTINFTRQR 9 66 3,11 0 0 0.051 0.40 0

LLGDNQIMPK 10 1/3 182 3,11 <0.0007 0.0001 0.022 0.016 0

SVMEVYDGR 9 219 3,11 <0.0006 0 0.059 0.32 0

HSAYGEPRK 9 229 3 0.0007 0 0.0070 0.0015 0

LLTQDLVQEK 10 238 3,11 <0.0007 0 0.0014 0.011 0 O

00

LTQDLVQEK 9 239 3,11 0.0011 0 0.0002 0.16 0

NYKHCFPEIF 10 135 24 0 0 0 0 0.26

LYIFATCLGL 10 115 24 <0.0007 0 0.0006 0 0.0035

NYPLWSQSY 9 16 24 <0.0006 0 0 0.0001 0.016

SYVLVTCL 8 168 24 0.0029 0.00025 0.0020 0.0002 0.0026

ETSYVKVLEY 10 0.075 0 0.0009 0.0004 0

TSYVKVLEY 9 275 3 0.082 0 0.23 0.013 0

FLWGPRALA 9 <0.0006 0.027 0.0015 0 0

•d

ALAETSYVKV 10 271 <0.0007 0.017 0.0011 0.0029 0 O H

RVRFFFPSLR 10 290 3 <0.0007 0 0.25 0.0035 0 CΛ vo 00

ALAETSYVK 9 <0.0006 0.0002 0.17 0.39 0 © Uol

LTQDLVQEKY 10 239 1 0.041 0 0 0.0002 0 Ul

Figure imgf000070_0001
VO

Table 5

Mage

Sequence AA Strain Mol. Pos. Motif Al A2.1 A3.2 All A24

NO NO

GFLLLKYRA 9 1 0.0004 0.0002 Ul

NO Ul

CFPEIFGKA 9 1 0 0 £>.

FFFPSLREA 9 1 0 0

FFPSLREAA 9 1 0 0

HCFPEIFGK 9 1 138 3,11 0.0017 0.0022

RSLHCKPEEA 10 1 0.0001 0.0008

EFLWGPRALA 10 1 0 0

RFFFPSLREA 10 , 1 0.0004 0

Figure imgf000071_0001
FPFPSLREAA 10 1 0 0 o

NO

O

H

NO 00

©

Ul

©

Ul

NO

Table 5

Sequence Antigen Strain Molecule Position Molif Al A2 A3 All A 24 MJIX. Binding Binding Binding Binding Binding Binding

FSPAFDNLYY c-ErbB2 1213 AOI 5.5000 , 00005 0.0010 5.5000

CMQIAKG SY c ErbB2 826 AOI "0.2967" ~t)(MH)3~ OOlMΪi 02967 NO NO

ESMPNPEGRY c-ErbB2 280 Aθi 0.Ϊ800 00003 00003 "ii J 00 in

NO in

ASCVTACPY c EιbB2 " 293 ΛOI 00552 00(H)8 00074 00552

FSPAFDNLY L ιbB2 12 i 3 AOI 0.0425 ii (MMΪ () (MΪ02 " 00425

ASPLDSTFY t-EιbB2 "997 Alii 00290 (j ()002~ 00004 "00290

RGTOLFEDNY c EιbB2 io A(ii 00205 00003" n (it)i 5 (10205

PASPLDSTΓY c-iϊιbB2 996 λiiP "θ()i48 oiiooi" 00001 00148

LSAFSLHSY iicv 2889 " A«)i )8U)0 001)02 ~ ij iii 102" 08UH)

KSTKVPAAΫ iicv i2Ϊfi A(ii" 7)0J 4 ϊ) 0009 ooooi " IMIM4

DSSVLCECY- "~ iicv Ϊ5M AOI 0.0110 0(KKJ2 O(MM)3 o.oiio

ETDPIGHLY MAGE-3a 3 analog "Ϊ6i A i 12.5000 12.5000

AVDPIGHLY MAGE-3a 3 anaiog "" i6i Aiii 8.0000 " 8 ()()()()

EVDPIAHLY MAGE a " 3 anaiog i6i ΛOI ~5.5θi)0 5.5000

EVDAΪGHLY" MAGE-3a 3 anaiog 161 Aiii 5.35()θ" 53500 σ

EVDPIGALY MAGE-3a 3 analog i6i AOΪ Tθ()OD 50000

EVDPIGUAY MAGE-.la 3 anaiog J6I Aiii 4"65(Hi 46500

EΛDPIGIII.Y AGE-Ja 3 anaiog i6i AOΪ 3.4500 " 4500

EVDPTGHLY MAGE-3a 3~ anaiog 161 Aiii 2.9500 29500

EVDPΪGUS MAGE- a 3" analog i6i Aiii 2.6667" 26667

EVDPAGHLY MAGE-3a 3 anaiog Ϊ6ϊ Aiii 2.4000" 2.4000

EVDPIGHLA MAGE-3a 3 anaiog Ϊ6i Aiii 0.3301) (13101)

EVAPΪGHLY MAGE-Ja 3 anaiog iόi ΛOI O.iWM)" - 01800

EVDPASNTY AGE-4 4 Ϊ6i ΛOI ϊ.500() " I 5000 O

H

VGSDCTTIHY p53 225 AOI 0.2600 0 (KK)3 0.0003 n.2 (itϊ

PSQKTYQGSY p53 98 AOI 0.0 ϊ 4(7 0.0003 0.0003 0.0140 NO o^o^

PLSEDQLLΫ PAP 147 AOΪ 1.2000" "0.0005 0.000*1 i.2000 ©

— — n

©

IPSΫKKL1MY~ PAP 277 AOΪ 0.5650 05650 Ol

NO

Figure imgf000072_0001
YASCHLTELY AP" 310 AOI 0.5467 ό.oδoT 0.0002 0.5467

Table 5

Sequence Antigen Strain Molecnle Position Motif Al A2 A3 All Λ24 Max. Binding Binding Binding Binding Binding Binding

RVLQGLPREY -ER 2 545 A03 0.0015 00350 00050 00350

NO

QLVTQLMPΫ c ERB2 795 A03 0()024 00112 00039 00112 NO in

VMΛGVGSPY c !ΞrbB2~ 773 A03 Ϊ) 04(H) 00575" 00079 00575 NO in

II.WKAGILY iinv adr POL" 724 A0 '" ϋ (iiii 7" 02667 OOOKi 02667

ILRGTSFVY iiiiv adr POL i.345 " A03 ii.iio i 7 00440 ~0(M)02 00440

K UWASQIΫ' HIV POL 958 A03 0.0070 o iifiii" ' (10006 (11 K.O ci.NKIVRMY iiiv GAG 274 A03 0.0017 θi() 00002 00ΪII3

I /GFLLLKY MAGE-I i()9 A(i3 ~ 00033 00563 ~ ϊi.CMl ϊ 2 00561

GTRVRAMAlΫ p53 ~ i54 Λ()3 " U.ΪH>27 (i 0365" (i. 002 01)365

KJQNFRVYY iiiv POL 1474 A03/AII 0.0056 0.U90 "iii 350 il.i350

SLYTKVVHY ~~ PSA "" 237 AO.VAli 0.0017 06750 ~'CMIMU 0.6750

LTCGFADlMGY iicv i26 AU 2.4500 00003 (iiii 20 o.iioiii" 2.45(H)

ETAYFLLK iiiv con 1351 AΪΪ 0(H)37 (λ0425 0.0425

RWGLLLALL c-EibB2 8 A24 i.2567 i.2567

PYVSRLLGI c-EιbB2 780 A24 0.i65() 0.1650

VYMΪMVKCW c-EιbB2 951 " A24 0 K.JO 01 (.10

AYSLTLQGL c-EιbB2 440 A24 01250 i) Ϊ250

SYGVTVWEL c-ErbB2 907 A24 01200 01200

LYISAWPDS c ErbB2 4 iii A24 00835 (10835

VWSYGVTVW c-ErbB2 9115 A24 _ 00800 00800

SYGVTVWELM c-ErbB2 907 A24 00630 " 0(16.10

TYLPT ASL '~ c-ErbB2 63 A24 00375 00375

VYMIMVKCWM c EιbB2 951 A24 00218 (UJ2i8

RFRELVSEF c ErbB2 " 968 A 24 ooiϋo 00IK0 n H

CYGLGMEML c-ErbB2 342 A24 (iiii 76 (iiii 76 c CΛ

NO

KWMALEsiL c ErbB2 ~ ~ 887 A24 00149 00149 00

EYLVPQQGFF -Eι l32 r≡ 1022 "Λ24~ 00121) 0.IH20 en

RYSEDPTVPL . _ c-EιbB2 iiii A24 Oθil7 00117 s NO

RFTUQs v ""

Figure imgf000073_0001
c-ErbB2 898 A24 0.0107 00107

Table 5

m ≥:

NO in

Sequence Antigen Strain Molecule Position Mollf Al A2 A3 Al l A 24 Max.

Binding Binding Binding Binding Binding Binding

EYLVSFGVWI HBV NUC 1 17 A24 00335 0.0335

WFHISCLTF IIBV NUC i()2 A24 0.0300 0.0300

QYLAGLSTL iicv _ _ ____ 1777 A24 0.0475 " 0.0475

TYSTYGKFL iicv J296 ~ A24 00225 0.0225

QYSPGQRVEF iicv 2614 A24 0 (M75 " O.OΪ75

KFMLCAGRW PSA 190 A24 iioo 0.0305 0.0305

Figure imgf000074_0001

n

CΛ NO 00 in

©

73 Table 6

AA SEQUENCE SOURCE

9 GLNKΓVRMY HIV GAG 274

9 KLNWASQIY HIV POL 958

9 KIQNFRVYY HIV POL 1474

9 TLWKAGILY HBV adr POL 724

9 ILRGTSFVY HBV adr POL 1345

9 SLYTKWHY PSA 237

9 NTSSSPQPK p53 311

9 NVKIPVAIK C-ERB2 745

10 TLGFGAYMSK HCV LORF 1261

10 GTRVRAMAIY p53 154

10 EAYSPVSTSK HBV adw POL 887

9 QIT IQNFR HIV POL 1471

9 NITGLILTR HIV ENV 2633

9 FLWEWASVR HBV adr ENV 324

9 RTPSPRRRR HBV adr CORE 549

9 SLARGNQGR HBV adr POL 805

10 VAYQATVCAR HCV LORF 1587

10 KTYQGSYGFR p53 101

9 WMCLRRFII HBV ayw 237

9 WMCLRRFII HBV ayw 237-245

9 KFMLCAGRW PSA 190

10 IMPKTGFLII MAGE 1 188

8 ETAYFLLK HIV con 1351

1 1 LTCGFAD1MGY HCV 126

9 CSPHHTALR HBV NUC;XNUCFUS 48

9 VMPKTGLLI MAGE 2 188

9 VMPKTGLLI MAGE2 188-196

9 VAELVHFLL MAGE 3 106

9 IMPKAGLL1 MAGE 3 188

10 VMPKTGLLII MAGE 2 188

10 VMPKTGLLII MAGE2 188-197

Figure imgf000075_0001
74

AA SEQUENCE SOURCE

9 ASCVTACPY c-ErbB2 293

9 VMAGVGSPY c-ErbB2 773

9 ASPLDSTFY c-ErbB2 997

9 FSPAFDNLY c-ErbB2 1213

9 KSTKVPAAY HCV 1236

9 DSSVLCECY HCV 1513

9 LSAFSLHSY HCV 2889

9 PLSEDQLLY PAP 147

9 YAVCDKCLK HPV 16 E6 67

9 CMSCCRSSR HPV 16 E6 143

9 RWGLLLALL c-ErbB2 8

9 TYLPTNASL c-ErbB2 63

9 CYGLGMEHL c-ErbB2 342

9 AYSLTLQGL c-ErbB2 440

9 PYVSRLLGI c-ErbB2 780

9 KWMALESIL c-ErbB2 887

9 RFTHQSDVW c-ErbB2 898

9 VWSYGVTVW c-ErbB2 905

9 SYGVTVWEL c-ErbB2 907

9 VYMIMVKCW c-ErbB2 951

9 RFRELVSEF c-ErbB2 968

9 WFHISCLTF HBV NUC 102

9 TYSTYGKFL HCV 1296

9 QYLAGLSTL HCV 1777

10 IPSYKKLIMY PAP 277

10 RGTQLFEDNY c-ErbB2 103

10 ESMPNPEGRY c-ErbB2 280

10 CMQIAKGMSY c-ErbB2 826

10 PASPLDSTFY c-ErbB2 996

10 FSPAFDNLYY c-ErbB2 1213

10 PSQKTYQGSY p53 98

10 VGSDCTTIHY p53 225

10 YASCHLTELY PAP 310

10 LYISAWPDSL c-ErbB2 410

Figure imgf000076_0001
75

AA SEQUENCE SOURCE

10 SYGVTVWELM c-ErbB2 907

10 VYMIMVKCWM c-ErbB2 951

10 EYLVPQQGFF c-ErbB2 1022

10 RYSEDPTVPL c-ErbB2 1111

10 EYLVSFGVWI HBV NUC 117

10 QYSPGQRVEF HCV 2614

9 VYNFATCGI LCMV glyco 35

9 GYCLTKWMI LCMV glyco 283

9 MFEALPHII LCMV glyco 7

9 IFALISFLL LCMV glyco 43

9 LFKTTVNSL LCMV glyco 342

9 LYTVKYPNL LCMV nucleo 204

9 PYIACRTSI LCMV nucleo 314

10 GYCLTKWMIL LCMV glyco 283

10 AYLVSIFLHL LCMV glyco 446

9 RWCIPWQRL CEA 10

9 IYPNASLLI CEA 101

9 LWWVNNQSL CEA 177

9 LYGPDAPTI CEA 234

9 VYAEPPKPF CEA 318

9 LWWVNNQSL CEA 355

9 LYGPDDPT1 CEA 412

9 TYYRPGVNL CEA 425

9 LYGPDTPI1 CEA 590

9 QYSWRINGI CEA 624

9 TYACFVSNL CEA 652

9 VWKTWGQYW gplOO 152

9 TWGQYWQFL gplOO 155

9 RYGSFSVTL gplOO 479

9 LMAWLASL gplOO 606

9 HWLRLPRIF gplOO 636

9 SYKHEQVYI PAP 96

9 AMTNLAALF PAP 116

9 VFLTLSVTW PSA 2

Figure imgf000077_0001
76

AA SEQUENCE SOURCE

9 TWIG,\APLI PSA 9

9 CYASGWGSI PSA 148

10 YMIMVKCWMI c-ErbB2 952

10 RWCIPWQRLL CEA 10

10 FWNPPTTAKL CEA 27

10 QYSWFVNGTF CEA 268

10 TFQQSTQELF CEA 276

10 VYAEPPKPFI CEA 318

10 YYRPGVNLSL CEA 426

10 QYSWLIDGNI CEA 446

10 SYLSGANLNL CEA 604

10 HFLRNQPLTF gplOO 231

10 LFPPEGVSIW PAP 123

10 TWIGAAPLIL PSA 9

10 HYRKWKDTI PSA 244

9 KLRKPKHKK P. falciparum CSP 104

9 KILSVFFLA P. falciparum EXP-1 2

9 ALFFIIFNK P. falciparum EXP-1 10

9 GTGSGVSSK P. falciparum EXP-1 28

9 VLYNTEKGR P. falciparum EXP-1 99

9 KYKLATSVL P. falciparum EXP-1 73

9 PSENERGYY P. falciparum LSA1 1664

9 FLKENKLNK P. falciparum LSA1 111

9 GVSENIFLK P. falciparum LSA1 105

9 ILVNLLIFH P. falciparum LSA1 12

9 KSLYDEHIK P. falciparum LSA1 1854

Figure imgf000078_0001
77

AA SEQUENCE SOURCE

9 LLIFHINGK P. falciparum LSA1 16

9 QSSLPQDNR P. falciparum LSA1 1676

9 QTNFKSLLR P. falciparum LSA1 94

9 RINEEKHEK P falciparum LSA1 49

9 SLYDEHKK P. falciparum LSA1 1855

9 VLAEDLYGR P. falciparum LSA1 1647

9 VLSHNSYEK P. falciparum LSA1 60

9 FYFILVNLL P. falciparum LSA1 9

9 YYIPHQSSL P. falciparum LSA1 1671

9 PSDGKCNLY P. falciparum TRAP 207

9 LACAGLAYK P. falciparum TRAP 511

9 LLACAGLAY P. falciparum TRAP 510

9 LSTNLPYGR P. falciparum TRAP 122

9 QGINVAFNR P. falciparum TRAP 192

9 RGDNFAVEK P. falciparum TRAP 307

9 RSRKREILH P. falciparum TRAP 262

9 SLLSTNLPY P. falciparum TRAP 120

9 KYLVIVFLI P. falcipamm TRAP 8

9 PYAGEPAPF P. falciparum TRAP 528

Figure imgf000079_0001
78

AA SEQUENCE SOURCE

10 VTCGNGIQVR P. falciparum CSP 375

10 GTGSGVSSKK P. falciparum EXP-1 28

10 LALFFIIFNK P. falciparum EXP-1 9

10 FQDEENIGIY P. falciparum LSA1 1794

10 FILVNLLIFH P. falciparum LSA1 11

10 HVLSHNSYEK P. falciparum LSA1 59

10 KSLYDEHIKK P. falciparum LSA1 1854

10 ALLACAGLAY P. falciparum TRAP 509

10 IIRLHSDASK P. falciparum TRAP 100

10 LLACAGLAYK P. falciparum TRAP 510

10 RLHSDASKNK P. falciparum TRAP 102

9 ILGFVFTLT-NH2 Flu Matrix 59-67

10 KGILGFVFTL- Flu Matrix 57-66 NH2

9 KLQCVPLHV PSA 166-174 P/D

9 KLQCVPLHV PSA 166-174 P/D

9 KLQCVPLHV PSA 166-174 P/D

11 KQVPLRPMTYK 940.03 N-terminal extension

9 LYEIVAKV A2.1 consensus

9 KLAEYVAKV A2.1 consensus

9 KLAEΓVYKV A2.1 consensus

9 KVFEYLINK A3.2 consensus

10 KVFPYALINK A3. consensus

9 AVFAYAAAK A3.2 consensus

9 ALEPAIAKY Al consensus

Figure imgf000080_0001
79

AA SEQUENCE SOURCE

9 YLEPAIAKY Al consensus

9 ALEPYIAKY Al consensus

9 YLEQYIEKY Al consensus

9 GTEKLLAKY Al consensus

9 ATEPAIAKY Al consensus

9 ATNYPAIQK Al l consensus

9 ATNVPAIQK Al l consensus

9 ATNAPYIQK Al l consensus

9 ATNAVYIQK Al l consensus

9 ATNAAYAQK Al l consensus

9 AVNAAYAQK Al l consensus

9 AVNAPYIQK Al l consensus

9 AVNAVYIQK Al l consensus

9 PTDPKLINY Al consensus

9 GTDPKLINY Al consensus

9 YTDPKLINF Al consensus

9 FTDPKLINY Al consensus

9 FTDQAVKY Al consensus

9 YTDQAVIKF Al consensus

9 YTDQKLINF Al consensus

9 STNPKPQKK HCV-core 2-10

11 STNPKPQKKNK HCV-core 2-12

9 SFFPEITYI self pepude of P815 analog, Y2 to F,

9 ATDPNFLLY Al consensus

9 ATDKNFLLY Al consensus

9 ALMEKIYQV A2.1 consensus peptide

9 ALSEKIYQV A2.1 consensus peptide

9 AVYDPIIQK A3.2 consensus peptide

9 AVYDKIIQK A3.2 consensus peptide

9 AVMNPMIQK Al l consensus peptide

Figure imgf000081_0001
80

AA SEQUENCE SOURCE

9 AVMNEMIQK Al l consensus peptide

9 AYMDMVNSF A24 consensus peptide

9 AY1DNVNSF A24 consensus peptide

9 KLAAAAAAK A3 2/A11 poly-A analog

9 DVFRDPALK Aw68 endogenous

9 GYKDGNEYI Lm listenolysin 91- 99

10 MMWYWGPSLY HBV

11 WMMWYWGPSL HBV Y

9 RYLRDQQLL HIV env

8 FLLLKYRA MAGE-1

9 IMPKTGFLI MAGE-1

9 VADLVGFLL MAGE-1

10 IMPKTGFLII MAGE-1

11 FLIIVLVMIAM MAGE-1

11 CILESCFRAVI MAGE-1

9 MYRPDAIQL P Yoeln SSP2 143

10 NYSPNGNTNL P Yoeln SSP2 119

9 KFNPMKTH1 Kd consensus peptide

9 AMKNLDFI Db consensus

9 AMKNLYFI Db consensus analog

11 STLPETYVVRR HCV 141-151 analog

9 QYDDAVYKL Cw4 consensus

10 FQDPQERPRK HPV16 E6

10 VFEFAFKDLF HPV18 E6

9 VVYRDSIPH HPV 18 E6

9 IFEANGNLI Flu HA 240-248

9 IYATVAGSL HA 529-537

Figure imgf000082_0001
81

AA SEQUENCE SOURCE

9 SYIPSAEKI P bergan CS 252- 260

9 KYQAVTTTL Tumour P198 14-22

10 MYPHFMPTNL MCMV pp89 167- 176

9 AYPNVSAKI Lm listenolysm 196- 204

9 AYTGGKINI Lm listenolysm 413- 421

9 SAISSILSK HBV ENV 159

9 QAGFFLLTK HBV ENV 190

9 SALYREALK HBV NUC 64

9 RAKWNNTLK HIV env 370

9 RATQIPSYK PAP 273

9 TAAHCIRNK PSA 58

9 MAVFIHNFK HIV pol 909

9 TAGILELLK HPV 6b El 192

9 RAALLGKFK HPV 6b El 205

9 CATMCRHYK HPV 6b El 406

9 TAACSHEGK Flu HA-1 132

9 NANANSAVK P. fal csp 304

9 GAFKVPGVK LCMV glyco 484

9 RARVHPTTR HBV POL 244

9 CALPFTSAR HBV X 69

9 NMLESILK LCMV nuc 259

9 WMILAAELK LCMV glyco 289

9 EMNLPGRWK HIV pol 107

9 SSLQSKHRK HBV POL 201

9 GSTHVSWPK HBV POL 398

9 TSDLEAYFK HBV X NUC FUS 105

9 ASQIYAGK HIV pol 438

9 ASCDKCQLK HIV pol 769

9 MSLAADLEK LCMV nuc 100

9 VSSKNLMEK Mel tyro 25

Figure imgf000083_0001
82

AA SEQUENCE SOURCE

9 LSTNLPYGK P. fal ssp2 122

9 STDHIPILY Al Nat. Processed

9 STAPPAHGV Breast mucin 9-17

9 LMAVVLASL gplOO

9 WSQKRSFVY gplOO

9 PLDCVLYRY gplOO

10 PSSVGSRSEY gplOO

9 YTAVVPLVY Hu J chain 102-110

Figure imgf000084_0001

83 Table 7

AA SEQUENCE SOURCE

8 LTELYFEK PAP 315

9 TISPSYTYY CEA 419

9 GTGCNGWFY HPV 16/18 El 11

9 LTEMVQWAY HPV6b/ll El 358

9 rrvNNSGSY CEA 289

9 CTGWFMVEA HPV6b/ll El 14

9 ATVQDLKRK HPV6b/ll El 77

10 9 AVESEISPR HPV6b/ll El 101

9 FLNSNMQϋ HPV6b/ll El 393

9 ΓΓRQTVIEH HPV6b/ll El 341

9 ΓVGPPDTGK HPV 6b/ 11 El 476

9 KLIEPLSLY HPV6b/ll El 254

15 9 KLWLHGTPK HPV 6b/ 11 El 462

9 KMSIKQWIK HPV6b/ll El 420

9 WAGFGIHH HPV6b/ll El 238

9 HLFGYSWYK CEA 61

9 ISPSYTYYR CEA 420

20 9 HTQVLFIAK CEA 636

9 ITVYAEPPK CEA 316

9 rrvsAELPK CEA 494

9 RLQLSNGNR CEA 190

9 RLQLSNGNR CEA 546

25 9 RINGIPQQH CEA 628

9 SNMQAKYVK HPV 6b/ 11 El 396

9 EWITRQTVI HPV6b/ll El 339

9 FFERLSSSL HPV6b/ll El 613

9 NWKPIVQFL HPV6b/ll El 439

30 10 PTISPSYTYY CEA 418

10 PTISPLNTSY CEA 240

10 HSASNPSPQY CEA 616

10 KLIEPLSLYA HPV6b/ll El 254

10 AIVGPPDTGK HPV6b/ll El 475

35 10 DCATMCRHYK HPV6b/16El 405

10 KLWLHGTPKK HPV 6b/ 11 El 462

10 WVVAGFGIHH HPV6b/ll El 237

Figure imgf000085_0001
84

AA SEQUENCE SOURCE

10 TΓΓVSAELPK CEA 493

10 TFWNPPTTAK CEA 26

10 TISPSYTYYR CEA 419

10 TISPLNTSYR CEA 241

10 RTLTLFNVTR , CEA 198

10 RTLTLFNVTR CEA 554

10 RTLTLLSVTR CEA 376

10 ATPGPAYSGR CEA 89

10 ASGHSRTTVK CEA 483

10 10 QFLRHQNIEF HPV6b/ll El 445

10 TFTFPNPFPF HPV 6b/ 11 El 586

9 RVDCTPLMY ProstCa PSM 463

9 LLSLYGIHK ProstCa PAP 243

9 SIVLPFDCR ProstCa PSM 590

15 9 KSLYESWTK Prost Ca PSM 491

9 SMKHPQEMK ProstCa PSM 615

9 SLYESWTKK ProstCa PSM 492

9 YSLVHNLTK Prost Ca PSM 471

9 HLTELYFEK ProstCa PAP 314

20 9 RATQIPSYK ProstCa PAP 273

9 ASGRARYTK ProstCa PSM 531

9 SLYGIHKQk ProstCa PAP 245

9 RDYAVVLRK ProstCa PSM 598

9 SSHDLMLLR ProstCa PSA 113

25 9 GAAPLILSR ProstCa PSA 12

9 KIVIARYGK ProstCa PSM 199

9 RAAPLLLAR Prost Ca PAP 2

9 VVLRKYADK ProstCa PSM 602

9 GLPDRPFYR ProstCa PSM 680

30 9 WLDRSVLAK ProstCa PAP 25

9 KVFRGNKVK ProstCa PSM 207

9 IVRSFGTLK ProstCa PSM 398

9 KIYSISMKH ProstCa PSM 610

9 RSVLAKELK ProstCa PAP 28

35 9 STNEVTRIY ProstCa PSM 348

Figure imgf000086_0001
9 GFFLLGFLF ProstCa PSM 31 85

AA SEQUENCE SOURCE

9 LYSDPADYF Prost Ca PSM 227

9 KYADKIYSI Prost Ca PSM 606

9 NYARTEDFF Prost Ca PSM 178

9 AYINADSSI Prost Ca PSM 448

9 SASFCGSPY HBV POL 165

9 AFTFSPTYK HBV POL 655

9 SVVRRAFPH HBV POL 524

9 RWMCLRRFI HBV ENV 236

9 SWLSLLVPF HBV ENV 334

10 9 SWWTSLNFL HBV ENV 197

9 PWTHKVGNF HBV POL 51

9 SFCGSPYSW HBV POL 167

10 NADSSIEGNY Prost Ca PSM 451

10 GLDSVELAHY Prost Ca PSM 104

15 10 RATQIPSYKK Prost Ca PAP 273

10 LGFLFGWFD Prost Ca PSM 35

10 SSIEGNYTLR Prost Ca PSM 454

10 KSLYESWTKK Prost Ca PSM 491

10 SLLSLYGIHK Prost Ca PAP 242

20 10 FLYNFTQIPH Prost Ca PSM 73

10 VIYAPSSHNK Prost Ca PSM 690

10 AVVLRKYADK Prost Ca PSM 601

10 KSPDEGFEGK Prost Ca PSM 482

10 IVRSFGTLKK Prost Ca PSM 398

25 10 RIYNVIGTLR Prost Ca PSM 354

10 LSLYGIHKQK Prost Ca PAP 244

10 MSLLKNRFLR Prost Ca PSA 99

10 ISMKHPQEMK Prost Ca PSM 614

10 RAVCGGVLVH Prost Ca PSA 43

30 10 GSAPPDSSWR Prost Ca PSM 311

10 SIPVHPIGYY Prost Ca PSM 291

10 CSGKIVIARY Prost Ca PSM 196

10 ETYELVEKFY Prost Ca PSM 557

10 RLLQERGVAY Prost Ca PSM 440

35 10 FYDPMFKYHL Prost Ca PSM 565

10 TYSVSFDSLF Prost Ca PSM 624

Figure imgf000087_0001
86

AA SEQUENCE SOURCE

10 LYNFTQIPHL Prost.Ca PSM 74

10 GWRPRRTILF Prost.Ca PSM 409

10 FAAPFTQCGY HBV POL 631

10 RWMCLRRFII HBV ENV 236

10 WFVGLSPTVW HBV ENV 345

10 SWPKFAVPNL HBV POL 392

10 VFADATPTGW HBV POL 686

9 FIFHKFQTK HTLV-I tax 276

9 FLTNVPYKR HTLV-I tax 182

10 9 ΓΓWDPIDGR HTLV-1 tax 54

9 SALQFLIPR HTLV-I tax 66

9 LSFPDPGLR HTLV-I tax 131

9 QSSSFIFHK HTLV-I tax 272

9 GLCSARLHR HTLV-1 tax 34

15 9 RLPSFPTQR HTLV-I tax 74

9 AMRKYSPFR HTLV-I tax 108

9 ISGGLCSAR HTLV-I tax 31

9 ALFTAQEAK HPV 16 El 69

9 ATMCRHYKR HPV 16 El 406

20 9 FMSFLTALK HPV 16 El 453

9 GVSFSELVR HPV 16 El 216

9 KAAMLAKFK HPV 16 El 204

9 LTNILNVLK HPV 16 El 191

9 LVRPFKSNK HPV 16 El 222

25 9 MSFLTALKR HPV 16 El 454

9 NSNASAFLK HPV 16 El 386

9 QMSMSQWIK HPV 16 El 419

9 RLKAICIEK HPV 16 El 109

9 SLFGMSLMK HPV 16 El 484

30 9 SMSQWKYR HPV 16 El 421

9 TAAALYWYK HPV 16 El 315

9 VVLLLVRYK HPV 16 El 274

9 ALLRYKCGK HPV 18 El 284

9 ATMCKHYRR HPV 18 El 413

35 9 CATMCKHYR HPV 18 El 412

9 FITFLGALK HPV 18 El 460

Figure imgf000088_0001
87

AA SEQUENCE SOURCE

9 GVLILALLR HPV 18 El 279

9 KLRAGQNHR HPV 18 El 647

9 LILALLRYK HPV 18 El 281

9 LTTNIHPAK HPV 18 El 571

9 NMSQWIRFR HPV 18 El 428

9 NSNAAAFLK HPV 18 El 393

9 SVAALYWYR HPV 18 El 322

9 WTYFDTYMR HPV 18 El 536

9 YVQAIVDKK HPV 18 El 19

10 9 ID NFDIPK GCDFP-15 36

9 VLAVQTELK GCDFP-15 55

10 IIKNFDIPK GCDFP-15 35

10 TACLCDDNPK GCDFP-15 87

10 AVLAVQTELK GCDFP-15 54

15 10 TFYWDFYTNR GCDFP-15 97

9 ASCHLTELY PAP 311

10 KGEYFVEMYY PAP 322

10 LTAAHCIRNK PSA 57

9 PLYDMSLLK PSA 95

20 9 QVHPQKVTK PSA 182

9 SLLKNRFLR PSA 100

9 YTKVVHYRK PSA 239

9 TLWKAGILY HBV pol 150

9 SLYTKVVHY PSA 237

25 9 PVNRPIDWK HBV POL 612

9 RHYLHTLWK HBV POL 719

11 HTLWKAGILYK HBV POL 149

11 GTDNSVVLSRK HBV POL 735

1 1 RVTGGVFLVDK HBV POL 357

30 8 ATQIPSYK PAP 274

9 WMNSTGFTK HCV consensus

9 RVLEDGVNY HCV consensus

9 RLLAPΓΓAY HCV consensus

9 GVLAALAAY HCV consensus

35 9 RVCEKMALY HCV consensus

Figure imgf000089_0001
88 TABLE 8

PEPTIDE AA SEQUENCE

1235.01 10 AVFDRKSDAK

26.0149 9 CALRFTSAR

26.0153 9 SSAGPCALR

F104.02 9 SLTPPHSAK

F105.01 9 AIFQSSMTK

F105.02 9 GIFQSSMTK

10 F105.03 9 AAFQSSMTK

F105.04 9 AIAQSSMTK

F105.05 9 AIFASSMTK

F105.06 9 AIFQASMTK

F105.07 9 AIFQSAMTK

15 F105.08 9 AIFQSSATK

F105.O9 9 AIFQSSMAK

F105.10 9 AIFQSSMTA

F105.l l 9 FIFQSSMTK

F105.12 9 SIFQSSMTK

20 F105.14 9 ANFQSSMTK

F105.16 9 AIFQCSMTK

F105.17 9 AIFQSSMTR

F105.19 9 AIFQSSMTY

F105.20 9 AILQSSMTR

25 F105.21 9 AIFQRSMTR

F105.24 10 PAIFQSSMTK

F105.25 10 AIFQSSMTKI

27.0103 9 AIILHQQQK

27.0104 9 YGFRLGFLH

30 27.0108 9 SSCMGGMNR

27.0235 10 TCTYSPALNK

27.0239 10 NSSCMGGMNR

27.0240 10 SSCMGGMNRR

27.0250 10 KSKKGQSTSR

35 27.0252 10 TSRHKKLMFK

28.0062 8 FMFSPTYK

28.0063 8 FVFSPTYK

Figure imgf000090_0001
28.0066 8 TMLXMXXK 89

PEPTIDE AA SEQUENCE

28 0322 9 SMICSWRR

28 0323 9 SVICSWRR

28 0324 9 KVGNFTGLK

28 0325 9 KVGNFTGLR

28 0326 9 VVFFSQFSR

28 0327 9 SVNRPIDWK

28 0328 9 TLWKAGILK

28 0329 9 TLWKAGILR

28 0330 9 TMWKAGILY

10 28 0331 9 TVWKAGILY

28 0332 9 RMYLHTLWK

28 0333 9 RVYLHTLWK

28 0334 9 AMTFSPTYK

28 0335 9 AVTFSPTYK

15 28 0336 9 SVVRRAFPR

28 0337 9 SVVRRAFPK

28 0338 9 ISEYRHYXY

28 0339 9 GTGXNGWFY

28 0340 9 ASXHLTELY

20 28 0341 9 ASXDKXQLK

28 0371 9 RVXEKMALY

28 0372 9 XTGWFMVEA

28 0374 9 HISXLTFGR

28 0375 9 AVXTRGVAK

25 28 0377 9 HLIFXHSKK

28 0378 9 HTMLXMXXK

28 0381 9 RLKAD IEK

28 0383 9 TLFXASDAK

28 0384 9 ALLRYKXGK

30 28 0387 9 ATMXRHYKR

28 0388 9 XATMXRHYK

28 0390 9 ATMXKHYRR

28 0391 9 LLAXAGLAY

28 0392 9 LAXAGLAYK

35 28 0393 9 SIVLPFDXR

28 0394 9 AAXWWAGIK

Figure imgf000091_0001
28 0628 10 OMFTFSPTYK 90

PEPTIDE AA SEQUENCE

28.0629 10 QVFTFSPTYK

28.0630 10 TMWKAGILYK

28.0631 10 TVWKAGILYK

28.0632 10 VMGGVFLVDK

28.0633 10 VVGGVFLVDK

28.0635 10 SVLPETTVVR

28.0638 10 HTLWKAGILK

28.0640 10 HMLWKAGILY

28.0395 9 SAD(SVVRR

10 28.0644 10 GTFNSVVLSR

28.0645 10 YMFDVVLGAK

28.0646 10 MMWYWGPSLK

28.0647 10 MMWYWGPSLR

28.0665 10 IVGGWEXEK

15 28.0667 10 IILEXVYXK

28.0668 10 SIPHAAXHK

28.0670 10 ΓVXPIXSQK

28.0671 10 LIRXLRXQK

28.0672 10 XTYSPALNK

20 28.0675 10 TVXAGGXAR

28.0676 10 HISXLTFGR

28.0677 10 XVNXSQFLR

28.0678 10 LIFXHSKKK

28.0679 10 FVLGGXRHK

25 28.0713 10 TSAIXSVVRR

28.0714 10 HLIFXHSKKK

28.0715 10 LLIRXINXQK

28.0716 10 GΓVXPIXSQK

28.0717 10 LLIRXLRXQK

30 28.0718 10 SLEQRSLHXK

28.0720 10 RTVGGWEXEK

28.0721 10 DIILEXVYXK

28.0722 10 XVYXKQQLLR

28.0723 10 RAVXGGVLVH

35 28.0725 10 LTAAHXIRNK

28.0728 10 KAAXWWAGIK

Figure imgf000092_0001
28.0730 10 VVRRXPHHER 91

PEPTIDE AA SEQUENCE

28 0731 10 LLGIWGXSGK

28 0732 10 TTLFXASDAK

28 0734 10 RTVXAGGXAR

28 0736 10 GTQRXEKXSK

28 0737 10 LVQNANPDXK

28 0738 10 VTXGNGIQVR

28 0739 10 DXATMXRHYK

28 0740 10 GLAXHQLXAR

28 0741 10 ALLAXAGLAY

10 28 0742 10 LLAXAGLAYK

28 0743 10 XVARXPSGVK

28 0745 10 LVEIXTEMEK

28 0746 10 LLNWXMQIAK

28 0824 1 1 HMLWKAGILYK

15 28 0825 11 HVLWKAGILYK

28 0826 11 SMLPETTVVRR

28 0827 11 SVLPETTVVRR

28 0828 11 GMDNSVVLSRK

28 0829 1 1 GVDNSVVLSRK

20 28 0830 11 GTFNSVVLSRK

28 0369 9 GLAXHQLXA

1259 02 9 DTVDTVLEK

1259 10 9 PVTIGECPK

1259 14 10 FTAVGKEFNK

25 1259 16 11 RTLDFHDSNVK

1259 21 11 KTRPILSPLTK

1259 26 11 GTHPSSSAGLK

1259 28 11 ILWILDRLFFK

1259 29 9 WILDRLFFK

30 1259 30 11 CIYRRFKYGLK

1259 31 9 KSMREEYRK

1259 33 9 YIQMCTELK

1259 37 10 MVMELVRMK

1259 38 9 VMELVRMIK

35 1259 41 11 LIRPNENPAHK

26 0023 8 VSFGVWIR

Figure imgf000093_0001
26 0024 8 VSIPWTHK 92

PEPTIDE AA SEQUENCE

26 0026 8 ASFCGSPY

26 0035 9 TSPYELSLY

26 0036 9 TSIPFLHEY

26 0041 9 FNDPGPGTY

26 0045 9 YVDLGALRY

26 0051 9 DADRSFIEY

26 0055 9 NMDKAVKLY

26 0056 9 TTDNFYRNY

26 0058 9 HSAEALQKY

10 26 0059 9 LTAGLDFAY

26 0061 9 LTYKYNQFY

26 0062 9 CSNDKSLVY

26 0063 9 RSARASSRY

26 0065 9 ASADKPYSY

15 26 0067 9 STTAGPNEY

26 0069 9 LSGNGHFHY

26 0073 9 NTFVQANLY

26 0074 9 GTATYLPPY

26 0081 9 RLDAFRQTY

20 26 0082 9 KAEVHTFYY

26 0083 9 VAEGDTVIY

26 0084 9 LTEIDIRDY

26 0085 9 HTEFEGQVY

26 0086 9 VSDGGPNLY

25 26 0092 9 ΠEDQYNRY

26 0093 9 FLDQWWTEY

26 0095 9 FVEDPNGKY

26 0096 9 ISDESYRVY

26 0156 9 YLAEADLSY

30 26 0197 9 ALLAVGATK

26 0198 9 ALNFPGSQK

26 0199 9 AVGATKVPR

26 0203 9 FSVSVSQLR

26 0204 9 GTATLRLVK

35 26 0205 9 GVSRQLRTK

26 0207 9 LIYRRRLMK

Figure imgf000094_0001
26 021 1 9 OLVLHOILK 93

PEPTIDE AA SEQUENCE

26 0212 9 SSHWLRLPR

26 0214 9 TMEVTVYHR

26 0216 9 VLASLIYRR

26 0217 9 VSCQGGLPK

26 0218 9 VVLASLIYR

26 0227 9 GTQCALTRR

26 0251 9 FTIPYWDWR

26 0252 9 GTPEGPLRR

26 0253 9 KSYLEQASR

10 26 0255 9 LVSLLCRHK

26 0256 9 MVPFIPLYR

26 0258 9 QTSAGHFPR

26 0259 9 SIFEQWLRR

26 0260 9 SLLCRHKRK

15 26 0261 9 SSWQIVCSR

26 0267 10 NMQIGGVLTY

26 0273 10 RMAQNFAMRY

26 0274 10 FTVQGSLSGY

26 0275 10 QTSPYELSLY

20 26 0276 10 SSNAILSLSY

26 0280 10 TSQPWWPADY

26 0284 10 VSDVSIIIPY

26 0285 10 ASDAQSANKY

26 0286 10 FTETNLAGEY

25 26 0287 10 YVDGFEPNGY

26 0291 10 FNDPGPGTYY

26 0296 10 FLDQWWTEYY

26 0299 10 AAEFATETAY

26 0309 10 NAEVVLNQLY

30 26 0311 10 FVDGDSLFEY

26 0316 10 PSEDAQVAVY

26 0317 10 MSDNIRTGLY

26 0318 10 ESELREILNY

26 0319 10 CMESVRNGTY

35 26 0320 10 KTENGΓΓRLY

26 0321 10 LTEIDIRDYY

Figure imgf000095_0001
26 0397 10 LLVLMAWLA 94

PEPTIDE AA SEQUENCE

26 0424 10 AVVLASLIYR

26 0425 10 GALLAVGATK

26 0426 10 GTATLRLVKR

26 0427 10 HTMEVTVYHR

26 0428 10 IALNFPGSQK

26 0432 10 QLRALDGGNK

26 0433 10 QVPLDCVLYR

26 0434 10 SLIYRRRLMK

26 0435 10 SSSHWLRLPR

10 26 0438 10 TVSCQGGLPK

26 0442 10 VVLASLIYRR

26 0466 10 YVKVLHHTLK

26 0473 10 LIGCWYCRRR

26 0474 10 LLIGCWYCRR

15 26 0485 10 SSMHNALHIY

26 0504 10 CVSSKNLMEK

26 0510 10 FSSWQΓVCSR

26 0511 10 GLVSLLCRHK

26 0518 10 YMVPFIPLYR

20 26 0535 11 GVWIRTPPAYR

26 0539 11 RLVVDFSQFSR

26 0545 1 1 TLPETTVVRRR

26 0549 11 LLPIFFCLWVY

11 STLPETTWRR

25

Figure imgf000096_0001
26 0550 11 RAFPHCLAFSY

95

*

O o o co n o o o o o o p . o vn 00 O o o o o o o o o o l o o o O o O o o o o O

3 o o O l o o o o v v d

ω 01

4→ oo J~ C f CM

H

ON 00 R

£ s s 51 ? SI S 3 5 VO δ ω

«M N M *N M

8 σ» o» t CM OΛ σ> o» «* CM *

> >

2 > -I u CO •J •J u ω u iJ

I u u

Q u •J §1 (0 Q fa. I O

8 u •J W Bu H § H ϋ

OT to (0 n I ω U ω •J < 3

2 X •J ϋ t >- b.

2 II K O •J co Si s u u X Mage

Sequence Aλ Strain Mol. POB. Motif λl A2.1 A3.2 All A24

0 NO

AISRKMVELV 10 2 101 2.1 NO n

MVELVHFLLL 10 2 106 2.1 0.0017 NO in

KLPGLLSROL 10 2 135 2.1 0

LLSROLQQSL 10 2 139 2.1 0.0007

SLPTTMNYPL 10 3 63 2.1 0.0035

DLESEFQAAL 10 3 93 2.1 0.0001

ALSRKVAELV 10 3 101 2.1 0.0001

KVAELVHFLL 10 3 105 2.1 0.012

VIFSKASSSL 10 3 142 2.1 0

SLQLVFGIEL 10 3 150 2.1 0.0049

LMEVDPIGHL 10 3 159 2.1 0.0005 NO

ON

FLIIVLVMI 9 194 2.1 0.0005

GLLGDNQIM 9 181 2.1 0.0051

SLHCKPEEA 9 7 2.1 0.013 <0.0002 0

ALGLVCVQA 9 22 2.1 0.015 <0.0002 <0.0002

CKPEEALEA 9 10 Random <0.0002

QQBALGLVC 9 19 Random <0.0002

VQAATSSSS 9 28 Random <0.0002

PLVLGTLEB 9 37 Random <0.0002 "o0

VPTAGSTDP 9 46 Random <0.0002

PQSPQGASA 9 55 Random <0.0002 NO 00

©

Figure imgf000098_0001
FPTTINFTR 9 64 Random <0.0002 in

©

1*1 NO

Mage

Sequence AA Strain Mol. Poβ. Motif Al A2.1 A3.2 All A24

NO

QRQPSEGSS 9 73 Random <0 0002 NO in

SREEEGPST 9 82 Random <0 0002 NO in

AVITKKVAD 9 100 Random <0.0002

EMLESVIKN 9 127 Random <0.0002 0

YKHCFPEIF 9 136 Random <0.0002

GKASESLQL 9 145 Random <0.0002

VFGIDVKEA 9 154 Random <0.0002 <0.0002 0

DPTGHSYVL 9 163 Random <0.0002

VTCLGLSYD 9 172 Random <0.0002

PKTGFLIIV 9 190 Random <0.0002 NO

LVMIAMEGG 9 199 Random <0.0002

HAPEEEIHE 9 208 Random <0.0002

ELSVMEVYD 9 217 Random <0.0002

GREHSAYGE 9 226 Random <0.0002

PRKLLTQDL 9 235 Random 0.0002

VQEKYLEYG 9 244 Random <0.0002

RCRTVIPHA 9 253 Random <0.0002

MSSCGVQGP 9 262 Random <0.0002

ILESLFRAVI 10 93 2.1 0.0002 O H

FLIIVLVMIA 10 194 2.1 0.0003 0.0093 0.0030

LVFGIDVKEA 10 153 2.1 0.0002 <0.0002 0 NO 00

©

EVYDGRBHSA 10 222 2.1 0 <0.0002 0 ion

Figure imgf000099_0001

NO

Mage

Sequence AA Strain Mol. Pos. Motif Al A2.1 A3.2 All A24

NO

GVQGPSLKPA 10 266 2.1 0.0001 NO in

QLVFGIDV 8 152 2.1 0 NO n

KLLTQDLV 8 237 2.1 0.0004

GLLGDNQI 8 181 2.1 0

DLVGFLLL 8 108 2.1 0

GLSYDGLL 8 176 2.1 0.0001

DLVQEKYL 8 242 2.1 0

LLGDNQIM 8 182 2.1 0

FLIIVLVM 8 194 2.1 0

ALBAQQEA 8 15 2.1 0 NO 00

TLEEVPTA 8 42 2.1 0

IMPKTGFL 8 188 2.1 0.0001

PVTKAEML 8 122 2.1 0

IVLVMIAM 8 197 2.1 0.0001

AVITKKVA 8 100 2.1 0

EIHBELSV 8 213 2.1 0

LIIVLVMI 8 195 2.1 0.0001

IIVLVMIA 8 196 2.1 0.0002

SLFRAVITKKV 11 96 2.1 0.0001 0

O

H

LLLKYRAREPV 11 113 2.1 0.0001

YLEYGRCRTVI 11 248 2.1 NO

0.0006 00 β

Ul

Figure imgf000100_0001
ALBAQQEALGL 11 15 2.1 0.0001 o W

NO

Mage

Sequence AA Strain Mol. Poβ. Motif Al A2.1 A3.2 All A24

FLIIVLVMIAM 194 2.1 0.0041 NO NO

VLGTLEEVPTA 39 2.1 0.0002 in

NO n i-

QLVFGIDVKEA 152 2.1 0.0001

AVITKKVADLV 100 2.1 0

PVTKAEMLESV 122 2.1 0

KVADLVGFLLL 105 2.1 0.020

GVQGPSLKPAM 266 2.1 0

LVGFLLLKYRA 109 2.1 0.0004

LVMIAMEGGHA 199 2.1 0.0005

CILESLFRAVX 92 2.1 0.0030

EALEAQQEA 9 14 2.1 0 <0.0002 0 NO NO

EAQQEALGL 9 17 2.1 0 •θ.0002

AATSSSSPL 9 30 2.1 0 <0.0002

ATSSSSPLV 9 31 2.1 0.0007

GTLEEVPTA 9 41 2.1 0.013 <0.0002 0

GASAFPTTI 9 60 2.1 0 <0.0002

STSCILESL 9 89 2.1 0.0002

RAVITKKVA 9 99 2.1 0 <0.0002 0

ITKKVADLV 9 102 2.1 0 o

RAREPVTKA 9 118 2.1 0

KAEMLESVI 9 125 2.1 0 <0.0002 CΛ

NO 00

Figure imgf000101_0001
KASESLQLV 9 146 2.1 0.0009 © o in l

NO

Mage

Sequence AA Strain Mol. Pos. Motif Al A2.1 A3.2 All A24

PTGHSYVLV 9 164 2.1 0 NO NO

KTGFLIIVL 9 191 2.1 0.0006 CΛ

NO

LIIVLVMIA 0 0.0022 0.0006 in

9 195 2.1

IIVLVMIAM 9 196 2.1 0.0007

MIAMEGGHA 9 201 2.1 0.0005 <0.0002 0.0002

EIWEELSVM 9 213 2.1 0

SAYGEPRKL 9 230 2.1 0.0002 <0.0002

YLEYGRCRT 9 248 2.1 0

EALGLVCVQA 10 21 2.1 0.0005 <0.0002 0

QAATSSSSPL 10 29 2.1 0 <0.0002 o o

VTKAEMLESV 10 123 2.1 0

EADPTGHSYV 10 161 2.1 0

VLGTLEEVPT 10 39 2.1 0.0004

SAFPTTIN^ 10 62 2.1 0

GIDVKEADPT 10 156 2.1 0

PTGHSYVLVT 10 164 2.1 0

FLWGPRALA 9 new 265 2.1 0.042 0.0017 0

LAETSYVKV 9 new 272 2.1 0

YVKVLEYVI 9 new 277 2.1 0.0002

RVRFFFPSL 9 new 290 2.1 0.0001 n "0

LAETSYVKVL 10 new 272 2.1 0 <0.0002 CΛ NO 00

Figure imgf000102_0001
VLEYVIKVSA 10 new 280 2.1 0.0002 0.0002 0 © ion l

NO

Mage

Sequence AA Strain Mol. Poa. Motif Al A2.1 A3.2 All A24

AALREEEEGV 10 new 301 2.1 0 NO NO J≥

SMHCKPEEV 9 new (a) 7 2.1 0.018 CΛ

NO CΛ

AMGLVCVQV 9 new (a) 22 2.1 0.012

LMLGTLEEV 9 new (a) 38 2.1 0.13

LQLVFGIDV 9 new 151 2.1 0.0004

GLSYDGLLG 9 new 176 2.1 0

GLSYDGLLV 9 new (a) 176 2.1 0.0047

LLGDNQIMP 9 new 182 2.1 0.0001

LLGDNQIMV 9 new (a) 182 2.1 0.043

WEELSVMEV 9 new 215 2.1 0

WMELSVMEV 9 new (a) 215 2.1 0.041

RKLLTQDLV 9 new 236 2.1 0

YEFLWGPRA 9 new 262 2.1 0

YMFLWGPRV 9 new (a) 262 2.1 0.22

AATSSSSPLV 10 new 30 2.1 0

ATSSSSPLVL 10 new 31 2.1 0

KMADLVGFLV 10 new (a) 105 2.1 1.5

VADLVGFLLL 10 new 106 2.1 0.0008 0.0003

SESLQLVFGI 10 new 148 2.1 0

O

VMVTCLGLSV 10 new (a) 170 2.1 0.30 H

QIMPKTGFLI 10 new 187 2.1 0.0009 CΛ NO 0-^0

Figure imgf000103_0001
QMMPKTGFLV 10 new (a) 187 2.1 0.050 © CΛ s NO

Mage

Sequence AA Strain Mol. Poβ. Motif Al A2.1 A3.2 All A24

NO

KTGFLIIVLV 10 1 new 191 2.1 0.0012 NO

C £Λ:

LIIVLVMIAM 10 1 new 195 2.1 0.0003 NO CΛ

4-.

VMIAMEGGHV 10 1 new (a) 200 2.1 0.053

SAYGEPRKLL 10 1 new 230 2.1 0 0.0008

ALAETSYVKVL 11 1 N 270 2.1 0.012

KMVELVHFLLL 11 2 52 2.1 0.67

ELMEVDPIGHL 11 3 105 2.1 0.026

HLYIFATCLGL 11 3 114 2.1 0.041

LLLKYRAREPV 11 3 60 2.1 0.0001

QLVFGIELMEV 11 3 99 2.1 0.34 o

NJ

IMPKAGLLIIV 11 3 135 2.1 0.013

VLVTCLGLSYDGL 13 1 n B6 170 2.1 0.0017

KLLTQDLVQEKYL 13 1 n E6 237 2.1 0.0060

DLVQEKYLEYRQV 13 1 n E6 242 2.1 0

SLFRAVITKKVADLV 15 1 n POL 96 2.1 0.0004 .

DLESEFQAAISRKMV 15 2 POL 40 2.1 0

MLGSWGNWQYFFPV 15 3 POL 75 2.1 0.012

GASSFSTTI 9 2 60 2.1 0 0.0002

DLESEFQAA 9 2.3 93 2.1 0 n H

QAAISRKMV 9 2 99 2.1 0

KAEMLESVL 9 2 125 2.1 0 0 NO go ©

KASEYLQLV 9 2 146 2.1 0.011 CΛ

Figure imgf000104_0001
O Ul

NO

Mage

Sequence AA Strain Mol. Pos. Motif Al A2.1 A3.2 All A24

NO

QLVFGIEW 9 2 152 2.1 0.0038 NO

≥ CΛ:

WPISHLYI 9 2 162 2.1 0.0002 NO CΛ

PISHLYILV 9 2 164 2.1 0.0005

HLYILVTCL 9 2 167 2.1 0.0034

YILVTCLGL 9 2 169 2.1 0.0014

GLLGDNQVM 9 2 181 2.1 0.0038

QVMPKTGLL 9 2 187 2.1 0

VMPKTGLLI 9 2 188 2.1 0.0010 0.230

KTGLLIIVL 9 2 191 2.1 0.0002

GLLIIVLAI 9 2.3 193 2.1 0.0002 o

LLIIVLAII 9 2,3 194 2.1 0.0001 >

LIIVLAIIA 9 2,3 195 2.1 0.0008

IIVLAIIAI 9 2 196 2.1 0.0009

IIAIEGDCA 9 2 201 2.1 0

GASSLPTTM 9 3 60 2.1 0 0.0010

QAALSRKVA 9 3 99 2.1 0

VAELVHFLL 9 3 106 2.1 0 0.039

KAEMLGS 9 3 125 2.1 0

KASSSLQLV 9 3 146 2.1 0.0005 n

QLVFGIELM 9 3 152 2.1 0.0010

PIGHLYIFA 9 3 164 2.1 0 NO 00

©

Figure imgf000105_0001
IMPKAGLLI 9 3 188 2.1 0.0064 CΛ β Ul

NO

Mage

Sequence AA Strain Mol. Pos. Motif Al A2.1 A3.2 All Λ2

KAGLLIIVL 9 3 191 2.1 0.0002 0 NO

NO

S

IIAREGDCA 9 3 201 2.1 0 CΛ:

NO CΛ

EALEAQQEAL 10 1 new 14 2.1 0 0

EAQQEALGLV 10 1 new 17 2.1 0

DLESEFQAAI 10 2 93 2.1 0

AAISRKMVBL 10 2 100 2.1 0 0

VIFSKASEYL 10 2 142 2.1 0.0014

YLQLVFGIEV 10 2 150 2.1 0.37

LVFGIEWEV 10 2 153 2.1 0.012

GIEWEWPI 10 2 156 2.1 <0.0002 o

WE PISHL 10 2 159 2.1 <0.0002

E PISHLYI 10 2 161 2.1 <0.0002

WPISHLYIL 10 2 162 2.1 0.0002

PISHLYILVT 10 2 164 2.1 0.0003

QVMPKTGLLI 10 2 187 2.1 0.0002

VMPKTGLLII 10 2 188 2.1 0.0009 0.058

KTGLLIIVLA 10 2 191 2.1 <0.0002

GLLIIVLAII 10 2,3 193 2.1 0.0005

LLIIVLAIIA 10 2,3 194 2.1 <0.0002 -a o

LIIVLAIIAI 10 2 195 2.1 0.0013 H

AIIAIEGDCA 10 2 200 2.1 0.0023 NO 00

Figure imgf000106_0001
AALSRKVAEL 10 3 100 2.1 0.0007 0 © o CΛ l

NO

Mage

Sequence AA Strain Mol. Pos. Motif Al A2.1 A3.2 All A24

VAELVHFLLL 10 3 106 2.1 0.0009 0.0018 NO NO

VTKAEMLGSV 10 3 123 2.1 <0.0002 CΛ

NO C*Λ-.

GIELMEVDPI 10 3 156 2.1 <0.0002

EVDPIGHL I 10 3 161 2.1 <0.0002

PIGHLYIFAT 10 3 164 2.1 0.0003

QIMPKAGLLI 10 3 187 2.1 0.0006

IMPKAGLLII 10 3 188 2.1 0.0015

KAGLLIIVLA 10 3 191 2.1 <0.0002

AIIAREGDCA 10 3 200 2.1 <0.0002

FLWGPRALI 9 2 271 A02

GLEARGEAL 9 3 15 A02 o

EARGEALGL 9 3 17 A02

ALGLVGAQA 9 3 22 A02/A03

GLVGAQAPA 9 3 24 A02 A03

LVGAQAPAT 9 3 25 A02

PATEEQEAA 9 3 31 A02/A03

EAASSSSTL 9 3 37 A02

AASSSSTLV 9 3 38 A02

LVEVTLGEV 9 3 45 A02 n

EVTLGEVPA 9 3 47 A02 A03 H

VTLGEVPAA 9 3 48 A02 A03 NO go ©

Figure imgf000107_0001
KIWEELSVL 9 3 220 A02 CΛ

O Ul

NO

Mage

Sequence AA Strain Mol. Pos. Motif Al A2.1 A3.2 All A24

SILGDPKKL 9 3 237 A02 NO NO

ILGDPKKLL 9 3 238 A02 CΛ

NO CΛ

FLWGPRALV 9 3 271 A02 *.

RALVETSYV 9 3 276 A02

LVETSYVKV 9 3 278 A02

YVKVLHHMV 9 3 283 A02

KVLHHMVKI 9 3 285 A02

EARGEALGLV 10 3 17 A02

EALGLVGAQA 10 3 21 A02/A03

GLVGAQAPAT 10 3 24 A02

QAPATEEQEA 10 3 29 A02/A03 o O

EAASSSSTLV 10 3 37 A02

TLVEVTLGEV 10 3 44 A02

EVTLGEVPAA 10 3 47 A02/A03

EVFEGREDSI 10 3 229 A02

SILGDPKKLL 10 3 237 A02

ILGDPKKLLT 10 3 238 A02

ALVETSYVKV 10 3 277 A02

LVETSYVKVL 10 3 278 A02

MVKISGGPHI 10 3 290 A02 n T3

LVLGTLEEV 9 1 38 2.1 <0.0006 0.032 0 0 0.0003 CΛ

NO OO

Figure imgf000108_0001
KVADLVGFLL 10 1 105 0.0005 0.041 0.0039 0.0030 0.0070 ©

© Ul

NO

Mage

Sequence AA Strain Mol. Pos. Motif Al A2.1 A3.2 All A24

LVFGIELMEV 10 3 153 2.1 0.17 j£

I LWQPI V 9 3 <0.0007 1.4 0.0048 0.0048 0 *o

EVDPIGHLY 9 3 3.7 0.0022

KMVELVHFL 9 2 <0.0007 0.13 0.0007 0 0.0043

KMVELVHFLL 10 2 105 <0.0008 0.071 0.0004 0.0001 0.0008

LVFGIBLMBV 10 3 0.0030 0.065 0.0007 0 0

KVAELVHFL 9 3 105 2.1 0 0.073 0.011 0.0047 0.0005

CILESLFRA 9 1 92 2.1 0.0001 0.073 0 0.0002 0

VMIAMEGGHA 10 1 200 2.1 <0.00008 0.0023 0 0 0

MLESVIKNYK 10 1 0 0 0.034 0.0045 0

ETSYVKVLBY 10 1 0.075 0 0.0009 0.0004 0

KVLEYVIKV 9 1 new 279 2.1 <0.0005 0.095 0.022 0.015 0

FLHGPRALA 9 1 <0.0006 0.027 0.0015 0 0

ALREBEEGV 9 1 302 2.1 <0.0006 0.0056 0 0 0

ALAETSYVKV 10 1 271 <0.0007 0.017 0.0011 0.0029 0

YVIKVSARV 9 1 283 2.1 0.0005 0.018 0 0 0

RALAETSYV 9 1 270 2.1 <0.0006 0.014 0.0003 0.0005 0

ALAETSYVK 9 1 <0.0006 0.0002 0.17 0.39 0

VLGTLEEV 8 1 39 2.1 <0.0007 0.0088 0 0 0 n

SLQLVFGI 8 1 150 2.1 <0.0007 0.0094 0 0.0001 0

ILESLFRA 8 1 93 2.1 <0.0004 0.0017 0.0003 0 0.0001 00

Figure imgf000109_0001
FLLLKYRA 8 1 112 2.1 0.0036 0.0007 ©-

0.0003 0.0001 0 CΛ s

Mage

Sequence AA Strain Mol. Pos. Motif Al A2.1 A3.2 All A24

NO

GLVCVQAA 8 24 2.1 0.0016 0.0008 0.0008 0 0 NO

VLVTCLGL 8 170 2.1 <0.0007 0.0010 0.0001 0 0 NO CΛ

KVADLVGFL 9 105 2.1 <0.0008 0.0091 0.0013 0.0005 0

YVLVTCLGL 9 169 2.1

IMPKTGFLI 9 188 2.1 <0.0008 0.0035 0 0 3.2

GLLGDNQIM 9 A2.1 <0.0008 0.0054 0 0 0.0002

GLVCVQAAT 9 24 2.1 0.0030 0.0007 0.0026 0 0.0001

VADLVGFLL 9 106 2.1 0.032 0.0011 0.0054 0.0008 0.0007

YLEYGRCRTV 10 248 2.1 0.0008 0.0097 0.0001 0 0

SLQLVFGIDV 10 150 2.1 0.0028 0.0047 0.0013 0.0001 0.0001 o 00

IMPKTGFLII 10 188 2.1 <0.0008 0.0007 0 0 0.050

ALGLVCVQAA 10 22 A2.1 0.0011 0.0002 0.0003 0 0

EIHEBLSVMEV 11 213 A2.1 0.0007 0.013 0.0001 0.0001 0

FLIIVLVMIAM 11 A2.1 0.023 0.0031 0.016 0.0014 0.0011

VIPHAMSSCGV 11 257 2.1 <0.0009 1.4 0 0 0

CILESCFRAVI 11 A2.1 0.079 0.0017 0.058 0.0005 0.0008

QIMPKTGFLII 11 187 2.1 <0.0009 0.0003 0 0 0.0030

GFLLLKYRA 9 0.0004 0.0002

CFPBIFGKA 9 0 0 n

FFFPSLREA 9 0 0 H

FFPSLREAA 9 0 0 NO 00

©

RSLHCKPEEA 10 0.0001 0.0008 CΛ

Figure imgf000110_0001
© Ul

NO

Mage

Sequence AA Strain Mol. Pos. Motif Al A2.1 A3.2 All A24

0 0 NO

EFLWGPRALA 10 1 NO

≤ CΛ:

RFFFPSLREA 10 1 0.0004 0 NO CΛ

Figure imgf000111_0001
FFFPSLREAA 10 1 0 0

o NO

O H

CΛ NO 00

© CΛ

O Ul

NO

Sequence Antigen Strain Molecule Position Motif Al A2 Λ3 A l l A24 Mux.

Binding Binding Binding Binding Binding Binding

ALF GF GAA HIV MN gpI6U 518 A02 0 4950 j 0 4950 NO NO

MLQLTVWGI HIV N gplβO 566 A02 0 2450 0 2 150 CΛ

NO IV 0 i%3 0 1961 CΛ RVIEVLQRA H MN gplβO 829 A 2

KLTPLCVTL HIV MN gpl60 12(1 A02 (1 1600 0 1600

LLIAARIVEL HIV MN gpl60 776 A02 0.1550 0 1550

SLLNATDIAV HIV MN gpl60 814 A02 O.Ϊ05U 0 1050

ALFLGFLGA HIV MN gplβO 518 A02 0.0945 0 0945 HMLQLTV GI HIV MN gpl60 565 A02 0.0677 0 0677 NATDIAV HIV MN gplβO 815 A02 0 (1607 00607

ALLYKLDIV IIIV MN g l60 Ϊ 79 A02 " (1.0362 0 0362 WLWYIKIFI HIV MN gpI60 679 ~A02 0.0155 0 0 55

TIIVHLNESV HIV MN gplβO 288 A02 0.0350 00150

LLQYWSQEL HIV MN gpl60 800 A02 0.0265 0 0265 IMIVGGLVGL HIV MN gpl60 687 A02 0.0252 00252

LLYKLDIVSI HIV MN gpl60 180 A02 0.0245 0 0245

FLAI IWVDL HIV MN gpl60 753 A02 0.0233 00231

TLQCKIKQII HIV MN gp!60 415 A02 0.i)20() — 00200

GLVGLRIVFA HIV MN g I60 692 A02 0.0195 0 0195

FLGAAGSTM HIV MN gplβO 523 A02 "o.ϊϊii o 0 0190

I ISLWDQSL HIV MN gplβO 107 A02 00179 00179

TVWGIKQLQA HIV MN g l 0 570 A02 0.0150 0 0150

LLGRRGWEV HIV MN gpl60 785 A02 Iiii i 42 00142

Figure imgf000112_0001
AVLSIVNRV HIV MN g i60 701 A02 0.0132 0.0132 o

CΛ NO OO

Co oΛ

Ul

NO

Sequence Antigen Strain Molecule Position Motif Al A2 A3 All A24 Mux.

Binding Binding Binding Binding Binding Binding

FIMIVGGLV HIV MN gplόO 686 A02 0.0131 001 1

LLNATDIAVA HIV MN g lβO 815 A02 0.0117 0(1117 NO NO FLYGALLLA PLP Human 80 A02 " i .906 1.9000

SLLTFMIAA PLP Human 253 A02 0.5300 NO

— _ _ 0.5300 CΛ

4^

FMIAATYNFAV PLP Human 257 A02 0.495(1 (14950

- - -

RMYGVLPWI PLP Human 205 A02 (11650 0.1650

IAATYNFAV PLP Human 259 A02 0054(1 00540

GLLECCARCLV PLP Human 2 A02 0.1)515 00 15

YALTWWLL PLP Human 157 A02 0.(14 i 5 00 J5

ALTWWLLV PLP Human 158 A02 0.0.390 00390

FLYGALLL PLP Human 80 A02 0.0345 0(13 5

SLCADARMYGV PLP Human 199 A02 (1.0140 0.0140

LLVFACSAV PLP

Figure imgf000113_0001
Human 164 A02 αoiiπ 00107

"o0

CΛ NO 00

© o CΛ

Ul

NO

112 Table 10

AA SEQUENCE SOURCE

9 YIFATCLGL MAGE 3 109

9 IMPKTGFLI MAGE 1 188

10 IMPKTGFLII MAGE 1 188

15 ' MLGSWGNWQYFFPV MAGE 3 POL 75

9 VMPKTGLLI MAGE 2 188

9 IMPKAGLLI MAGE 3 188

10 10 IMPKAGLLII MAGE 3 188

9 RLWHYPCTV HCV Env2 614

9 RLWHYPCTI HCV Env2 614

9 FLLLADAR1 HCV Env2

9 GVWPLLLLL HCV Env2 792

15 9 GMWPLLLLL HCV Env2 792

9 YLNTPGLPV HCV NS3/NS4 1542

9 YMNTPGLPV HCV NS3/NS4 1542

9 VILDSFDPL HCV NS5 2251

9 ILMTHFFSI HCV NS5 2843

20 9 ILMTHFFSV HCV NS5 2843

9 LMAVVLASL gplOO 606

9 SLSLGFLFL PAP 13

10 YMIMVKCWMI c-ErbB2 952

10 GLHGQDLFGI PAP 196

25 9 AILSVSSFL P. falcipamm CSP 6

9 GLIMVLSFL P. falcipamm CSP 425

9 VLLGGVGLV P. falcipamm EXP-1 91

9 GLLGNVSTV P. falcipamm EXP-1 83

9 LLGNVSTVL P. falcipamm EXP-1 84

30 9 VLAGLLGNV P. falcipamm EXP-1 80

Figure imgf000114_0001
113

AA SEQUENCE SOURCE

9 KILSVFFLA P. falcipamm EXP-1 2

9 FLIFFDLFL P. falcipamm TRAP 14

9 LIFFDLFLV P. falcipamm TRAP 15

9 FMKAVCVEV P. falcipamm TRAP 230

9 LLMDCSGSI P. falcipamm TRAP 51

10 ILSVSSFLFV P. falcipamm CSP 7

10 VLLGGVGLVL P. falcipamm EXP-1 91

10 GLLGNVSTVL P. falcipamm EXP-1 83

10 FLIFFDLFLV P. falcipamm TRAP 14

10 10 GLALLACAGL P. falcipamm TRAP 507

9 KIWEELSML MAGE2 220

9 TLMSAMTNL Prost.Ca PAP 112

9 LLLARAASL Prost.Ca PAP 6

9 ALDVYNGLL Prost.Ca PAP 299

15 9 VTWIGAAPL PSA 8

10 ALIETSYVKV MAGE2 277

10 SLSLGFLFLL Prost.Ca PAP 13

10 RTLMSAMTNL PAP 111

10 FLPSDFFPSV(CONH2) HBc 18-27

20 10 FLPSDFFPSV-NH2 HBc 18-27

9 ILGFVFTLT-NH2 Flu Matrix 59-67

10 KGILGFVFTL-NH2 Flu Matrix 57-66

11 FLPSDFFPSVR HBc 18-28

9 FLPSDFFPS HBc 18-26

25 9 GILGKVFTL Flu Matrix 58-66 analog

9 FLSKQYLNL HBV polymerase

9 KLQCVPLHV PSA 166-174 P/D

Figure imgf000115_0001
114

AA SEQUENCE SOURCE

9 KLQCVPLHV PSA 166-174 P/D

9 KLQCVPLHV PSA 166-174 P/D

9 KLYEIVAKV A2 1 consensus

9 KLAEYVAKV A2 1 consensus

9 KLAEΓVYKV A2 1 consensus

9 TLTSCNTSV HIV gp 120 env RE trans 197

9 ALMEKIYQV A2 1 consensus peptide

9 ALSEKIYQV A2 1 consensus peptide

9 FLMSYFPSV 941 01 9-mer analog

10 9 FLPSYFPSV 941 01 9-mer analog

10 FLMSDYFPSV 941 01 M2 analog

9 FLYCYFALV Chiron consensus

9 FMYCYFALV Chiron consensus

10 SLVGFGILCV Chiron consensus

15 10 SLMGCGLFWV Chiron consensus

8 GLLGPLLV HBVadr-ENV

9 AMAKAAAAI A2 1 poly-A

10 MMWYWGPSLY HBV

9 FLPSYFPSA analog of 994 02 chiron comb

20 9 FAPSYFPSV analog of 994 02 chiron comb

9 FLPSYFPSS analog of 994 02 chiron comb

9 FSPSYFPSV analog of 994 02 chiron comb

9 IMPKTGFLI MAGE-1

9 VADLVGFLL MAGE-1

25 11 EΓWEELSVMEV MAGE-1

11 FLIIVLVMIAM MAGE-1

11 VIPHAMSSCGV MAGE-1

11 CILESCFRAVI MAGE-1

9 YIFATCLGL MAGE3

Figure imgf000116_0001
115

AA SEQUENCE SOURCE

9 YIFATCLGL MAGE3

11 KMVELWHFLLL MAGE2 112-122

11 HLFIYATCLGL MAGE3 174-184

9 GLQDCTMLV HCV NS5 2727-2735

8 TLGIVSPI HPV, analog of 1088.01

8 TLGΓVXPI HPV, analog of 1088.01

10 FLLAQFTSAI HBV POL 513

11 VLLDYQGMLPV HBV env

11 CILLLCLIFLL HBV env

10 9 FLGGSPVCL HBV env

11 TVIEYLVSFGV HBV core 114-124

1 1 TVLEYLVSFGV HBV core 114-124

10 FLLAQFTSAI HBV pol

9 GLYSSTVPI HBV pol

15 9 GLYSSTAPI HBV pol

9 GLDVLTAKV HIV form VIN.

9 RILGAVAKV HIV form VIN.

9 LLFGYPVYV HTLV, tax 11-19

9 ALFGYPVYV tax 11-19, SAAS

20 9 LLFGAPVYV tax 11-19, SAAS

9 LLFGYAVYV tax 11-19, SAAS

9 LLFGYPVAV tax 11-19, SAAS

9 AAGIGILTV MARTI 27-35

9 GILTVILGV MARTI 31-39

25 9 ILTVILGVL MARTI 32-40

9 VILGVLLLI MARTI 35-43

9 ALMDKSLHV MARTI 56-64

10 TVILGVLLL1 MARTI

10 LLDGTATLRL MARTI

30 10 ILSVSSFLFV Plas. falcip. CSA-A 7-16

9 GLIMVLSFL Plas. falcip. CSA-A 401-409

Figure imgf000117_0001
116

AA SEQUENCE SOURCE

9 IMVLSFLFL Plas. falcip. CSA-A 403-411

10 FLIFFDLFLV Plas. falcip. TRAP-A 14-23

9 FMKAVCVEV Plas. falcip. TRAP-A 200-207

9 IMPGQEAGL gplOO

9 GLGQVPLΓV gplOO

9 LMAVVLASL gplOO

9 RLMKQDFSV gplOO

9 HLAVIGALL gplOO

9 LLAVGATKV gplOO

10 9 MLGTHTMEV gplOO

10 LLDGTATLRL gplOO

10 VLYRYGSFSV gpioo

10 VLPSPACQLV gpioo

10 SLADTNSLAV gplOO

15 10 VLMAVVLASL gplOO

10 LMAVVLASLI gplOO

10 RLDCWRGGQV gplOO

10 AMLGTHTMEV gplOO

10 ALDGGNKHFL gplOO

20 9 YLEPGPVTA gplOO

10 LLNATALAVA

11 SLLNATAIAVA

9 KTWGQYWQV gplOO

9 ΓΓDQVPFSV gplOO

25 9 YLEPGPVTA gplOO

10 LLDGTATLRL gplOO

10 VLYRYGSFSV gplOO

10 ALDGGNKHFL gpioo

9 GILTVILGV MARTI 31-39

30 9 YMNGTMSQV Human Tyrosinase

9 MLLAVLYBL Human Tyrosinase

9 LLWSFQTSA Human Tyrosinase

Figure imgf000118_0001
117

AA SEQUENCE SOURCE

9 YLTLAKHTI Human Tyrosinase

9 FLPWHRLFL Human Tyrosinase

9 FLLRWEQEI Human Tyrosinase

9 RIWSWLLGA Human Tyrosinase

9 LLGAAMVGA Human Tyrosinase

9 AMVGAVLTA Human Tyrosinase

9 VLTALLAGL Human Tyrosinase

9 ALLAGLVSL Human Tyrosinase

9 LLAGLVSLL Human Tyrosinase

10 10 BLLWSFQTSA Human Tyrosinase

10 WMHYYVSMDA Human Tyrosinase

10 FLPWHRLFLL Human Tyrosinase

10 WLLGAAMVGA Human Tyrosinase

10 AMVGAVLTAL Human Tyrosinase

15 10 VLTALLAGLV Human Tyrosinase

10 TALLAGLVSL Human Tyrosinase

10 ALLAGLVSLL Human Tyrosinase

9 NLTDALLQV P. falcipamm SSP2 132

9 SAWENVKNV P. falcipamm SSP2 218

20 10 FLIFFDLFLV P. falcipamm SSP2 14

9 NLNDNAIHL P. falcipamm SSP2 80

10 YLLMDCSGSI P. falcipamm SSP2 51

9 TLQDVSLEV controls

Figure imgf000119_0001

25 118 Table 11

AA SEQUENCE SOURCE

9 ALYWFRTGI HPVόb/11 El 319

LLDGNPMSI HPV6b/ll El 540

9 NAWGMVLLV HPV6b/ll El 270

9 SLYAHIQWL HPV6b/ll El 260

9 TLIKCPPLL HPV6b/ll El 556

10 9 GIYDALFDI PSMAg 707

9 YLSGANLNL CEA 605

9 VLYGPDTPI CEA 589

9 IMIGVLVGV CEA 691

9 LLTFWNPPT CEA 24

15 9 KLTEMVQWA HPV6b/ll El

357

9 YMDTYMRNL HPV6b/ll El

532

10 NLLDGNPMSI HPV6b/ll El 539

10 SLYAHIQWLT HPV6b/llEl 260

10 TLKCPPLLV HPV6b/ll El 556

20 10 MVFELANSrV PSMAg 583

10 YLWWVNNQSL CEA 176

10 YLWWVNNQSL CEA 354

10 YLWWVNGQSL CEA 532

10 GIMIGVLVGV CEA 690

25 10 VLYGPDAPTI CEA 233

10 KLIEPLSLYA HPV6b/ll El 254

10 WLCAGALVLA PSMAg 20

10 IMIGVLVGVA CEA 691

Figure imgf000120_0001
119

AA SEQUENCE SOURCE

9 YLYQLSPPI HTLV-I tax 155

9 LLFEEYTNI HTLV-I tax 307

9 QLGAFLTNV HTLV-I tax 178

9 TLTAWQNGL HTLV-I tax 226

9 ALQFLIPRL HTLV-I tax 67

9 TLGQHLPTL HTLV-1 tax 123

9 FAFKDLFVV HPV 18 E6

47

9 RLLQLLFRA GCDFP-15 2

9 CMWKTYLI GCDFP-15 65

10 9 LLLVLCLQL GCDFP-15 15

9 ILYAHIQCL HPV18 El 266

9 SLACSWGMV HPV16 El 266

9 CLYLHIQSL HPV 16 El 259

9 YLVSPLSDI HPV16 El 90

15 9 VMFLRYQGV HPV16 El 443

9 KLLSKLLCV HPV16 El 292

9 ALDGNPISI HPV18 El 546

9 AVFKDTYGL HPV18 El 216

9 LLTTNIHPA HPV18 El 570

20 9 LLQQYCLYL HPV 16 El

254

Figure imgf000121_0001
120

AA SEQUENCE SOURCE

9 AMLAKFKEL HPV16 El 206

9 ALDGNLVSM HPV 16 El 539

9 FLGALKSFL HPV18 El 463

9 FIHFIQGAV HPV18 El 497

10 TLLLVLCLQL GCDFP-15

14

10 LLFRASPATL GCDFP-15 6

10 SLMKFLQGSV HPV16 El 489

10 SLACSWGMVV HPV16 El 266

10 FLQGSVICFV HPV16 El 493

10 10 FIQGAVISFV HPV18 El 500

10 KLLCVSPMCM HPV16 El 296

10 FILYAHIQCL HPV18 El 265

10 FVNSTSHFWL HPV18 El 508

10 ILLTTNIHPA HPV18 El 569

15 10 TLLQQYCLYL HPV16 El 253

9 GLLGWSPQA HBV ENV 62

9 GLACHQLCA HER2/neu

9 ILDEAYVMA HER2/neu

9 SIISAVVGI HER2/neu

20 9 VVLGWFGI HER2/neu

9 YMIMVKCWM HER2/neu

10 ALCRWGLLLA HER2/neu

10 QLFEDNYALA HER2/neu

Figure imgf000122_0001
121

AA SEQUENCE SOURCE

9 HMWNFISG1 HCV consensus

9 VIYQYMDDL HIV POL 358

9 SLYNTVATL HIV GAG 77

10 TVWGKQLQA HIV ENV

735

9 LLLEAGALV MSH 99

9 VLETAVGLL MSH 92

9 CLALSDLLV MSH 79

9 FLSLGLVSL MSH 45

9 SLVENALW MSH 52

10 9 AIIDPLIYA MSH 291

9 FLCWGPFFL MSH 251

9 FLALIICNA MSH 283

9 TILLGIFFL MSH 244

9 RLLGSLNST MSH 9

15 9 SLYNTVATL HIV pl7/5B 77-8

9 VIYQYMDDL HIV RT/50A 346-

9 ILKEPVHGV HIV RT/IV9 476-

Figure imgf000123_0001

122 Table 12

PEPTIDE NO PEPTIDE LENGTH SEQUENCE

1237 01 9 FLWGPQALV

1237 02 9 FLWGPNALV

1237 03 9 FLWGPHALV

1237 04 9 FLWGPKALV

1237 05 9 FLWGPFALV

26 0158 9 AVIGALLAV

26 0172 9 LLHLAVIGA

26 0186 9 SLADTNSLA

26 0192 9 VMGTTLAEM

26 0240 9 LLAVLYCLL

26 0383 10 FLRNQPLTFA

26 0390 10 HLAVIGALLA

26 0395 10 LAVIGALLAV

26 0418 10 TLAEMSTPEA

26 0423 10 YLAEADLSYT

26 0497 10 MLLAVLYCLL

1183 10 10 VLYRYGSFSV

27 0007 9 ILSSLGLPV

27 0012 9 LLFLGWFL

27 0019 9 GLYGAQYDV

27 0022 9 FVVALIPLV

27 0023 9 GLMTAVYLV

27 0027 9 ALVLLMLPV

27 0028 9 ILLSIARVV

27 0029 9 SLYFGGICV

27 0030 9 QLIPCMDVV

27 0031 9 VLQQSTYQL

27 0032 9 AIHNVVHAI

27 0034 9 GLHGVGVSV

27 0035 9 GLVDFVKHI

27 0036 9 LLFRFMRPL

27 0038 9 LMLPGMNGI

27 0043 9 TVLRFVPPL

27 0044 9 MLGNAPSVV

27 0050 9 YLDLALMSV

Figure imgf000124_0001
27 0064 9 RMPEAAPPV 123

PEPTIDE NO PEPTIDE LENGTH SEQUENCE

27 0082 9 FLLPDAQSI

27 0083 9 MTYAAPLFV

27 0088 9 LLPLGYPFV

27 0089 9 GLYYLTTEV

27 0090 9 MALLRLPLV

27 0091 9 RLPLVLPAV

27 0093 9 RMFAANLGV

27 0095 9 RLLDDTPEV

27 0096 9 YLYVHSPAL

27 0100 9 GLYLSQIAV

27 0101 9 YLSQIAVLL

27 0102 9 SLAGFVRML

27 0137 10 ATYDKGILTV

27 0146 10 KIFMLVTAVV

27 0151 10 FLLADERVRV

27 0153 10 MLATDLSLRV

27 0154 10 RLQPQVGWEV

27 0161 10 FLMPVEDVF1

27 0165 10 RMSRVTTFTV

27 0168 10 LALVLLMLPV

27 0169 10 ALVLLMLPVV

27 0170 10 GΓVSGILLSI

27 0171 10 SLYFGGICVI

27 0173 10 QLIPCMDVVL

27 0181 10 LLFRFMRPLI

27 0183 10 VLLEDGGVEV

27 0184 10 AMPAYNWMTV

27 0186 10 GLAGTVLRFV

27 0188 10 VLIAFGRFPI

27 0189 10 FLTCDANLAV

27 0197 10 AIAWGAWGEV

27 0204 10 LLLETSWEA1

27 0217 10 RMPEAAPPVA

27 0223 10 WMAETTLGRV

27 0226 10 AMALLRLPLV

27 0229 10 FMSLAOFVRM

Figure imgf000125_0001
27 0266 11 SLLTEVETYVL 124

PEPTIDE NO PEPTIDE LENGTH SEQUENCE

27 0268 GILGFVFTLTV

27 0269 VLDVGDAYFSV

27 0271 KIWEELSMLEV

27 0272 STLVEVTLGEV

27 0273 GLAPPQHLIRV

27 0274 HLIRVEGNLRV

27 0005 9 YLLALRYLA

27 0013 9 GLYRQWALA

27 0017 9 LLWQDPVPA

27 0040 9 ALLSDWLPA

27 0045 9 WLLIDTSNA

27 0046 9 MLASTLTDA

27 0081 9 YLSEGDMAA

27 0094 9 LLACAVIHA

27 0144 10 LLCCSGVATA

27 0191 10 LLATVFKLTA

27 0192 10 KLTADGVLTA

27 0195 10 GLGGLGLFFA

28 0064 8 TLGIVXPI

28 0065 8 ALGTTXYA

28 0293 9 FLLTRILTV

28 0294 9 ALMPLYACV

28 0295 9 LLAQFTSAV

28 0296 9 LLPFVQWFV

28 0297 9 FLLAQFTSV

28 0298 9 KLHLYSHPV

28 0299 9 KLFLYSHPI

28 0300 9 LLSSNLSWV

28 0301 9 FLLSLGIHV

28 0302 9 MMWYWGPSV

28 0303 9 VLQAGFFLV

28 0304 9 PLLPIFFCV

28 0305 9 FLLPIFFCL

28 0306 9 VLLDYQGMV

28 0307 9 YMDDVVLGV

28 0308 9 YMFDVVLGA

Figure imgf000126_0001
28 0309 9 GLLGWSPOV 125

PEPTIDE NO PEPTIDE LENGTH SEQUENCE

28 0342 9 YMIMVKXWM

28 0343 9 YIFATXLGL

28 0345 9 SLHXKPEEA

28 0346 9 ALGLVXVQA

28 0348 9 LLMDXSGSI

28 0349 9 FAFRDLXIV

28 0352 9 GTLGΓVXPI

28 0353 9 TLGΓVXPIX

28 0354 9 LLWFHISXL

28 0355 9 KLTPLXVTL

28 0356 9 ALVEIXTEM

28 0357 9 LTFGWXFKL

28 0359 9 KLQXVDLHV

28 0360 9 FMKAVXVEV

28 0361 9 LLQQYXLYL

28 0362 9 XLYLHIQSL

28 0363 9 SLAXSWGMV

28 0364 9 ILYAHIQXL

28 0365 9 KLLSKLLXV

28 0366 9 PLLPIFFXL

28 0367 9 TLIKXPPLL

28 0368 9 ALMPLYAXI

28 0370 9 XILESLFRA

28 0609 10 FLLAQFTSAV

28 0610 10 YLHTLWKAGV

28 0611 10 YLFTLWKAGI

28 0612 10 YLLTLWKAGI

28 0613 10 LLFYQGMLPV

28 0614 10 LLLYQGMLPV

28 0615 10 LLVLQAGFFV

28 0616 10 ILLLCLIFLV

28 0650 10 ALXRWGLLL

28 0651 10 KLPDLXTEL

28 0652 10 HLYQGXQVV

28 0653 10 XILESLFRA

28 0654 10 KLQXVDLHV

Figure imgf000127_0001
28 0655 10 YIFATXLGL 126

PEPTIDE NO PEPTIDE LENGTH SEQUENCE

Fill 01 9 SLYNTVATL

Fill 02 9 ALYNTVATL

Fill 04 9 SLANTVATL

Fill 06 9 SLFNAVATL

Fill 07 9 SLFNLLATL

Fill 10 9 SLFNTIAVL

Fill 11 9 SLFNAVAVL

Fill 09 9 SLFNTIWL

Fill 12 9 SLFNAIAVL

Fill 13 9 SLFNTVAVL

Fill 14 9 SLFNTVCVI

Fill 15 9 SLHNTVATL

Fill 17 9 SLHNTVAVL

Fill 18 9 SLYATVATL

Fill 19 9 SLYNAVATL

Fill 21 9 SLYNTAATL

Fill 22 9 SLYNTIAVL

Fill 23 9 SLYNTSATL

Fill 25 9 SLYNTVAVL

Fill 26 9 SLYNTVATA

Fill 27 9 SLYNAIATL

Fill 28 9 SLYNLVAVL

Fill 29 9 SLFNLLAVL

FI 1132 9 SLFNTVVTL

Fill 34 9 SLYNTVAAL

1039031 9 MMWYWGPSL

121140 10 SLLNATAIAV

10 TIHDIILECV

9 FAFRDLCIV

9 GTLGIVCPI

9 TLGIVCPIC

Figure imgf000128_0001
127 Table 13

A SEQUENCE SOURCE A

9 IPQSLDSWW HBV ENV 191

9 IPIPSSWAF HBV ENV 313

9 TPARVTGGV HBV POL

365

9 LPIFFCLWV HBV ENV 379

9 HPAAMPHLL HBV POL

440

10 9 FPHCLAFSY HBV POL

541

9 DPSRGRLGL HBV POL

789

9 QPRGRRQPI HCV Core 57

9 SPRGSRPSW HCV Core 99

9 DPRRRSRNL HCV Core 111

15 9 LPGCSFSIF HCV Core 168

9 YPCTVNFTI HCV E2 622

9 LPALSTGLI HCV E2 681

9 HPNIEEVAL HCV NS3 1358

9 SPGALVVGV HCV NS4 1887

Figure imgf000129_0001
128

A SEQUENCE SOURCE

A

9 SPGQRVEFL HCV NS5 2615

9 APTLWARMI HCV NS5 2835

9 FPRIWLHJL HIV VPR 34

9 SPTRRELQV HIV POL 37

9 FPVRPQVPL HIV NEF 84

9 RPQVPLRPM HIV NEF 87

9 KPCVKLTPL HIV ENV 123

9 SPRTLNAWV HIV GAG

153

9 FPISPIETV HIV POL 171

10 9 SPAIFQSSM HIV POL 327

9 NPDIVIYQY HIV POL 346

9 GPGHKARVL HIV GAG

360

9 LPEKDSWTV HIV POL 417

9 YPLASLRSL HIV GAG

507

15 9 VPRRKAKII HIV POL 991

9 TPTLHEYML HPV 16 E7 5

9 KPLNPAEKL HPV 18 E6 110

9 NPAEKLRHL HPV 18 E6

113

9 VPISHLYIL MAGE2 170

20

Figure imgf000130_0001
9 MPKTGLLII MAGE2 196 129

A SEQUENCE SOURCE A

9 DPACYEFLW MAGE2 265

9 EPHISYPPL MAGE2 296

9 YPPLHERAL MAGE2 301

9 LPTTMNYPL MAGE3 71

9 DPIGHLYIF MAGE3 170

9 MPKAGLLII MAGE3 196

9 GPHISYPPL MAGE3 296

9 HPSDGKCNL P. falciparum S

9 RPRGDNFAV P. falciparum S

10 9 QPRPRGDNF P. falciparum S

9 LPNDKSDRY P. falciparum S

10 LPLDKGIKPY HBV POL

123

10 TPARVTGGVF HBV POL 365

10 FPHCLAFSYM HBV POL

541

15 10 LPRRGPRLGV HCV Core 37

10 APLGGAARAL HCV Core 142

10 LPGCSFSIFL HCV Core 168

10 VPASQVCGPV HCV E2 497

Figure imgf000131_0001
10 YPCTVNFTIF HCV E2 622 130

A SEQUENCE SOURCE

A

10 SPLLLSTTEW HCV E2 663

10 RPSGMFDSSV HCV NS3 1506

10 LPVCQDHLEF HCV NS3

1547

10 KPTLHGPTPL HCV NS3 1614

10 TPLLYRLGAV HCV NS3 1621

10 NPAIASLMAF HCV NS4 1783

10 LPAILSPGAL HCV NS4 1882

10 SPGALVVGVV HCV NS4 1887

10 APTLWARMIL HCV NS5 2835

10 10 IPVGEIYKRW HIV GAG

261

10 YPLASLRSLF HIV GAG

507

10 APTKAKRRVV HIV ENV 547

10 VPISHLYILV MAGE2 170

10 MPKTGLLIIV MAGE2 196

15 10 HPRKLLMQDL MAGE2 241

10 LPTTMNYPLW MAGE3 71

Figure imgf000132_0001
10 MPKAGLLIIV MAGE3 196 131

A SEQUENCE SOURCE A

10 IPYSPLSPKV P. falciparum S

10 TPYAGEPAPF P. falciparum S

9 FPDHQLDPA HBV ENV 14

9 YPALMPLYA HBV POL

640

9 LPVCAFSSA HBV X 58

9 APLGGAARA HCV 142

9 DPTTPLARA HCV 2806

9 FPYLVAYQA HCV 1582

9 LPAILSPGA HCV 1882

10 9 NPAIASLMA HCV 1783

9 TPIDTTIMA HCV 2551

9 TPLLYRLGA HCV 1621

9 WPLLLLLLA HCV 793

9 NPYNTPVFA HIV POL 225

15 9 APLLLARAA PAP 4

9 HPQWVLTAA PSA 52

10 IPIPSSWAFA HBV ENV 313

10 TPPAYRPPNA HBV NUC 128

10 APFTQCGYPA HBV POL

633

20 10 LPIHTAELLA HBV POL

712

Figure imgf000133_0001
10 GPCALRFTSA HBV X 67 132

A SEQUENCE SOURCE A

10 DPTTPLARAA HCV 2806

10 IPQAVVDMVA HCV 339

10 LPCSFTTLPA HCV 674

10 QPEKGGRKPA HCV 2567

10 VPHPNIEEVA HCV 1356

10 IPAETGQETA HIV POL 820

10 LPQGWKGSPA HIV POL 320

10 FPDLESEFQA MAGE2/3 98

10 DPIGHLYIFA MAGE3 170

10 9 EPLSLYAHI HPV 6b/ 11 El

2

9 PPLLVTSNI HPV 6b/ 11 El

5

9 SPRLDAIKL HPV 6b/ 11 El 1

9 TPKKNCIAI HPV 6b/ 11 El

4

9 FPFDRNGNA HPV 6b/ 11 El

5

15 10 CPPLLVTSNI HPV 6b/ 11 El

5

10 FPFDRNGNAV HPV 6b/ 11 El 5

8 GPLLVLQA HBV ENV 173

8 IPIPSSWA HBV ENV

Figure imgf000134_0001
313 133

A SEQUENCE SOURCE A

8 VPFVQWFV HBV ENV 340

8 LPIFFCLW HBV ENV 379

8 RPPNAPIL HBV NUC

133

8 MPLSYQHF HBV POL 1

8 HPAAMPHL HBV POL

429

8 SPFLLAQF HBV POL

511

8 YPALMPLY HBV POL

640

8 SPTYKAFL HBV POL

659

8 VPSALNPA HBV POL

769

10 8 HPvhAGPI HIV con. GAG

8 GPGvRyPL HIV con. NEF

8 SPIETVPV HIV con. POL

8 NPYNTPVF HIV con. POL

8 LPIQKETW HIV con.

Figure imgf000135_0001
POL 134

A SEQUENCE SOURCE A

8 VPRRKaKi HIV con. POL

8 VpLQLPPl HIV con. REV

8 VPLAMKLI P. falciparum

8 LPYGRTNL P. falciparum

8 RPRGDNFA P. falciparum

8 IPQQEPNI P. falciparum

8 TPFAGEPA P. falciparum

9 SPINTIAEA HPV 6b El 93

9 SPISNVANA HPV 11 El 93

10 9 SPRLDAIKL HPV 6b/ 11 El 1

9 EPLSLYAHI HPV 6b/ 11 El 2

9 EPPKIQSGV HPV 6b/ 11 El

3

9 IPFLTKFKL HPV 6b El 455

9 TPKKNCIAI HPV 6b/ 11 El 4

15 9 QPLTDAKVA HPV 11 El

512

9 PPLLVTSNI HPV 6b/ 11 El

Figure imgf000136_0001
5 135

A SEQUENCE SOURCE A

9 FPFDRNGNA HPV 6b/ 11 El

5

9 APLILSRIV PSA 14

9 HPEDTGQVF PSA 78

9 HPLYDMSLL PSA 94

9 HPQKVTKFM PSA 184

9 GPLVCNGVL PSA 211

9 RPSLYTKVV PSA 235

9 FPPEGVSIW PAP 124

9 NPILLWQPI PAP 133

10 9 LPFRNCPRF PAP 156

9 IPSYKKLIM PAP 277

9 LPPYASCHL PAP 307

9 SPSCPLERF PAP 348

9 CPLERFAEL PAP 351

15 9 GPTLIGANA gplOO 74

9 LPDGQVIWV gplOO 97

9 VPLAHSSSA gplOO 198

9 QPLTFALQL gplOO 236

9 DPSGYLAEA gplOO 246

20 9 EPGPVTAQV gplOO 282

9 MPTAESTGM gplOO 366

9 TPAEVSIVV gplOO 401

9 LPKEACMEI gplOO 520

9 LPSPACQLV gplOO 545

25 9 VPLIVGILL gplOO 596

Figure imgf000137_0001
9 LPHSSSHWL gplOO 630 136

A SEQUENCE SOURCE A

9 CPIGENSPL gplOO 647

9 SPLLSGQQV gplOO 653

9 MPREDAHFI MARTI 1

9 APLGPQFPF Tyrosinase 6

9 IPIGTYGQM Tyrosinase 1

9 TPMFNDINI Tyrosinase 1

9 LPWHRLFLL Tyrosinase 2

9 IPYWDWRDA Tyrosinase 2

9 SPASFFSSW Tyrosinase 2

10 9 LPSSADVEF Tyrosinase 3

9 SPLTGIADA Tyrosinase 3

9 DPIFLLHHA Tyrosinase 3

9 IPLYRNGDF Tyrosinase 4

9 YPELPKPSI CEA 141

15 9 LPVSPRLQL CEA 185

9 LPVSPRLQL CEA 363

9 NPPAQYSWL CEA 442

9 LPVSPRLQL CEA 541

9 IPQQHTQVL CEA 632

20 9 NPPAQYSWF CEA 264

9 LPSIPVHPI Prost.Ca PSM

9 IPVHPIGYY Prost.Ca PSM

9 RPFYRHVIY Prost.Ca PSM

9 TPKHNMKAF Prost.Ca PSM

25 9 FPGIYDALF Prost.Ca PSM

9 RPRWLCAGA Prost.Ca PSM

9 DPLTPGYPA Prost.Ca PSM

Figure imgf000138_0001
137

A SEQUENCE SOURCE A

9 RPRRTILFA Prost.Ca PSM

9 LPFDCRDYA Prost.Ca PSM

9 LPIHTAELL HBV POL

712

10 GPDAPTISPL CEA 236

10 IPQQHTQVLF CEA 632

10 QPIPVHTVPL Prost.Ca PAP

10 HPYKDFIATL Prost.Ca PAP

10 LPGCSPSCPL Prost.Ca PAP

10 LPSWATEDTM Prost.Ca PAP

10 10 VPLSEDQLLY Prost.Ca PAP

10 FPHPLYDMSL Prost.Ca PSA

10 RPGDDSSHDL Prost.Ca PSA

10 HPQKVTKFML Prost.Ca PSA

10 LPFDCRDYAV Prost.Ca PSM

15 10 YPNKTHPNYI Prost.Ca PSM

10 SPEFSGMPRI Prost.Ca PSM

10 RPRWLCAGAL Prost.Ca PSM

10 TPKHNMKAFL Prost.Ca PSM

10 RPFYRHVIYA Prost.Ca PSM

20 10 HPAAMPHLLV HBV POL

429

9 SPREGPLPA HER2/neu 1151

9 KPDLSYMPI HER2/neu 605

9 HPPPAFSPA HER2/neu 1208

Figure imgf000139_0001
138

A SEQUENCE SOURCE A

9 GPLPAARPA HER2/neu 1155

9 APQPHPPPA HER2/neu 1204

9 EPLTPSGAM HER2/neu 698

9 LPTHDPSPL HER2/neu 1101

9 DPLNNTTPV HER2/neu 121

9 SPLTSIISA HER2/neu 649

9 SPKANKEIL HER2/neu 760

9 LPTNASLSF HER2/neu 65

9 CPSGVKPDL HER2/neu 600

10 9 SPLAPSEGA HER2/neu 1073

9 MPNQAQMRI HER2/neu 706

9 LPAARPAGA HER2/neu 1157

9 LPQPPICTI HER2/neu 941

9 SPAFDNLYY HER2/neu 1214

Figure imgf000140_0001
139

A SEQUENCE SOURCE A

9 TPTAENPEY HER2/neu 1240

9 LPSETDGYV HER2/neu 1120

10 LPTNASLSFL HER2/neu 65

10 CPAEQRASPL HER2/neu 642

10 KPCARVCYGL HER2/neu 336

10 APQPHPPPAF HER2/neu 1204

10 SPGGLRELQL HER2/neu 133

10 SPLTSIISAV HER2/neu 649

10 MPNQAQMRIL HER2/neu 706

10 10 SPYVSRLLGI HER2/neu 779

10 HPPPAFSPAF HER2/neu 1208

10 SPREGPLPAA HER2/neu 1151

10 NPHQALLHTA HER2/neu 488

10 MPYGCLLDHV HER2/neu

Figure imgf000141_0001
801 140

A SEQUENCE SOURCE A

10 GPASPLDSTF HER2/neu 995

9 LPTTLFQPV HTLV-I tax

21

9 IPPSFLQAM HTLV-I tax

10

9 FPGFGQSLL HTLV-I tax

4

9 WPLLPHVIF HTLV-I tax 16

9 SPPITWPLL HTLV-I tax 16

9 VPYKRIEEL HTLV-I tax

18

9 RPQNLYTLW HTLV-I tax

13

9 CPKDGQPSL HTLV-I tax 26

10 9 RPNDEVTAV GCDFP-15

47

9 SPATLLLVL GCDFP-15 11

9 WPYLHNRLV HPV16 El

576

9 QPFILYAHI HPV18 El 263

9 SPRLKAICI HPV16 El 107

Figure imgf000142_0001
141

A SEQUENCE SOURCE A

9 SPLGERLEV HPV 18 El 97

9 SPRLQEISL HPV 18 El 110

9 RPIVQFLRY HPV 18 El

447

10 WPYLHNRLVV HPV 16 El

576

10 WPYLESRITV HPV 18 El

583

10 QPPKLRSSVA HPV18 El 315

10 EPPKLRSTAA HPV 16 El 308

9 DPSRGRLGL HBV POL

778

9 HPAAMPHLL HBV POL

429

10 9 IPIPSSWAF HBV ENV 313

10 TPARVTGGVF HBV POL

354

10 FPHCLAFSYM HBV POL

530

9 LPVCAFSSA HBV X 58

9 YPALMPLYA HBV POL 640

15 9 APLLLARAA PAP 4

Figure imgf000143_0001
142

A SEQUENCE SOURCE A

9 HPQWVLTAA PSA 52

9 HPSDGKCNL Pf SSP2 206

9 RPRGDNFAV Pf SSP2 305

9 QPRPRGDNF Pf SSP2 303

10 TPYAGEPAPF Pf SSP2 539

9 GPHISYPPL MAGE3 296

9 YPPLHERAL MAGE2 301

9 VPISHLYIL MAGE2 170

9 EPHISYPPL MAGE2 296

10 9 LPTTMNYPL MAGE3 71

9 MPKAGLLII MAGE3 196

10 HPRKLLMQDL MAGE2 241

Figure imgf000144_0001

143 Table 14

PEPTIDE AA SEQUENCE

25.0129 9 LPPLERLTL

26.0445 10 EPGPVTAQVV

26.0448 10 LPRIFCSCPI

26.0449 10 LPSPACQLVL

26.0455 10 VPLAHSSSAF

26.0458 10 VPRNQDWLGV

10 26.0476 10 APPAYEKLSA

26.0478 10 MPREDAHFIY

26.0519 10 APAFLPWHRL

26.0522 10 GPNCTERRLL

26.0523 10 IPLYRNGDFF

15 26.0529 10 TPRLPSSADV

19.0101 9 TPAEVSIVV

26.0554 11 APFTQCGYPAL

26.0561 11 NPADDPSRGRL

26.0564 11 RPPNAPILSTL

20 26.0566 11 SPFLLAQFTSA

26.0567 11 SPHHTALRQAI

Figure imgf000145_0001
26.0568 11 TPARVTGGVFL

Claims

144WHAT IS CLAIMED IS:
1. A composition comprising an immunogenic peptide having an HLA binding motif, which immunogenic peptide is a peptide shown in Tables 3-14 or a peptide comprising a conservative substitution of a residue in a peptide shown in Table 3-14.
2. The composition of claim 1, wherein the immunogenic peptide is linked to a second oligopeptide.
3. The composition of claim 2, wherein the second oligopeptide is a peptide that induces a helper T response.
4. A composition comprising a nucleic acid molecule encoding an immunogenic peptide as shown in Tables 3-14, or a peptide comprising a conservative substitution of a residue of a peptide shown in Table 3-14.
5. The composition of claim 4, wherein the nucleic acid further comprises a sequence encoding a second immunogenic peptide.
6. The composition of claim 4, wherein the nucleic acid further comprises a sequence encoding an oligopeptide that induces a helper T response.
7. A method of inducing a cytotoxic T cell response comprising contacting a cytotoxic T cell with a peptide of claim 1.
PCT/US1998/005039 1998-03-13 1998-03-13 Hla-binding peptides and their uses WO1999045954A1 (en)

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