WO2004113554A2 - Methods for determining susceptibility to psoriasis - Google Patents

Abstract

Methods and materials for determining susceptibility to psoriasis, based in part on newly discovered association between psoriasis and specific allelic variants found in polymorphic regions of human chromosome 17q24-q25. A first polymorphic region harboring EBP50/SLC9A3R1/NHERF and NAT9 includes five allelic variants shown herein to associate with susceptibility to psoriasis. A second polymorphic region harboring RAPTOR includes other allelic variants shown herein to associate with susceptibility to psoriasis.

Description

TITLE OF THE INVENTION METHODS FOR DETERMINING SUSCEPTIBILITY TO PSORIASIS

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims the priority benefit of U.S. Provisional Patent Application Serial

No. 60/479,377, filed June 16, 2003, which is incorporated by reference in its entirety.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT Research relating to the invention was supported in part by NIGH grants AR44577 and

AR04904901. The Government has certain rights in the invention.

REFERENCE TO A SEQUENCE LISTING

The Sequence Listing, which is a part of the present disclosure, includes a text file comprising nucleotide and/or amino acid sequences of the present invention on a floppy disk. The subject matter ofthe Sequence Listing is incorporated herein by reference in its entirety.

BACKGROUND OF THE INVENTION

1. Field ofthe Invention

The present invention relates to polymorphisms located on human chromosome 17q24- q25, and to methods and materials for analyzing the allelic variations, and to the use of genetic polymorphisms in the diagnosis and treatment of autoimmune diseases.

2. Description o the Related Art

Psoriasis is a debilitating, chronic inflammatory skin and nail disorder of unknown pathogenesis affecting 2-3% ofthe Western population (Menter, A. & Barker, J., Lancet 338, 231-234 (1991)). Approximately 20%-30% of psoriasis patients also have psoriatic arthritis (National Psoriasis Foundation Bulletin 33, 6 (2002)). Psoriatic arthritis is a specific type of arthritis causing inflammation in and around the joints, usually the wrists, knees, ankles, lower back and neck, and most commonly affecting the ends ofthe fingers and toes. On average, it appears about ten years after the first signs of psoriasis, typically between the ages of 30 and 50, and affecting men and women equally. Early diagnosis is important for preventing long-term damage to joints and tissue, but psoriatic arthritis can be difficult to diagnose, particularly in its milder forms and earlier stages. Most people with psoriatic arthritis also have psoriasis, although rarely, a person can have psoriatic arthritis without having psoriasis, or present with psoriatic arthritis symptoms before psoriasis has been diagnosed. Psoriatic arthritis is usually milder than rheumatoid arthritis, but some patients with psoriatic arthritis have disease symptoms comparable in severity to those of patients with rheumatoid arthritis.

While psoriasis and psoriatic arthritis are both complex diseases and the underlying mechanisms are not completely understood, it is known for example that the frequency of occurrence of psoriasis is elevated in patients with HIV infection (Duvic, M., J. Invest. Dermatol. 95, 38S-40S (1990)). Like rheumatoid arthritis, psoriatic arthritis is thought to be caused by interplay of immune system malfunction with genetic and environmental factors.

With respect to genetic factors, genetic analyses, including linkage studies of families with a history of psoriasis and association studies have identified the locations of susceptibility loci. Psoriasis is associated with HLA class I alleles (see, e.g., Gottlieb, A.B. & Krueger, J.G., Arch. Dermatol. 126, 1083-1086 (1990)). A second susceptibility locus for psoriasis and psoriatic arthritis has been identified on human chromosome 17q25 (Tomfohrde, J. et al., Science 264, 1141-1145 (1994)), and confirmed with independent families from the U.S., Germany, and Sweden (Enlund, F. et al., Hum. Hered. 49, 2-8 (1999); Nair, R.P. et al., Hum. Molec. Genet. 6, 1349-1356 (1997)).

The field of pharmacogenetics approaches treatment of disease using knowledge of genetics, such as awareness of alleles of particular genetic polymorphisms, to diagnose disease and identify patients most amenable to treatment using particular pharmaceutical agents. Polymorphisms, including single nucleotide polymorphisms (SNPs) in which a single nucleotide in a genetic sequence is exchanged for another, have been extremely useful for mapping the human genome and now continue to help elucidate the genetic component of diseases. Lists of previously identified polymorphisms are generally available, for example in online databases, but most are not yet known to have an association with any particular protein, function or disease. Ongoing basic research in all areas of medicine seeks to associate alleles of previously identified polymorphisms such as SNPs with specific human diseases and conditions to improve diagnostic capabilities. Pharmacogenetics can also be used in pharmaceutical research to assist the drug selection process. References that provide background details on pharmacogenetics and other uses of polymorphism detection include, for example, Linder et al., Clinical Chemistry 43, 254 (1997); Marshall, Nature Biotechnology 15, 1249 (1997); International Patent Application WO 97/40462, Spectra Biomedical; and Schafer et al., Nature Biotechnology 16, 33 (1998).

Advances in the fields of medicine and biotechnology have contributed to a greater understanding of diseases such as psoriasis. However, diagnostic testing for psoriasis and psoriatic arthritis remain limited, while at the same time, treatment of both psoriasis and psoriatic arthritis is thought to benefit greatly from early diagnosis and treatment. Currently, skin and nail changes characteristic of psoriasis must be demonstrated before a diagnosis can be made with certainty.

As is true for many autoimmune disorders, current treatment options are varied and typically limited in effectiveness. Initial treatment of psoriasis usually involves topical treatment with agents such as steroids or salicyclic acid, phototherapy, and for moderate to severe forms of the disease, the use of systemic drugs including NSAIDS, and immunosuppressants such as methotrexate. For psoriatic arthritis, corticosteroid injections directly into the joints, and systemic therapy with NSAIDS, hydroxychloroquine, sulfasalazine, and azathioprinecyclosporin have been used. However, topical treatments are not always very effective and are less useful in patients with extensive disease. Phototherapy is not effective for many patients, and systemic therapy, especially with immunosuppressants and other drugs, frequently involves serious side effects such as kidney or liver damage. Patients with joint destruction from advanced psoriatic arthritis may require surgery. Thus, a clear need remains for improved diagnostic methods and materials and for methods that promote continued drug development.

SUMMARY OF THE INVENTION

Briefly, therefore, there are provided methods and materials for determining whether a subject has a susceptibility to psoriasis.

In one embodiment, a method for determining whether a subject has a susceptibility to psoriasis includes, in a biological sample from the subject, analyzing a polynucleotide sequence to detect the presence or absence of an allelic variant of at least one polymorphic region of chromosome 17q24-q25 that is associated with susceptibility to psoriasis. The at least one polymorphic region is, for example, a first region harboring EBP50/SLC9A3R1/NHERF and NAT9, or a second region harboring RAPTOR. The allelic variant is, for example, one of multiple single nucleotide polymorphisms shown herein to be associated with psoriasis. .

In another embodiment, a method for determining whether a subject has a susceptibility to psoriasis includes, in a biological sample from the subject, analyzing a polynucleotide sequence to detect the presence or absence of at least one DNA marker from chromosome 17q24- q25, wherein the DNA marker is associated with susceptibility to psoriasis. The DNA marker is, for example, selected from the group of single nucleotide polymorphisms shown herein to be associated with psoriasis.

In another embodiment, a method for detecting the presence or absence in a subject of at least one allelic variant that is associated with psoriasis, includes detecting the presence or absence of at least one single nucleotide polymorphism (SNP) from a first polymorphic region of chromosome 17q24-q25, or from a second polymorphic region of 17q24-q25, wherein the at least one SNP is associated with psoriasis.

In another embodiment, a method for indicating a predisposition to psoriasis in a subject includes, on a chromosome 17q24-q25 obtained from the subject, detecting the presence or absence of at least one allelic variant of a polymorphic region of 17q24-q25 that is associated with psoriasis, wherein the polymorphic region harbors EBP50/SLC9A3R1/NHERF and NAT9, or the polymoφhic region harbors RAPTOR, and wherein the presence ofthe at least one allelic variant in the subject is indicative of a predisposition to psoriasis in the subject, as compared to a subject in which the allelic variant is not present.

In another embodiment, a method of screening for biologically active agents that modulate psoriasis symptoms includes combining a candidate agent with a cell that includes a polynucleotide having a sequence that encodes at least one allelic variant of a polymoφhic region of 17q24-q25, wherein the polymoφhic region harbors EBP50/SLC9A3R1/NHERF and NAT9, and wherein the polynucleotide is operably linked to a promoter such that the polynucleotide sequence is expressed in the cell as an EBP50 protein, and then determining the effect ofthe agent upon the expression and/or activity ofthe EBP50 protein.

In another embodiment, a method of screening for biologically active agents that modulate psoriasis symptoms includes combining a candidate agent with a cell that includes a polynucleotide having a sequence that encodes at least one allelic variant of a polymoφhic region of 17q24-q25, wherein the polymoφhic region harbors EBP50/SLC9A3R1/NHERF and NAT9, and wherein the polynucleotide is operably linked to a promoter such that the polynucleotide sequence is expressed in the cell as a NAT9 protein, and then determining the effect ofthe agent upon the expression and/or activity ofthe NAT9 protein.

In another embodiment, a method of screening for biologically active agents that modulate psoriasis symptoms includes combining the candidate agent with a cell comprising a polynucleotide having a sequence that encodes at least one allelic variant of a polymoφhic region of 17q24-q25, wherein the polymoφhic region harbors RAPTOR, and wherein the polynucleotide is operably linked to a promoter such that the polynucleotide sequence is expressed in the cell as a RAPTOR protein; and then determining the effect ofthe agent upon the expression and/or activity ofthe RAPTOR protein. In another embodiment, there is provided a primer or probe that specifically hybridizes adjacent to or at a first polymoφhic region of human chromosome 17q24-q25 that harbors EBP50/SLC9A3R1/NHERF and NAT9, in combination with a primer or probe that specifically hybridizes adjacent to or at a second polymoφhic region of human chromosome 17q24-q25 that harbors RAPTOR, wherein the first polymoφhic region and the second polymoφhic region are associated with psoriasis.

In another embodiment, a kit for indicating whether a subject has a predisposition to developing psoriasis includes at least one probe or primer that specifically hybridizes adjacent to or at the first polymoφhic region of chromosome 17q24-q25 that harbors EBP50/SLC9A3R1/NHERF and NAT9 and that is associated with psoriasis, along with instructions for use ofthe kit for indicating whether the subject has a predisposition to developing psoriasis. The kit may alternatively, or in addition to the first probe or primer, include at least one probe or primer that specifically hybridizes adjacent to or at the second polymoφhic region of 17q24-q25 that harbors RAPTOR and that is associated with psoriasis.

In another embodiment, there is provided a microarray including a nucleic acid having a sequence ofthe first polymorphic region of chromosome 17q24-q25 that harbors EBP50/SLC9A3R1/NHERF and NAT9.

In another embodiment, there is provided a microarray including a nucleic acid having a sequence ofthe second polymoφhic region of chromosome 17q24-q25 that harbors RAPTOR.

In another embodiment, there is provided a method for determining whether a subject has a susceptibility to an autoimmune disease including, in a biological sample from the subject, analyzing a polynucleotide sequence to detect the presence or absence of an allelic variant of at least one polymoφhic region wherein the allelic variant abolishes a RUNXl/AMLl binding site.

In another embodiment, there is provided a method for determining whether a subject has a susceptibility to psoriasis, said method comprising analyzing a polynucleotide sequence from a polymoφhic intragenic region on chromosome 17q24-q25 between EBP50 and NAT9 to determine the elimination of a RUNXl/AMLl binding site.

These and other features, aspects and advantages ofthe present invention will become better understood with reference to the following description, examples and appended claims.

BRIEF DESCRIPTION OF THE DRAWINGS

Figure 1 shows the results of family-based association mapping of psoriasis at 17q24-q25 using TDT-AE analyses, demonstrating association between psoriasis and DNA markers from two separate regions of chromosome 17q24-q25;

Figure 2a is a partial sequence ofthe intragenic region between the genes NHERF1/EBP50 and DKFZP564C103;

Figure 2b shows the results of electrophoretic mobility shift, super-shift and competition assays with Jurkat nuclear cell extract and allelic variants of rs734232;

Figure 3a shows staining of cross-sections of normal and psoriatic skin (involved and uninvolved) with EBP50 antibodies;

Figure 3b graphs results of FAC staining of keratinocyte cells (HaCAT line) and peripheral blood lymphocytes (primarily T cells) with EBP50 antibody conjugated with FITC; and

Figure 4 is a bar graph of results of quantitative RT-PCR on purified naive murine CD4

T cells, stimulated with anti-CD3 +/- IL-2 +/- anti-CD28 with primers for murine NAT9 cDNA.

DETAD ED DESCRIPTION OF THE PREFERRED EMBODIMENTS Abbreviations and Definitions

To facilitate understanding ofthe invention, a number of terms and abbreviations as used herein are defined below as follows:

"Activity": As used herein, "activity" refers to the level of functioning in which a gene or transcript participates; for example, high activity of a gene or gene product refers to an increase in the gene's function relative to its normal level of functioning. "Allele": As used herein, the term "allele" refers to any ofthe two or more alternative forms of a gene that occur at the same locus on a chromosome.

"Associated": As used herein in connection with the relationship between certain allelic variants and psoriasis, the term "associated" refers to the characteristic of co-occurrence of the allelic variants and psoriasis in subjects, as established using TDT-AE analysis as described herein.

"Association": As used herein in connection with the relationship between certain allelic variants and psoriasis, the term "association" refers to the co-occurrence of the allelic variants and psoriasis in subjects, as established using TDT-AE analysis as described herein.

"Autoimmune disease": As used interchangeably herein, the terms "autoimmune disease" and "autoimmune diseases and conditions" are broadly defined to include psoriasis and psoriatic arthritis, as well as other disorders that are or will be associated with loss of RUNXl/AMLl binding sites, including lupus erythematosus.

"EBP50": As used herein, the term "EBP50" refers to a protein, also known as SLC9A3R1 and as NHERFl, which is encoded by the gene sequence of EMBL/GenBank/DDBJ accession no. AF015926 (SEQ ID NO: 1), and to the gene sequence of accession no. AF015926, and refers also to alleles ofthe EBP50 gene sequence.

"NAT9": As used herein, the term "NAT9" refers to a protein, also known as N acetyl transferase 9, which is encoded by the gene sequence of EMBL/GenBank/DDBJ accession number EMBL/GenBank/DDBJ accession no. AL050269 (SEQ ID NO: 2), and to the gene sequence of accession no. AL050269, and refers also to alleles ofthe EBP50 gene.

"Psoriasis": As used herein the term "psoriasis" includes the common, non-contagious chronic skin condition characterized by squamous dermatosis which is marked by exacerbations and remissions, and in well-developed cases produces distinct histological findings known as Munro microabscesses and spongiform pustules, as well as the arthritis which is associated with psoriasis known as psoriatic arthritis. "RAPTOR": As used herein, the term "RAPTOR" refers to a protein which is encoded by any of the gene sequences of EMBL/GenBank/DDBJ accession nos. AY090663 (SEQ ID NO: 3), AK055912 (SEQ ID NO: 4), AB082951 (SEQ ID NO: 5), and to the nucleotide sequences of accession nos. AY090663, AK055912 and AB082951, and refers also to alleles ofthe RAPTOR gene sequences.

"Subject": As used herein, the term "subject" refers to both a human having or suspected of having psoriatic disease and an asymptomatic human who may be tested for predisposition or susceptibility to psoriatic disease, including psoriasis and psoriatic arthritis. At each position the human may be homozygous for an allele or the human may be a heterozygote.

"Susceptible": As used herein, the term "susceptible" and "susceptibility" refer to the characteristic of having a predisposition to developing psoriasis or psoriatic arthritis in the sense the subject has a greater risk of developing such disease than the risk reflected in the general population, wherein the increased risk of the subject is identified by the presence or absence of one or more identified allelic variants in the subject, for example such as those allelic variants described herein.

Methods and materials for determining susceptibility to psoriasis and psoriatic arthritis are based in part on the discovery that SNPs from two separate regions of chromosome 17q24- q25 are associated with psoriasis. Results of previous studies were consistent with an association of psoriasis with genetic regions close to D17S1301 (Speckman, R.A. et al., Hum. Genet. 112, 34-41 (2002)). The association is demonstrated by genotyping of multiple nuclear families. In the present case, to determine the boundaries of this association and to identify the causative variants, 242 nuclear families were genotyped for 54 additional single nucleotide polymoφhisms (SNPs) mapping to 17q24-q25. Complete descriptions of all SNPs employed herein, including sequences, genomic location and observed alleles are publicly available online at: The SNP Consortium, Ltd. database, http://snp.cshl.org/, or in the databases of the National Center for Biotechnology Information (NCBI) at http://www.ncbi.nlm.nih.gov/SNP/. The descriptions of the SNP's used herein and described in the specified online databases are herein incoφorated by reference in their entirety.

The associated SNPs lie in two regions: a first, proximal peak of association is in or near SLC9A3R1 (also known as EBP50 and NHERF1) and NAT9. SLC9A3R1/EBP50 (EMBL/GenBank/DDBJ accession number AF015926) is a PDZ domain-containing phosphoprotein that associates with members of the ezrin-radixin-moesin family (Reczek, D._s et al., Identification of EBP50: A PDZ-containing Phosphoprotein that Associates with Members of the Ezrin-Radixin-Moesin Family, J. Cell Biol. 139(1), 169-79 (1997)), and is a multifunctional scaffold protein implicated in diverse aspects of epithelial membrane biology and immune synapse formation in T cells (Voltz, J.W., Weinman, EJ. & Shenolikar, S. Expanding the role of NHERF, a PDZ-domain containing protein adapter, to growth regulation. Oncogene 20, 6309-14 (2001)). NAT9 (N-acetyl transferase 9; EMBL/GenBank/DDBJ accession number AL050269) is a novel member ofthe N-acetyl transferase superfamily. A distal peak of association is within RAPTOR (pl50 target of rapamycin (TOR)-scaffold protein containing WD-repeats) ((Hara, K. et al. Raptor, a binding partner of target of rapamycin (TOR), mediates TOR action. Cell 110, 177-89 (2002)); EMBL/GenBank/DDBJ accession nos. AY090663, AK055912, AB082951). TOR is a component of the T-cell interleukin-2 signaling pathway. The findings support important roles for the proteins EBP50 and RAPTOR in the pathogenesis of psoriatic disease, including psoriasis and psoriatic arthritis.

The genes presented here are involved in psoriasis pathogenesis and will be targets for drug discovery efforts. The associated SNPs described here are useful in risk assessment of psoriasis and likely also of other autoimmune diseases of the skin and joints, including atopic dermatitis and rheumatoid arthritis. The findings described herein also support a general role for RUNX1 in preventing autoimmune disease via regulation of expression of organ-specific genes, or genes involved in T cell development. Current topical, phototherapeutic, and systemic agents used to treat psoriasis have multiple undesirable side effects. The identification of therapeutic alternatives is greatly facilitated by knowledge ofthe underlying genetic and biochemical defects responsible for the disease.

The results described herein support the existence of two psoriasis susceptibility regions at chromosome 17q24-q25. Clustering of genes for complex traits is not unusual. For example, a cluster of genes for murine systemic lupus erythematosus (SLE) exists on chromosome lq (Morel, L., Blenman, K.R., Croker, B.P. & Wakeland, E.K. The major murine systemic lupus erythematosus susceptibility locus, Slel, is a cluster of functionally related genes. Proc. Natl. Acad. Sci., U.S.A. 98, 1787-92 (2001)), and there are likely to be two Crohn's disease loci within approximately 20cM on chromosome 16q (Adeniji, O.A., Mrug, M.M. & DiPalma, J.A. Not one but two inflammatory bowel disease susceptibility loci map to chromosome 16. Am. J. Gastroenterol. 97, 2464-5 (2002)). As with any complex disease study it will be necessary to examine association of these variants with other psoriasis cohorts, as well as with other inflammatory diseases such as rheumatoid arthritis and atopic dermatitis where linkage to 17q24- q25 has also been demonstrated (Cookson, W.O. et al. Genetic linkage of childhood atopic dermatitis to psoriasis susceptibility loci. Nat. Genet. 27, 372-3 (2001)).

Accordingly, provided are methods and related materials for determining the susceptibility of a subject to psoriasis. A method for determining whether a subject has a susceptibility to psoriasis includes, for example, taking a biological sample from the subject, and analyzing a polynucleotide sequence in the sample to detect the presence or absence of an allelic variant of at least one polymoφhic region of chromosome 17q24-q25, wherein the allelic variant has an established association with psoriasis, for example such as those described herein. For example, the allelic variant is any one of the SNPs established herein through TDT-AE analysis to be associated with psoriasis. These SNPs include those from the first polymoφhic region described herein, namely rs745318, rs734232, rs895691, rsl2797 and rs2305214, as well as those from the second polymorphic region described herein, namely rs869190, rsl48530, rsl564864, rs2019154 and rs9906827. The first polymoφhic region is that described herein as harboring EBP50/SLC9A3R1/NHERF and NAT9, and the second polymoφhic region is that described herein as harboring RAPTOR.

In another aspect, the methods encompass a method for determining whether a subject has a susceptibility to psoriasis, including analyzing a polynucleotide sequence in a biological sample from the subject, to detect the presence or absence of at least one DNA marker from chromosome 17q24-q25, wherein the DNA marker is associated with susceptibility to psoriasis. The DNA marker is, for example, one ofthe SNPs identified herein as being associated with psoriasis.

In another aspect, the methods encompass a method for detecting the presence or absence in a subject of at least one allelic variant that is associated with psoriasis, including detecting the presence or absence of at least one of the previously identified SNPs from the first polymoφhic region of chromosome 17q24-q25 or from the second polymoφhic region of 17q24-q25.

In another aspect, the methods encompass a method for indicating a predisposition to psoriasis in a subject, including, on a chromosome 17q24-q25 obtained from the subject, detecting the presence or absence of at least one allelic variant of a polymoφhic region of 17q24- q25 that is associated with psoriasis, wherein the polymoφhic region comprises EBP50/SLC9A3R1/NHERF and NAT9, or the polymoφhic region comprises RAPTOR, and wherein the presence of the at least one allelic variant in the subject is indicative of a predisposition to psoriasis in the subject as compared to a subject in which the allelic variant is not present. The at least one allelic variant is, for example, one ofthe SNPs identified herein.

The materials and methods also give rise a method of screening for biologically active agents that modulate psoriasis symptoms. Such a method includes, for example, combining a candidate agent with a cell, wherein the cell includes a polynucleotide having a sequence that encodes at least one allelic variant, such as the SNPs described herein, ofthe polymoφhic region of 17q24-q25 that harbors EBP50/SLC9A3R1/NHERF and NAT9, the polynucleotide operably linked to a promoter such that the polynucleotide sequence is expressed in the cell as the EBP50 protein, and then determining the effect of the candidate agent upon the expression and/or activity ofthe EBP50 protein.

Similarly, the materials and methods give rise in another aspect to a method of screening for biologically active agents that modulate psoriasis symptoms, including combining the candidate agent with a cell comprising a polynucleotide having a sequence that encodes at least one allelic variant of that polymorphic region of 17q24-q25 comprising RAPTOR, the polynucleotide operably linked to a promoter such that the polynucleotide sequence is expressed in the cell as a RAPTOR protein, and then determining the effect of the agent upon the expression and/or activity ofthe RAPTOR protein.

The materials also encompass a primer or probe that specifically hybridizes adjacent to or at the first polymoφhic region of human chromosome 17q24-q25 harboring EBP50/SLC9A3R1/NHERF and NAT9, in combination with a primer or probe that specifically hybridizes adjacent to or at the second polymorphic region of human chromosome 17q24-q25 harboring RAPTOR. For example, the first polymoφhic region includes at least one allelic variant comprising a single nucleotide polymoφhism selected from the group consisting of rs745318, rs734232, rs895691, rsl2797 and rs2305214, and the second polymoφhic region comprises an allelic variant comprising a single nucleotide polymoφhism selected from the group consisting of rs869190, rsl48530, rsl564864, rs2019154 and rs9906827. A diagnostic primer is defined as a nucleic acid and an allele specific primer that is used, generally together with a constant primer, in an amplification reaction such as a PCR reaction, which provides the discrimination between alleles through selective amplification of one allele at a particular sequence position, such as used for ARMS.TM assays. The diagnostic primer is preferably 10- 50 nucleotides. Provided are diagnostic primers or probes including combinations of sequences encompassing the allelic variations identified here as associating with psoriasis. The primers may be manufactured using any convenient method of synthesis. Examples of such methods may be found in standard textbooks, for example "Protocols for Oligonucleotides and Analogues; Synthesis and Properties," Methods in Molecular Biology Series, Vol. 20; Ed. Sudhir Agrawal, Humana ISBN: 0-89603-247-7; 1993; 1st Edition. If required the primer(s) may be labelled with signal-generating materials to facilitate detection.

In another aspect, there is provided a kit for indicating whether a subject has a predisposition to developing psoriasis. The kit includes at least one probe or primer that specifically hybridizes adjacent to or at the first polymoφhic region of chromosome 17q24-q25 comprising EBP50/SLC9A3R1/NHERF and NAT9, and instructions for use of the kit for indicating whether the subject has a predisposition to developing psoriasis. The kit may also include at least one probe or primer that specifically hybridizes adjacent to or at a second polymoφhic region of 17q24-q25 comprising RAPTOR and that is associated with psoriasis. With respect to the kit, the first polymorphic region can include at least one allelic variant comprising a single nucleotide polymoφhism selected from the group consisting of rs745318, rs734232, rs895691, rsl2797 and rs2305214, and the second polymoφhic region can include an allelic variant comprising a single nucleotide polymoφhism selected from the group consisting of: rs869190, rsl48530, rsl564864, rs2019154 and rs9906827. The kit instructions, for example, may identify the five SNPs in the polymoφhic region harboring EBP50/SLC9A3R1/NHERF and NAT9, and the SNPs associated with RAPTOR that are associated here with psoriasis as described herein, and may further describe how to detect the presence or absence of any such variants within a biological sample taken from a subject. The kits may comprise appropriate packaging and may further comprise appropriate buffer(s) and polymerase(s) such as thermostable polymerases, for example Taq polymerase.

Alternatively, the kit for indicating whether a subject has a predisposition to developing psoriasis includes at least one probe or primer that specifically hybridizes adjacent to or at the polymorphic region of chromosome 17q24-q25 comprising RAPTOR and that is associated with psoriasis, along with instructions for use of the kit for indicating whether the subject has a predisposition to developing psoriasis. The kit includes, for example, an allelic variant comprising a single nucleotide polymoφhism selected from the group consisting of: rs869190, rsl48530, rsl564864, rs2019154 and rs9906827.

In another aspect, microarrays useful for diagnosis are provided which include, for example, a nucleic acid having a sequence of a first polymoφhic region of chromosome 17q24- q25 harboring EBP50/SLC9A3R1/NHERF and NAT9, and that is associated with psoriasis. With respect to the microarray, for example, the first polymoφhic region comprises at least one allelic variant comprising a single nucleotide polymorphism selected from the group consisting of rs745318, rs734232, rs895691, rsl2797 and rs2305214. Also contemplated is a microarray further comprising a sequence of the second polymoφhic region of chromosome 17q24-q25 comprising RAPTOR and that is associated with psoriasis, wherein the second polymoφhic region comprises an allelic variant comprising a single nucleotide polymoφhism selected from the group consisting of rs869190, rsl48530, rsl564864, rs2019154 and rs9906827.

A test sample of nucleic acid suitable for diagnostic testing according to the methods described herein, is conveniently a sample of blood, sputum, or other body fluid or tissue obtained from an individual. It will be appreciated that the test sample may equally be a nucleic acid sequence corresponding to the sequence in the test sample, that is to say that all or a part of the region in the sample nucleic acid may firstly be amplified using any convenient technique, such as PCR, before use in the analysis of the first polymoφhic region harboring EBP50 or the second polymoφhic region harboring RAPTOR.

In yet another aspect, there is provided a method for determining whether a subject has a susceptibility to an autoimmune disease, the method including, in a biological sample from the subject, analyzing a polynucleotide sequence to detect the presence or absence of an allelic variant of at least one polymorphic region wherein the allelic variant abolishes a RUNXl/AMLl binding site. The autoimmune disease is, for example, psoriasis and the method includes analyzing chromosome 17q24-q25 to detect the presence or absence of rs734232. Alternatively, a method for determining whether a subject has a susceptibility to psoriasis includes analyzing a polynucleotide sequence from a polymoφhic intragenic region on chromosome 17q24-q25 between EBP50 and NAT9, to determine the elimination of a RUNXl/AMLl binding site. The method may include, for example, detecting the presence or absence of rs734232.

Methods used for diagnosis are, for example, those in which the sequence is determined by a method such as amplification refractory mutation system and restriction fragment length polymoφhism. It will be apparent to the person skilled in the art that there are a large number of analytical procedures that may be used to detect the presence or absence of variant nucleotides at one or more of the SNP positions described herein with respect to EBP50 and RAPTOR. In general, the detection of allelic variation requires a mutation discrimination technique, optionally an amplification reaction and a signal generation system.

Mutation detection techniques can be based, for example, on the PCR. Exemplary techniques, without limitation, include the following: general techniques such as DNA sequencing, sequencing by hybridization; scanning techniques such as PJT*, SSCP, DOGE, TGGE, Cleavase, Heteroduplex analysis, CMC, Enzymatic mismatch cleavage; hybridization based solid phase hybridization such as dot blots, MASDA, reverse dot blots, oligonucleotide arrays (DNA Chips); solution phase hybridization such as Taqman.TM. (U.S. Pat. Nos. 5,210,015 & 5,487,972, Hoffmann-La Roche); molecular beacons such as that described by Tyagi et al (1996), Nature Biotechnology 14, 303 and WO 95/13399 (Public Health Inst, New York); extension based techniques such as ARMS.TM., ALEX.TM. (European Patent No. EP 332435 Bl, Zeneca Limited) and COPS (Gibbs et al, Nucleic Acids Research, 17, 2347 (1989); incoφoration based techniques such as mini-sequencing, and APEX; restriction enzyme based, such as RFLP, restriction site generating PCR; ligation based such as OLA; and other techniques such as invader assays. These techniques will often be used in combination with a number of signal generation systems.

Signal detection techniques include, for example, fluorescence-based techniques such as FRET, fluorescence quenching, fluorescence polarization (United Kingdom Patent No. 2228998, Zeneca Limited); colorimetric assays such as hybridization protection assay; mass spectrometry, and other signal detection techniques such as chemiluminescence, electrochemiluminescence, Raman specfroscopy and radioactivity signal detection.

Many current methods for the detection and amplification of allelic variation can be found in recent reviews, such as that by Nollau et al., Clin. Chem. 43, 1114-1120 (1997), and also in standard textbooks, such as, for example "Laboratory Protocols for Mutation Detection", Ed. by U. Landegren, Oxford University Press, (1996), and "PCR", 2nd Ed., Newton & Graham, BIOS Scientific Publishers Limited, (1997).

Individuals who carry the particular allelic variants of the EBP50/SLC9A3R1/NHERF and NAT9, or of RAPTOR, may therefore exhibit differences in their ability to produce or regulate the subject proteins or protein isoforms under different physiological conditions and will display altered abilities to react to different factors that play a role in psoriatic disease pathogenesis. In addition, differences in protein expression and regulation arising as a result of allelic variation may have a direct effect on the response of an individual to drug therapy. The polymoφhisms described herein may therefore have the greatest effect on the efficacy of drugs designed to modulate the activity of EBP50/SLC9A3R1/NHERF, NAT9 or RAPTOR. The diagnostic methods ofthe invention may therefore be useful both to predict the clinical response to such drug agents and to determine therapeutic dose.

In a further aspect, the diagnostic methods ofthe invention are used in the development of new drug therapies that selectively target one or more allelic variants of EBP50/SLC9A3R1/NHERP, NAT9 or RAPTOR. Identification of a link between a particular allelic variant and predisposition to disease development or response to drug therapy may have a significant impact on the design of new drugs. Drugs may be designed to regulate the biological activity of variants implicated in the disease process whilst minimizing effects on other variants. For example, RAPTOR, which is likely to play a role in the interleukin-2 signaling pathway, and alleles of RAPTOR including those that may be associated with other T-cell mediated autoimmune diseases, are potential drug targets. More specifically, for example, with respect to RAPTOR, the variants can be used to screen agents that modify TOR kinase activity.

General molecular biology procedures can be followed from any of the methods described in MOLECULAR CLONING~A LABORATORY MANUAL, 2^nd ed., Sambrook, Fritsch and Maniatis (Cold Spring Harbor Laboratory, 1989).

EXAMPLES

Without further elaboration, it is believed that one skilled in the art can, using the preceding description, utilize the present invention to its fullest extent. The following specific examples are offered by way of illustration and not by way of limiting the remaining disclosure.

Example 1 - Genotyping and Association Analyses

Ascertainment and characteristics of psoriasis families are described elsewhere in Speckman, R.A. et al, Hum.Genet. 112, 34-41 (2002), which is herein incoφorated by reference. 242 nuclear families with 572 individuals diagnosed with psoriasis were used. Approximately 20% of patients had joint involvement indicative of psoriatic arthritis and 2/3 of these had been conclusively diagnosed by a rheumatologist. Semi-automated genotyping

SNPs were identified by re-sequencing pooled DNA samples of 10-30 unrelated affected and unaffected individuals as described in Speckman, RA. et al., (2002), supra. All SNPs identified as of May 28, 2003 by re-sequencing were also all found in public databases. SNPs were genotyped with fluorescently-labeled allele-specific primer extension assayed by fluorescence polarization template-directed dye incoφoration (FP-TDI) (Chen, X., Levine, L. & Kwok, P.-Y. Fluorescence polarization in homogeneous nucleic acid analysis. Genome Res. 9, 492-498 (1999).). Unlabeled dideoxynucleotides (Boehringer Mannheim) were used for the liquid chromatography assay. Association analyses

PEDMANAGER (Whitehead Institute for Biomedical Research,) was used to check for non- Mendelian inheritance of alleles. Mega (Mukhopadhyay, N., Almasy, L., Schroeder, M., Mulvihill, W.P. & Weeks, D.E. Mega2, a data-handling program for facilitating genetic linkage and association analyses. Am. J. Hum. Genet. 65, A436 (1999)) was used to prepare family data for input to SIMWALK2. Mega2 SIMWALK2 uses simulated annealing to reconstruct the most likely haplotypes in families. In re-examining haplotype subsets from SIMWALK2, excluded were families with apparent recombinations in the region. For counts of transmitted and untransmitted haplotypes, removed from the haplotype pool were cases where one or more marker alleles in the SIMWALK output were of unknown phase or were inferred. SIMWALK haplotypes were also used to calculate disequilibrium coefficient D', chi-square of association, and p-values for all pairwise combinations of markers via the GOLD-HaploXT program. HTML- based plots ofthe results were generated with in-house programs. Further errors were detected in the process of haplotype reconstruction as described below.

Association studies were first performed with the transmission disequilibrium test (TDT)

(Spielman, R.S., McGinnis, R.E., and Ewens ,W.J. Transmission test for linkage disequilibrium: the insulin gene region and insulin-dependent diabetes mellitus (IDDM). Am. J. Hum. Genet. 52,

506-516 (1993).) (using the TDT-AE method (Gordon, D., Heath, S.C., Liu, X. & Ott, J. A transmission/disequilibrium test that allows for genotyping errors in the analysis of single- nucleotide polymoφhism data. Am. J. Hum, Genet. 69, 371-80 (2001))). This was used because a number of the marker loci (particularly microsatellites) showed genotyping errors, and it has been demonstrated that removing Mendelian inconsistencies from the genotyping data and performing TDT analysis can lead to substantial increases in the type I error rate of the TDT statistic. The TDT-AE method uses a likelihood approach to correct for genotyping error and thus remains valid in the presence of data with genotyping error. For SNP and other loci with only 2 alleles, the uncorrected and corrected p-values are identical. For marker loci with numbers, k, of alleles exceeding 2, the TDT-AE statistic is computed k times, by down-coding all alleles at a locus to 2 alleles; the allele of interest vs. all other alleles. The maximum likelihood ratio test statistic is chosen among all alleles, and the corresponding uncorrected p-value multiplied by the number of alleles for the particular locus. The product of this number and the uncorrected p-value is the corrected p-value. Complete results from the TDT-AE method are presented as supplemental data.

For association analyses with haplotypes, all data in the families were used to construct haplotypes in the parents and children. For each haplotype construction/TDT analysis a specified

! set of markers was used (starting with 1 marker, and going up to >7). Haplotypes were reconstructed with PATCH (Wijsman, E.M. A deductive method of haplotype analysis in pedigrees. Am. J. Hum. Genet. 41, 356-373 (1987).) or SIMWALK2 (Mukhopadhyay, N., Almasy, L., Schroeder, M., Mulvihill, W.P. & Weeks, D.E. Mega2, a data-handling program for facilitating genetic linkage and association analyses. Am. J. Hum. Genet. 65, A436 (1999)). For all pedigrees with at least one parent where transmission could be determined, one affected child was chosen at random. The total number of transmitted vs. untransmitted chromosomes was determined for all such pedigrees. Pedigrees for which it was not possible to definitively determine phase-known, noninferred transmissions from at least one parent were not used. With this table of transmitted and untransmitted chromosomes, the marginal test of homogeneity was then used to test for non- random transmission of haplotypes (a multiallelic TDT based on total transmissions and non- transmissions) (Bickeboller, H. & Clerget-Darpoux, F. Statistical properties of the allelic and genotypic transmission/disequilibrium test for multiallelic markers. Genet. Epidemiol. 12, 865-70 (1995)). Haplotypes reconstructed with either method were essentially identical. EBP50 expression

Immunohistochemistry was performed on frozen tissue sections obtained from psoriasis patients and normal controls. EBP-50 antibody from BD Transduction Laboratories (Cat #: 611160, Clone 6, Mouse IgGl) and from Abeam Limited (Cat #: ab9526, Clone EBP-10, Mouse IgG2b) were applied to tissue sections for 90 minutes. Bound antibody was visualized using the avidin-biotin complex (Vectastain ABC, Vector Laboratories, Inc.). 3-amino-9-ethylcarbazol was the chromagen used. Flow cytometry

Whole blood and HaCat cells were fixed and lysed (FACS Lyse, BD), then extracted with 0.1% Triton-X-100 in PBS. The cells were stained using the EBP-50 antibody from BD Transduction Laboratories, labeled with a fluorescein-Zenon mouse IgG labeling reagent (from Molecular Probes, Inc.). The sample was then analyzed through the use of FACSCalibur and CellQuest Software (Becton Dickinson). Transcription factor binding site identification

The TFSEARCH database (available at http: //ιnolsunl.cbrc.aist.ga.jp/research/db/TFSEΛRCH.htmI) was used to predict binding sites (Heinemeyer, T. et al. Databases on transcriptional regulation: TRANSFAC, TRRD and COMPEL. Nucl. Acids Res. 26, 364-370 (1998).). Electrophoretic mobility and supershift assays

[γ-³²P] -labeled (Amersham) double-stranded oligonucleotide and Jurkat cell nuclear extract (Oncogene Research Products) were incubated at 25°C for 20 minutes using the Gel Shift Assay System from Promega (Cat #:E3050). The reaction mixture was separated on 4% PAGE and visualized by autoradiography. Unlabeled oligonucleotide at 50-fold molar excess was added to the reaction for competition. The identity ofthe DNA-binding protein in the assay was confirmed by using a RUNX1 specific antibody from Santa Cruz Biotechnology, Inc. or the non-specific EBP-50 antibody. Similar results were obtained with Promega buffer (20% glycerol, 5mM MgC12, 2.5mM EDTA, 2.5mM DTT, 250mM Nacl, 50mM Tris-HCl (pH 7.5), 0.25mg/ml poly(dI-dC)(poly(dI-dC)) and in-house buffer (2mM Hepes, lOmM Tris-HCl (pH7.5), 25mM NaCl, lOmM KC1, 1.5mM EDTA, O.lmM ZnSO4, 15% glycerol, 0.25mg/ml BSA, 0.6mM DTT, 0.2mg/ml poly(dI-dC)(poly(dI-dC)). The sequences of the oligonucleotide probes are as follows: RUNX1-A:gcttggtgtagtcagtgt (SEQ ID NO: 6); RUNX1-G:gcttggtgtggtcagtgt (SEQ ID NO: 7); pl-.attcgatcggggcggggcgagc (SEQ ID NO: 8) and their reverse complements.

Electronic database information

TDT-AE version 1.0 is available at ftp://linkage.rockefeller.edu/software/tdtae. SNP primers are available at http://hg.wustl.edu/bowcock/2003/.

Figure 1 shows the results of family-based association mapping of psoriasis at 17q24-q25 using TDT-AE analyses (described in Spielman, R.S., et al., Am. J. Hum. Genet. 52, 506-516 (1993), and Gordon, D., et al., Am. J. Hum. Genet. 69, 371-80 (2001)) demonstrating association between psoriasis and specific DNA markers from two separate regions of chromosome 17q24- q25. TDT-AE analysis revealed two peaks where evidence for association was significant. More specifically, as shown in Figure 1, two regions separated by 5.4Mb are associated with psoriasis. Seventy-eight (78) SNPs and thirty (30) microsatellites distributed along the length of 17q24-q25 were genotyped in 242 nuclear psoriasis families and association with psoriasis was evaluated with the TDT-AE. The -logio transformation of the corrected TDT p-values are plotted against physical location of markers (see, e.g., http://genome.ucsc.edu/index.html?org=Human&db=hgl3&hgsid=20285318), so that the more significant p-values appear higher than less significant p-values. The p-values reported for the TDT-AE method are corrected for multiple testing. The first peak extends from marker rs745318, with a p-value of 0.0012, [-log(p-value)=2.92], to rs878906, with a p-value of 0.0015 [-log(p-value)=2.82]. The marker with the most significant p-value in this interval is rs2305214 (marker 15), with a p-value of 0.0002 [-log(p-value)=3.70]. This marker also has the most significant p-value over the entire set of markers. The length of this interval, from marker rs745318 to marker rs878906, is 5.355kb. The other interval consisted of a single point, at marker rs869190. The p-value corresponding to this marker is 0.0005 [-log(p-value)=3.30]. The

TDT-AE method is powerful even in the presence of observed genotyping errors. In fact, marker rs2305214, for which the TDT-AE gave the most significant p-value, has maximum likelihood error parameter estimates ^=0.0367 and ε₂=Q under the alternative hypothesis of linkage and

association (HI). Here,^ is the probability that a "1" allele is miscoded as a "2" allele and £₂is the probability that a "2" allele is miscoded as a "1" allele, assuming there are two alleles at the locus. This error model is described in more detail in Gordon, D., et al., Am. J. Hum. Genet. 69, 371-80 (2001).

Associated SNPs in the proximal peak lie in or near SLC9A3R1 (also known as EBP50 and NHERF1) and NAT9. As explained supra, SLC9A3R1/EBP50 is a PDZ domain-containing phosphoprotein that associates with members of the ezrin-radixin-moesin family. SLC9A3R1/EBP50 is a multifunctional scaffold protein implicated in diverse aspects of epithelial membrane biology and immune synapse formation in T cells (Voltz, J.W., Weinman, E.J. & Shenolikar, S. Expanding the role of NHERF, a PDZ-domain containing protein adapter, to growth regulation. Qncogene 20, 6309-14 (2001)). NAT9 (N-acetyl transferase 9) is a novel member of the N-acetyl transferase superfamily. The distal peak of association was within RAPTOR (pi 50 target of rapamycin (TOR)~scaffold protein containing WD-repeats) (Hara, K. et al. Raptor, a binding partner of target of rapamycin (TOR), mediates TOR action. Cell 110, 177- 89 (2002)). TOR is a component ofthe T-cell interleukin-2 signaling pathway.

Expression of SLC9A3R1 is highest in the uppermost stratum Malpighi of psoriatic and normal skin and in inactive versus active T cells. A disease-associated SNP lying between SLC9A3R1 and NAT9 leads to loss of RUNXl binding, representing a second example of loss of a RUNXl binding site associated with susceptibility to an autoimmune disease (Prokunina, L. et al. A regulatory polymorphism in PDCD1 is associated with susceptibility to systemic lupus erythematosus in humans. Nat. Genet. 32, 666-669 (2002)), which is also consistent with defective regulation of SLC9A3R1 or NAT9 by RUNXl as a susceptibility factor for psoriasis. These genes are separated by 5.4Mb, suggesting that they confer independent contributions to psoriasis susceptibility. EBP50 protein was detected in T cells and in both normal and psoriatic skin with highest levels of expression in the uppermost stratum Malpighi.

Sequences of EBP50 (accession no. AF015926), and RAPTOR (accession nos. AY090663, AK055912, AB082951) are available, respectively, in: Reczek et al., Identification of EBP50: A PDZ-containing phosphoprotein that associates with members ofthe ezrin-radixin- moesin family, J. Cell Biol. 139:169-79 (1997)(AF015926); Kim et al., mTOR interacts with raptor to form a nutrient-sensitive complex that signals to the cell growth machinery, Cell 110, 163-75 (2002)(AY090663); and Hara, K. et al., Raptor, a binding partner of target of rapamycin (TOR), mediates TOR action, Cell 110, 177-89 (2002)(AB082951 and AB082952).

More specifically, the first peak lies 80kb distal to D17S1301 and harbors EBP50/NHERF (Na+/H+ exchange regulatory factor)/SLC9A3Rl (Voltz, J.W., Weinman, E.J. & Shenolikar, S. Expanding the role of NHERF, a PDZ-domain containing protein adapter, to growth regulation. Oncogene 20, 6309-14 (2001).) and DKFZP564C103 genes. These are transcribed in tail-to-tail orientation and are separated by only 1.2kb. DKFZP564C103 encodes NAT9. Resequencing ofthe region in patients and controls, followed by genotyping of SNPs in the region revealed other associated SNPs (see Table la, supplemental data, infra) but no psoriasis-associated mutations, suggesting that predisposing variants are common in the population. All associated SNPs were polymoφhic in other Caucasian, African and Asian populations (see Table lb, in supplemental data, infra). All pairwise combinations of associated markers were in LD with each other (see supplemental data, infra).

Haplotypes reconstructed along the length of this region in families yielded significant differences between the numbers of transmitted and untransmitted haplotypes when a multiallelic TDT approach was used (Bickeboller, H. & Clerget-Daφoux, F. Statistical properties of the allelic and genotypic transmission/disequilibrium test for multiallelic markers. Genet. Epidemiol. 12, 865-70 (1995)). The most common over-transmitted and overlapping 5-marker haplotypes are shown in Table 2a (see supplemental data, infra). When haplotypes comprised of greater than (>) 5 markers were analyzed, power to detect association was lost since an increasing number of haplotypes was discarded due to our criteria for inclusion. However, over the region of association herein described, even haplotypes with 8 or more markers yielded significant results at p < 0.01 (see supplemental data, infra, for complete TDT tables and remaining haplotypes).

In order to identify a core region or set of SNPs driving this association we constructed overlapping five-marker haplotypes from rs3178300 to rs878907 (#6-#16) and determined the over- and under-transmitted haplotypes (Table 2b, supplemental data, infra)). The most common transmitted and untransmitted haplotypes harbored complementary bases suggesting the existence of susceptibility and resistance haplotypes. Five SNPs from this region had one allele that was consistently overtransmitted and one that was consistently undertransmitted. These SNPs are rs745318 (#7), rs734232 (#9), rs895691(#ll), rsl2797 (#12), and rs2305214(#15). For each of these markers it was the allele that was less common in the Northern European population that was over-transmitted to affecteds (Table lb, see supplemental data, infra). The SNP rs745318 lies within the intron of EBP50 gene between exons 3 and 4, rs734232 and rs895691 lie in the 1.2kb intragenic region between EBP50 and NAT9 (rs734232 is 234bp from the 3' end of the EBP50 gene), rsl2797 lies in exon7 of NAT9, and rs2305214 lies in the intron between exons 4 and 5 of NAT9. Table 2c (see supplemental data, infra) displays comparison of allele frequencies of SLC9A3R1/NAT9 associated SNPs and the five marker haplotype in cases from the 242 families and unrelated Caucasian individuals from the U.S. and reveals strong evidence for association with the haplotype. This suggests that the combination of associated alleles of markers 7, 9, 11, 12 and 15 predisposes to disease.

Figure 2a is a partial sequence (SEQ ID NO: 9) of the intragenic region between the genes NHERF1/EBP50 and DKFZP564C103. The predicted binding site for the transcription factor AML-1/RUNX1 is shown in bold. This site is disrupted by the psoriasis associated A allele of SNP rs734232. Figure 2b shows the results of electrophoretic mobility shift, super-shift and competition assays with Jurkat nuclear cell extract and allelic variants of rs734232. The 18-bp oligonucleotides containing the G and A alleles of rs734232, representing native and mutated RUNXl binding sites were assayed with Jurkat cell extracts. Binding was not observed with an oligonucleotide containing rs734232A (lanes 9-12) but was present with oligonucleotides containing rs734232G (lanes 1-8) when Jurkat extract was present. Binding to the wildtype G allele resulted in a complex that was competed by 50X excess of unlabeled rs734232G oligonucleotide (lane 7) but not by the same amount of an unrelated oligonucleotides (Spl binding site) (lane 8). Antiserum against AML-1/RUNXl (anti-AML) revealed a super-shifted band (lane 5) whereas unrelated serum did not (lane 6).

Immunohistochemical analyses and FAC staining were performed to evaluate the expression of EBP50 protein in the skin and T cells. Figure 3a shows staining of cross-sections of normal, non-lesional (uninvolved) and lesional (involved) psoriatic skin with EBP50 antibodies. The staining revealed the presence of EBP50 in the epidermal layer in both patients and controls. EBP50 is expressed in all viable epidermal layers in normal and psoriatic skin. However, in both patients and controls expression is highest in the uppermost stratum Malpigi (i.e. the granular layer of normal epidermis). There are also scattered positive cells at the dermal- epidemal junction.

The localization of the associated EBP50 SNPs with respect to known TF binding sites was investigated. The psoriasis-associated allele (A) of rs734232 eliminated a binding site for the runt-related transcription factor RUNXl/AMLl (Erickson, P. et al. Identification of breakpoints in t(8;21) acute myelogenous leukemia and isolation of a fusion transcript, AMLl/ETO, with similarity to Drosophila segmentation gene, runt. Blood 80, 1825-31 (1992).). Figure 3b shows FAC staining of keratinocyte cells (HaCAT line) and peripheral blood lymphocytes (primarily T cells) with EBP50 antibody conjugated with FITC. This was confirmed by supershift binding on addition of antibodies against RUNXl. The binding was competed by 50-fold excess of unlabeled oligonucleotide. However, no binding to the psoriasis- associated site (allele A), at any concentration of the nuclear extract, was found. It is therefore concluded, without being bound, that the target protein is expressed in most keratinocytes and T cells but that its level in the skin increases in the granular layer where terminal differentiation occurs.

A recent study on systemic lupus erythematosus provided evidence of association with the A allele of a SNP lying within an intron of PDCDl that also abolished a binding site for RUNXl/AMLl (Prokunina, L. et al. A regulatory polymoφhism in PDCDl is associated with susceptibility to systemic lupus erythematosus in humans. Nat. Genet. 32, 666-669 (2002)). The associated SNP described herein lies in the 1.2kb intragenic region between EBP50 and NAT9 and 234bp from the 3' to the end of EBP50. This intragenic region is predicted to harbor 15 RUNXl transcription factor binding sites. RUNXl is involved in hematopoietic and endothelial cell development (Lacaud, G. et al. Runxl is essential for hematopoietic commitment at the hemangioblast stage of development in vitro. Blood 100, 458-66 (2002).), CD4 silencing (Taniuchi, I. et al. Differential requirements for Runx proteins in CD4 repression and epigenetic silencing during T lymphocyte development. Cell 111, 621-633 (2002).)and the development of acute myelogenous leukemia (Osato, M., Yanagida, M., Shigesada, K. & Ito, Y. Point mutations ofthe RUNxl/AMLl gene in sporadic and familial myeloid leukemias. Int. J. Hematol. 74, 245- 51 (2001).). The loss of RUNXl sites in alleles associated with two different autoimmune diseases supports an important role for RUNXl in tolerance in general.

A psoriasis-associated allele of a second SNP (rs745318) lies within a GATA1 site whereas the untransmitted allele lies within a binding site for the transcriptional repressor deltaE. However, although EMS As with oligonucleotides harboring the two alleles of rs745318 revealed binding to nuclear extracts from T cells, the addition of GATA1 and GATA2 antibodies did not reveal a supershift suggesting binding by a different transcription factor. These experiments support the conclusion that one causative variant is the A allele of rs734232, but the involvement of some ofthe other associated SNPs described herein cannot be ruled out.

Northern analysis of EBP50 in inactive versus activated T cells revealed two transcripts of 3.8 and 2.0kb that are down-regulated 3-5 fold upon T cell activation with PMA and ionomycin. Without being bound it is believed that the RAPTOR variants may alter regulation or alternative splicing of RAPTOR mRNA.

Example 2 - NAT9 Involvement in Disease Process

Although there is a biologically plausible role for SLC9A3R1 in psoriasis, since it is expressed in polarized epithelial cells, and is a negative regulator ofthe immune synapse, NAT9 cannot be excluded as being involved in disease. For example, gly cosy lation affects protein folding, assembly, quality control, loading into MHC class I and presentation to the T cell receptor (TCR) complex. Cell-surface glycosylation also changes with T cell development. Changes in the populations of immunoglobulin G glycoforms isoforms have been noted in rheumatoid arthritis and systemic lupus erythematosus and mice defective in the pathway of protein N-glycosylation due to a mutation in the Mgat5 gene (Dl,6 N- acetylglucosaminyltransferase V) develop kidney autoimmune disease, enhanced delayed-type hypersensitivity, and increased susceptibility to experimental autoimmune encephalomyelitis accompanied by increased clustering of TCRs.

To determine the role of these genes in T cell activation, purified naive murine CD4 T cells were stimulated with anti-CD3 +/- IL-2 +/- anti-CD28 with primers for murine NAT9 cDNA. Figure 4 is a bar graph ofthe results of quantitative RT-PCR which was performed on the resultant CD4 T cells, revealing that Nat9 transcripts are diminished in expression in response to anti-CD3 and particularly IL-2. This type of pattern is only seen for a few other genes such as Tob and LKLF. To date these other genes have all been involved in the maintenance of T cell quiescence. The evidence supports roles of both SLC9A3R1 and NAT9 in the disease process of psoriasis.

Example 3 - Analysis of SNPs from the proximal and distal peaks of association

Genome- wide scans have repeatedly mapped a major disease susceptibility locus (PSORS1) to the Major Histocompatibility Complex (MHC), on chromosome 6p21 (reviewed by Capon et al.(Capon F, Munro M, Barker J, et al. Searching for the major histocompatibility complex psoriasis susceptibility gene. J Invest Dermatol 2002;118(5):745-51). Outside of the MHC, at least eight additional susceptibility intervals have been reported (PSORS2-9) (reviewed by Capon et al (Capon F, Munro M, Barker J, et al. Searching for the major histocompatibility complex psoriasis susceptibility gene. J Invest Dermatol 2002;118(5):745-51.) The PSORS2 interval [MIM 602723] was originally mapped to chromosome 17q25, in a sample of extended pedigrees presenting with disease segregation across multiple generations(Tomfohrde J, Silverman A, Barnes R, et al. Gene for familial psoriasis susceptibility mapped to the distal end of human chromosome 17q. Science 1994;264(5162):1141-5). Linkage to PSORS2 was later replicated in independently ascertained cohorts (Nair RP, Henseler T, Jenisch S, et al. Evidence for two psoriasis susceptibility loci (HLA and 17q) and two novel candidate regions (16q and 20p) by genome-wide scan. Hum Mol Genet 1997;6(8): 1349-56). Conversely, two distinct genome-wide scans carried out by our group failed to detect any evidence for linkage to PSORS2, in UK cohorts of European descent (Trembath RC, Clough RL, Rosbotham JL, et al. Identification of a major susceptibility locus on chromosome 6p and evidence for further disease loci revealed by a two stage genome-wide search in psoriasis. Hum Mol Genet 1997;6(5):813- 20). However, High-density genetic analysis of the PSORS2 interval has identified two distinct association peaks, both defined by a small number of non-coding SNPs, as described herein and elsewhere (Helms C, Cao L, Krueger JG, et al. As described herein, a RUNXl binding site variant between SLC9A3R1 and NAT9 is associated with susceptibility to psoriasis. (See also Nat Genet 2003; 35:349-56). The proximal peak spans a 20 kb genomic segment where a putative susceptibility allele, mapping between the SLC9AR1 and NAT9 genes, abolishes a RUNXl binding site. The less characterized distal region of association lies 6Mb away, within intron 3 of the RAPTOR gene [MIM *607130] (Helms C, Cao L, Krueger JG, et al. A putative RUNXl binding site variant between SLC9A3R1 and NAT9 is associated with susceptibility to psoriasis. Nat Genet 2003; 35:349-56). In order to define the relevance of PSORS2 genetic variation in the UK, eight (8) representative SNPs were analyzed, selected from both association peaks. The results provide evidence for association between familial psoriasis and RAPTOR SNPs.

The patient cohort included a total of 233 independent parent-offspring trios of Northern European origin. Of these, 116 were sampled from the family cohort previously described by Veal et al. (Veal CD, Clough RL, Barber RQ et al. Identification of a novel psoriasis susceptibility locus at lp and evidence of epistasis between PSORSl and candidate loci. J Med Genet 2001;38(1):7-13). The 117 remaining trios were ascertained through an affected proband, as detailed in Veal et al., (2001).

Based on the reported significance of disease association the following five markers were selected from the proximal association peak: SNP8 (rs7420); SNP9 (rs734232, abolishing the RUNXl site); SNP11 (rs895691); SNP12 (rsl2797); SNP15 (rs2305214). Based on the same criterion, three (3) further SNPs (rsl564864, rs2019154 and rs869190) were selected from the distal association peak. Following DNA extraction from blood lymphocytes, SNP genotyping was carried out by fluorescence polarization template directed dye incoφoration (FP-TDI) as described by Speckman et al (Speckman RA, Wright Daw JA, Helms C, et al. Novel immunoglobulin superfamily gene cluster, mapping to a region of human chromosome 17q25, linked to psoriasis susceptibility. Hum Genet 2003;112(1):34-41.) or with Sequenom MassArray technology (Sequenom Inc). Family based association analysis was carried out using the TRANSMIT 2.5 software (Clayton D. A generalization of the transmission/disequilibrium test for uncertain- haplotype transmission. Am J Hum Genet 1999;65(4): 1170-7.) to examine the transmission rates of marker alleles.

Table 3b shows TDT-AE p values showing association between psoriasis and SNPs in RAPTOR (ALL FAMS). Stratification of families with the PSORSl risk allele (SNP9) revealed stronger evidence for association with psoriasis, indicating interaction between PSORSl (the major psoriasis determinant in the HLA class I region), and RAPTOR . Hence RAPTOR is a modifier of this locus. Without being bound, RAPTOR may determine in part who with HLA- Cw6 or the nearby susceptibility allele in the class I region (known as PSORSl), gets psoriasis. Stratification on SNP9 - allele 2 (T) (reported in Veal et al. 2002), which lies upstream of HLA- C, gives improved results over using HLA-Cw6 itself. RISK applies to families where at least one affected child had the SNP9 - allele 2. Non-risk applies to families where no affected child had the SNP9 - allele 2 (T).

Association analysis results are summarized in Table 4 (see supplemental data, Table 4, infra). The entire dataset was first examined and revealed that rs2019154 (distal peak) was the only marker supporting evidence for association (P = 0.027). In order to reduce the heterogeneity of our cohort, subsequent analysis was restricted to the 116 trios that had been sampled from extended pedigrees, thus defining a subset of patients with a well documented family history of psoriasis. This stratification did not modify the outcome of the proximal peak genetic analysis. However, the significance of disease association increased for all 3 SNPs mapping to RAPTOR intron 3, with rs2019154 yielding the lowest P value (P = 0.008) ( ee supplemental data, Table 4, infra).

The failure to detect association with SNPs from the SLC9AR1/NAT9 genomic segment is in keeping with the low relative risk that is conferred by these variants (Helms C, Cao L, Krueger JG, et al. As described supra, a RUNXl binding site variant between SLC9A3R1 and NAT9 is associated with susceptibility to psoriasis, indicating that a larger dataset might be needed to replicate the significance values previously reported (Helms C, Cao L, Krueger JG, et al. However, the observation of increased RAPTOR association in the familial subset of the present sample supports the use of strict selection criteria in patient recruitment. Noteworthy is the fact that the location of the RAPTOR gene closely matches that of the original PSORS2 interval, as defined by parametric linkage analysis of multi-generation pedigrees, which implicates RAPTOR SNPs in familial psoriasis, for example by acting as a modifier of major susceptibility loci.

The observation of significant association at the RAPTOR locus contrasts with previous efforts to detect linkage with the PSORS2 interval (Trembath RC, Clough RL, Rosbotham JL, et al. Identification of a major susceptibility locus on chromosome 6p and evidence for further disease loci revealed by a two stage genome-wide search in psoriasis. Hum Mol Genet 1997;6(5):813-20). This discrepancy can be explained by several factors, including the informativity and spacing of the microsatellites used in the genome scans. Moreover, the psoriasis-associated alleles from this region are found on multiple haplotypes in families and are likely to have a small effect upon disease susceptibility. Mathematical modelling has clearly shown that association studies offer a greater power to detect minor susceptibility loci, compared to linkage analysis (Risch NJ. Searching for genetic determinants in the new millennium. Nature 2000;405(6788):847-56). The presently disclosed findings, which replicate the above-described observation (see Example 1) of significant association of psoriasis at the RAPTOR locus in an independent set of individuals, are important for demonstrating the value of association studies in the characterization of genomic intervals linked to complex traits.

Other Embodiments

When introducing elements of the present invention or the preferred embodiments thereof, the articles "a", "an", "the" and "said" are intended to mean that there are one or more of the elements. The terms "comprising", "including" and "having" are intended to be inclusive and mean that there may be additional elements other than the listed elements. As various changes could be made in the above constructions without departing from the scope ofthe invention, it is intended that all matter contained in the above description or shown in the accompanying drawings shall be inteφreted as illustrative and not in a limiting sense. Indeed, various modifications of the invention in addition to those shown and described herein will become apparent to those skilled in the art from the foregoing description which do not depart from the spirit or scope of the present inventive discovery. Such modifications are also intended to fall within the scope ofthe appended claims.

References Cited

All publications, patents, patent applications and other references cited in this application are incoφorated herein by reference in their entirety for all puφoses to the same extent as if each individual publication, patent, patent application or other reference was specifically and individually indicated to be incoφorated by reference in its entirety for all puφoses. Citation of a reference herein shall not be construed as an admission that such is prior art to the present invention.

SUPPLEMENTAL DATA

Table la. Detailed location of exons and SNPs with corresponding GENEHUNTER TDT and TDT-AE p values. Marker numbers refer to marker position in the 27-marker haplotypes described in text and subsequent tables. Locations of SNPs and exons are taken from the UCSC June 2002 assembly ofthe genome (http://genome.ucsc.edu/). SNPs with rs# are described according to their reference identification number from the SNP database. Polymoφhism and associated alleles are derived from the coding strand of EBP50/SLC9A3R1. n.s. (not significant)

Table lb. Frequencies of associated SNP alleles in different human populations. (Marker numbers refer to marker position in 27-marker haplotype. ND= not determined)

Table 2a. Most common over-transmitted five-marker haplotypes found for markers 1-22. Freq.: Also presented are: Freq.: haplotype frequency, T: number of transmitted and UT: untransmitted haplotypes; TOTAL: total number of haplotypes identified in the families for each set of five markers; D² values comparing distribution of over-and under-transmitted haplotypes in each set as described in Methods, d.f. (no. haplotypes -1), and corresponding p values.

Marker

[Haplotype 1 β [3 |4 |5 |6 |7 |8 |9 |10 |ll |12 |13 |14 |15 |16 |17 |l8 |l9 |20 |21 ]22 |Freq T UT TOTAL D² df p-value

1 0.3 60 44350 18.46 15 0.239 2 0.26 69 51 462 21.9 19 0.289 3 0.12 39 13 432 32.91 23 0.083 4 0.11 32 12410 30.89 21 0.076 5 0.12 34 15410 30.02 21 0.092 6 0.19 51 30424 25.22 12 0.014 7 2 112 90458 21.8 11 0.026 2 2 0.45 118 89458 17.09 8 0.029

9 2 2 0.45 125 92482 17.73 7 0.013

10 2 2 0.45 122 95480 10.96 4 0.027

11 2 2 2 0.5 118 86454 15.93 6 0.014

12 2 2 0.44 118 85456 16.36 6 0.012

13 2 2 0.45 114 85440 15.2 5 0.01

14 2 2 0.45 101 77392 21.01 5 0.0008

15 2 2 2 0.48 78 63 296 18.3 7 0.0107

16 2 2 2 0.47 84 74334 9.54 7 0.216

17 2 2 2 2 0.3 55 40314 22.52 10 0.013

18 2 2 2 0.37 61 57318 11.08 11 0.437

Table 2b. Most probable haplotypes constructed by successive haplotype extensions of 5 marker overlaps, covering markers rs5181157 to rs939537 [positions 1-22]. OT: overtransmitted (major haplotype). UT: undertransmitted (major haplotype). OM: overtransmitted minor haplotype, UM: undertransmitted minor haplotype. Only haplotypes with an excess of five over- or five under-transmissions were used except for a few cases where an excess of four transmissions were used to obtain overlaps for an existing haplotype or haplotype extension. Marker numbers are along the top.

Table 2c. Comparison of allele frequencies of SLC9A3R1/NAT9 associated SNPs and the five marker haplotype in cases from the 242 families and unrelated Caucasian individuals from the U.S.

Table 3a. SNPs from RAPTOR associated with psoriasis with family-based methods. Locations of SNPs and exons are taken from the UCSC April 2003 assembly ofthe genome (http://genome.ucsc.edu/).

SNP Assoc. TDT-^

(polymorphism) /exon Location Allele (base)GH TDT i p value p valut

Raptor Exon 2 79161699-79161802 rs901065 79161864 2 0.0543 0.0532

Raptor Exon 3 79179736-79179819 rsl007850 79181643 - 0.5279 0.4171 rsl531946 79193016 - 0.6121 0.7883 rsl 872431 79197409 - 0.7576 0.3763 rsl485330 79203031 1 (C) 0.0047 0.0154 rsl564864 79204254 2 (T) 0.0064 0.0088 rs2019154 79216553 1 (C) 0.0001 0.0002 rs756075 79225118 - 0.3805 0.283 rs756076 79225127 - 0.8415 0.8367 rs869190 79230802 1 (G) 0.0003 0.0005 rsl471791 79232580 - 0.6698 0.6693 rs2306690 79243799 - 0.7868 0.8568

Raptor Exon 4 79243849-79244008 rs2315923 79255887 - 0.5465 0.5483

Table 3b. TDT-AE p values showing association between psoriasis and SNPs in RAPTOR (ALL FAMS). Stratification of families with the PSORSl risk allele (SNP9) revealed stronger evidence for association with psoriasis, indicating interaction between PSORSl and RAPTOR

RISK NO RISK ALL FAMS

Pval

Marker ChiSq Pval (SUM) ChiSq Pval (SUM) ChiSq (SUM) rs930552 0.174 0.6767 0.1 0.7518 0.273 0.6015 rs8132 0.045 0.8312 0.25 0.6171 0.010.9223 csl8 0.731 0.3924 0.381 0.5371 1.110.2921 rs755340 1.515 0.2184 0.154 0.6949 1.565 0.2109 csll 0.853 0.3558 0.875 0.3545 0.066 0.7977 rsl0931 0.04 0.8415 0.048 0.8273 0.074 0.7851 rs4303599 0.216 0.6419 1.143 0.285 0.121 0.7277 rs901063 0.037 0.8474 0.053 0.8185 0 1 rs901065 2.286 0.1306 0.533 0.4652 2.817 0.0933 rs 1007850 1.424 0.2328 0.758 0.3741 0.412 0.5211 rs4889872 0.462 0.4969 0.243 0.6219 0.077 0.7815 rsl531946 0.043 0.8348 0.25 0.6171 0.2310.631 rsl 872431 0.043 0.8348 0.067 0.7963 0.105 0.7456 rsl485330 8.711 0.0032 0 ^" 1 7.538 0.006 rsl 564864 7.442 0.0064 0 ' 1 6.837 0.0089 rs20191S4 13.828 0.0002 0.25 0.6171 13.226 0.0003 rs756075 3.366 0.0665 3.27 0.0705 0.595 0.4404 rs756076 1.6 0.2059 0.818 0.3651 0.048 0.8273 s9906827 - ,0,835 ^~, ~ 0.3608 ^{^ "}2,788 » 67095,6 2.714 0.0995' rs869190 12 0.0005 0.0474 0-4913 11.946 0.0005 rsl471791 0.301 0.5831 2.455 0.1172 0.138 0.7103 rs4062178 0.527 0.4679 2.314 0.1282 0.031 0.8608 rs2306690 0.097 0.7557 0.72 0.9361 0.063 0.8019 rs2315923 0.36 0.5485 0.059 0.8084 0.381 0.5371 rs3764371 2.51 0.1131 0.806 0.3692 0.591 0.4419 rs2291359 0.78 0.377 0.806 0.3692 0.080.777 8 rap55 0.778 0.3778 0.29 0.59 0.190.6799 rs908238 0.333 0.5637 2 0.1573 0.015 0.9028 rs7219896 0.056 0.8137 4.571 0.0325 0.931 0.3346 rs2672871 0.891 0.3452 0.692 0.4054 1.754 0.1854 rs3751945(rap

38) 0.019 0.8907 0.2 0.6547 0.069 0.7928 rs2589156 0 1 0.36 0.5485 0.209 0.6473 rs2672890 0.97 0.3248 0.31 0.5775 1.5 0.2207 rs2289759 0.134 0.714 0.783 0.3763 0.214 0.6439 rs2016817 0.397 0.5287 0.857 0.3545 0.083 0.7738 rs2289763 0.111 0.7389 2 0.1573 0.0910.763 rs2280147 1.724 0.1892 1.286 0.2568 0.287 0.5919 rs868432 0.316 0.5737 0 1 0.221 0.6381 rs2271602 0.056 0.8137 0.029 0.8658 0.084 0.7718 rs2271608 0.091 0.763 0.36 0.5485 0.229 0.6326 rsl 877926 0.45 0.5023 0.385 0.5351 0.986 0.3206 rs2292639 0.01 0.9215 0.032 0.8515 0.329 0.5663 rsl567962 0.134 0.715 0.571 0.4497 0 1 rs2271612 0.2 0.6547 0.032 0.8575 0.221 0.6381 rs3751940 0.036 0.8501 0.016 0.8997 0.006 0.9397 rsl 059672 0.036 0.8488 0.72 0.3961 0.304 0.5812

Table 4. TRANSMIT output for the analysed PSORS2 SNPs

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Claims

CLAIMS:

1. A method for determining whether a subject has a susceptibility to psoriasis, said method comprising:

in a biological sample from the subject, analyzing a polynucleotide sequence to detect the presence or absence of an allelic variant of at least one polymoφhic region of chromosome 17q24-q25 that is associated with susceptibility to psoriasis.

2. A method in accordance with claim 1 wherein the at least one polymoφhic region is selected from a first region comprising EBP50/SLC9A3R1/NHERF and NAT9, and a second region comprising RAPTOR.

3. A method in accordance with claim 1 wherein the at least one polymoφhic region comprises the first region comprising EBP50/SLC9A3R1/NHERF and NAT9 and wherein the allelic variant of the at least one polymoφhic region comprises a single nucleotide polymoφhism.

4. A method in accordance with claim 3 wherein the single nucleotide polymoφhism is selected from the group consisting of rs745318, rs734232, rs895691, rsl2797 and rs2305214.

5. A method in accordance with claim 1 wherein the at least one polymoφhic region comprises the second region comprising RAPTOR and wherein the allelic variant of the polymoφhic region comprises a single nucleotide polymoφhism.

6. A method in accordance with claim 5 wherein the single nucleotide polymoφhism is selected from the group consisting of rs869190, rsl48530, rsl564864 and rs2019154.

7. A method for determining whether a subject has a susceptibility to psoriasis, said method comprising: in a biological sample from the subject, analyzing a polynucleotide sequence to detect the presence or absence of at least one DNA marker from chromosome 17q24-q25, wherein the DNA marker is associated with susceptibility to psoriasis.

8. A method in accordance with claim 7 wherein the at least one DNA marker comprises at least one single nucleotide polymorphism (SNP) selected from the group consisting of rs745318, rs734232, rs895691, rsl2797, rs2305214, rs869190, rsl48530, rsl564864 and rs2019154.

9. A method in accordance with claim 7 wherein the at least one DNA marker comprises at least one SNP selected from the group consisting of rs745318, rs734232, rs895691, rsl2797 and rs2305214.

10. A method in accordance with claim 7 wherein the at least one DNA marker comprises at least one SNP selected from the group consisting of rs869190, rsl48530, rsl564864 and rs2019154.

11. A method in accordance with claim 7 wherein the at least one DNA marker comprises at least one SNP selected from the group consisting of rs 745318, rs734232, rs895691, rs 12797 and rs2305214., and at least one SNP selected from the group consisting of rs869190, rsl48530, rsl564864 and rs2019154.

12. A method for detecting the presence or absence in a subject of at least one allelic variant that is associated with psoriasis, said method comprising:

detecting the presence or absence of at least one single nucleotide polymoφhism (SNP) from a first polymoφhic region of chromosome 17q24-q25 or from a second polymorphic region of 17q24-q25, wherein the at least one SNP is associated with psoriasis.

13. A method in accordance with claim 12 wherein the first polymoφhic region comprises EBP50/SLC9A3R1/NHERF and NAT9, and the second polymoφhic region comprises RAPTOR.

14. A method in accordance with claim 13 wherein the at least one SNP is selected from the group consisting of rs745318, rs734232, rs895691, rsl2797, rs2305214., rs869190, rsl48530, rsl564864 and rs2019154..

15. A method in accordance with claim 13 comprising detecting the presence or absence of at least two SNPs, wherein at least a first SNP is from the first polymoφhic region of chromosome 17q24-q25 and at least a second SNP is from the second polymoφhic region of 17q24-q25.

16. A method for indicating a predisposition to psoriasis in a subject, comprising:

on a chromosome 17q24-q25 obtained from the subject, detecting the presence or absence of at least one allelic variant of a polymorphic region of 17q24-q25 that is associated with psoriasis, wherein the polymoφhic region comprises EBP50/SLC9A3R1/NHERF and NAT9, or the polymoφhic region comprises RAPTOR, and wherein the presence of the at least one allelic variant in the subject is indicative of a predisposition to psoriasis in the subject as compared to a subject in which the allelic variant is not present.

17. A method in accordance with claim 16 wherein the polymoφhic region comprises EBP50/SLC9A3R1/NHERF and NAT9 and the at least one allelic variant comprises a single nucleotide polymoφhism selected from the group consisting of rs745318, rs734232, rs895691, rsl2797 and rs2305214.

18. A method in accordance with claim 16 wherein the polymoφhic region comprises RAPTOR and the at least one allelic variant comprises a single nucleotide polymoφhism selected from the group consisting of rs869190, rsl48530, rsl564864 and rs2019154.

19. A method in accordance with claim 16 wherein detecting the presence or absence of the at least one allelic variant comprises a method selected from the group consisting of: allele specific hybridization, primer specific extension, oligonucleotide ligation assay, restriction enzyme site analysis and single-stranded conformation polymoφhism analysis.

20. A method of screening for biologically active agents that modulate psoriasis symptoms, comprising:

combining a candidate agent with a cell comprising a polynucleotide having a sequence that encodes at least one allelic variant of a polymoφhic region of 17q24-q25 comprising EBP50/SLC9A3R1/NHERF and NAT9, said allelic variant associated with susceptibility to psoriasis, the polynucleotide operably linked to a promoter such that the polynucleotide sequence is expressed in the cell as an EBP50 protein; and

(b) determining the effect of the agent upon the expression and/or activity of the EBP50 protein.

21. A method in accordance with claim 20 wherein the at least one allelic variant of the polymoφhic region comprises a single nucleotide polymorphism selected from the group consisting ofrs745318, rs734232, rs895691, rsl2797 and rs2305214.

22. A method of screening for biologically active agents that modulate psoriasis symptoms, comprising:

combining a candidate agent with a cell comprising a polynucleotide having a sequence that encodes at least one allelic variant of a polymoφhic region of 17q24-q25 comprising RAPTOR, said allelic variant associated with susceptibility to psoriasis, the polynucleotide operably linked to a promoter such that the polynucleotide sequence is expressed in the cell as a RAPTOR protein; and

(b) deteπnining the effect of the agent upon the expression and/or activity of the RAPTOR protein.

23. A method in accordance with claim 22 wherein the at least one allelic variant ofthe polymoφhic region comprises a single nucleotide polymoφhism selected from the group consisting of: rs869190, rsl48530, rsl564864 and rs2019154.

24. A primer or probe that specifically hybridizes adjacent to or at a first polymorphic region of human chromosome 17q24-q25 comprising EBP50/SLC9A3R1/NHERF and NAT9, in combination with a primer or probe that specifically hybridizes adjacent to or at a second polymoφhic region of human chromosome 17q24-q25 comprising RAPTOR, wherein the first polymoφhic region and the second polymoφhic region are associated with psoriasis.

25. A primer or probe in accordance with claim 24 wherein the first polymoφhic region comprises at least one allelic variant comprising a single nucleotide polymoφhism selected from the group consisting of rs745318, rs734232, rs895691, rsl2797 and rs2305214.

26. A primer or probe in accordance with claim 24 wherein the second polymoφhic region comprises an allelic variant comprising a single nucleotide polymoφhism including rs869190, rsl48530, rsl564864, rs2019154 and rs9906827.

27. A kit for indicating whether a subject has a predisposition to developing psoriasis, comprising: at least one probe or primer that specifically hybridizes adjacent to or at a first polymoφhic region of chromosome 17q24-q25 comprising EBP50/SLC9A3R1/NHERF and NAT9 and that is associated with psoriasis; and

instructions for use of the kit for indicating whether the subject has a predisposition to developing psoriasis.

28. A kit in accordance with claim 27 further comprising at least one probe or primer that specifically hybridizes adjacent to or at a second polymoφhic region of 17q24-q25 comprising RAPTOR and that is associated with psoriasis.

29. A kit in accordance with claim 28 wherein the first polymorphic region comprises at least one allelic variant comprising a single nucleotide polymorphism selected from the group consisting of rs745318, rs734232, rs895691, rsl2797 and rs2305214.

30. A kit in accordance with claim 28 wherein the second polymoφhic region comprises an allelic variant comprising a single nucleotide polymorphism selected from the group consisting of: rs869190, rsl48530, rsl564864, rs2019154 and rs9906827.

31. A kit for indicating whether a subject has a predisposition to developing psoriasis, comprising:

at least one probe or primer that specifically hybridizes adjacent to or at a polymoφhic region of chromosome 17q24-q25 comprising RAPTOR and that is associated with psoriasis; and

instructions for use of the kit for indicating whether the subject has a predisposition to developing psoriasis.

32. A kit in accordance with claim 31 wherein the polymoφhic region comprises an allelic variant comprising a single nucleotide polymoφhism selected from the group consisting of: rs869190, rsl48530, rsl564864 and rs2019154.

33. A microarray, comprising a nucleic acid having a sequence of a first polymoφhic region of chromosome 17q24-q25 comprising EBP50/SLC9A3R1/NHERF and NAT9, and that is associated with psoriasis.

34. A microarray in accordance with claim 33 wherein the first polymoφhic region comprises at least one allelic variant comprising a single nucleotide polymoφhism selected from the group consisting of rs745318, rs734232, rs895691, rsl2797 and rs2305214.

35. A microarray in accordance with claim 33 further comprising a sequence of a second polymoφhic region of chromosome 17q24-q25 comprising RAPTOR and that is associated with psoriasis, wherein the second polymoφhic region comprises an allelic variant comprising a single nucleotide polymoφhism selected from the group consisting of rs869190, rsl48530, rsl564864, rs2019154 and rs9906827.

36. A method for determining whether a subject has a susceptibility to an autoimmune disease, said method comprising:

in a biological sample from the subject, analyzing a polynucleotide sequence to detect the presence or absence of an allelic variant of at least one polymoφhic region wherein the allelic variant abolishes a RUNXl/AMLl binding site.

37. A method in accordance with claim 36 wherein the autoimmune disease is psoriasis and the method comprises analyzing chromosome 17q24-q25 to detect the presence or absence of rs734232.

38. A method for determining whether a subject has a susceptibility to psoriasis, said method comprising analyzing a polynucleotide sequence from a polymoφhic intragenic region on chromosome 17q24-q25 between EBP50 and NAT9 to determine the elimination of a RUNXl/AMLl binding site.

39. A method in accordance with claim 38 comprising detecting the presence or absence ofrs734232.

40. A method of screening for biologically active agents that modulate psoriasis symptoms, comprising:

combining a candidate agent with a cell comprising a polynucleotide having a sequence that encodes at least one allelic variant of a polymoφhic region of 17q24-q25 comprising EBP50/SLC9A3R1/NHERF and NAT9, said allelic variant associated with susceptibility to psoriasis, the polynucleotide operably linked to a promoter such that the polynucleotide sequence is expressed in the cell as a NAT9 protein; and

(b) determining the effect of the agent upon the expression and/or activity of the NAT9 protein.

41. A method in accordance with claim 40 wherein the at least one allelic variant ofthe polymoφhic region comprises a single nucleotide polymorphism selected from the group consisting ofrs745318, rs734232, rs895691, rsl2797 and rs2305214.