AU2000278349A1 - Drug target isogenes: polymorphisms in the interleukin 13 gene - Google Patents

Description

What is Claimed is: 1. An isolated polynucleotide comprising a nucleotide sequence selected from the group consisting of:

(a) a first nucleotide sequence which is a polymorphic variant of a reference sequence for interleukin 13 (IL13) gene or a fragment thereof, wherein the reference sequence comprises SEQ ID NO:l, and the polymorphic variant comprises at least one polymorphism selected from the group consisting of thymine at PS1, guanine at PS2, guanine at PS3, thymine at PS4, cytosine at PS5, adenine at PS6, thymine at PS7, adenine at PS8, thymine at PS9, thymine at PS10, adenine at PS11, thymine at PS12, thymine at PS13 and adenine at PS14; and

(b) a second nucleotide sequence which is complementary to the first nucleotide sequence.

2. The isolated polynucleotide of claim 1 which comprises an IL13 isogene.

3. The isolated polynucleotide of claim 1 which is a DNA molecule and comprises both the first and second nucleotide sequences and further comprises expression regulatory elements operably linked to the first nucleotide sequence.

4. A recombinant nonhuman organism transformed or transfected with the isolated polynucleotide of claim 1, wherein the organism expresses an IL13 protein encoded by the first nucleotide sequence.

5. The recombinant organism of claim 4 which is a nonhuman transgenic animal.

6. The isolated polynucleotide of claim 1 , wherein the first nucleotide sequence is a polymorphic variant of a fragment of the IL13 gene, the fragment comprising one or more polymorphisms selected from the group consisting of thymine at PS1, guanine at PS2, guanine at PS3, thymine at PS4, cytosine at PS5, adenine at PS6, thymine at PS7, adenine at PS8, thymine at PS9, thymine at PS10, adenine at PS11, thymine at PS12, thymine at PS13 and adenine at PS14.

7. An isolated polynucleotide comprising a nucleotide sequence which is a polymorphic variant of a reference sequence for the IL13 cDNA or a fragment thereof, wherein the reference sequence comprises SEQ ID NO:2 and the polymorphic variant comprises at least one polymorphism selected from the group consisting of adenine at a position corresponding to nucleotide 111 and adenine at a position corresponding to nucleotide 386.

8. A recombinant nonhuman organism transformed or transfected with the isolated polynucleotide of claim 7, wherein the organism expresses a interleukin 13 (IL13) protein encoded by the polymorphic variant sequence.

9. The recombinant organism of claim 8 which is a nonhuman transgenic animal.

10. An isolated polypeptide comprising an amino acid sequence which is a polymorphic variant of a reference sequence for the IL13 protein or a fragment thereof, wherein the reference sequence comprises SEQ ID NO: 3 and the polymorphic variant comprises glutamine at a position corresponding to amino acid position 129.

11. An isolated antibody specific for and immunoreactive with the isolated polypeptide of claim 10.

12. A method for screening for drugs targeting the isolated polypeptide of claim 10 which comprises

40 contacting the IL13 polymorphic variant with a candidate agent and assaying for binding activity.

13. A composition comprising at least one genotyping oligonucleotide for detecting a polymoφhism in the interleukin 13 (IL13) gene at a polymoφhic site selected from PS1-PS14.

14. The composition of claim 13, wherein the genotyping oligonucleotide is an allele-specific oligonucleotide that specifically hybridizes to an allele of the IL13 gene at a region containing the polymoφhic site.

15. The composition of claim 14, wherein the allele-specific oligonucleotide comprises a nucleotide sequence selected from the group consisting of of SEQ ID NOS:4-31, the complements of SEQ ID NOS: 4-31, and SEQ ID NOS:32-87.

16. The composition of claim 13, wherein the genotyping oligonucleotide is a primer-extension oligonucleotide.

17. A method for genotyping the interleukin 13 (IL13) gene of an individual, comprising determining for the two copies of the IL13 gene present in the individual the identity of the nucleotide pair at one or more polymoφhic sites (PS) selected from PS 1 -PS 14.

18. The method of claim 17, wherein the determining step comprises:

(a) isolating from the individual a nucleic acid mixture comprising both copies of the IL13 gene, or a fragment thereof, that are present in the individual;

(b) amplifying from the nucleic acid mixture a target region containing at least one of the polymoφhic sites;

(c) hybridizing a primer extension oligonucleotide to one allele of the amplified target region;

(d) performing a nucleic acid template-dependent, primer extension reaction on the hybridized genotyping oligonucleotide in the presence of at least two different terminators of the reaction, wherein said terminators are complementary to the alternative nucleotides present at the polymoφhic site; and

(e) detectmg the presence and identity of the terminator in the extended genotyping oligonucleotide.

19. A method for haplotyping the interleukin 13 (IL13) gene of an individual which comprises determining, for one copy of the IL13 gene present in the individual, the identity of the nucleotide at one or more polymoφhic sites (PS) selected from PS 1 -PS 14.

20. The method of claim 19, wherein the determining step comprises

(a) isolating from the individual a nucleic acid molecule containing only one of the two copies of the IL13 gene, or a fragment thereof, that is present in the individual;

(b) amplifying from the nucleic acid molecule a target region containing at least one of the polymoφhic sites;

(c) hybridizing a primer extension oligonucleotide to one allele of the amplified target region;

(d) performing a nucleic acid template-dependent, primer extension reaction on the hybridized genotyping oligonucleotide in the presence of at least two different terminators of the

41 reaction, wherein said terminators are complementary to the alternative nucleotides present at the polymoφhic site; and

(e) detecting the presence and identity of the terminator in the extended genotyping oligonucleotide.

21. A method for predicting a haplotype pair for the interleukin 13 (IL13) gene of an individual comprising:

(a) identifying an IL13 genotype for the individual at two or more of polymoφhic sites selected from PS 1 -PS 14; (b) enumerating all possible haplotype pairs which are consistent with the genotype;

(c) accessing data containing the IL13 haplotype pairs determined in a reference population; and

(d) assigning a haplotype pair to the individual that is consistent with the data.

22. A method for identifying an association between a trait and at least one genotype or haplotype of the interleukin 13 gene which comprises comparing the frequency of the genotype or haplotype in a population exhibiting the trait with the frequency of the genotype or haplotype in a reference population, wherein the genotype or haplotype comprises a nucleotide pair or nucleotide located at one or more polymoφhic sites selected from PS 1 -PS 14, wherein a higher frequency of the genotype or haplotype in the trait population than in the reference population indicates the trait is associated with the genotype or haplotype. 23 The method of claim 22, wherein the haplotype is selected from haplotype numbers 1-21 shown in Table 4.

24. The method of claim 23, wherein the trait is a clinical response to a drug targeting IL13 .

25. A computer system for storing and analyzing polymoφhism data for the interleukin 13 gene, comprising:

(a) a central processing unit (CPU); (b) a communication interface;

(c) a display device;

(d) an input device; and

(e) a database containing the polymoφhism data; wherein the polymoφhism data comprises the genotypes and haplotype pairs shown in Table 3 and the haplotypes shown in Table 4.

26. A genome anthology for the interleukin 13 (IL13) gene which comprises IL13 isogenes defined by haplotypes 1-21 shown in Table 4.

42 DRUG TARGET ISOGENES: POLYMORPHISMS IN THE INTERLEUKIN 13 GENE

RELATED APPLICATIONS This application is a continuation-in-part of, and claims priority to, U.S. Provisional

Application Serial No. 60/156,489 filed September 28, 1999.

FIELD OF THE INVENTION

This invention relates to variation in genes that encode pharmaceutically important proteins. In particular, this invention provides genetic variants of the human Interleukin 13 (IL13) gene and methods for identifying which variant(s) of this gene is/are possessed by an individual.

BACKGROUND OF THE INVENTION

Current methods for identifying pharmaceuticals to treat disease often start by identifying, cloning, and expressing an important target protein related to the disease. A determination of whether an agonist or antagonist is needed to produce an effect that may benefit a patient with the disease is then made. Then, vast numbers of compounds are screened against the target protein to find new potential drugs. The desired outcome of this process is a drug that is specific for the target, thereby reducing the incidence of the undesired side effects usually caused by a compound's activity at non- intended targets.

What this approach fails to consider, however, is that natural variability exists in any and every population with respect to a particular protein. A target protein currently used to screen drugs typically is expressed by a gene cloned from an individual who was arbitrarily selected. However, the nucleotide sequence of a particular gene may vary tremendously among individuals. Subtle alteration(s) in the primary nucleotide sequence of a gene encoding a target protein may be manifested as significant variation in expression of or in the structure and/or function of the protein. Such alterations may explain the relatively high degree of uncertainty inherent in treatment of individuals with drugs whose design is based upon a single representative example of the target. For example, it is well-established that some classes of drugs frequently have lower efficacy in some individuals than others, which means such individuals and their physicians must weigh the possible benefit of a larger dosage against a greater risk of side effects. In addition, variable information on the biological function or effects of a particular protein may be due to different scientists unknowingly studying different isoforms of the gene encoding the protein. Thus, information on the type and frequency of genomic variation that exists for pharmaceutically important proteins would be useful. The organization of single nucleotide variations (polymoφhisms) in the primary sequence of a gene into one of the limited number of combinations that exist as units of inheritance is termed a haplotype. Each haplotype therefore contains significantly more information than individual

1 unorganized polymoφhisms. Haplotypes provide an accurate measurement of the genomic variation in the two chromosomes of an individual.

It is well-established that many diseases are associated with specific variations in gene sequences. However while there are examples in which individual polymoφhisms act as genetic markers for a particular phenotype, in other cases an individual polymoφhism may be found in a variety of genomic backgrounds and therefore shows no definitive coupling between the polymoφhism and the causative site for the phenotype (Clark AG et al. 1998 Am J Hum Genet 63:595-612; Ulbrecht M et al. 2000 Am J Respir Crit Care Med 161: 469-74). In addition, the marker may be predictive in some populations, but not in other populations (Clark AG et al. 1998 supra). In these instances, a haplotype will provide a superior genetic marker for the phenotype (Clark AG et al. 1998 supra; Ulbrecht M et al. 2000, supra; Ruano G & Stephens JC Gen EngNews 19 (21), December 1999).

Analysis of the association between each observed haplotype and a particular phenotype permits ranking of each haplotype by its statistical power of prediction for the phenotype. Haplotypes found to be strongly associated with the phenotype can then have that positive association confirmed by alternative methods to minimize false positives. For a gene suspected to be associated with a particular phenotype, if no observed haplotypes for that gene show association with the phenotype of interest, then it may be inferred that variation in the gene has little, if any, involvement with that phenotype (Ruano & Stephens 1999, supra). Thus, information on the observed haplotypes and their frequency of occurrence in various population groups will be useful in a variety of research and clinical applications.

One possible drug target for the treatment of cancers, inflammatory and immune disorders is the Interleukin 13 (IL13) gene or its encoded product. IL13 is a pro-inflammatory cytokine expressed by activated human T lymphocytes (Minty et al., Nature 362:248-250, 1993; McKenzie et al., Proc. Natl. Acad. Sci. USA 90:3735-3739, 1993). IL-13 shares some biological activities with IL4 and these two T-cell cytokines may also share a common signaling pathway through the IL-4 receptor (Punnonen et al., Proc. Natl. Acad. Sci. 90:3730-3734, 1993). Several recent reports have suggested a role for IL13 in the pathogenesis of asthma. For example, IL-13 was found to be necessary and sufficient for the expression of allergic asthma in mice (Wills-Kaφ et al., Science 282:2258-2261, 1998; Grunig et al., Science 282:2261-2263, 1998) and targeted pulmonary expression of IL-13 in transgenic mice produced responses similar to those observed in asthma (Zhu et al., J. Clin. Invest. 103:779-788, 1999). In addition, IL-13 expression is elevated in the airways of both allergic and nonallergic asthma patients (Walker et al., Am. Rev. Respir. Dis. 146:109, 1992; Humbert et al, J. Allergy Clin. Immunol. 99:657, 1997; Huang, S.K., J. Immunol. 155:2688, 1995). Finally, human asthma has been linked genetically to the region of chromosome 5q that contains both the IL-13 and IL-4 genes (Marsh et al., Science 264: 1152, 1996).

IL13 has also been implicated in the pathogenesis of diseases characterized by fibrosis.

2 Studies on normal (NF) and keloid (KF) fibroblasts have shown that IL13 stimulates collagen production in both NF and KF cells by the expression of genes for procollagen 1 alpha 1. In NF, IL13 inhibited matrix metalloproteinase-3 (MMP-3) production and enhanced tissue inhibitor of metalloproteinase (TIMP)-l generation, whereas in KF, IL13 enhanced MMP-3 production but the levels of TIMP-1 remained unaffected. These data show the importance of IL13 in collagen homeostasis and the differential regulation of its effectors in fibroblasts (Oriente et al., J. Pharmacol. Exp. Ther 2000 Mar;292(3):988-94).

Kanai et al., (Br. J. Cancer 2000 May;82(10):1717-23) studied the role of IL13 in colon cancer and found that IL13 inhibited colon cancer cell-cell adhesion by down-regulating the expression of E-cadherin and carcinoembryonic antigen (CEA) molecules.

In the vast majority of patients with high-grade gliomas (HGG), mutated IL13-based cytotoxins, directed specifically towards glioma-associated sites, are known to be the most active anti- glioma agents (Debinski W and Gibo DM Mol Med 2000 May;6(5):440-9). A mutagenized IL13, known as hIL13.E13K (glutamic acid at position 13 changed to lysine), was fused to Pseudomonas exotoxin A. This mutagenized IL13 was less active and less toxic on normal cells than gliomas and therefore served as an antitumor agent (Debinski et al., Nat. Biotechnol 1998 may;16(5):449-53).

The Interleukin 13 gene is located on chromosome 5q31 and contains 4 exons that encode a 131 amino acid protein. Reference sequences for the IL13 gene (SEQ ID NO: 1), coding sequence, and protein are shown in Figures 1, 2 and 3, respectively. One single nucleotide polymoφhism of a guanine or adenine at nucleotide position 4165 in

Figure 1, reported in the NCBI SNP Database (Ref SNP#20541), released on December 21, 1999 was originally reported in U.S Provisional Application Serial No._60/156,489 filed September 28, 1999.

This polymoφhism results in a variation of arginine or glutamine at amino acid position 129 in Figure 3. Heinzmann et al. (Hum. Mol. Genet. 2000 Mar l;9(4):549-59) have shown that this Argl29Gln variant affects the interaction of IL13 with its receptor and was found to be associated with asthma in their study population from Britain and Japan. Because of the potential for polymoφhisms in the IL13 gene to affect the expression and function of the encoded protein, it would be useful to determine whether additional polymoφhisms exist in the IL13 gene, as well as how such polymoφhisms are combined in different copies of the gene. Such information would be useful for studying the biological function of IL 13 as well as in identifying drugs targeting this protein for the treatment of disorders related to its abnormal expression or function.

SUMMARY OF THE INVENTION

Accordingly, the inventors herein have discovered 14 novel polymoφhic sites in the IL13 gene. These polymoφhic sites (PS) correspond to the following nucleotide positions in Figure 1 : 1100 (PS1), 1408 (PS2), 1477 (PS3), 1842 (PS4), 2080 (PS5), 2233 (PS6), 2385 (PS7), 3248 (PS8), 3280 (PS9), 3807 (PS10), 4014 (PS11), 4033 (PS12), 4044 (PS13) and 4165 (PS14). The

3 polymoφhisms at these sites are cytosine or thymine at PS1, adenine or guanine at PS2, adenine or guanine at PS3, cytosine or thymine at PS4, thymine or cytosine at PS5, cytosine or adenine at PS6, cytosine or thymine at PS7, guanine or adenine at PS8, cytosine or thymine at PS9, cytosine or thymine at PS10, guanine or adenine at PS11, cytosine or thymine at PS12, cytosine or thymine at PS13 and guanine or adenine at PS14. In addition, the inventors have determined the identity of the alternative nucleotides present at these sites in a human reference population of 79 unrelated individuals self-identified as belonging to one of four major population groups: African descent, Asian, Caucasian and Hispanic/Latino. It is believed that IL13-encoding polynucleotides containing one or more of the novel polymoφhic sites reported herein will be useful in studying the expression and biological function of IL 13, as well as in developing drugs targeting this protein. In addition, information on the combinations of polymoφhisms in the IL13 gene may have diagnostic and forensic applications.

Thus, in one embodiment, the invention provides an isolated polynucleotide comprising a nucleotide sequence which is a polymoφhic variant of a reference sequence for the IL13 gene or a fragment thereof. The reference sequence comprises SEQ ID NO: 1 and the polymoφhic variant comprises at least one polymoφhism selected from the group consisting of thymine at PS1, guanine at PS2, guanine at PS3, thymine at PS4, cytosine at PS5, adenine at PS6, thymine at PS7, adenine at PS8, thymine at PS9, thymine at PS10, adenine at PS11, thymine at PS12, thymine at PS13 and adenine at PS 14. A particularly preferred polymoφhic variant is a naturally-occurring isoform (also referred to herein as an "isogene") of the IL13 gene. An IL13 isogene of the invention comprises cytosine or thymine at PS1, adenine or guanine at PS2, adenine or guanine at PS3, cytosine or thymine at PS4, thymine or cytosine at PS5, cytosine or adenine at PS6, cytosine or thymine at PS7, guanine or adenine at PS8, cytosine or thymine at PS9, cytosine or thymine at PS 10, guanine or adenine at PS11, cytosine or thymine at PS12, cytosine or thymine at PS13 and guanine or adenine at PS14. The invention also provides a collection of IL13 isogenes, referred to herein as an IL13 genome anthology. An IL13 isogene may be defined by the combination and order of these polymoφhisms in the isogene, which is referred to herein as an IL 13 haplotype. Thus, the invention also provides data on the number of different IL13 haplotypes found in the above four population groups. This haplotype data is useful in methods for deriving an IL13 haplotype from an individual's genotype for the IL13 gene and for determining an association between an IL13 haplotype and a particular trait.

In another embodiment, the invention provides a polynucleotide comprising a polymoφhic variant of a reference sequence for an IL13 cDNA or a fragment thereof. The reference sequence comprises SEQ ID NO:2 (Fig. 2) and the polymoφhic cDNA comprises at least one polymoφhism selected from the group consisting of adenine at a position corresponding to nucleotide 111 and adenine at a position corresponding to nucleotide 386.

Polynucleotides complementary to these IL13 genomic and cDNA variants are also provided by the invention.

4 In other embodiments, the invention provides a recombinant expression vector comprising one of the polymoφhic genomic variants operably linked to expression regulatory elements as well as a recombinant host cell transformed or transfected with the expression vector. The recombinant vector and host cell may be used to express ILl 3 for protein structure analysis and drug binding studies. In yet another embodiment, the invention provides a polypeptide comprising a polymoφhic variant of a reference amino acid sequence for the ILl 3 protein. The reference amino acid sequence comprises SEQ ID NO:3 (Fig. 3) and the polymoφhic variant comprises glutamine at a position corresponding to amino acid position 129. A polymoφhic variant of ILl 3 is useful in studying the effect of the variation on the biological activity of ILl 3 as well as studying the binding affinity of candidate drugs targeting ILl 3 for the treatment of cancers, inflammatory and immune disorders. The present invention also provides antibodies that recognize and bind to the above polymoφhic ILl 3 protein variant. Such antibodies can be utilized in a variety of diagnostic and prognostic formats and therapeutic methods.

In other embodiments, the invention provides methods, compositions, and kits for haplotyping and/or genotyping the ILl 3 gene in an individual. The methods involve identifying the nucleotide or nucleotide pair present at one or more polymoφhic sites selected from PS 1 -PS 14 in one or both copies of the ILl 3 gene from the individual. The compositions contain oligonucleotide probes and primers designed to specifically hybridize to one or more target regions containing, or that are adjacent to, a polymoφhic site. The methods and compositions for establishing the genotype or haplotype of an individual at the novel polymoφhic sites described herein are useful for studying the effect of the polymoφhisms in the etiology of diseases affected by the expression and function of the ILl 3 protein, studying the efficacy of drugs targeting ILl 3, predicting individual susceptibility to diseases affected by the expression and function of the ILl 3 protein and predicting individual responsiveness to drugs targeting ILl 3. In yet another embodiment, the invention provides a method for identifying an association between a genotype or haplotype and a trait. In preferred embodiments, the trait is susceptibility to a disease, severity of a disease, the staging of a disease or response to a drug. Such methods have applicability in developing diagnostic tests and therapeutic treatments for cancers, inflammatory and immune disorders. The present invention also provides transgenic animals comprising one of the ILl 3 genomic polymoφhic variants described herein and methods for producing such animals. The transgenic animals are useful for studying expression of the ILl 3 isogenes in vivo, for in vivo screening and testing of drugs targeted against ILl 3 protein, and for testing the efficacy of therapeutic agents and compounds for cancers, inflammatory and immune disorders in a biological system. The present invention also provides a computer system for storing and displaying polymoφhism data determined for the ILl 3 gene. The computer system comprises a computer processing unit; a display; and a database containing the polymoφhism data. The polymoφhism data

5 includes the polymoφhisms, the genotypes and the haplotypes identified for the ILl 3 gene in a reference population. In a preferred embodiment, the computer system is capable of producing a display showing ILl 3 haplotypes organized according to their evolutionary relationships.

BRIEF DESCRIPTION OF THE DRAWINGS

Figure 1 illustrates a reference sequence for the IL13 gene (contiguous lines; SEQ ID NO:l), with the start and stop positions of each region of coding sequence indicated below the sequence by the numbers within the brackets and the polymoφhic sites and polymoφhisms identified by Applicants in a reference population indicated by the variant nucleotide positioned below the polymoφhic site in the sequence.

Figure 2 illustrates a reference sequence for the ILl 3 coding sequence (contiguous lines; SEQ ID NO:2) with the polymoφhic sites and polymoφhisms identified by Applicants in a reference population indicated by the variant nucleotide positioned below the polymoφhic site in the sequence. Figure 3 illustrates a reference sequence for the ILl 3 protein (contiguous lines; SEQ ID NO:3), with the variant amino acids caused by the polymoφhisms of Fig. 2 positioned below the polymoφhic site in the sequence.

DESCRIPTION OF THE PREFERRED EMBODIMENTS

The present invention is based on the discovery of novel variants of the ILl 3 gene. As described in more detail below, the inventors herein discovered 14 novel polymoφhic sites by characterizing the ILl 3 gene found in genomic DNAs isolated from an Index Repository IA that contains immortalized cell lines from one chimpanzee and 93 human individuals and Index Repository IB that contains 70 individuals. These two repositories contain 10 individuals in common.

The human individuals in Index Repository IA included a reference population of 79 unrelated individuals self-identified as belonging to one of four major population groups: Caucasian (22 individuals), African descent (20 individuals) Asian (20 individuals) Hispanic/Latino (17 individuals). To the extent possible, the members of this reference population were organized into population subgroups by the self-identified ethnogeographic origin of their four grandparents as shown in Table 1 below.

Table 1. Population Groups in the Index Repository

In addition, the Index Repository contains three unrelated indigenous American Indians (one from each of North, Central and South America), one three-generation Caucasian family (from the CEPH Utah cohort) and one two-generation African-American family. Index Repository IB contains a reference population of 70 human individuals comprised of 4 three-generation families (from the CEPH Utah cohort) as well as unrelated African-American, Asian and Caucasian individuals. A total of 38 individuals in this reference population are unrelated. Using the ILl 3 genotypes identified in the Index Repository and the methodology described in the Examples below, the inventors herein also determined the haplotypes found on each chromosome for most human members of this repository. The ILl 3 genotypes and haplotypes found in the repository include those shown in Tables 3 and 4, respectively. The polymoφhism and haplotype data disclosed herein are useful for studying population diversity, anthropological lineage, the significance of diversity and lineage at the phenotypic level, paternity testing, forensic applications, and for identifying associations between the ILl 3 genetic variation and a trait such as level of drug response or susceptibility to disease.

In the context of this disclosure, the following terms shall be defined as follows unless otherwise indicated: Allele - A particular form of a genetic locus, distinguished from other forms by its particular

7 nucleotide sequence.

Candidate Gene - A gene which is hypothesized to be responsible for a disease, condition, or the response to a treatment, or to be correlated with one of these.

Gene - A segment of DNA that contains all the information for the regulated biosynthesis of an RNA product, including promoters, exons, introns, and other untranslated regions that control expression.

Genotype - An unphased 5 ' to 3 ' sequence of nucleotide pair(s) found at one or more polymoφhic sites in a locus on a pair of homologous chromosomes in an individual. As used herein, genotype includes a full-genotype and/or a sub-genotype as described below. Full-genotype - The unphased 5 ' to 3 ' sequence of nucleotide pairs found at all known polymoφhic sites in a locus on a pair of homologous chromosomes in a single individual.

Sub-genotype - The unphased 5' to 3' sequence of nucleotides seen at a subset of the known polymoφhic sites in a locus on a pair of homologous chromosomes in a single individual.

Genotyping - A process for determining a genotype of an individual. Haplotype - A 5 ' to 3 ' sequence of nucleotides found at one or more polymoφhic sites in a locus on a single chromosome from a single individual. As used herein, haplotype includes a full- haplotype and or a sub-haplotype as described below.

Full-haplotype - The 5' to 3' sequence of nucleotides found at all known polymoφhic sites in a locus on a single chromosome from a single individual. Sub-haplotype - The 5 ' to 3 ' sequence of nucleotides seen at a subset of the known polymoφhic sites in a locus on a single chromosome from a single individual.

Haplotype pair - The two haplotypes found for a locus in a single individual.

Haplotyping - A process for determining one or more haplotypes in an individual and includes use of family pedigrees, molecular techniques and/or statistical inference. Haplotype data - Information concerning one or more of the following for a specific gene: a listing of the haplotype pairs in each individual in a population; a listing of the different haplotypes in a population; frequency of each haplotype in that or other populations, and any known associations between one or more haplotypes and a trait.

Isoform - A particular form of a gene, mRNA, cDNA or the protein encoded thereby, distinguished from other forms by its particular sequence and/or structure.

Isogene - One of the isoforms of a gene found in a population. An isogene contains all of the polymoφhisms present in the particular isoform of the gene.

Isolated - As applied to a biological molecule such as RNA, DNA, oligonucleotide, or protein, isolated means the molecule is substantially free of other biological molecules such as nucleic acids, proteins, lipids, carbohydrates, or other material such as cellular debris and growth media. Generally, the term "isolated" is not intended to refer to a complete absence of such material or to absence of water, buffers, or salts, unless they are present in amounts that substantially interfere with the methods of the present invention.

Locus - A location on a chromosome or DNA molecule corresponding to a gene or a physical or phenotypic feature.

Naturally-occurring - A term used to designate that the object it is applied to, e.g., naturally- occurring polynucleotide or polypeptide, can be isolated from a source in nature and which has not been intentionally modified by man.

Nucleotide pair - The nucleotides found at a polymoφhic site on the two copies of a chromosome from an individual.

Phased - As applied to a sequence of nucleotide pairs for two or more polymoφhic sites in a locus, phased means the combination of nucleotides present at those polymoφhic sites on a single copy of the locus is known.

Polymorphic site (PS) - A position within a locus at which at least two alternative sequences are found in a population, the most frequent of which has a frequency of no more than 99%.

Polymorphic variant - A gene, mRNA, cDNA, polypeptide or peptide whose nucleotide or amino acid sequence varies from a reference sequence due to the presence of a polymoφhism in the gene.

Polymorphism - The sequence variation observed in an individual at a polymoφhic site. Polymoφhisms include nucleotide substitutions, insertions, deletions and microsatellites and may, but need not, result in detectable differences in gene expression or protein function. Polymorphism data - Information concerning one or more of the following for a specific gene: location of polymoφhic sites; sequence variation at those sites; frequency of polymoφhisms in one or more populations; the different genotypes and/or haplotypes determined for the gene; frequency of one or more of these genotypes and/or haplotypes in one or more populations; any known association(s) between a trait and a genotype or a haplotype for the gene. Polymorphism Database - A collection of polymoφhism data arranged in a systematic or methodical way and capable of being individually accessed by electronic or other means.

Polynucleotide - A nucleic acid molecule comprised of single-stranded RNA or DNA or comprised of complementary, double-stranded DNA.

Population Group - A group of individuals sharing a common ethnogeographic origin. Reference Population - A group of subjects or individuals who are predicted to be representative of the genetic variation found in the general population. Typically, the reference population represents the genetic variation in the population at a certainty level of at least 85%, preferably at least 90%, more preferably at least 95% and even more preferably at least 99%. Single Nucleotide Polymorphism (SNP) - Typically, the specific pair of nucleotides observed at a single polymoφhic site. In rare cases, three or four nucleotides may be found.

Subject - A human individual whose genotypes or haplotypes or response to treatment or disease state are to be determined.

9 Treatment - A stimulus administered internally or externally to a subject. Unphased - As applied to a sequence of nucleotide pairs for two or more polymoφhic sites in a locus, unphased means the combination of nucleotides present at those polymoφhic sites on a single copy of the locus is not known. The inventors herein have discovered 14 novel polymoφhic sites in the ILl 3 gene. The polymoφhic sites identified by the inventors are referred to as PS 1-14 to designate the order in which they are located in the gene (see Table 2 below).

Thus, in one embodiment, the invention provides an isolated polynucleotide comprising a polymoφhic variant of the ILl 3 gene or a fragment of the gene which contains at least one of the novel polymoφhic sites described herein. The nucleotide sequence of a variant ILl 3 gene is identical to the reference genomic sequence for those portions of the gene examined, as described in the Examples below, except that it comprises a different nucleotide at one or more of the novel polymoφhic sites PS 1 -PS 14. Similarly, the nucleotide sequence of a variant fragment of the ILl 3 gene is identical to the corresponding portion of the reference sequence except for having a different nucleotide at one or more of the novel polymoφhic sites described herein. Thus, the invention specifically does not include polynucleotides comprising a nucleotide sequence identical to the reference sequence (or other reported ILl 3 sequences) or to portions of the reference sequence (or other reported ILl 3 sequences), except for genotyping oligonucleotides as described below.

The location of a polymoφhism in a variant gene or fragment is identified by aligning its sequence against SEQ ID NO: 1. The polymoφhism is selected from the group consisting of thymine at PS1, guanine at PS2, guanine at PS3, thymine at PS4, cytosine at PS5, adenine at PS6, thymine at PS7, adenine at PS8, thymine at PS9, thymine at PS 10, adenine at PS11, thymine at PS 12, thymine at PS 13 and adenine at PS 14. In a preferred embodiment, the polymoφhic variant comprises a naturally- occurring isogene of the ILl 3 gene which is defined by any one of haplotypes 1-21 shown in Table 4 below.

Polymoφhic variants of the invention may be prepared by isolating a clone containing the ILl 3 gene from a human genomic library. The clone may be sequenced to determine the identity of the nucleotides at the polymoφhic sites described herein. Any particular variant claimed herein could be prepared from this clone by performing in vitro mutagenesis using procedures well-known in the art.

ILl 3 isogenes may be isolated using any method that allows separation of the two "copies" of the ILl 3 gene present in an individual, which, as readily understood by the skilled artisan, may be the same allele or different alleles. Separation methods include targeted in vivo cloning (TIVC) in yeast as described in WO 98/01573, U.S. Patent No. 5,866,404, and U.S. Patent No. 5,972,614. Another method, which is described in U.S. Patent No. 5,972,614, uses an allele specific oligonucleotide in combination with primer extension and exonuclease degradation to generate hemizygous DNA targets. Yet other methods are single molecule dilution (SMD) as described in Ruano et al., Proc. Natl. Acad.

10 Sci. 87:6296-6300, 1990; and allele specific PCR (Ruano et al., 17 Nucleic Acids. Res. 8392, 1989; Ruano et al., 19 Nucleic Acids Res. 6877-6882, 1991; Michalatos-Beloin et al., 24 Nucleic Acids Res. 4841-4843, 1996).

The invention also provides ILl 3 genome anthologies, which are collections of ILl 3 isogenes found in a given population. The population may be any group of at least two individuals, including but not limited to a reference population, a population group, a family population, a clinical population, and a same sex population. An IL13 genome anthology may comprise individual IL13 isogenes stored in separate containers such as microtest tubes, separate wells of a microtitre plate and the like. Alternatively, two or more groups of the ILl 3 isogenes in the anthology may be stored in separate containers. Individual isogenes or groups of isogenes in a genome anthology may be stored in any convenient and stable form, including but not limited to in buffered solutions, as DNA precipitates, freeze-dried preparations and the like. A preferred ILl 3 genome anthology of the invention comprises a set of isogenes defined by the haplotypes shown in Table 4 below.

An isolated polynucleotide containing a polymoφhic variant nucleotide sequence of the invention may be operably linked to one or more expression regulatory elements in a recombinant expression vector capable of being propagated and expressing the encoded ILl 3 protein in a prokaryotic or a eukaryotic host cell. Examples of expression regulatory elements which may be used include, but are not limited to, the lac system, operator and promoter regions of phage lambda, yeast promoters, and promoters derived from vaccinia virus, adenovirus, retroviruses, or SV40. Other regulatory elements include, but are not limited to, appropriate leader sequences, termination codons, polyadenylation signals, and other sequences required for the appropriate transcription and subsequent translation of the nucleic acid sequence in a given host cell. Of course, the correct combinations of expression regulatory elements will depend on the host system used. In addition, it is understood that the expression vector contains any additional elements necessary for its transfer to and subsequent replication in the host cell. Examples of such elements include, but are not limited to, origins of replication and selectable markers. Such expression vectors are commercially available or are readily constructed using methods known to those in the art (e.g., F. Ausubel et al., 1987, in "Current Protocols in Molecular Biology", John Wiley and Sons, New York, New York). Host cells which may be used to express the variant ILl 3 sequences of the invention include, but are not limited to, eukaryotic and mammalian cells, such as animal, plant, insect and yeast cells, and prokaryotic cells, such as E. coli, or algal cells as known in the art. The recombinant expression vector may be introduced into the host cell using any method known to those in the art including, but not limited to, microinjection, electroporation, particle bombardment, transduction, and transfection using DEAE- dextran, lipofection, or calcium phosphate (see e.g., Sambrook et al. (1989) in "Molecular Cloning. A Laboratory Manual", Cold Spring Harbor Press, Plainview, New York). In a preferred aspect, eukaryotic expression vectors that function in eukaryotic cells, and preferably mammalian cells, are used. Non-limiting examples of such vectors include vaccinia virus vectors, adenovirus vectors,

11 heφes virus vectors, and baculovirus transfer vectors. Preferred eukaryotic cell lines include COS cells, CHO cells, HeLa cells, NIH 3T3 cells, and embryonic stem cells (Thomson, J. A. et al., 1998 Science 282: 1145-1147). Particularly preferred host cells are mammalian cells.

As will be readily recognized by the skilled artisan, expression of polymoφhic variants of the ILl 3 gene will produce ILl 3 mRNAs varying from each other at any polymoφhic site retained in the spliced and processed mRNA molecules. These mRNAs can be used for the preparation of an ILl 3 cDNA comprising a nucleotide sequence which is a polymoφhic variant of the ILl 3 reference coding sequence shown in Figure 2. Thus, the invention also provides IL13 mRNAs and corresponding cDNAs which comprise a nucleotide sequence that is identical to SEQ ID NO:2 (Fig. 2), or its corresponding RNA sequence, except for having one or both polymoφhisms selected from the group consisting of adenine at a position corresponding to nucleotide 111 and adenine at a position corresponding to nucleotide 386. Fragments of these variant mRNAs and cDNAs are included in the scope of the invention, provided they contain the novel polymoφhisms described herein. The invention specifically excludes polynucleotides identical to previously identified and characterized ILl 3 cDNAs and fragments thereof. Polynucleotides comprising a variant RNA or DNA sequence may be isolated from a biological sample using well-known molecular biological procedures or may be chemically synthesized.

Genomic and cDNA fragments of the invention comprise at least one novel polymoφhic site identified herein and have a length of at least 10 nucleotides and may range up to the full length of the gene. Preferably, a fragment according to the present invention is between 100 and 3000 nucleotides in length, and more preferably between 200 and 2000 nucleotides in length, and most preferably between 500 and 1000 nucleotides in length.

In describing the polymoφhic sites identified herein, reference is made to the sense strand of the gene for convenience. However, as recognized by the skilled artisan, nucleic acid molecules containing the ILl 3 gene may be complementary double stranded molecules and thus reference to a particular site on the sense strand refers as well to the corresponding site on the complementary antisense strand. Thus, reference may be made to the same polymoφhic site on either strand and an oligonucleotide may be designed to hybridize specifically to either strand at a target region containing the polymoφhic site. Thus, the invention also includes single-stranded polynucleotides which are complementary to the sense strand of the IL13 genomic variants described herein.

Polynucleotides comprising a polymoφhic gene variant or fragment may be useful for therapeutic puφoses. For example, where a patient could benefit from expression, or increased expression, of a particular ILl 3 protein isoform, an expression vector encoding the isoform may be administered to the patient. The patient may be one who lacks the ILl 3 isogene encoding that isoform or may already have at least one copy of that isogene.

In other situations, it may be desirable to decrease or block expression of a particular ILl 3 isogene. Expression of an ILl 3 isogene may be turned off by transforming a targeted organ, tissue or

12 cell population with an expression vector that expresses high levels of untranslatable mRNA for the isogene. Alternatively, oligonucleotides directed against the regulatory regions (e.g., promoter, introns, enhancers, 3' untranslated region) of the isogene may block transcription. Oligonucleotides targeting the transcription initiation site, e.g., between positions -10 and +10 from the start site are preferred. Similarly, inhibition of transcription can be achieved using oligonucleotides that base-pair with region(s) of the isogene DNA to form triplex DNA (see e.g., Gee et al. in Huber, B.E. and B.I. Can, Molecular and Immunologic Approaches, Futura Publishing Co., Mt. Kisco, N.Y., 1994). Antisense oligonucleotides may also be designed to block translation of ILl 3 mRNA transcribed from a particular isogene. It is also contemplated that ribozymes may be designed that can catalyze the specific cleavage of IL 13 mRNA transcribed from a particular isogene.

The oligonucleotides may be delivered to a target cell or tissue by expression from a vector introduced into the cell or tissue in vivo or ex vivo. Alternatively, the oligonucleotides may be formulated as a pharmaceutical composition for administration to the patient. Oligoribonucleotides and/or oligodeoxynucleotides intended for use as antisense oligonucleotides may be modified to increase stability and half-life. Possible modifications include, but are not limited to phosphorothioate or 2' O-methyl linkages, and the inclusion of nontraditional bases such as inosine and queosine, as well as acetyl-, methyl-, thio-, and similarly modified forms of adenine, cytosine, guanine, thymine, and uracil which are not as easily recognized by endogenous nucleases.

The invention also provides an isolated polypeptide comprising a polymoφhic variant of the reference ILl 3 amino acid sequence shown in Figure 3. The location of a variant amino acid in an ILl 3 polypeptide or fragment of the invention is identified by aligning its sequence against SEQ ID NO:3 (Fig. 3). An IL13 protein variant of the invention comprises an amino acid sequence identical to SEQ ID NO: 3 except for having glutamine at a position conesponding to amino acid position 129. The invention specifically excludes amino acid sequences identical to those previously identified for IL13, including SEQ ID NO:3, and previously described fragments thereof. IL13 protein variants included within the invention comprise all amino acid sequences based on SEQ ID NO: 3 and having glutamine at a position conesponding to amino acid position 129.

The invention also includes ILl 3 peptide variants, which are any fragments of an ILl 3 protein variant that contains glutamine at a position conesponding to amino acid position 129. An ILl 3 peptide variant is at least 6 amino acids in length and is preferably any number between 6 and 30 amino acids long, more preferably between 10 and 25, and most preferably between 15 and 20 amino acids long. Such ILl 3 peptide variants may be useful as antigens to generate antibodies specific for one of the above ILl 3 isoforms. In addition, the ILl 3 peptide variants may be useful in drug screening assays. An IL13 variant protein or peptide of the invention may be prepared by chemical synthesis or by expressing one of the variant ILl 3 genomic and cDNA sequences as described above. Alternatively, the ILl 3 protein variant may be isolated from a biological sample of an individual

13 having an ILl 3 isogene which encodes the variant protein. Where the sample contains two different IL13 isoforms (i.e., the individual has different IL13 isogenes), a particular IL13 isoform of the invention can be isolated by immunoaffinity chromatography using an antibody which specifically binds to that particular IL13 isoform but does not bind to the other IL13 isoform. The expressed or isolated ILl 3 protein may be detected by methods known in the art, including Coomassie blue staining, silver staining, and Western blot analysis using antibodies specific for the isoform of the ILl 3 protein as discussed further below. ILl 3 variant proteins can be purified by standard protein purification procedures known in the art, including differential precipitation, molecular sieve chromatography, ion-exchange chromatography, isoelectric focusing, gel electrophoresis, affinity and immunoaffϊnity chromatography and the like. (Ausubel et. al., 1987, In Cunent Protocols in Molecular Biology John Wiley and Sons, New York, New York). In the case of immunoaffinity chromatography, antibodies specific for a particular polymoφhic variant may be used.

A polymoφhic variant ILl 3 gene of the invention may also be fused in frame with a heterologous sequence to encode a chimeric ILl 3 protein. The non-IL13 portion of the chimeric protein may be recognized by a commercially available antibody. In addition, the chimeric protein may also be engineered to contain a cleavage site located between the ILl 3 and non-IL13 portions so that the ILl 3 protein may be cleaved and purified away from the non-IL13 portion.

An additional embodiment of the invention relates to using a novel ILl 3 protein isoform in any of a variety of drug screening assays. Such screening assays may be performed to identify agents that bind specifically to all known ILl 3 protein isoforms or to only a subset of one or more of these isoforms. The agents may be from chemical compound libraries, peptide libraries and the like. The ILl 3 protein or peptide variant may be free in solution or affixed to a solid support. In one embodiment, high throughput screening of compounds for binding to an ILl 3 variant may be accomplished using the method described in PCT application WO84/03565, in which large numbers of test compounds are synthesized on a solid substrate, such as plastic pins or some other surface, contacted with the ILl 3 protein(s) of interest and then washed. Bound ILl 3 protein(s) are then detected using methods well-known in the art.

In another embodiment, a novel ILl 3 protein isoform may be used in assays to measure the binding affinities of one or more candidate drugs targeting the ILl 3 protein. In another embodiment, the invention provides antibodies specific for and immunoreactive with one or more of the novel ILl 3 variant proteins described herein. The antibodies may be either monoclonal or polyclonal in origin. The ILl 3 protein or peptide variant used to generate the antibodies may be from natural or recombinant sources or produced by chemical synthesis using synthesis techniques known in the art. If the ILl 3 protein variant is of insufficient size to be antigenic, it may be conjugated, complexed, or otherwise covalently linked to a carrier molecule to enhance the antigenicity of the peptide. Examples of carrier molecules, include, but are not limited to, albumins

14 (e.g., human, bovine, fish, ovine), and keyhole limpet hemocyanin (Basic and Clinical Immunology, 1991, Eds. D.P. Stites, and A.I. Ten, Appleton and Lange, Norwalk Connecticut, San Mateo, California).

In one embodiment, an antibody specifically immunoreactive with one of the novel ILl 3 protein isoforms described herein is administered to an individual to neutralize activity of the ILl 3 isoform expressed by that individual. The antibody may be formulated as a pharmaceutical composition which includes a pharmaceutically acceptable carrier.

Antibodies specific for and immunoreactive with one of the novel ILl 3 protein isoform described herein may be used to immunoprecipitate the ILl 3 protein variant from solution as well as react with ILl 3 protein isoforms on Western or immunoblots of polyacrylamide gels on membrane supports or substrates. In another prefened embodiment, the antibodies will detect ILl 3 protein isoforms in paraffin or frozen tissue sections, or in cells which have been fixed or unfixed and prepared on slides, coverslips, or the like, for use in immunocytochemical, immunohistochemical, and immunofmorescence techniques. In another embodiment, an antibody specifically immunoreactive with one of the novel ILl 3 protein variants described herein is used in immunoassays to detect this variant in biological samples. In this method, an antibody of the present invention is contacted with a biological sample and the formation of a complex between the ILl 3 protein variant and the antibody is detected. As described, suitable immunoassays include radioimmunoassay, Western blot assay, immunofluorescent assay, enzyme linked immunoassay (ELISA), chemiluminescent assay, immunohistochemical assay, immunocytochemical assay, and the like (see, e.g., Principles and Practice of Immunoassay, 1991, Eds. Christopher P. Price and David J. Neoman, Stockton Press, New York, New York; Cunent Protocols in Molecular Biology, 1987, Eds. Ausubel et al., John Wiley and Sons, New York, New York). Standard techniques known in the art for ELISA are described in Methods in Immunodiagnosis, 2nd Ed., Eds. Rose and Bigazzi, John Wiley and Sons, New York 1980; and

Campbell et al., 1984, Methods in Immunology, W.A. Benjamin, Inc.). Such assays may be direct, indirect, competitive, or noncompetitive as described in the art (see, e.g., Principles and Practice of Immunoassay, 1991, Eds. Christopher P. Price and David J. Neoman, Stockton Pres, NY, NY; and Oellirich, M., 1984, J. Clin. Chem. Clin. Biochem., 22:895-904). Proteins may be isolated from test specimens and biological samples by conventional methods, as described in Cunent Protocols in Molecular Biology, supra.

Exemplary antibody molecules for use in the detection and therapy methods of the present invention are intact immunoglobulin molecules, substantially intact immunoglobulin molecules, or those portions of immunoglobulin molecules that contain the antigen binding site. Polyclonal or monoclonal antibodies may be produced by methods conventionally known in the art (e.g., Kohler and Milstein, 1975, Nature, 256:495-497; Campbell Monoclonal Antibody Technology, the Production and Characterization of Rodent and Human Hybridomas, 1985, In: Laboratory Techniques in

15 Biochemistry and Molecular Biology, Eds. Burdon et al., Volume 13, Elsevier Science Publishers, Amsterdam). The antibodies or antigen binding fragments thereof may also be produced by genetic engineering. The technology for expression of both heavy and light chain genes in E. coli is the subject of PCT patent applications, publication number WO 901443, WO 901443 and WO 9014424 and in Huse et al., 1989, Science, 246:1275-1281. The antibodies may also be humanized (e.g., Queen, C. et al. 1989 Proc. Natl. Acad. Sci. 86;10029).

Effect(s) of the polymoφhisms identified herein on expression of ILl 3 may be investigated by preparing recombinant cells and/or organisms, preferably recombinant animals, containing a polymoφhic variant of the ILl 3 gene. As used herein, "expression" includes but is not limited to one or more of the following: transcription of the gene into precursor mRNA; splicing and other processing of the precursor mRNA to produce mature mRNA; mRNA stability; translation of the mature mRNA into ILl 3 protein (including codon usage and tRNA availability); and glycosylation and/or other modifications of the translation product, if required for proper expression and function. To prepare a recombinant cell of the invention, the desired ILl 3 isogene may be introduced into the cell in a vector such that the isogene remains extrachromosomal. In such a situation, the gene will be expressed by the cell from the extrachromosomal location. In a prefened embodiment, the ILl 3 isogene is introduced into a cell in such a way that it recombines with the endogenous ILl 3 gene present in the cell. Such recombination requires the occunence of a double recombination event, thereby resulting in the desired ILl 3 gene polymoφhism. Vectors for the introduction of genes both for recombination and for extrachromosomal maintenance are known in the art, and any suitable vector or vector construct may be used in the invention. Methods such as electroporation, particle bombardment, calcium phosphate co-precipitation and viral transduction for introducing DNA into cells are known in the art; therefore, the choice of method may lie with the competence and preference of the skilled practitioner. Examples of cells into which the ILl 3 isogene may be introduced include, but are not limited to, continuous culture cells, such as COS, NIH 3T3, and primary or culture cells of the relevant tissue type, i.e., they express the ILl 3 isogene. Such recombinant cells can be used to compare the biological activities of the different protein variants.

Recombinant organisms, i.e., transgenic animals, expressing a variant ILl 3 gene are prepared using standard procedures known in the art. Preferably, a construct comprising the variant gene is introduced into a nonhuman animal or an ancestor of the animal at an embryonic stage, i.e., the one- cell stage, or generally not later than about the eight-cell stage. Transgenic animals carrying the constructs of the invention can be made by several methods known to those having skill in the art. One method involves transfecting into the embryo a retrovirus constructed to contain one or more insulator elements, a gene or genes of interest, and other components known to those skilled in the art to provide a complete shuttle vector harboring the insulated gene(s) as a transgene, see e.g., U.S. Patent No. 5,610,053. Another method involves directly injecting a transgene into the embryo. A third method involves the use of embryonic stem cells. Examples of animals into which the ILl 3

16 isogenes may be introduced include, but are not limited to, mice, rats, other rodents, and nonhuman primates (see "The Introduction of Foreign Genes into Mice" and the cited references therein, In: Recombinant DNA, Eds. J.D. Watson, M. Gilman, J. Witkowski, and M. Zoller; W.H. Freeman and Company, New York, pages 254-272). Transgenic animals stably expressing a human ILl 3 isogene and producing human ILl 3 protein can be used as biological models for studying diseases related to abnormal ILl 3 expression and/or activity, and for screening and assaying various candidate drugs, compounds, and treatment regimens to reduce the symptoms or effects of these diseases.

An additional embodiment of the invention relates to pharmaceutical compositions for treating disorders affected by expression or function of a novel ILl 3 isogene described herein. The pharmaceutical composition may comprise any of the following active ingredients: a polynucleotide comprising one of these novel ILl 3 isogenes; an antisense oligonucleotide directed against one of the novel ILl 3 isogenes, a polynucleotide encoding such an antisense oligonucleotide, or another compound which inhibits expression of a novel ILl 3 isogene described herein. Preferably, the composition contains the active ingredient in a therapeutically effective amount. By therapeutically effective amount is meant that one or more of the symptoms relating to disorders affected by expression or function of a novel ILl 3 isogene is reduced and/or eliminated. The composition also comprises a pharmaceutically acceptable carrier, examples of which include, but are not limited to, saline, buffered saline, dextrose, and water. Those skilled in the art may employ a formulation most suitable for the active ingredient, whether it is a polynucleotide, oligonucleotide, protein, peptide or small molecule antagonist. The pharmaceutical composition may be administered alone or in combination with at least one other agent, such as a stabilizing compound. Administration of the pharmaceutical composition may be by any number of routes including, but not limited to oral, intravenous, intramuscular, intra-arterial, intramedullary, intrathecal, intraventricular, intradermal, transdermal, subcutaneous, intraperitoneal, intranasal, enteral, topical, sublingual, or rectal. Further details on techniques for formulation and administration may be found in the latest edition of Remington's Pharmaceutical Sciences (Maack Publishing Co., Easton, PA).

For any composition, determination of the therapeutically effective dose of active ingredient and/or the appropriate route of administration is well within the capability of those skilled in the art. For example, the dose can be estimated initially either in cell culture assays or in animal models. The animal model may also be used to determine the appropriate concentration range and route of administration. Such information can then be used to determine useful doses and routes for administration in humans. The exact dosage will be determined by the practitioner, in light of factors relating to the patient requiring treatment, including but not limited to severity of the disease state, general health, age, weight and gender of the patient, diet, time and frequency of administration, other drugs being taken by the patient, and tolerance/response to the treatment.

Information on the identity of genotypes and haplotypes for the ILl 3 gene of any particular individual as well as the frequency of such genotypes and haplotypes in any particular population of

17 individuals is expected to be useful for a variety of basic research and clinical applications. Thus, the invention also provides compositions and methods for detecting the novel ILl 3 polymoφhisms identified herein.

The compositions comprise at least one ILl 3 genotyping oligonucleotide. In one embodiment, an ILl 3 genotyping oligonucleotide is a probe or primer capable of hybridizing to a target region that is located close to, or that contains, one of the novel polymoφhic sites described herein. As used herein, the term "oligonucleotide" refers to a polynucleotide molecule having less than about 100 nucleotides. A prefened oligonucleotide of the invention is 10 to 35 nucleotides long. More preferably, the oligonucleotide is between 15 and 30, and most preferably, between 20 and 25 nucleotides in length. The oligonucleotide may be comprised of any phosphorylation state of ribonucleotides, deoxyribonucleotides, and acyclic nucleotide derivatives, and other functionally equivalent derivatives. Alternatively, oligonucleotides may have a phosphate-free backbone, which may be comprised of linkages such as carboxymethyl, acetamidate, carbamate, polyamide (peptide nucleic acid (PNA)) and the like (Varma, R. in Molecular Biology and Biotechnology, A Comprehensive Desk Reference, Ed. R. Meyers, VCH Publishers, Inc. (1995), pages 617-620). Oligonucleotides of the invention may be prepared by chemical synthesis using any suitable methodology known in the art, or may be derived from a biological sample, for example, by restriction digestion. The oligonucleotides may be labeled, according to any technique known in the art, including use of radiolabels, fluorescent labels, enzymatic labels, proteins, haptens, antibodies, sequence tags and the like.

Genotyping oligonucleotides of the invention must be capable of specifically hybridizing to a target region of an IL13 polynucleotide, i.e., an IL13 isogene. As used herein, specific hybridization means the oligonucleotide forms an anti-parallel double-stranded structure with the target region under certain hybridizing conditions, while failing to form such a structure when incubated with a non-target region or a non-IL13 polynucleotide under the same hybridizing conditions. Preferably, the oligonucleotide specifically hybridizes to the target region under conventional high stringency conditions. The skilled artisan can readily design and test oligonucleotide probes and primers suitable for detecting polymoφhisms in the ILl 3 gene using the polymoφhism information provided herein in conjunction with the known sequence information for the IL13 gene and routine techniques. A nucleic acid molecule such as an oligonucleotide or polynucleotide is said to be a "perfect" or "complete" complement of another nucleic acid molecule if every nucleotide of one of the molecules is complementary to the nucleotide at the conesponding position of the other molecule. A nucleic acid molecule is "substantially complementary" to another molecule if it hybridizes to that molecule with sufficient stability to remain in a duplex form under conventional low-stringency conditions. Conventional hybridization conditions are described, for example, by Sambrook J. et al., in Molecular Cloning, A Laboratory Manual, 2^nd Edition, Cold Spring Harbor Press, Cold Spring Harbor, NY (1989) and by Haymes, B.D. et al. in Nucleic Acid Hybridization, A Practical Approach,

18 IRL Press, Washington, D.C. (1985). While perfectly complementary oligonucleotides are prefened for detecting polymoφhisms, departures from complete complementarity are contemplated where such departures do not prevent the molecule from specifically hybridizing to the target region. For example, an oligonucleotide primer may have a non-complementary fragment at its 5 ' end, with the remainder of the primer being complementary to the target region. Alternatively, non-complementary nucleotides may be interspersed into the oligonucleotide probe or primer as long as the resulting probe or primer is still capable of specifically hybridizing to the target region.

Prefened genotyping oligonucleotides of the invention are allele-specific oligonucleotides. As used herein, the term allele-specific oligonucleotide (ASO) means an oligonucleotide that is able, under sufficiently stringent conditions, to hybridize specifically to one allele of a gene, or other locus, at a target region containing a polymoφhic site while not hybridizing to the conesponding region in another allele(s). As understood by the skilled artisan, allele-specificity will depend upon a variety of readily optimized stringency conditions, including salt and formamide concentrations, as well as temperatures for both the hybridization and washing steps. Examples of hybridization and washing conditions typically used for ASO probes are found in Kogan et al., "Genetic Prediction of Hemophilia A" in PCR Protocols, A Guide to Methods and Applications, Academic Press, 1990 and Ruano et al., 87 Proc. Natl. Acad. Sci. USA 6296-6300, 1990. Typically, an allele-specific oligonucleotide will be perfectly complementary to one allele while containing a single mismatch for another allele.

Allele-specific oligonucleotide probes which usually provide good discrimination between different alleles are those in which a central position of the oligonucleotide probe aligns with the polymoφhic site in the target region (e.g., approximately the 7^th or 8^th position in a 15 mer, the 8^th or 9^th position in a 16mer, the 10^th or 11^th position in a 20 mer). A prefened ASO probe for detecting IL13 gene polymoφhisms comprises a nucleotide sequence, listed 5' to 3', selected from the group consisting of:

AGGAAAACGAGGGAA (SEQ ID NO: 4) and its complement, AGGAAAA GAGGGAA (SEQ ID NO: 5) and its complement, ACAAAACAAAAAAAC (SEQ ID NO: 6) and its complement, ACAAAACGAAAAAAC (SEQ ID NO: :7) and its complement, CCTGGAAATCTGAAC (SEQ ID NO: :8) and its complement, CCTGGAAGTCTGAAC (SEQ ID NO: :9) and its complement, TGCCTGCCGCTGGAA (SEQ ID NO: :10 and its complement, TGCCTGCTGCTGGAA (SEQ ID NO: :11 and its complement, CCCAGCCTATGCATC (SEQ ID NO: :12 and its complement, CCCAGCCCATGCATC (SEQ ID NO: :13 and its complement, AGCTGGTCAACATCA (SEQ ID NO: :14 and its complement, AGCTGGTAAACATCA (SEQ ID NO: :15 and its complement, ACCAAGGCCCGGCCC (SEQ ID NO: :16 and its complement, ACCAAGGTCCGGCCC (SEQ ID NO: :17 and its complement, TGGCCTGGGCTGCCA (SEQ ID NO: 18 and its complement, TGGCCTGAGCTGCCA (SEQ ID NO: ;19 and its complement, CTGCCAGCACTCTGC (SEQ ID NO: :20 and its complement, CTGCCAGTACTCTGC (SEQ ID NO: 21 and its complement,

19 GAATATCCATGGTGT (SEQ ID NO 22) and its complement,

GAATATCTATGGTGT (SEQ ID NO 23) and its complement,

TTTGTGCGAGTCGTC (SEQ ID NO 24) and its complement,

TTTGTGCAAGTCGTC (SEQ ID NO 25) and its complement,

CCTCTGGCGTTCTAC (SEQ ID NO 26) and its complement,

CCTCTGGTGTTCTAC (SEQ ID NO 27) and its complement,

CTACTCACGTGCTGA (SEQ ID NO 28) and its complement,

CTACTCATGTGCTGA (SEQ ID NO 29) and its complement,

GAGGGACGGTTCAAC (SEQ ID NO 30) and its complement, and

GAGGGACAGTTCAAC (SEQ ID NO 31) and its complement .

An allele-specific oligonucleotide primer of the invention has a 3' terminal nucleotide, or preferably a 3 ' penultimate nucleotide, that is complementary to only one nucleotide of a particular SNP, thereby acting as a primer for polymerase-mediated extension only if the allele containing that nucleotide is present. Allele-specific oligonucleotide primers hybridizing to either the coding or noncoding strand are contemplated by the invention. A prefened ASO primer for detecting ILl 3 gene polymoφhisms comprises a nucleotide sequence, listed 5 ' to 3', selected from the group consisting of:

ACTTCTAGGAAAACG (SEQ ID NO 32) ^• CTGCTCTTCCCTCGT SEQ ID NO 33) ACTTCTAGGAAAATG (SEQ ID NO 34) ^• CTGCTCTTCCCTCAT SEQ ID NO 35) AACAAAACAAAACAA (SEQ ID NO 36) ^• TTTGGTGTTTTTTTG SEQ ID NO 37) AACAAAACAAAACGA (SEQ ID NO 38) ^■ TTTGGTGTTTTTTCG SEQ ID NO 39) TGGAGACCTGGAAAT (SEQ ID NO 40) ^■ GTCAAAGTTCAGATT SEQ ID NO 41) TGGAGACCTGGAAGT (SEQ ID NO 42) ^• GTCAAAGTTCAGACT SEQ ID NO 43) GCCCCTTGCCTGCCG (SEQ ID NO 44) ^• GTTTAATTCCAGCGG SEQ ID NO 45) GCCCCTTGCCTGCTG (SEQ ID NO 46) GTTTAATTCCAGCAG SEQ ID NO 47) AAGCCACCCAGCCTA (SEQ ID NO 48) ^• GGAGCGGATGCATAG SEQ ID NO 49) AAGCCACCCAGCCCA (SEQ ID NO 50) GGAGCGGATGCATGG SEQ ID NO 51) TTGAGGAGCTGGTCA (SEQ ID NO 52) TCTGGGTGATGTTGA SEQ ID NO 53) TTGAGGAGCTGGTAA (SEQ ID NO 54) ^• TCTGGGTGATGTTTA SEQ ID NO 55) CCATGGACCAAGGCC (SEQ ID NO 56) ^■ ATGGCTGGGCCGGGC SEQ ID NO 57) CCATGGACCAAGGTC (SEQ ID NO 58) ATGGCTGGGCCGGAC SEQ ID NO 59) CAGACCTGGCCTGGG (SEQ ID NO 60) ^• CTGCCCTGGCAGCCC SEQ ID NO 61) CAGACCTGGCCTGAG (SEQ ID NO 62) ^■ CTGCCCTGGCAGCTC SEQ ID NO 63) CAACCCCTGCCAGCA (SEQ ID NO 64) ^• CAGTGAGCAGAGTGC SEQ ID NO 65) CAACCCCTGCCAGTA (SEQ ID NO 66) CAGTGAGCAGAGTAC SEQ ID NO 67) CTGGCTGAATATCCA (SEQ ID NO 68) GGACACACACCATGG SEQ ID NO 69) CTGGCTGAATATCTA (SEQ ID NO 70) GGACACACACCATAG SEQ ID NO 71) CCCTGGTTTGTGCGA (SEQ ID NO 72) , GGCCGGGACGACTCG SEQ ID NO 73) CCCTGGTTTGTGCAA (SEQ ID NO 74), GGCCGGGACGACTTG SEQ ID NO 75) TCCCGGCCTCTGGCG (SEQ ID NO 76), ACGTGAGTAGAACGC SEQ ID NO 77) TCCCGGCCTCTGGTG (SEQ ID NO 78) , ACGTGAGTAGAACAC SEQ ID NO 79) GGCGTTCTACTCACG (SEQ ID NO 80) , AAGAGGTCAGCACGT SEQ ID NO 81) GGCGTTCTACTCATG (SEQ ID NO 82) , AAGAGGTCAGCACAT SEQ ID NO 83) TTTCGCGAGGGACGG (SEQ ID NO 84) , GTTTCAGTTGAACCG SEQ ID NO 85) TTTCGCGAGGGACAG (SEQ ID NO: 86) , and GTTTCAGTTGAAC :TG SEQ ID NO π:

Other genotyping oligonucleotides of the invention hybridize to a target region located one to several nucleotides downstream of one of the novel polymoφhic sites identified herein. Such oligonucleotides are useful in polymerase-mediated primer extension methods for detecting one of the novel polymoφhisms described herein and therefore such genotyping oligonucleotides are refened to

20 herein as "primer-extension oligonucleotides". In a prefened embodiment, the 3 '-terminus of a primer-extension oligonucleotide is a deoxynucleotide complementary to the nucleotide located immediately adjacent to the polymoφhic site. A particularly prefened oligonucleotide primer for detecting ILl 3 gene polymoφhisms by primer extension terminates in a nucleotide sequence, listed 5' to 3', selected from the group consisting of:

TCTAGGAAAA (SEQ ID NO: :88); CTCTTCCCTC SEQ ID NO: :89) ; AAAACAAAAC (SEQ ID NO: :90) ; GGTGTTTTTT SEQ ID NO: :91); AGACCTGGAA (SEQ ID NO: :92) ; AAAGTTCAGA SEQ ID NO: :93) ; CCTTGCCTGC (SEQ ID NO: :94) ; TAATTCCAGC SEQ ID NO: :95); CCACCCAGCC (SEQ ID NO: :96), GCGGATGCAT SEQ ID NO: :97) ; AGGAGCTGGT (SEQ ID NO: :98); GGGTGATGTT SEQ ID NO: :99) ; TGGACCAAGG (SEQ ID NO: :100) GCTGGGCCGG SEQ ID NO: :101); ACCTGGCCTG (SEQ ID NO: :102) CCCTGGCAGC SEQ ID NO: :103) ; CCCCTGCCAG (SEQ ID NO: :104) TGAGCAGAGT SEQ ID NO: :105) ; GCTGAATATC (SEQ ID NO: :106) CACACACCAT SEQ ID NO: :107) ; TGGTTTGTGC (SEQ ID NO: :108) CGGGACGACT SEQ ID NO: :109) ; CGGCCTCTGG (SEQ ID NO: :110) TGAGTAGAAC SEQ ID NO: :111); GTTCTACTCA (SEQ ID NO: :112) AGGTCAGCAC SEQ ID NO: :113); CGCGAGGGAC (SEQ ID NO: :114) and TCAGTTGAAC (SEQ ID NO:! L15

In some embodiments, a composition contains two or more differently labeled genotyping oligonucleotides for simultaneously probing the identity of nucleotides at two or more polymoφhic sites. It is also contemplated that primer compositions may contain two or more sets of allele-specific primer pairs to allow simultaneous targeting and amplification of two or more regions containing a polymoφhic site.

ILl 3 genotyping oligonucleotides of the invention may also be immobilized on or synthesized on a solid surface such as a microchip, bead, or glass slide (see, e.g., WO 98/20020 and WO 98/20019). Such immobilized genotyping oligonucleotides may be used in a variety of polymoφhism detection assays, including but not limited to probe hybridization and polymerase extension assays. Immobilized ILl 3 genotyping oligonucleotides of the invention may comprise an ordered anay of oligonucleotides designed to rapidly screen a DNA sample for polymoφhisms in multiple genes at the same time.

In another embodiment, the invention provides a kit comprising at least two genotyping oligonucleotides packaged in separate containers. The kit may also contain other components such as hybridization buffer (where the oligonucleotides are to be used as a probe) packaged in a separate container. Alternatively, where the oligonucleotides are to be used to amplify a target region, the kit may contain, packaged in separate containers, a polymerase and a reaction buffer optimized for primer extension mediated by the polymerase, such as PCR.

The above described oligonucleotide compositions and kits are useful in methods for genotyping and/or haplotyping the IL13 gene in an individual. As used herein, the terms "IL13 genotype" and "ILl 3 haplotype" mean the genotype or haplotype contains the nucleotide pair or nucleotide, respectively, that is present at one or more of the novel polymoφhic sites described herein

21 and may optionally also include the nucleotide pair or nucleotide present at one or more additional polymoφhic sites in the ILl 3 gene. The additional polymoφhic sites may be cunently known polymoφhic sites or sites that are subsequently discovered.

One embodiment of the genotyping method involves isolating from the individual a nucleic acid mixture comprising the two copies of the ILl 3 gene, or a fragment thereof, that are present in the individual, and determining the identity of the nucleotide pair at one or more of the polymoφhic sites selected from PS 1 -PS 14 in the two copies to assign an ILl 3 genotype to the individual. As will be readily understood by the skilled artisan, the two "copies" of a gene in an individual may be the same allele or may be different alleles. In a particularly prefened embodiment, the genotyping method comprises determining the identity of the nucleotide pair at each of PS1-14.

Typically, the nucleic acid mixture is isolated from a biological sample taken from the individual, such as a blood sample or tissue sample. Suitable tissue samples include whole blood, semen saliva, tears, urine, fecal material, sweat, buccal, skin and hair. The nucleic acid mixture may be comprised of genomic DNA, mRNA, or cDNA and, in the latter two cases, the biological sample must be obtained from an organ in which the ILl 3 gene is expressed. Furthermore it will be understood by the skilled artisan that mRNA or cDNA preparations would not be used to detect polymoφhisms located in introns or in 5' and 3' nontranscribed regions. If an ILl 3 gene fragment is isolated, it must contain the polymoφhic site(s) to be genotyped.

One embodiment of the haplotyping method comprises isolating from the individual a nucleic acid molecule containing only one of the two copies of the ILl 3 gene, or a fragment thereof, that is present in the individual and determining in that copy the identity of the nucleotide at one or more of the polymoφhic sites PS 1 -PS 14 in that copy to assign an ILl 3 haplotype to the individual. The nucleic acid may be isolated using any method capable of separating the two copies of the ILl 3 gene or fragment such as one of the methods described above for preparing ILl 3 isogenes, with targeted in vivo cloning being the prefened approach. As will be readily appreciated by those skilled in the art, any individual clone will only provide haplotype information on one of the two ILl 3 gene copies present in an individual. If haplotype information is desired for the individual's other copy, additional ILl 3 clones will need to be examined. Typically, at least five clones should be examined to have more than a 90% probability of haplotyping both copies of the ILl 3 gene in an individual. In a particularly prefened embodiment, the nucleotide at each of PS 1-14 is identified.

In a prefened embodiment, an ILl 3 haplotype pair is determined for an individual by identifying the phased sequence of nucleotides at one or more of the polymoφhic sites selected from PS 1 -PS 14 in each copy of the ILl 3 gene that is present in the individual. In a particularly prefened embodiment, the haplotyping method comprises identifying the phased sequence of nucleotides at each of PS1-14 in each copy of the IL13 gene. When haplotyping both copies of the gene, the identifying step is preferably performed with each copy of the gene being placed in separate containers. However, it is also envisioned that if the two copies are labeled with different tags, or are

22 otherwise separately distinguishable or identifiable, it could be possible in some cases to perform the method in the same container. For example, if first and second copies of the gene are labeled with different first and second fluorescent dyes, respectively, and an allele-specific oligonucleotide labeled with yet a third different fluorescent dye is used to assay the polymoφhic site(s), then detecting a combination of the first and third dyes would identify the polymoφhism in the first gene copy while detecting a combination of the second and third dyes would identify the polymoφhism in the second gene copy.

In both the genotyping and haplotyping methods, the identity of a nucleotide (or nucleotide pair) at a polymoφhic site(s) may be determined by amplifying a target region(s) containing the polymoφhic site(s) directly from one or both copies of the ILl 3 gene, or fragment thereof, and the sequence of the amplified region(s) determined by conventional methods. It will be readily appreciated by the skilled artisan that only one nucleotide will be detected at a polymoφhic site in individuals who are homozygous at that site, while two different nucleotides will be detected if the individual is heterozygous for that site. The polymoφhism may be identified directly, known as positive-type identification, or by inference, refened to as negative-type identification. For example, where a SNP is known to be guanine and cytosine in a reference population, a site may be positively determined to be either guanine or cytosine for an individual homozygous at that site, or both guanine and cytosine, if the individual is heterozygous at that site. Alternatively, the site may be negatively determined to be not guanine (and thus cytosine/cytosine) or not cytosine (and thus guanine/guanine). In addition, the identity of the allele(s) present at any of the novel polymoφhic sites described herein may be indirectly determined by genotyping a polymoφhic site not disclosed herein that is in linkage disequilibrium with the polymoφhic site that is of interest. Two sites are said to be in linkage disequilibrium if the presence of a particular variant at one site enhances the predictability of another variant at the second site (Stevens, JC 1999, Mol. Diag. 4: 309-17). Polymoφhic sites in linkage disequilibrium with the presently disclosed polymoφhic sites may be located in regions of the gene or in other genomic regions not examined herein. Genotyping of a polymoφhic site in linkage disequilibrium with the novel polymoφhic sites described herein may be performed by, but is not limited to, any of the above-mentioned methods for detecting the identity of the allele at a polymoφhic site. The target region(s) may be amplified using any oligonucleotide-directed amplification method, including but not limited to polymerase chain reaction (PCR) (U.S. Patent No. 4,965,188), ligase chain reaction (LCR) (Barany et al., Proc. Natl. Acad. Sci. USA 88: 189-193, 1991; WO90/01069), and oligonucleotide ligation assay (OLA) (Landegren et al., Science 241: 1077-1080, 1988). Oligonucleotides useful as primers or probes in such methods should specifically hybridize to a region of the nucleic acid that contains or is adjacent to the polymoφhic site. Typically, the oligonucleotides are between 10 and 35 nucleotides in length and preferably, between 15 and 30 nucleotides in length. Most preferably, the oligonucleotides are 20 to 25 nucleotides long. The exact

23 length of the oligonucleotide will depend on many factors that are routinely considered and practiced by the skilled artisan.

Other known nucleic acid amplification procedures may be used to amplify the target region including transcription-based amplification systems (U.S. Patent No. 5,130,238; EP 329,822; U.S. Patent No. 5,169,766, WO89/06700) and isothermal methods (Walker et al., Proc. Natl. Acad. Sci. USA 89:392-396, 1992).

A polymoφhism in the target region may also be assayed before or after amplification using one of several hybridization-based methods known in the art. Typically, allele-specific oligonucleotides are utilized in performing such methods. The allele-specific oligonucleotides may be used as differently labeled probe pairs, with one member of the pair showing a perfect match to one variant of a target sequence and the other member showing a perfect match to a different variant. In some embodiments, more than one polymoφhic site may be detected at once using a set of allele- specific oligonucleotides or oligonucleotide pairs. Preferably, the members of the set have melting temperatures within 5°C, and more preferably within 2°C, of each other when hybridizing to each of the polymoφhic sites being detected.

Hybridization of an allele-specific oligonucleotide to a target polynucleotide may be performed with both entities in solution, or such hybridization may be performed when either the oligonucleotide or the target polynucleotide is covalently or noncovalently affixed to a solid support. Attachment may be mediated, for example, by antibody-antigen interactions, poly-L-Lys, streptavidin or avidin-biotin, salt bridges, hydrophobic interactions, chemical linkages, UV cross-linking baking, etc. Allele-specific oligonucleotides may be synthesized directly on the solid support or attached to the solid support subsequent to synthesis. Solid-supports suitable for use in detection methods of the invention include substrates made of silicon, glass, plastic, paper and the like, which may be formed, for example, into wells (as in 96-well plates), slides, sheets, membranes, fibers, chips, dishes, and beads. The solid support may be treated, coated or derivatized to facilitate the immobilization of the allele-specific oligonucleotide or target nucleic acid.

The genotype or haplotype for the ILl 3 gene of an individual may also be determined by hybridization of a nucleic sample containing one or both copies of the gene to nucleic acid arrays and subarrays such as described in WO 95/11995. The arrays would contain a battery of allele-specific oligonucleotides representing each of the polymoφhic sites to be included in the genotype or haplotype.

The identity of polymoφhisms may also be determined using a mismatch detection technique, including but not limited to the RNase protection method using riboprobes (Winter et al., Proc. Natl. Acad. Sci. USA 82:7575, 1985; Meyers et al., Science 230:1242, 1985) and proteins which recognize nucleotide mismatches, such as the E. coli mutS protein (Modrich, P. Ann. Rev. Genet. 25:229-253, 1991). Alternatively, variant alleles can be identified by single strand conformation polymoφhism (SSCP) analysis (Orita et al., Genomics 5:874-879, 1989; Humphries et al., in Molecular Diagnosis of

24 Genetic Diseases, R. Elles, ed., pp. 321-340, 1996) or denaturing gradient gel electrophoresis (DGGE) (Wartell et al., Nucl. Acids Res. 18:2699-2706, 1990; Sheffield et al, Proc. Natl. Acad. Sci. USA 86:232-236, 1989).

A polymerase-mediated primer extension method may also be used to identify the polymoφhism(s). Several such methods have been described in the patent and scientific literature and include the "Genetic Bit Analysis" method (W092/15712) and the ligase/polymerase mediated genetic bit analysis (U.S. Patent 5,679,524. Related methods are disclosed in W091/02087, WO90/09455, W095/17676, U.S. Patent Nos. 5,302,509, and 5,945,283. Extended primers containing a polymoφhism may be detected by mass spectrometry as described in U.S. Patent No. 5,605,798. Another primer extension method is allele-specific PCR (Ruano et al., Nucl. Acids Res. 17:8392,

1989; Ruano et al., Nucl. Acids Res. 19, 6877-6882, 1991; WO 93/22456; Turki et al, J. Clin. Invest. 95:1635-1641, 1995). In addition, multiple polymoφhic sites may be investigated by simultaneously amplifying multiple regions of the nucleic acid using sets of allele-specific primers as described in Wallace et al. (WO89/10414). In another aspect of the invention, an individual's ILl 3 haplotype pair is predicted from its

ILl 3 genotype using information on haplotype pairs known to exist in a reference population. In its broadest embodiment, the haplotyping prediction method comprises identifying an ILl 3 genotype for the individual at two or more polymoφhic sites selected from PS 1 -PS 14, enumerating all possible haplotype pairs which are consistent with the genotype, accessing data containing ILl 3 haplotype pairs identified in a reference population, and assigning a haplotype pair to the individual that is consistent with the data. In one embodiment, the reference haplotype pairs include the ILl 3 haplotype pairs shown in Table 3.

Generally, the reference population should be composed of randomly-selected individuals representing the major ethnogeographic groups of the world. A prefened reference population for use in the methods of the present invention comprises an approximately equal number of individuals from Caucasian, African American, Asian and Hispanic-Latino population groups with the minimum number of each group being chosen based on how rare a haplotype one wants to be guaranteed to see. For example, if one wants to have a q% chance of not missing a haplotype that exists in the population at a p% frequency of occurring in the reference population, the number of individuals (n) who must be sampled is given by 2n=log(l-q)/log(l-p) where p and q are expressed as fractions. A prefened reference population allows the detection of any haplotype whose frequency is at least 10% with about 99% certainty and comprises about 20 unrelated individuals from each of the four population groups named above. A particularly prefened reference population includes a 3-generation family representing one or more of the four population groups to serve as controls for checking quality of haplotyping procedures.

In a prefened embodiment, the haplotype frequency data for each ethnogeographic group is examined to determine whether it is consistent with Hardy- Weinberg equilibrium. Hardy- Weinberg

25 equilibrium (D.L. Hartl et al., Principles of Population Genomics, Sinauer Associates (Sunderland, MA), 3^rd Ed., 1997) postulates that the frequency of finding the haplotype pair H_x I H₂ is equal to p_H __w (H IH₂ ) = 2p(H_x )p(H₂ ) if H, ≠ H₂ and p_H__w (H, I H₂ ) = p(H_x )p(H₂ ) if H = H₂ .

A statistically significant difference between the observed and expected haplotype frequencies could be due to one or more factors including significant inbreeding in the population group, strong selective pressure on the gene, sampling bias, and or enors in the genotyping process. If large deviations from Hardy- Weinberg equilibrium are observed in an ethnogeographic group, the number of individuals in that group can be increased to see if the deviation is due to a sampling bias. If a larger sample size does not reduce the difference between observed and expected haplotype pair frequencies, then one may wish to consider haplotyping the individual using a direct haplotyping method such as, for example, CLASPER System^™ technology (U.S. Patent No. 5,866,404), SMD, or allele-specific long- range PCR (Michalotos-Beloin et al, Nucleic Acids Res. 24:4841-4843, 1996).

In one embodiment of this method for predicting an ILl 3 haplotype pair, the assigning step involves performing the following analysis. First, each of the possible haplotype pairs is compared to the haplotype pairs in the reference population. Generally, only one of the haplotype pairs in the reference population matches a possible haplotype pair and that pair is assigned to the individual. Occasionally, only one haplotype represented in the reference haplotype pairs is consistent with a possible haplotype pair for an individual, and in such cases the individual is assigned a haplotype pair containing this known haplotype and a new haplotype derived by subtracting the known haplotype from the possible haplotype pair. In rare cases, either no haplotypes in the reference population are consistent with the possible haplotype pairs, or alternatively, multiple reference haplotype pairs are consistent with the possible haplotype pairs. In such cases, the individual is preferably haplotyped using a direct molecular haplotyping method such as, for example, CLASPER System^™ technology (U.S. Patent No. 5,866,404), SMD, or allele-specific long-range PCR (Michalotos-Beloin et al., Nucleic Acids Res. 24:4841-4843, 1996).

The invention also provides a method for determining the frequency of an ILl 3 genotype or ILl 3 haplotype in a population. The method comprises determining the genotype or the haplotype pair for the ILl 3 gene that is present in each member of the population, wherein the genotype or haplotype comprises the nucleotide pair or nucleotide detected at one or more of the polymoφhic sites PS 1 -PS 14 in the ILl 3 gene; and calculating the frequency any particular genotype or haplotype is found in the population. The population may be a reference population, a family population, a same sex population, a population group, a trait population (e.g., a group of individuals exhibiting a trait of interest such as a medical condition or response to a therapeutic treatment).

In another aspect of the invention, frequency data for ILl 3 genotypes and/or haplotypes found in a reference population are used in a method for identifying an association between a trait and an ILl genotype or an ILl 3 haplotype. The trait may be any detectable phenotype, including but not

26 limited to susceptibility to a disease or response to a treatment. The method involves obtaining data on the frequency of the genotype(s) or haplotype(s) of interest in a reference population as well as in a population exhibiting the trait. Frequency data for one or both of the reference and trait populations may be obtained by genotyping or haplotyping each individual in the populations using one of the methods described above. The haplotypes for the trait population may be determined directly or, alternatively, by the predictive genotype to haplotype approach described above. In another embodiment, the frequency data for the reference and or trait populations is obtained by accessing previously determined frequency data, which may be in written or electronic form. For example, the frequency data may be present in a database that is accessible by a computer. Once the frequency data is obtained, the frequencies of the genotype(s) or haplotype(s) of interest in the reference and trait populations are compared. In a prefened embodiment, the frequencies of all genotypes and/or haplotypes observed in the populations are compared. If a particular genotype or haplotype for the ILl 3 gene is more frequent in the trait population than in the reference population at a statistically significant amount, then the trait is predicted to be associated with that ILl 3 genotype or haplotype. Preferably, the ILl 3 genotype or haplotype being compared in the trait and reference populations is selected from the full-genotypes and full-haplotypes shown in Tables 3 and 4, respectively, or from sub-genotypes and sub-haplotypes derived from these genotypes and haplotypes.

In a prefened embodiment of the method, the trait of interest is a clinical response exhibited by a patient to some therapeutic treatment, for example, response to a drug targeting ILl 3 or response to a therapeutic treatment for a medical condition. As used herein, "medical condition" includes but is not limited to any condition or disease manifested as one or more physical and/or psychological symptoms for which treatment is desirable, and includes previously and newly identified diseases and other disorders. As used herein the term "clinical response" means any or all of the following: a quantitative measure of the response, no response, and adverse response (i.e., side effects). In order to deduce a conelation between clinical response to a treatment and an ILl 3 genotype or haplotype, it is necessary to obtain data on the clinical responses exhibited by a population of individuals who received the treatment, hereinafter the "clinical population". This clinical data may be obtained by analyzing the results of a clinical trial that has already been run and/or the clinical data may be obtained by designing and carrying out one or more new clinical trials. As used herein, the term "clinical trial" means any research study designed to collect clinical data on responses to a particular treatment, and includes but is not limited to phase I, phase II and phase HI clinical trials. Standard methods are used to define the patient population and to enroll subjects.

It is prefened that the individuals included in the clinical population have been graded for the existence of the medical condition of interest. This is important in cases where the symptom(s) being presented by the patients can be caused by more than one underlying condition, and where treatment of the underlying conditions are not the same. An example of this would be where patients experience breathing difficulties that are due to either asthma or respiratory infections. If both sets were treated

27 with an asthma medication, there would be a spurious group of apparent non-responders that did not actually have asthma. These people would affect the ability to detect any conelation between haplotype and treatment outcome. This grading of potential patients could employ a standard physical exam or one or more lab tests. Alternatively, grading of patients could use haplotyping for situations where there is a strong conelation between haplotype pair and disease susceptibility or severity.

The therapeutic treatment of interest is administered to each individual in the trial population and each individual's response to the treatment is measured using one or more predetermined criteria. It is contemplated that in many cases, the trial population will exhibit a range of responses and that the investigator will choose the number of responder groups (e.g., low, medium, high) made up by the various responses. In addition, the IL13 gene for each individual in the trial population is genotyped and/or haplotyped, which may be done before or after administering the treatment.

After both the clinical and polymoφhism data have been obtained, conelations between individual response and ILl 3 genotype or haplotype content are created. Conelations may be produced in several ways. In one method, individuals are grouped by their ILl 3 genotype or haplotype (or haplotype pair) (also refened to as a polymoφhism group), and then the averages and standard deviations of clinical responses exhibited by the members of each polymoφhism group are calculated.

These results are then analyzed to determine if any observed variation in clinical response between polymoφhism groups is statistically significant. Statistical analysis methods which may be used are described in L.D. Fisher and G. vanBelle, "Biostatistics: A Methodology for the Health Sciences", Wiley-Interscience (New York) 1993. This analysis may also include a regression calculation of which polymoφhic sites in the ILl 3 gene give the most significant contribution to the differences in phenotype. One regression model useful in the invention is described in the PCT Application entitled "Methods for Obtaining and Using Haplotype Data", filed June 26, 2000. A second method for finding conelations between ILl 3 haplotype content and clinical responses uses predictive models based on enor-minimizing optimization algorithms. One of many possible optimization algorithms is a genetic algorithm (R. Judson, "Genetic Algorithms and Their Uses in Chemistry" in Reviews in Computational Chemistry, Vol. 10, pp. 1-73, K. B. Lipkowitz and D. B. Boyd, eds. (VCH Publishers, New York, 1997). Simulated annealing (Press et al., "Numerical Recipes in C: The Art of Scientific Computing", Cambridge University Press (Cambridge) 1992, Ch. 10), neural networks (E. Rich and K. Knight, "Artificial Intelligence", 2^nd Edition (McGraw-Hill, New York, 1991, Ch. 18), standard gradient descent methods (Press et al., supra Ch. 10), or other global or local optimization approaches (see discussion in Judson, supra) could also be used. Preferably, the conelation is found using a genetic algorithm approach as described in PCT Application entitled "Methods for Obtaining and Using Haplotype Data", filed June 26, 2000.

Conelations may also be analyzed using analysis of variation (ANOVA) techniques to determine how much of the variation in the clinical data is explained by different subsets of the

28 polymoφhic sites in the ILl 3 gene. As described in PCT Application entitled "Methods for Obtaining and Using Haplotype Data", filed June 26, 2000, ANOVA is used to test hypotheses about whether a response variable is caused by or conelated with one or more traits or variables that can be measured (Fisher and vanBelle, supra, Ch. 10). From the analyses described above, a mathematical model may be readily constructed by the skilled artisan that predicts clinical response as a function of ILl 3 genotype or haplotype content. Preferably, the model is validated in one or more follow-up clinical trials designed to test the model. The identification of an association between a clinical response and a genotype or haplotype (or haplotype pair) for the ILl 3 gene may be the basis for designing a diagnostic method to determine those individuals who will or will not respond to the treatment, or alternatively, will respond at a lower level and thus may require more treatment, i.e., a greater dose of a drug. The diagnostic method may take one of several forms: for example, a direct DNA test (i.e., genotyping or haplotyping one or more of the polymoφhic sites in the ILl 3 gene), a serological test, or a physical exam measurement. The only requirement is that there be a good conelation between the diagnostic test results and the underlying ILl 3 genotype or haplotype that is in turn conelated with the clinical response. In a prefened embodiment, this diagnostic method uses the predictive haplotyping method described above.

Any or all analytical and mathematical operations involved in practicing the methods of the present invention may be implemented by a computer. In addition, the computer may execute a program that generates views (or screens) displayed on a display device and with which the user can interact to view and analyze large amounts of information relating to the ILl 3 gene and its genomic variation, including chromosome location, gene structure, and gene family, gene expression data, polymoφhism data, genetic sequence data, and clinical data population data (e.g., data on ethnogeographic origin, clinical responses, genotypes, and haplotypes for one or more populations). The IL13 polymoφhism data described herein may be stored as part of a relational database (e.g., an instance of an Oracle database or a set of ASCII flat files). These polymoφhism data may be stored on the computer's hard drive or may, for example, be stored on a CD ROM or on one or more other storage devices accessible by the computer. For example, the data may be stored on one or more databases in communication with the computer via a network. Prefened embodiments of the invention are described in the following examples. Other embodiments within the scope of the claims herein will be apparent to one skilled in the art from consideration of the specification or practice of the invention as disclosed herein. It is intended that the specification, together with the examples, be considered exemplary only, with the scope and spirit of the invention being indicated by the claims which follow the examples.

29 EXAMPLES The Examples herein are meant to exemplify the various aspects of carrying out the invention and are not intended to limit the scope of the invention in any way. The Examples do not include detailed descriptions for conventional methods employed, such as in the performance of genomic DNA isolation, PCR and sequencing procedures. Such methods are well-known to those skilled in the art and are described in numerous publications, for example, Sambrook, Fritsch, and Maniatis, "Molecular Cloning: A Laboratory Manual", 2^nd Edition, Cold Spring Harbor Laboratory Press, USA, (1989).

Example IA This example illustrates examination of various regions of the ILl 3 gene for polymoφhic sites using DNA from Index Repository 1 A.

Amplification of Target Regions

The following target regions of the ILl 3 gene were amplified using the PCR primer pairs listed below, with the sequences presented in the 5' to 3' direction and nucleotide positions shown for each region conesponding to Figure 1

Fragment 1

Forward Primer

960-979 AGCCTGAGCAGGCAGAGAGG (SEQ ID NO: 116)

Reverse Primer

Complement of 1515-1496 CTTGGCCCCACTGTGAGAGG (SEQ ID NO: 117) PCR product 556 nt

Fragment 2 Forward Primer

1273-1295 CCAGACACGTGCACACTACTTCC (SEQ ID NO: 118) Reverse Primer

Complement of 1771-1750 CAACCCTGAGTACCTGGACAGC (SEQ ID NO: 119) PCR product 499 nt

Fragment 3 Forward Primer

1510-1531 GCCAAGGAGGAATTAGGCAAGC (SEQ ID NO: 120)

Reverse Primer

Complement of 2218-2197 AGCTCCCTGAGGGCTGTAGAGG (SEQ ID NO: 121)

PCR product 709 nt

Fragment 4

Forward Primer

1880-1903 CCCTGGACCCTTCTCAATAAGTCC (SEQ ID NO: 122)

Reverse Primer Complement of 2416-2396 CAGCTCCTCTCTCCCTCATGG (SEQ ID NO: 123)

PCR product 537 nt

30 Fragment 5 Forward Primer

1923-1946 CCTTTATGCGACACTGGATTTTCC (SEQ ID NO:124) Reverse Primer

Complement of 2495-2474 AGGCCAGGAGAGCAGGTAGTCC (SEQ ID NO: 125) PCR product 573 nt

Fragment 6 Forward Primer

3146-3168 CAAAGCAGAAAACGAAGCTCAGG (SEQ ID NO: 126)

Reverse Primer

Complement of 3568-3546 TTTGTGAGTCTGCAGGAAGATGG (SEQ ID NO: 127)

PCR product 423 nt

Fragment 7

Forward Primer

3451-3472 GTTCCAAGCAAGCTTCAAGTGC (SEQ ID NO: 128)

Reverse Primer Complement of 3914-3893 TGAGGCCCAGGTAGGAGTTAGG (SEQ ID NO: 129)

PCR product 464 nt

Fragment 8 Forward Primer 3900-3920 CCTACCTGGGCCTCAATTTCC (SEQ ID NO: 130) Reverse Primer

Complement of 4527-4507 GTGTGAAGTGGGTCCCTGTCC (SEQ ID NO: 131) PCR product 628 nt

These primer pairs were used in PCR reactions containing genomic DNA isolated from immortalized cell lines for each member of the Index Repository. The PCR reactions were carried out under the following conditions:

Reaction volume = 20 μl 10 x Advantage 2 Polymerase reaction buffer (Clontech) = 2 μl

100 ng of human genomic DNA = 1 μl

10 mM dNTP = 0.4 μl

Advantage 2 Polymerase enzyme mix (Clontech) = 0.2 μl

Forward Primer (10 μM) = 0.4 μl Reverse Primer (10 μM) = 0.4 μl

Water =15.6μl

Amplification profile: 94°C - 2 min. 1 cycle

10 cycles

35 cycles

31 Sequencing of PCR Products

The PCR products were purified by Solid Phase Reversible Immobilization using the protocol developed by the Whitehead Genome Center. A detailed protocol can be found at http://www.genome.wi.mit.edu/sequencing/protocols/pure/SPRI_pcr.html. Briefly, five μl of carboxyl coated magnetic beads (10 mg/ml) and 60 μl of HYB BUFFER

(2.5M NaCl/20% PEG 8000) were added to each PCR reaction mixture (20 μl). The reaction mixture was mixed well and incubated at room temperature (RT) for 10 min. The microtitre plate was placed on a magnet for 2 min and the beads washed twice with 150 μl of 70% EtOH. The beads were air dried for 2 min and the DNA was eluted in 25 μl of distilled water and incubated at RT for 5 min. The beads were magnetically separated and the supernatant removed for testing and sequencing.

The purified PCR products were sequenced in both directions using the primer sets described previously or those listed, in the 5 ' to 3 ' direction, below.

Fragment 1 Forward Primer 961-980 GCCTGAGCAGGCAGAGAGGG (SEQ ID NO: 132)

Reverse Primer Complement of 1514-1495 TTGGCCCCACTGTGAGAGGG (SEQ ID NO: 133)

Fragment 2 Forward Primer

1275-1296 AGACACGTGCACACTACTTCCA (SEQ ID NO: 134)

Reverse Primer

Complement of 1769-1749 ACCCTGAGTACCTGGACAGCT (SEQ ID NO: 135) Fragment 3

Forward Primer

1635-1655 CCCCAAATTCCCATAGCTGGT (SEQ ID NO: 136)

Reverse Primer

Complement of 2152-2133 GCAATGACCGTGGTCAACAA (SEQ ID NO: 137)

Fragment 4

Forward Primer

1930-1949 GCGACACTGGATTTTCCACA (SEQ ID NO: 138)

Reverse Primer Complement of 2387-2368 GGCCTTGGTCCATGGAGATT (SEQ ID NO: 139)

Fragment 5 Forward Primer

1989-2010 GTGCCTGAAAAAGCAGAGACCA (SEQ ID NO: 140) Reverse Primer

Complement of 2447-2428 AGGTCCATCCACAGTGCTGA (SEQ ID NO: 141)

Fragment 6 Forward Primer 3190-3208 CTGCCTCTGTGCCACACCA (SEQ ID NO: 142) Reverse Primer Complement of 3493-3475 ATTATGGCGGGAGGGAGGA (SEQ ID NO: 143)

32 Fragment 7 Forward Primer

3477-3496 CTCCCTCCCGCCATAATCTG (SEQ ID NO: 144) Reverse Primer Complement of 3871-3852 TAAATCCCGAAGGCCACGTC (SEQ ID NO: 145)

Fragment 8 Forward Primer

3949-3968 ACCCACCTCATGGGGACTTC (SEQ ID NO: 146) Reverse Primer

Complement of 4349-4330 GGTCGGCTAGGCTGAAGACG (SEQ ID NO: 147)

Example IB This example illustrates examination of the ILl 3 gene for polymoφhic sites in several regions spanning about 2100 base pairs upstream of the ATG start site to about 115 base pairs downstream of the termination codon.

Amplification of Target Regions

The locations of the PCR primer pairs, which were designed based on Figure 1 are set forth below:

Fragment 1 (Promoter region) Forward primer

21-43 GAAACAAGCAACAGGACCCTCTG (SEQ ID NO: 148)

Reverse primer complement of 622-598 GGAACTACCTTGGTCTGTGCAACTC (SEQ ID NO: 149) PCR Product 602 nt

Fragment 2 (Promoter region) Forward primer: 560-581 GGGATAAGGGGCGTTGACTCAC (SEQ ID NO: 150)

Reverse primer: complement of 1248-1223 CCATCCTTCTGGGAAACTCTTAACTG (SEQ ID NO: 151) PCR Product 689 nt Fragment 3 (Promoter region)

Forward primer:

1101-1076 GTTTCTGGAGGACTTCTAGGAAAACG (SEQ ID NO: 152)

Reverse primer: complement of 1667-1644 TGACCACAGTCTACCAGCTATGGG (SEQ ID NO: 153) PCR Product 592 nt

Fragment 4 (Promoter region) Forward primer:

1361-1384 GCAACATAGTGAGACCCCATCTCC (SEQ ID NO: 154)

Reverse primer: complement of 2058-2035 GCGTCTTGTGGCAGCTTTTATAGG (SEQ ID NO: 155) PCR Product 698 nt

33 Fragment 5 (Promoter region Forward primer: 1635-1657 CCCCAAATTCCCATAGCTGGTAG (SEQ ID NO: 156) Reverse primer: complement of 2267-2246 GCCGACACTCTCCTTCTGGTTC (SEQ ID NO: 157) PCR Product 633 nt

Fragment 6 (Exon 1) Forward primer: 1985-2009 GATAGTGCCTGAAAAAGCAGAGACC (SEQ ID NO: 158) Reverse primer: complement of 2454-2432 CCTCCATAGGTCCATCCACAGTG (SEQ ID NO: 159) PCR Product 470 nt

Fragment 7 (Exon 2 and 3) Forward primer: 3126-3146 TCACCCCTATGCCTGCTGTTC (SEQ ID NO: 160

)

Reverse primer: complement of 3906-3883 AGGTAGGAGTTAGGAGCCCTTGAG (SEQ ID NO: 161) PCR Product 781 nt

Fragment 8 (Exon 4) Forward primer: 3982-4002 TGAGACAGTCCCTGGAAAGCC (SEQ ID NO: 162) Reverse primer: complement of 4304-4281 AAGGAATTTTACCCCTCCCTAACC (SEQ ID NO: 163) PCR Product 324 nt

These primer pairs were used in PCR reactions containing genomic DNA isolated from immortalized cell lines for each member of the Index Repository. The PCR reactions were carried out under the following conditions:

Reaction volume = 20 μl

10 x Advantage 2 Polymerase reaction buffer (Clontech) = 2 μl

100 ng of human genomic DNA = 1 μl

10 mM dNTP = 0.4 μl

Advantage 2 Polymerase enzyme mix (Clontech) = 0.2 μl

Forward Primer (10 μM) = 0.4 μl

Reverse Primer (10 μM) = 0.4 μl

Water =15.6μl

Amplification profile:

94°C - 2 min. 1 cycle

94°C - 30 sec. 70°C - 45 sec. 10 cycles 72°C - 1 min.

94°C - 30 sec. 64°C - 45 sec. 35 cycles 72°C - 1 min.

34 Sequencing of PCR Products

The PCR products were purified by Solid Phase Reversible Immobilization using the protocol developed by the Whitehead Genome Center. A detailed protocol can be found at http://www.genome.wi.mit.edu/sequencing/protocols/pure/SPRI_pcr.html. Briefly, carboxyl coated magnetic beads (10 mg/ml) were washed three times with wash buffer (0.5 M EDTA, pH 8.0). Ten μl of washed beads and 50 μl of HYB BUFFER (2.5M NaCl/20% PEG 8000) were added to each PCR reaction mixture (50 μl). The reaction mixture was mixed well and incubated at room temperature (RT) for 10 min. The microtitre plate was placed on a magnet for 2 min and the beads washed twice with 150 μl of 70% EtOH. The beads were air dried for 2 min and resuspend in 20 μl of elution buffer (10 mM trisacetate, pH 7.8) and incubated at RT for 5 min. The beads were magnetically separated and the supernatant removed for testing and sequencing.

The purified PCR products were sequenced in both directions using the above PCR primer sets except where indicated below, with nucleotide positions of the primers referring to Fig. 1.

Fragment 1

Forward primer:

26-49 AAGCAACAGGACCCTCTGATGTAG (SEQ ID NO: 164)

Reverse primer: complement of 620-597 AACTACCTTGGTCTGTGCAACTCC (SEQ ID NO: 165)

Fragment 3

Forward primer:

1089-1111 TTCTAGGAAAACGAGGGAAGAGC (SEQ ID NO: 166)

Reverse primer: complement of 1667-1644 TGACCACAGTCTACCAGCTATGGG (SEQ ID NO: 167)

Fragment 4 Forward primer:

1443-1468 GAATCTTTCTGGATCTCTCAGTGGAG (SEQ ID NO: 168) Reverse primer: complement of 2032-2012 CAAGTGGTGACGCCTGACTCC (SEQ ID NO: 169)

Fragment 5 Forward primer: 1683-1707 AAGACTATCTGCTCAGCACTTCTGG (SEQ ID NO: 170)

Reverse primer: complement of 2241-2219 TGATGTTGACCAGCTCCTCAATG (SEQ ID NO: 171)

Fragment 6 (exon 1) Forward primer:

2066-2085 ACAAGCCACCCAGCCTATGC (SEQ ID NO: 172)

Reverse primer: complement of 2442-2423 CATCCACAGTGCTGAGCCCCCCAGCCCAGC (SEQID NO: 173)

35 Fragment 7 (exon 2) Forward primer: 3202-3221 CACACCAGGGATGCTTGTGG (SEQ ID NO: 174] Reverse primer: complement of 3556-3536 CTGGAAGATGGGGCTGAGATG (SEQ ID NO: 175)

Fragment 8 (exon 3)

Forward primer:

3336-3358 TCCCTGATCAACGTGTCAGGCTGCAGTGCCATC (SEQ ID NO: 176;

Reverse primer: complement of 3805-3784 TATTCAGCCAGCTTCCCTTCAG (SEQ ID NO: 177)

Fragment 9 (exon 4)

Forward primer:

4003-4022 CCTGGTTTGTGCGAGTCGTC (SEQ ID NO: 178;

Reverse primer: complement of 4293-4274 CCCCTCCCTAACCCTCCTTC (SEQ ID NO: 179)

Analysis of Sequences for Polymoφhic Sites

Sequences were analyzed for the presence of polymoφhisms using the Polyphred program (Nickerson et al., Nucleic Acids Res. 14:2745-2751, 1997). The presence of a polymoφhism was confirmed on both strands. The polymoφhisms and their locations in the ILl 3 gene are listed in Table 2 below. Table 2. Polymoφhic Sites Identified in the ILl 3 Gene

Polymoφhic Reference Variant Examp]

Site Number Nucleotide Position Allele Allele

PS1 ^R 1100 C T IA, IB

PS2 ^R 1408 A G IA, IB

PS3 1477 A G IA

PS4 1842 C T IA

PS5 2080 T C IA

PS6 2233 C A IA

PS7 2385 C T IA

PS8 3248 G A IA

PS9 ^R 3280 C T IA, IB

PS10 3807 C T IA

PS11 4014 G A IA

PS12 4033 C T IA

PS13 ^R 4044 C T IA, IB

PS14^R 4165 G A IA, IB

R: These polymoφhic sites have previously been mapped to nucleotide positions 1100, 1408, 3281, 4045 and 4166, respectively, in the GenBank Accession No. U10307.1 in Application No. 60,156,489 filed on September 28, 1999.

Example 2 This example illustrates analysis of the ILl 3 polymoφhisms identified in the Index Repositories IA and IB for human genotypes and haplotypes.

36 The different genotypes containing these polymoφhisms that were observed in the reference population are shown in Table 3 below, with the haplotype pair indicating the combination of haplotypes determined for the individual using the haplotype derivation protocol described below. In Table 3, homozygous positions are indicated by one nucleotide and heterozygous positions are indicated by two nucleotides. Missing nucleotides in any given genotype in Table 3 can typically be infened based on linkage disequilibrium and/or Mendelian inheritance.

Table 3 (Parti). Genotypes and Haplotype Pairs Observed for IL13 Gene

Genotype PO: Lymor;phic Sites

Number PS1 PS2 PS3 PS4 PS5 PS6 PS7 PS8 PS9 PS10 HAP Pai.

1 C A A C T C c G c C 3 3

2 T A A C T C c G c c 14 14

3 C A A C T C c G C c 4 4

4 C A A C T C c G c c 5 5

5 T A G C T C c G c c 19 19

6 T A A C T C c G c c 15 15

7 c A A C T c c G c c 3 6

8 c A A C T c c G c c 4 6

9 c/τ A A C/T T c c G c c 3 17

10 T A A/G C T c c G c c 14 18

11 c A A C T c C/T G c c 3 9

12 c A/G A C T c c G c c 3 10

13 C/T A A/G C T c c G c c 4 19

14 C/T A A/G C T c c G C/T c 3 21

15 C A A C T c c G C c 3 5

16 T A A C T C/A c G c C/T 14 12

17 C/T A A C T C/A c G c c 3 11

18 c A A C T C c G c C/T 3 7

19 c A A C T C c G c C/T 5 7

20 C/T A A/G C T C c G c c 3 20

21 c A A C T C c G c c 4 5

22 τ/c A G/A C T C c G c C/T 19 7

23 C/T A A C T C c G c C 3 16

24 C/T A A C T c c G c C 3 15

25 c A A C T c c G/A c c 3 2

26 C/T A A/G c T c c G c c 3 19

27 C A A c T/C c c G c c 4 1

28 C A A c T c c G c c 3 4

29 C/T A A/G c T c c G c c 3 18

30 T/C A A c T c c G c c 14 4

31 C A A c T c c G C/T c 5 8

32 T/C A G/A c T c c G c c 19 5

33 T/C A G/A c T c c G C/T c 19 8

34 C/T A A c T c c G C c 3 13

35 T A A/G c T c c G C c 14 19

36 C/T A A c T c c G C c 3 14

37 Table 3(Part2). Genotypes and Haplotype Pairs Observed for IL13 Gene Genotype Polymorphic Sites

Number PS11 PS12 PS13 PS14 HAP Pai

1 G c c G 3 3

2 G c T A 14 14

3 G c T A 4 4

4 G c T G 5 5

5 G c T G 19 19

6 G c T G 15 15

7 G C/T c G 3 6

8 G C/T T/C A/G 4 6

9 G C C/T G 3 17

10 G C T/C A/G 14 18

11 G C C/T G/A 3 9

12 G C C/T G 3 10

13 G C T A/G 4 19

14 G/A C C/T G 3 21

15 G C C/T G 3 5

16 G C T/C A/G 14 12

17 G c C/T G/A 3 11

18 G c C/T G/A 3 7

19 G c T G/A 5 7

20 G C/T C/T G 3 20

21 G c T A/G 4 5

22 G c T G/A 19 7

23 G C/T c G 3 16

24 G c C/T G 3 15

25 G c C/T G/A 3 2

26 G c C/T G 3 19

27 G c T A 4 1

28 G c C/T G/A 3 4

29 G c c G 3 18

30 G c T A 14 4

31 G c T/C G 5 8

32 G c T G 19 5

33 G c T/C G 19 8

34 G c C G 3 13

35 G c T A/G 14 19

36 G c C/T G/A 3 14

The haplotype pairs shown in Table 3 were estimated from the unphased genotypes using an extension of Clark's algorithm (Clark, A.G. (1990) Mol Bio Evol 1, 111-122), as described in U.S. Provisional Patent Application filed April 19, 2000 and entitled "A Method and System for Determining Haplotypes from a Collection of Polymoφhisms". In this method, haplotypes are assigned directly from individuals who are homozygous at all sites or heterozygous at no more than one of the variable sites. This list of haplotypes is then used to deconvolute the unphased genotypes in the remaining (multiply heterozygous) individuals.

By following this protocol, it was determined that the Index Repositories examined herein and, by extension, the general population contains the 21 human ILl 3 haplotypes shown in Table 4 below.

38 Table 4. Haplotypes Identifieid in the IL13 Gene

Haplotype Polymorph:ic : Sites

PS PS PS PS 1 PS PS PS PS PS PS PS PS PS P:

Number 1 2 3 4 5 6 7 8 9 10 11 12 13 1.

1 C A A C c c C G c c G c T A

2 C A A C T c C A c c G c T A

3 C A A c T c C G C c G c c G

4 C A A c T c C G C c G C T A

5 C A A c T c C G C c G C T G

6 C A A c T c C G C c G T c G

7 C A A c T c C G C T G C T A

8 C A A c T c C G T c G C c G

9 C A A c T c T G C c G C T A

10 C G A c T c C G C c G C T G

11 T A A c T A C G C c G C T A

12 T A A c T A c G c T G C c G

13 T A A c T c c G c c G C c G

14 T A A c T c c G c c G c T A

15 T A A c T c c G c c G c T G

16 T A A c T c c G c c G T c G

17 T A A T T c c G c c G c T G

18 T A G c T c c G c c G c c G

19 T A G c T c c G c c G c T G

20 T A G c T c c G c c G T T G

21 T A G c T c c G T c A c T G

In view of the above, it will be seen that the several advantages of the invention are achieved and other advantageous results attained. As various changes could be made in the above methods and compositions without departing from the scope of the invention, it is intended that all matter contained in the above description and shown in the accompanying drawings shall be inteφreted as illustrative and not in a limiting sense. All references cited in this specification, including patents and patent applications, are hereby incoφorated in their entirety by reference. The discussion of references herein is intended merely to summarize the assertions made by their authors and no admission is made that any reference constitutes prior art. Applicants reserve the right to challenge the accuracy and pertinency of the cited references.

39