WO2002026765A2 - Haplotypes of the muc1 gene - Google Patents

Abstract

Novel genetic variants of the Mucin 1, Transmembrane (MUC1) gene are described. Various genotypes, haplotypes, and haplotype pairs that exist in the general United States population are disclosed for the MUC1 gene. Compositions and methods for haplotyping and/or genotyping the MUC1 gene in an individual are also disclosed. Polynucleotides defined by the haplotypes disclosed herein are also described.

Description

HAPLOTYPES OF THE MUCl GENE

RELATED APPLICATIONS

This application claims the benefit of U.S. Provisional Application Serial No. 60/236,113 filed September 28, 2000.

FIELD OF THE TNVENTION

This invention relates to variation in genes that encode pharmaceutically-important proteins. In particular, this invention provides genetic variants ofthe human mucin 1, transmembrane (MUCl) 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 lead compound that is specific for the target, thereby reducing the incidence ofthe undesired side effects usually caused by activity at non-intended targets. The lead compound identified in this screening process then undergoes further in vitro and in vivo testing to determine its absorption, disposition, metabolism and toxicological profiles. Typically, this testing involves use of cell lines and animal models with limited, if any, genetic diversity.

What this approach fails to consider, however, is that natural genetic variability exists between individuals in any and every population with respect to pharmaceutically-important proteins, including the protein targets of candidate drugs, the enzymes that metabolize these drugs and the proteins whose activity is modulated by such drug targets. Subtle alteration(s) in the primary nucleotide sequence of a gene encoding a pharmaceutically-important protein may be manifested as significant variation in expression, structure and/or function ofthe protein. Such alterations may explain the relatively high degree of uncertainty inherent in the treatment of individuals with a drug whose design is based upon a single representative example ofthe target or enzyme(s) involved in metabolizing the drug. For example, it is well-established that some 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. Also, there is significant variation in how well people metabolize drugs and other exogenous chemicals, resulting in substantial interindividual variation in the toxicity and/or efficacy of such exogenous substances (Evans et al., 1999, Science 286:487-491). This variability in efficacy or toxicity of a drug in genetically-diverse patients makes many drugs ineffective or even dangerous in certain groups ofthe population, leading to the failure of such drugs in clinical trials or their early withdrawal from the market even though they could be highly beneficial for other groups inthe population. This problem significantly increases the time and cost of drug discovery and development, which is a matter of great public concern. It is well-recognized by pharmaceutical scientists that considering the impact ofthe genetic variability of pharmaceutically-important proteins in the early phases of drug discovery and development is likely to reduce the failure rate of candidate and approved drugs (Marshall A 1997 Nature Biotech 15: 1249-52; Kleyn PW et al. 1998 Science 281: 1820-21; Kola 1 1999 Curr Opin Biotech 10:589-92; Hill AVS et al. 1999 in Evolution in Health and Disease Stearns SS (Ed.) Oxford University Press, New York, pp 62-76; Meyer U. A. 1999 in Evolution in Health and Disease Stearns SS (Ed.) Oxford University Press, New York, pp 41-49; Kalow W et al. 1999 Clin. Pharm. Therap. 66:445-7; Marshall, E 1999 Science 284:406-7; Judson R et al. 2000 Pharmacogenomics 1:1-12; Roses AD 2000 Nature 405:857-65). However, in practice this has been difficult to do, in large part because of the' time and cost required for discovering the amount of genetic variation that exists in the population (Chakravarti A 1998 Nature Genet 19:216-7; Wang DG et al 1998 Science 280: 1077- 82; Chakravarti A 1999 Nat Genet 21:56-60 (suppl); Stephens JC 1999 Mol. Diagnosis 4:309-317; Kwo PY and Gu S 1999 Mol. Med. Today 5:538-43; Davidson S 2000 Nature Biotech 18: 1134-5). The standard for measuring genetic variation among individuals is the haplotype, which is - the ordered combination of polymorphisms in the sequence of each form of a gene that exists in the population. Because haplotypes represent the variation across each form of a gene, they provide a more accurate and reliable measurement of genetic variation than individual polymorphisms. For example, while specific variations in gene sequences have been associated with a particular phenotype such as disease susceptibility (Roses AD supra; Ulbrecht M et al. 2000 Am JRespir Crit Care Med 161: 469-74) and drug response (Wolfe CR et al. 2000 BMJ 320:987-9-0; Dahl BS 1997 Acta Psychiatr Scand 96 (Suppl 391): 14-21), in many other cases an individual polymorphism may be found in a variety of genomic backgrounds, i.e., different haplotypes, and therefore shows no definitive coupling between the polymorphism and the causative site for the phenotype (Clark AG et al. 1998 Am JHum Genet 63:595-612; Ulbrecht M et al. 2000 supra; Drysdale et al. 2000 PNAS 97:10483-10488). Thus, there is an unmet need in the pharmaceutical industry for information on what haplotypes exist in the population for pharmaceutically-important genes. Such haplotype information would be useful in improving the efficiency and output of several steps in the drug discovery and development process, including target validation, identifying lead compounds, and early phase clinical trials (Marshall et al., supra).

One pharmaceutically-important gene for the treatment of cancer is the mucin 1 , transmembrane (MUCl) gene or its encoded product. Mucins are major epithelial luminal surface proteins that function as a physical barrier protecting mucous epithelia. The glycosylation of mucins is important for tissue-specific interaction with the surrounding environment (Irimura et al., J Biochem (Tokyo) 1999; 126:975-985). MUCl contains three distinct regions: an amino terminus consisting of a putative signal peptide and degenerate repeats; a carboxyl terminus consisting of degenerate tandem repeats; and a unique sequence containing a transmembrane sequence and a cytoplasmic tail. The tandem repeat regions in the protein are a characteristic structural feature of MUCl. Potential O-glycosylation sites make up for about one-fourth ofthe total amino acids (Gendler et al., JBiol Chem. 1990; 265:15286-15293).

Mucins are potential targets for cancer immunotherapy because they are expressed 10-fold higher in adenocarcinomas. They have an altered expression wherein they become ubiquitous, and due to their altered glycosylation, they harbor new epitopes on the cell surface which are otherwise absent from cells of normal tissues (Apostolopoulos and McKenzie, Crit Rev Immunol 1994; 14:293- 309). MUCl is a carcinoma-associated marker protein whose expression correlates with the clinical stage of cancer. The MUCl immune response is known to provide a host defense mechanism against cancer and the role of MUCl in carcinoma-host interactions is believed to be dependent on its glycosylation status (Denda-Nagai and Irimura, Glycoconj. J2000; 17:649-658). MUC 1 is also highly expressed in breast cancer. In mice, MUC 1 , conjugated to oxidized mannan (MUCl-mannam fusion protein [M-FP]), targets the.mannose receptor and induces a high frequency of cytotoxic T lymphocytes and anti-tumor responses. Similarly, patients with adenocarcinoma were found to have a high titer of MUCl IgGl response (Apostolopoulos and McKenzie, Crit Rev Immunol 1994; 14:293-309; Karanikas et al., JImmunother. 2001; 24:172-183). Since MUCl is involved in the immune response to cancers, mechanisms that alter the glycosylation of MCU1 may have serious in the deveopment of immunotherapy for various types of cancer.

The mucin 1, transmembrane gene is located on chromosome Iq21-q23 and contains 7 exons that encode a 475 amino acid protein. A reference sequence for the MUCl gene is shown in the contiguous lines of Figure l(Genaissance Reference No. 14830314; SEQ ID NO: 1). Reference sequences for the coding sequence (GenBank Accession No. J05581.1) and protein are shown in Figures 2 (SEQ ID NO: 2) and 3 (SEQ ID NO: 3), respectively.

Because ofthe potential for variation in the MUCl gene to affect the expression and function ofthe encoded protein, it would be useful to know whether polymorphisms exist in the MUCl gene, as well as how such polymorphisms are combined in different copies ofthe gene. Such information could be applied for studying the biological function of MUC 1 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 11 novel polymorphic sites in the MUCl gene. These polymorphic sites (PS) correspond to the following nucleotide positions in Figure 1:

718 (PS1), 805 (PS2), 917 (PS3), 2511 (PS4), 2714 (PS5), 2797 (PS6), 3460 (PS7), 4474 (PS8), 4478 (PS9), 4547 (PS10) and 4803 (PS11). The polymorphisms at these sites are cytosine or thymine at PS1, adenine or thymine at PS2, guanine or adenine at PS3, thymine or cytosine at PS4, cytosine or thymine at PS5, guanine or adenine at PS6, guanine or adenine at PS7, cytosine or thymine at PS8, guanine or adenine at PS9, cytosine or thymine at PS 10 and cytosine or thymine at PS 11. In addition, the inventors have determined the identity ofthe alleles 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. From this information, the inventors deduced a set of haplotypes and haplotype pairs for PS1-PS11 in the MUCl gene, which are shown below in Tables 4 and 3, respectively. Each of these MUCl haplotypes constitutes a code that defines the variant nucleotides that exist in the human population at this set of polymorphic sites in the MUCl gene. Thus each MUCl haplotype also represents a naturally-occurring isoform (also referred to herein as an "isogene") ofthe MUCl gene. The frequency of each haplotype and haplotype pair within the total reference population and within each ofthe four major population groups included in the reference population was also determined.

Thus, in one embodiment, the invention provides a method, composition and kit for genotyping the MUCl gene in an individual. The genotyping method comprises identifying the nucleotide pair that is present at one or more polymorphic sites selected from the group consisting of PS1, PS2, PS3, PS4, PS5, PS6, PS7, PS8, PS9, PS10 and PSl l in both copies ofthe MUCl gene from the individual. A genotyping composition ofthe invention comprises an oligonucleotide probe or primer which is designed to specifically hybridize to a target region containing, or adjacent to, one of these novel MUCl polymorphic sites. A genotyping kit ofthe invention comprises a set of oligonucleotides designed to genotype each of these novel MUCl polymorphic sites. The genotyping method, composition, and kit are useful in determining whether an individual has one of the haplotypes in Table 4 below or has one ofthe haplotype pairs in Table 3 below.

The invention also provides a method for haplotyping the MUCl gene in an individual. In one embodiment, the haplotyping method comprises determining, for one copy ofthe MUCl gene, the identity ofthe nucleotide at one or more polymorphic sites selected from the group consisting of PS1, PS2, PS3, PS4, PS5, PS6, PS7, PS8, PS9, PS10 and PS11. In another embodiment, the haplotyping method comprises determining whether one copy ofthe individual's MUCl gene is , defined by one ofthe MUCl haplotypes shown in Table 4, below, or a sub-haplotype thereof. In a preferred embodiment, the haplotyping method comprises determining whether both copies ofthe individual's MUCl gene are defined by one ofthe MUCl haplotype pairs shown in Table 3 below, or a sub-haplotype pair thereof. Establishing the MUCl haplotype or haplotype pair of an individual is useful for improving the efficiency and reliability of several steps in the discovery and development of drugs for treating diseases associated with MUCl activity, e.g., cancer. For example, the haplotyping method can be used by the pharmaceutical research scientist to validate MUCl as a candidate target for treating a specific condition or disease predicted to be associated with MUC 1 activity. Determining for a particular population the frequency of one or more ofthe individual MUCl haplotypes or haplotype pairs described herein will facilitate a decision on whether to pursue MUCl as a target for treating the specific disease of interest. In particular, if variable MUCl activity is associated with the disease, then one or more MUCl haplotypes or haplotype pairs will be found at a higher frequency in disease cohorts than in appropriately genetically matched controls. Conversely, if each ofthe observed MUCl haplotypes are of similar frequencies in the disease and control groups, then it may be inferred that variable MUCl activity has little, if any, involvement with that disease. In either case, the pharmaceutical research scientist can, without a priori knowledge as to the phenotypic effect of any MUCl haplotype or haplotype pair, apply the information derived from detecting MUCl haplotypes in an individual to decide whether modulating MUC 1 activity would be useful in treating the disease.

The claimed invention is also useful in screening for compounds targeting MUCl to treat a specific condition or disease predicted to be associated with MUCl activity. For example, detecting which ofthe MUCl haplotypes or haplotype pairs disclosed herein are present in individual members of a population with the specific disease of interest enables the pharmaceutical scientist to screen for a compound(s) that displays the highest desired agonist or antagonist activity for each ofthe MUCl isoforms present in the disease population, or for only the most frequent MUCl isoforms present in the disease population. Thus, without requiring any a priori knowledge ofthe phenotypic effect of any particular MUCl haplotype or haplotype pair, the claimed haplotyping method provides the scientist with a tool to identify lead compounds that are more likely to show efficacy in clinical trials. Haplotyping the MUC 1 gene in an individual is also useful in the design of clinical trials of candidate drugs for treating a specific condition or disease predicted to be associated with MUCl activity. For example, instead of randomly assigning patients with the disease of interest to the treatment or control group as is typically done now, detennining which ofthe MUCl haplotype(s) disclosed herein are present in individual patients enables the pharmaceutical scientist to distribute MUCl haplotypes and/or haplotype pairs evenly to treatment and control groups, thereby reducing the potential for bias in the results that could be introduced by a larger frequency of a MUCl haplotype or haplotype pair that is associated with response to the drug being studied in the trial, even if this association was previously unknown. Thus, by practicing the claimed invention, the scientist can more confidently rely on the information learned from the trial, without first deterrmning the phenotypic effect of any MUC 1 haplotype or haplotype pair.

In another embodiment, the invention provides a method for identifying an association between a trait and a MUCl genotype, haplotype, or haplotype pair for one or more ofthe novel polymorphic sites described herein. The method comprises comparing the frequency ofthe MUCl genotype, haplotype, or haplotype pair in a population exhibiting the trait with the frequency ofthe MUCl genotype or haplotype in a reference population. A higher frequency ofthe MUCl genotype, haplotype, or haplotype pair in the trait population than in the reference population indicates the trait is associated with the MUCl genotype, haplotype, or haplotype pair. In preferred embodiments, the trait is susceptibility to a disease, severity of a disease, the staging of a disease or response to a drug. In a particularly preferred embodiment, the MUCl haplotype is selected from the haplotypes shown in Table 4, or a sub-haplotype thereof. Such methods have applicability in developing diagnostic tests and therapeutic treatments for cancer. In yet another embodiment, the invention provides an isolated polynucleotide comprising a nucleotide sequence which is a polymorphic variant of a reference sequence for the MUCl gene or a fragment thereof. The reference sequence comprises the contiguous sequences shown in Figure 1 and the polymorphic variant comprises at least one polymorphism selected from the group consisting of thymine at PS1, thymine at PS2, adenine at PS3, cytosine at PS4, thymine at PS5, adenine at PS6, adenine at PS7, thymine at PS8, adenine at PS9, thymine at PS 10 and thymine at PS11.

A particularly preferred polymorphic variant is an isogene ofthe MUCl gene. A MUCl isogene ofthe invention comprises cytosine or thymine at PS1, adenine or thymine at PS2, guanine or adenine at PS3, thymine or cytosine at PS4, cytosine or thymine at PS5, guanine or adenine at PS6, guanine or adenine at PS7, cytosine or thymine at PS8, guanine or adenine at PS9, cytosine or thymine at PS 10 and cytosine or thymine at PS 11. The invention also provides a collection of MUC 1 isogenes, referred to herein as a MUCl genome anthology.

In another embodiment, the invention provides a polynucleotide comprising a polymorphic variant of a reference sequence for a MUCl cDNA or a fragment thereof. The reference sequence comprises SEQ ID NO:2 (Fig.2) and the polymorphic cDNA comprises adenine at a position corresponding to nucleotide 1009. A particularly preferred polymorphic cDNA variant comprises the coding sequence of a MUCl isogene defined by haplotypes 6 and 12.

Polynucleotides complementary to these MUCl genomic and cDNA variants are also provided by the invention. It is believed that polymorphic variants ofthe MUCl gene will be useful in studying the expression and function of MUC 1 , and in expressing MUC 1 protein for use in screening for candidate drugs to treat diseases related to MUCl activity.

In other embodiments, the invention provides a recombinant expression vector comprising one ofthe polymorphic genomic and cDNA 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 MUCl for protein structure analysis and drug binding studies.

In yet another embodiment, the invention provides a polypeptide comprising a polymorphic variant of a reference amino acid sequence for the MUCl protein. The reference amino acid sequence comprises SEQ ID NO:3 (Fig.3) and the polymorphic variant comprises methionine at a position corresponding to amino acid position 337. A polymorphic variant of MUCl is useful in studying the effect of the variation on the biological activity of MUC 1 as well as on the bmding affinity of candidate drugs targeting MUCl for the treatment of cancer.

The present invention also provides antibodies that recognize and bind to the above polymorphic MUCl protein variant. Such antibodies can be utilized in a variety of diagnostic and prognostic formats and therapeutic methods.

The present invention also provides nonhuman transgenic animals comprising one or more of the MUCl polymorphic genomic variants described herein and methods for producing such animals. The transgenic animals are useful for studying expression ofthe MUCl isogenes in vivo, for in vivo screening and testing of drugs targeted against MUCl protein, and for testing the efficacy of therapeutic agents and compounds for cancer in a biological system. .

The present invention also provides a computer system for storing and displaying polymorphism data determined for the MUCl gene. The computer system comprises a computer processing unit; a display; and a database containing the polymorphism data. The polymorphism data includes one or more ofthe following: the polymorphisms, the genotypes, the haplotypes, and the haplotype pairs identified for the MUCl gene in a reference population. In a preferred embodiment, the computer system is capable of producing a display showing MUCl haplotypes organized according to their evolutionary relationships..

BRIEF DESCRIPTION OF THE DRAWINGS

Figure 1 illustrates a reference sequence for the MUCl gene (Genaissance Reference No. 14830314; contiguous lines), with the start and stop positions of each region of coding sequence indicated with a bracket ([ or ]) and the numerical position below the sequence and the polymorphic site(s) and polymorphism(s) identified by Applicants, in a reference population indicated by the variant nucleotide positioned below the polymorphic site in the sequence. SEQ ID NO: 1 is equivalent to Figure 1, with the two alternative allelic variants of each polymorphic site indicated by the appropriate nucleotide symbol (R= G or A, Y= T or C, M= A or C, K= G or T, S= G or C, and W= A or T; WTPO standard ST.25). SEQ ID NO:61 is a modified version of SEQ ID NO: 1 that shows the context sequence of each polymorphic site, PSl-PSl l, in a uniform format to facilitate electronic searching. For each polymorphic site, SEQ ID NO:61 contains a block of 60 bases ofthe nucleotide sequence encompassing the centrally-located polymorphic site at the 30^th position, followed by 60 bases of unspecified sequence to represent that each PS is separated by genomic sequence whose composition is defined elsewhere herein. Figure 2 illustrates a reference sequence for the MUCl coding sequence (contiguous lines;

SEQ ID NO:2), with the polymorphic site(s) and polymorphism(s) identified by Applicants in a reference population indicated by the variant nucleotide positioned below the polymorphic site in the sequence.

Figure 3 illustrates a reference sequence for the MUCl protein (contiguous lines; SEQ ID NO:3), with the variant amino acid(s) caused by the polymorphism(s) of Figure 2 positioned below the polymorphic site in the sequence. DESCRIPTION OF THE PREFERRED EMBODIMENTS

The present invention is based on the discovery of novel variants ofthe MUCl gene. As described in more detail below, the inventors herein discovered 13 isogenes ofthe MUCl gene by characterizing the MUCl gene found in genomic DNAs isolated from an Index Repository that contains immortalized cell lines from one chimpanzee and 93 human individuals. The human individuals included a reference population of 79 umelated individuals self-identified as belonging to one of four major population groups: Caucasian (21 individuals), African descent (20 individuals), Asian (20 individuals), or Hispanic/Latino (18 individuals). To the extent possible, the members of this reference population were organized into population subgroups by their self-identified ethnogeographic origin as shown in Table 1 below.

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.

The MUCl isogenes present in the human reference population are defined by haplotypes for 11 polymorphic sites in the MUCl gene, all of which are believed to be novel. The novel MUCl polymorphic sites identified by the inventors are referred to as PS 1-PS 11 to designate the order in which they are located in the gene (see Table 2 below). Using the genotypes identified in the Index Repository for PS 1 -PS 11 and the methodology described in the Examples below, the inventors herein also determined the pair of haplotypes for the MUCl gene present in individual human members of this repository. The human genotypes and haplotypes found in the repository for the MUCl gene include those shown in Tables 3 and 4, respectively. The polymorphism and haplotype data disclosed herein are useful for validating whether MUC 1 is a suitable target for drugs to treat cancer, screening for such drugs and reducing bias in clinical trials of such drugs.

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 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 polymorphic 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 polymorphic sites examined herein 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 ofthe polymorphic sites examined herein 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 polymorphic 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^r to 3' sequence of nucleotides found at all polymorphic sites examined herein in a locus on a single chromosome from a single individual. Sub-haplotype - The 5 ' to 3 ' sequence of nucleotides seen at a subset ofthe polymorphic sites examined herein 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 ofthe following for a specific gene: a listing ofthe haplotype pairs in each individual in a population; a listing ofthe 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.

Isof orm - 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 ofthe isoforms (e.g., alleles) of a gene found in a population. An isogene (or allele) contains all ofthe polymorphisms present in the particular isoform ofthe 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, where physical features include polymorphic sites.

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 polymorphic site on the two copies of a chromosome from an individual.

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

Polymorphic site (PS) - A position on a chromosome or DNA molecule at which at least two alternative sequences are found in a population.

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 polymorphism in the gene.

Polymorphism - The sequence variation observed in an individual at a polymorphic site. Polymorphisms 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 ofthe following for a specific gene: location of polymorphic sites; sequence variation at those sites; frequency of polymorphisms 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 polymorphism 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 ofthe 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 polymorphic 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.

Treatment - A stimulus administered internally or externally to a subject. Unphased - As applied to a sequence of nucleotide pairs for two or more polymorphic sites in a locus, unphased means the combination of nucleotides present at those polymorphic sites on a single copy ofthe locus is not known. As discussed above, information on the identity of genotypes and haplotypes for the MUC 1 gene of any particular individual as well as the frequency of such genotypes and haplotypes in any particular population of individuals is useful for a variety of drug discovery and development applications. Thus, the invention also provides compositions and methods for detecting the novel MUCl polymorphisms, haplotypes and haplotype pairs identified herein. The compositions comprise at least one oligonucleotide for detecting the variant nucleotide or nucleotide pair located at a novel MUCl polymorphic site in one copy or two copies ofthe MUCl gene. Such oligonucleotides are referred to herein as MUCl haplotyping oligonucleotides or genotyping oligonucleotides, respectively, and collectively as MUCl oligonucleotides. In one embodiment, a MUCl haplotyping or genotyping oligonucleotide is a probe or primer capable of hybridizing to a target region that contains, or that is located close to, one ofthe novel polymoφhic sites described herein.

As used herein, the term "oligonucleotide" refers to a polynucleotide molecule having less ^' than about 100 nucleotides. A preferred oligonucleotide ofthe 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 exact length ofthe oligonucleotide will depend on many factors that are routinely considered and practiced by the skilled artisan. The ohgonucleotide 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 ofthe 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. Haplotyping or genotyping oligonucleotides ofthe invention must be capable of specifically hybridizing to a target region of a MUCl polynucleotide. Preferably, the target region is located in a MUCl 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 another. region in the MUCl polynucleotide or with a non-MUCl 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 polymorphisms in the MUCl gene using the polymoφhism information provided herein in conjunction with the known sequence information for the MUCl 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 ofthe molecules is complementary to the nucleotide at the corresponding position ofthe 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, URL Press, Washington, D.C. (1985). While perfectly complementary oligonucleotides are preferred 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 ofthe primer being complementary to the target region. Alternatively, non- complementary nucleotides may be interspersed into the probe or primer as long as the resulting probe or primer is still capable of specifically hybridizing to the target region.

Preferred haplotyping or genotyping oligonucleotides ofthe 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 corresponding 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 ASO will be perfectly complementary to one allele while containing a single mismatch for another allele.

Allele-specific oligonucleotides ofthe invention include ASO probes and ASO primers. ASO probes which usually provide good discrimination between different alleles are those in which a central position ofthe oligonucleotide probe aligns with the polymoφhic site in the target region (e.g., approximately the 7^th or 8^th position in a 15mer, the 8^th or 9^th position in a 16mer, and the 10^th or 11^th position in a 20mer). An ASO primer ofthe 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. ASO probes and primers hybridizing to either the coding or noncoding strand are contemplated by the invention. ASO probes and primers listed below use the appropriate nucleotide symbol (R= G or A, Y= T or C, M= A or C, K= G or T, S= G or C, and W= A or T; WTPO standard ST.25) at the position ofthe polymoφhic site to represent that the ASO contains either ofthe two alternative allelic variants observed at that polymoφhic site.

A preferred ASO probe for detecting MUCl gene polymoφhisms comprises a nucleotide sequence, listed 5' to 3', selected from the group consisting of:

CAGACTGYCCCTCCC (SEQ ID NO 4 and its complement,

TTGAGCGWTTAGAGC (SEQ ID NO 5 and its complement,

CTAGGGCRGGCGGGC_. (SEQ ID NO 6 and its complement,

CGAGTCCYTTCCCTC (SEQ ID, NO 7 and its complement,

TGAAGTGYCCATTTC (SEQ ID NO 8 and its complement,

CCACGACRTGGAGAC (SEQ ID NO 9 and its complement,

GGAAGAGRTGAGAAG (SEQ ID NO: 10) and its complement,

AGGGGCAYGTCGCCC (SEQ ID NO: 11) and its complement,

GCACGTCRCCCGCTG (SEQ ID NO: 12) and its complement,

GCCCCTGYACCCTGT (SEQ ID NO: 13) and its complement, and

TGTGACCYGTGGGCA (SEQ ID NO: 14) and its complement.

A preferred ASO primer for detecting MUCl gene polymoφhisms comprises a nucleotide sequence, listed 5' to 3', selected from the group consisting of:

AAGTTCCAGACTGYC (SEQ ID NO 15) GGAGGGGGGAGGGRC (SEQ ID NO: 16)

AGGGGGTTGAGCG T (SEQ ID NO 17) ACAAGGGCTCTAAWC (SEQ ID NO: 18)

CTGTGCCTAGGGCRG (SEQ ID NO 19) CTCCCCGCCCGCCYG (SEQ ID NO: 20)

CAAGCCCGAGTCCYT (SEQ ID NO 21) GGGTGAGAGGGAARG (SEQ ID NO: 22)

CGTGGCTGAAGTGYC (SEQ ID NO 23) CACAGGGAAATGGRC (SEQ ID NO: 24)

CAATGTCCACGACRT (SEQ ID NO 25) AACTGTGTCTCCAYG (SEQ ID NO: 26)

GAGCTTGGAAGAGRT (SEQ ID NO 27) ACGCCACTTCTCAYC (SEQ ID NO: 28)

ACTTGTAGGGGCAYG (SEQ ID NO 29) CTCAGCGGGCGACRT (SEQ ID NO: 30)

GTAGGGGCACGTCRC (SEQ ID NO 31) TCAGCTCAGCGGGYG (SEQ ID NO: 32)

GCCAGAGCCCCTGYA (SEQ ID NO 33) GCCCAAACAGGGTRC (SEQ ID NO: 34)

TTCATCTGTGACCYG (SEQ ID NO 35) and CCCTGCTGCCCACRG (SEQ ID NO 36) Other oligonucleotides ofthe invention hybridize to a target region located one to several nucleotides downstream of one ofthe 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 oligonucleotides are referred to herein as "primer-extension oligonucleotides". In a preferred 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 preferred oligonucleotide primer for detecting MUCl gene polymoφhisms by primer extension terminates in a nucleotide sequence, listed 5 ' to 3 ', selected from the group consisting of:

TTCCAGACTG (SEQ ID NO:37); GGGGGGAGGG ( SEQ ID NO : 38 ) ;

GGGTTGAGCG (SEQ ID NO: 39); AGGGCTCTAA (SEQ ID NO : 40 ) ;

TGCCTAGGGC (SEQ ID NO: 41); CCCGCCCGCC (SEQ ID NO : 42 ) ;

GCCCGAGTCC (SEQ ID NO: 43); TGAGAGGGAA ( SEQ ID NO : 4.4 ) ;

GGCTGAAGTG (SEQ ID NO:45); AGGGAAATGG ( SEQ ID NO : 46 ) ;

TGTCCACGAC (SEQ ID NO:47); TGTGTCTGCA ( SEQ ID NO : 48 )

CTTGGAAGAG (SEQ ID NO: 49); CCACTTCTCA ( SEQ ID NO : 50 )

TGTAGGGGCA (SEQ ID.NO:51); AGCGGGCGAC (SEQ ID NO : 52 )

GGGGCACGTC (SEQ ID NO:^'53); GCTCAGCGGG ( SEQ ID NO : 54 )

AGAGCCCCTG (SEQ ID NO:55); CAAACAGGGT ( SEQ ID NO : 56) ;

ATCTGTGACC (SEQ ID NO:57); and TGCTGCCCAC ( SEQ ID NO : 58 )

In some embodiments, a composition contains two or more differently labeled MUCl oligonucleotides for simultaneously probing the identity of nucleotides or nucleotide pairs 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.

MUCl oligonucleotides ofthe 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 oligonucleotides may be used in a variety of polymoφhism detection assays, including but not limited to probe hybridization and polymerase extension assays. Immobilized MUCl oligonucleotides ofthe invention may comprise an ordered array 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 MUCl 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 MUCl gene in an individual. As used herein, the terms "MUCl genotype" and "MUCl haplotype" mean the genotype or haplotype contains the nucleotide pair or nucleotide, respectively, that is present at one or more ofthe novel polymoφhic sites described herein and may optionally also include the nucleotide pair or nucleotide present at one or more additional polymoφhic sites in the MUCl gene. The additional polymoφhic sites may be currently known polymoφhic sites or sites that are subsequently discovered.

One embodiment of a genotyping method ofthe invention involves isolating from the individual a nucleic acid sample comprising the two copies ofthe MUCl gene, mRNA transcripts thereof or cDNA copies thereof, or a fragment of any ofthe foregoing, that are present in the individual, and determining the identity ofthe nucleotide pair at one or more polymoφhic sites selected from the group consisting of PS1, PS2, PS3, PS4, PS5, PS6, PS7, PS8, PS9, PS10 and PS11 in the two copies to assign a MUCl genotype to the individual. As will be readily understood by the skilled artisan, the two "copies" of a gene, mRNA or cDNA (or fragment of. such MUCl molecules) in an individual may be the same allele or may be different alleles. In another embodiment, a genotyping method ofthe invention comprises determining the identity ofthe nucleotide pair at each ofPSl-PSl l.

Typically, the nucleic acid sample 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 sample may be comprised of genomic DNA, mRNA, or cDNA and, in the latter two cases, the biological sample must be obtained from a tissue in which the MUCl 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 ' untranslated regions if not present in the mRNA or cDNA. If a MUC 1 gene fragment is isolated, it must contain the polymoφhic site(s) to be genotyped.

One embodiment of a haplotyping method ofthe invention comprises isolating from the individual a nucleic acid sample containing only one ofthe two copies ofthe MUCl gene, mRNA or cDNA, or a fragment of such MUC 1 molecules, that is present in the individual and determining in that copy the identity ofthe nucleotide at one or more polymoφhic sites selected from the group consisting of PS1, PS2, PS3, PS4, PS5, PS6, PS7, PS8, PS9, PS 10 and PS 11 in that copy to assign a MUCl haplotype to the individual.

The nucleic acid used in the above haplotyping methods ofthe invention may be isolated using any method capable of separating the two copies ofthe MUCl gene or fragment such as one of the methods described above for preparing MUCl isogenes, with targeted in vivo cloning being the preferred approach. As will be readily appreciated by those skilled in the art, any individual clone will typically only provide haplotype information on one ofthe two MUCl gene copies present in an individual. If haplotype information is desired for the individual's other copy, additional MUCl clones will usually need to be examined. Typically, at least five clones should be examined to have more than a 90% probability of haplotyping both copies ofthe MUCl gene in an individual. In some cases, however, once the haplotype for one MUCl allele is directly determined, the haplotype for the other allele may be inferred if the individual has a known genotype for the polymoφhic sites of interest or if the haplotype frequency or haplotype pair frequency for the individual's population groμp is known. In a particularly preferred embodiment, the nucleotide at each of PS1-PS11 is identified.

In another embodiment, the haplotyping method comprises determining whether an individual has one or more ofthe MUCl haplotypes shown in Table 4. This can be accomplished by identifying, for one or both copies of the individual' s MUC 1 gene, the phased sequence of nucleotides present at each of PS1-PS11. This identifying step does not necessarily require that each of PS1-PS11 be directly examined. Typically only a subset of PS1-PS11 will need to be directly examined to assign to an individual one or more ofthe haplotypes shown in Table 4. This is because at least one polymoφhic site in a gene is frequently in strong linkage disequilibrium with one or more other polymoφhic sites in that gene (Drysdale, CM et al. 2000. PNAS 97: 10483-10488; Rieder MJ et al. 1999 Nature Genetics 22:59-62). 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 (Stephens, JC 1999, Mol. Diag. 4:309-317). Techniques for determining whether any two polymoφhic sites are in linkage disequilibrium are well-known in the art (Weir B.S. 1996 Genetic Data Analysis II, Sinauer Associates, Inc. Publishers, Sunderland, MA).

In another embodiment of a haplotyping method ofthe invention, a MUCl haplotype pair is determined for an individual by identifying the phased sequence of nucleotides at one or more polymoφhic sites selected from the group consisting of PS1, PS2, PS3, PS4, PS5, PS6, PS7, PS8, PS9, PS10 and PS11 in each copy ofthe MUCl gene that is present in the individual. In a particularly preferred embodiment, the haplotyping method comprises identifying the phased sequence of nucleotides at each of PS1-PS11 in each copy ofthe MUCl gene.

When haplotyping both copies ofthe gene, the identifying step is preferably performed with each copy ofthe gene being placed in separate containers. However, it is also envisioned that if the two copies are labeled with different tags, or are 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 ofthe 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 ofthe 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 ofthe MUCl gene, or a fragment thereof, and the sequence ofthe 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, referred 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 guamne/guanine).

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). 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 ofthe 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 ofthe 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 ofthe 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 ofthe allele-specific oligonucleotide or target nucleic acid.

The genotype or haplotype for the MUCl gene of an individual may also be determined by hybridization of a nucleic acid sample containing one or both copies ofthe gene, mRNA, cDNA or fragment(s) thereof, 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 ofthe 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., Genornics 5:874-879, 1989; Humphries et al., in Molecular Diagnosis of 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 WO91/02087, 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 ofthe nucleic acid using sets of allele-specific primers as described in Wallace et al. (WO89/10414).

In addition, the identity ofthe allele(s) present at any ofthe novel polymoφhic sites described herein may be indirectly determined by haplotyping or genotyping another polymoφhic site that is in linkage disequilibrium with the polymoφhic site that is of interest.' 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. Detection ofthe allele(s) present at a polymoφhic site in linkage disequihbrium with the novel polymoφhic sites described herein may be performed by, but is not limited to, any ofthe above-mentioned methods for detecting the identity of the allele at a polymoφhic site.

In another aspect ofthe invention, an individual's MUCl haplotype pair is predicted from its MUCl genotype using information on haplotype pairs known to exist in a reference population. In its broadest embodiment, the haplotyping prediction method comprises identifying a MUCl genotype for the individual at two or more MUCl polymoφhic sites described herein, accessing data containing MUCl haplotype pairs identified in a reference population, and assigning a haplotype pair to the individual that is consistent with the genotype data. In one embodiment, the reference haplotype pairs include the MUCl haplotype pairs shown in Table 3. The MUCl haplotype pair can be assigned by comparing the individual's genotype with the genotypes corresponding to the haplotype pairs known to exist in the general population or in a specific population group, and determining which haplotype pair is consistent with the genotype ofthe individual. In some embodiments, comparison ofthe genotype ofthe individual to the haplotype pairs identified in a reference population and determination of which haplotype pair is consistent with the genotype ofthe individual may be performed by visual inspection (for example, by consulting Table 3). When the genotype ofthe individual is consistent with more than one haplotype pair, haplotype pair frequency data (such as that presented in Table 6) may be used to determine which of these haplotype pairs is most likely to be present in the individual. This determination may also be performed in some embodiments by visual inspection upon consulting Table 6. If a particular MUC 1 haplotype pah- consistent with the genotype ofthe individual is more frequent in the reference population than others consistent with the genotype, then that haplotype pair with the highest frequency is the most likely to be present in the individual. In other embodiments, the comparison may be made by a computer-implemented algorithm with the genotype ofthe individual and the reference haplotype data stored in computer-readable formats. For example, as described in PCT/USOl/12831, filed April 18, 2001, one computer-implemented algorithm to perform this comparison entails enumerating all possible haplotype pairs which are consistent with the genotype, accessing data containing MUCl haplotype pairs frequency data determined in a reference population to determine a probability that the individual has a possible haplotype pair, and analyzing the determined probabilities to assign a haplotype pair to the individual.

Generally, the reference population should be composed of randomly-selected individuals representing the major ethnogeographic groups ofthe world. A preferred reference population for use in the methods ofthe present invention comprises an approximately equal number of individuals from Caucasian, African-descent, 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 preferred 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 ofthe four population groups named above. A particularly preferred reference population includes a 3- generation family representing one or more ofthe four population groups to serve as controls for checking quality of haplotyping procedures.

In a preferred embodiment, the haplotype frequency data for each ethnogeographic group is examined to determine whether it is consistent with Hardy- Weinberg equilibrium. Hardy- Weinberg 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. / H₂ is equal to p_H__w(H_λ IH₂) = 2p(H₁)p(H₂) if H. ≠ H₂ and p_H__w(H I H₂) = />(HXH₂) 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 errors 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), single molecule dilution, 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 a MUCl haplotype pair for an individual, the assigning step involves performing the following analysis. First, each ofthe possible haplotype pairs is compared to the haplotype pairs in the reference population. Generally, only one ofthe 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. Alternatively, the haplotype pair in an individual may be predicted from the individual's genotype for that gene using reported methods (e.g., Clark et al. 1990 Mol Bio Evol 7: 111-22; copending PCT/USOl/12831 filed April 18, 2001 ) or through a commercial haplotyping service such as offered by Genaissance Pharmaceuticals, Inc. (New Haven, CT). 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., supra). The invention also provides a method for determining the frequency of a MUCl genotype, haplotype, or haplotype pair in a population. The method comprises, for each member ofthe population, detennining the genotype or the haplotype pair for the novel MUCl polymoφhic sites described herein, and calculating the frequency any particular genotype, haplotype, or haplotype pah- is found in the population. The population may be e.g., a reference population, a family population, a same gender population, a population group, or 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 ofthe invention, frequency data for MUCl genotypes, haplotypes, and/or haplotype pairs are determined in a reference population and used in a method for identifying an association between a trait and a MUCl genotype, haplotype, or haplotype pair. The trait may be any detectable phenotype, including but not limited to susceptibility to a disease or response to a treatment. In one embodiment, the method involves obtaining data on the frequency ofthe genotype(s), haplotype(s), or haplotype pair(s) of interest in a reference population as well as in a population exhibiting the trait. Frequency data for one or both ofthe reference and trait populations may be obtained by genotyping or haplotyping each individual in the populations using one or more ofthe methods described above. The haplotypes for the trait population may be determined directly or, alternatively, by a predictive genotype to haplotype approach as 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 ofthe genotype(s), haplotype(s), or haplotype pair(s) of interest in the reference and trait populations are compared. In a prefened embodiment, the frequencies of all genotypes, haplotypes, and/or haplotype pairs observed in the populations are compared. If a particular MUCl genotype, haplotype, or haplotype pair 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 MUCl genotype, haplotype or haplotype pair. Preferably, the MUCl genotype, haplotype, or haplotype pair being compared in the trait and reference populations is selected from the full-genotypes and full-haplotypes shown in Tables 3 and 4, 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 MUCl 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 ofthe following: a quantitative measure ofthe response, no response, and/or adverse response (i.e., side effects). In order to deduce a conelation between clinical response to a treatment and a MUCl genotype, haplotype, or haplotype pair, 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 IH 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 ofthe 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 ofthe 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 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 MUCl 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 MUCl genotype or haplotype content are created. Conelations may be produced in several ways. In one method, individuals are grouped by their MUCl 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 MUCl gene give the most significant contribution to the differences in phenotype. One regression model useful in the invention is described in WO 01/01218, entitled "Methods for Obtaining and Using Haplotype Data".

A second method for finding conelations between MUCl 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 WO 01/01218. Conelations may also be analyzed using analysis of variation (ANOVA) techniques to determine how much ofthe variation in the clinical data is explained by different subsets ofthe polymoφhic sites in the MUCl gene. As described in WO 01/01218, 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 MUCl 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 MUCl 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 ofthe polymoφhic sites in the MUCl 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 MUCl genotype or haplotype that is in turn correlated with the clinical response. In a prefened embodiment, this diagnostic method uses the predictive haplotyping method described above.

In another embodiment, the invention provides an isolated polynucleotide comprising a polymoφhic variant ofthe MUCl gene or a fragment ofthe gene which contains at least one ofthe novel polymoφhic sites described herein. The nucleotide sequence of a variant MUCl gene is identical to the reference genomic sequence for those portions ofthe gene examined, as described in the Examples below, except that it comprises a different nucleotide at one or more ofthe novel polymoφhic sites PS1, PS2, PS3, PS4, PS5, PS6, PS7, PS8, PS9, PS10 and PS11. Similarly, the nucleotide sequence of a variant fragment ofthe MUCl gene is identical to the conesponding portion ofthe reference sequence except for having a different nucleotide at one or more ofthe novel polymoφhic sites described herein. Thus, the invention specifically does not include polynucleotides comprising a nucleotide sequence identical to the reference sequence ofthe MUCl gene, which is defined by haplotype 9, (or other reported MUCl sequences) or to portions ofthe reference sequence (or other reported MUCl sequences), except for the haplotyping and genotyping oligonucleotides described above.

The location of a polymoφhism in a variant MUCl gene or fragment is preferably identified by aligning its sequence against SEQ ID NO:l. The polymoφhism is selected from the group consisting of thymine at PS1, thymine at PS2, adenine at PS3, cytosine at PS4, thymine at PS5, adenine at PS6, adenine at PS 7, thymine at P_.S8, adenine at PS9, thymine at PS 10 and thymine at PS 11. In a prefened embodiment, the polymoφhic variant comprises a naturally-occurring isogene ofthe MUCl gene which is defined by any one of haplotypes 1-8 and 10-13 shown in Table 4 below. Polymoφbic variants ofthe invention may be prepared by isolating a clone containing the

MUCl gene from a human genomic library. The clone may be sequenced to determine the identity ofthe nucleotides at the novel polymoφhic sites described herein. Any particular variant or fragment thereof, that is claimed herein could be prepared from this clone by performing in vitro mutagenesis using procedures well-known in the art. Any particular MUCl variant or fragment thereof may also be prepared using synthetic or semi-synthetic methods known in the art.

MUCl isogenes, or fragments thereof, may be isolated using any method that allows separation ofthe two "copies" ofthe MUCl 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. Sci. 87:6296-6300, 1990; and allele specific PCR (Ruano et al., 1989, supra; Ruano et al., 1991, supra; Michalatos-Beloin et al., supra).

The invention also provides MUCl genome anthologies, which are collections of at least two MUCl 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 gender population. A MUCl genome anthology may comprise individual MUCl isogenes stored in separate containers such as microtest tubes, separate wells of a microtitre plate and the like. Alternatively, two or more groups ofthe MUCl isogenes in the anthology may be stored in separate containers. Individual isogenes or groups of such 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 prefened MUCl genome anthology ofthe invention comprises a set of isogenes defined by the haplotypes shown in Table 4 below. A MUCl genome anthology is useful in providing control nucleic acids for kits ofthe invention. An isolated polynucleotide containing a polymoφhic variant nucleotide sequence ofthe 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 MUCl 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 ofthe nucleic acid sequence in a given host cell. Of course, the conect 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 "Cunent Protocols in Molecular Biology", John Wiley and Sons, New York, New York). Host cells which may be used to express the variant MUCl sequences ofthe 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 prefened 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, heφes virus vectors, and baculovirus transfer vectors. Prefened eukaryotic cell lines include COS cells, CHO cells, HeLa cells, NTH/3T3 cells, and embryonic stem cells (Thomson, J. A. et al., 1998 Science 282: 1145-1147). Particularly prefened host cells are mammalian cells.

As will^'be readily recognized by the skilled artisan, expression of polymoφhic variants of the MUCl gene will produce MUCl 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 a MUCl cDNA comprising a nucleotide sequence which is a polymoφhic variant of the MUCl reference coding sequence shown in Figure 2. Thus, the invention also provides MUCl mRNAs and conesponding cDNAs which comprise a nucleotide sequence that is identical to SEQ ID NO:2 (Fig. 2), or its conesponding RNA sequence, for those regions of SEQ ID NO:2 that correspond to the examined portions ofthe MUCl gene (as described in the Examples below), except for having adenine at a position conesponding to nucleotide 1009. A particularly prefened polymoφhic cDNA variant comprises the coding sequence of a MUCl isogene defined by any one of haplotypes 6 and 12. Fragments of these variant mRNAs and cDNAs are included in the scope of the invention, provided they contain the novel polymoφhism described herein. The invention specifically excludes polynucleotides identical to previously identified and characterized MUCl mRNAs, cDNAs or fragments thereof. Polynucleotides comprising a variant MUCl RNA or DNA sequence may be isolated from a biological sample using well-known molecular biological procedures or may be chemically synthesized.

As used herein, a polymoφhic variant of a MUCl gene, mRNA or cDNA fragment comprises at least one novel polymoφhism identified herein and has a length of at least 10 nucleotides and may range up to the full length ofthe gene. Preferably, such fragments are 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 MUCl polymoφhic sites identified herein, reference is made to the sense strand ofthe gene for convenience. However, as recognized by the skilled artisan, nucleic acid molecules containing the MUCl gene or cDNA may be complementary double stranded molecules and thus reference to a particular site on the sense strand refers as well to the conesponding 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 ofthe MUCl genomic, mRNA and cDNA variants described herein.

Polynucleotides comprising a polymoφhic gene variant or fragment ofthe invention may be useful for therapeutic puφoses. For example, where a patient could benefit from expression, or increased expression, of a particular MUCl protein isoform, an expression vector encoding the isoform may be administered to the patient. The patient may be one who lacks the MUCl 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 MUCl isogene. Expression of a MUCl isogene may be turned off by transforming a targeted organ, tissue or cell population with an expression vector that expresses high levels of untranslatable mRNA or antisense RNA for the isogene or fragment thereof. Alternatively, oligonucleotides directed against the regulatory regions (e.g., promoter, introns, enhancers, 3' untranslated region) ofthe isogene may block transcription. Oligonucleotides targeting the transcription initiation site, e.g., between positions -10 and +10 from the start site are prefened. Similarly, inhibition of transcription can be achieved using oligonucleotides that base-pair with region(s) ofthe isogene DNA to form triplex DNA (see e.g., Gee et al. in Huber, B.E. and B.I. Can, Molecular and hnmunologic Approaches, Futura Publishing Co., Mt. Kisco, N.Y., 1994). Antisense oligonucleotides may also be designed to block translation of MUCl mRNA transcribed from a particular isogene. It is also contemplated that ribozymes may be designed that can catalyze the specific cleavage of MUCl mRNA transcribed from a particular isogene.

The untranslated mRNA, antisense RNA or antisense 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, such molecules 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-, thio¹, 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 (a) the reference MUCl amino acid sequence shown in Figure 3 or (b) a fragment of this reference sequence. The location of a variant amino acid in a MUCl polypeptide or fragment ofthe invention is identified by aligning its sequence against SEQ ID NO: 3 (Fig. 3). A MUCl protein variant ofthe invention comprises an amino acid sequence identical to SEQ ID NO: 3 for those regions of SEQ ID NO:3 that are encoded by examined portions ofthe MUCl gene (as described in the Examples below), except for having methionine at a position corresponding to amino acid position 337. Thus, a MUCl fragment ofthe invention, also refened to herein as a MUCl peptide variant, is any fragment of a MUCl protein variant that contains methionine at a position conesponding to amino acid position 337. The invention specifically excludes amino acid sequences identical to those previously identified for MUCl, including SEQ ID NO:3, and previously described fragments thereof. In prefened embodiments, a MUCl protein variant ofthe invention is encoded by an isogene defined by one ofthe observed haplotypes, 6 and 12, shown in Table 4.

A MUCl peptide variant ofthe invention 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 MUCl peptide variants may be useful as antigens to generate antibodies specific for one ofthe above MUCl isoforms. In addition, the MUCl peptide variants may be useful in drug screening assays.

A MUCl variant protein or peptide ofthe invention may be prepared by chemical synthesis or by expressing an appropriate variant MUC 1 genomic or cDNA sequence described above.

Alternatively, the MUCl protein variant may be isolated .from a biological sample of an individual having a MUCl isogene which encodes the variant protein. Where the sample contains two different MUCl isoforms (i.e., the individual has different MUCl isogenes), a particular MUCl isoform ofthe invention can be isolated by immunoaffinity chromatography using an antibody which specifically binds to that particular MUCl isoform but does not bind to the other MUCl isoform.

The expressed or isolated MUCl protein or peptide 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 ofthe MUCl. protein or peptide as discussed further below. MUCl variant proteins and peptides 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 immunoaffinity chromatography and the like. (Ausubel et. al., 1987, In Current 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 MUC 1 gene ofthe invention may also be fused in frame with a heterologous sequence to encode a chimeric MUCl protein. The non-MUCl portion ofthe 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 MUCl and non-MUCl portions so that the MUCl protein may be cleaved and purified away from the non-MUCl portion. An additional embodiment ofthe invention relates to using a novel MUCl protein isoform, or a fragment thereof, in any of a variety of drug screening assays. Such screening assays may be . performed to identify agents that bind specifically to all known MUCl 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 MUCl 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 a MUCl 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 MUCl protein(s) of interest and then washed. Bound MUCl protein(s) are then detected using methods well-known in the art.

In another embodiment, a novel MUCl protein isoform may be used in assays to measure the binding affinities of one or more candidate drugs targeting the MUCl protein. In yet another embodiment, when a particular MUC 1 haplotype or group of MUC 1 haplotypes encodes a MUCl protein variant with an amino acid sequence distinct from that of MUCl protein isoforms encoded by other MUCl haplotypes, then detection of that particular MUCl haplotype or group of MUCl haplotypes may be accomplished by detecting expression ofthe encoded MUCl protein variant using any of the. methods described herein or otherwise commonly known to the skilled artisan.

In another embodiment, the invention provides antibodies specific for and immunoreactive with one or more ofthe novel MUCl variant proteins described herein. The antibodies may be either monoclonal or polyclonal in origin. The MUCl 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 MUCl 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 ofthe peptide. Examples of carrier molecules, include, but are not limited to, albumins (e.g., human, bovine, fish, ovine), and keyhole limpet hemocyanin (Basic and Clinical Immunology, 1991, Eds. DP. Stites, and A.I. Ten, Appleton and Lange, Norwalk Connecticut, San Mateo, California).

In one embodiment, an antibody specifically immunoreactive with one ofthe novel protein isoforms described herein is admimstered to an individual to neutralize activity ofthe MUCl 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 ofthe novel protein isoforms described herein may be used to immunoprecipitate the MUCl protein variant from solution as well as react with MUCl protein isoforms on Western or immunoblots of polyacrylamide gels on membrane supports or substrates. In another prefened embodiment, the antibodies will detect MUCl 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 immunofluorescence techniques. In another embodiment, an antibody specifically immunoreactive with one of the novel

MUCl protein variants described herein is used in immunoassays to detect this variant in biological samples. In this method, an antibody ofthe present invention is contacted with a biological sample and the formation of a complex between the MUC 1 protein variant and the antibody is detected. As described, suitable immunoassays include radioimmunoassay, Western blot assay, immune-fluorescent 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 hnmunodiagnosis, 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 ofthe 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 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.USA 86;10029).

Effect(s) ofthe polymoφhisms identified herein on expression of MUCl maybe investigated by preparing recombinant cells and/or nonhuman recombinant organisms, preferably recombinant animals, containing a polymoφhic variant ofthe MUCl gene. As used herein, "expression" includes but is not limited to one or more ofthe following: transcription ofthe gene into precursor mRNA; splicing and other processing ofthe precursor mRNA to produce mature mRNA; mRNA stability; translation ofthe mature mRNA into MUCl 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 MUC 1 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 MUCl isogene is introduced into a cell in such a way that it recombines with the endogenous MUCl gene present in the cell. Such recombination requires the occunence of a double recombination event, thereby resulting in the desired MUC 1 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 ofthe skilled practitioner. Examples of cells into which the MUCl isogene may be introduced include, but are not limited to, continuous culture cells, such as COS, NIH/3T3, and primary or culture cells ofthe relevant tissue type, i.e., they express the MUCl isogene. Such recombinant cells can be used to compare the biological activities ofthe different protein variants. Recombinant nonhuman organisms, i.e., transgenic animals, expressing a variant MUCl 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 ofthe 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 ofthe 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 MUCl 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 MUCl isogene and producing the encoded human MUCl protein can be used as biological models for studying diseases related to abnormal MUCl 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 ofthe invention relates to pharmaceutical compositions for treating disorders affected by expression or function of a novel MUCl isogene described herein. The pharmaceutical composition may comprise any ofthe following active ingredients: a polynucleotide comprising one of these novel MUCl isogenes; an antisense oligonucleotide directed against one of the novel MUCl isogenes, a polynucleotide encoding such an antisense oligonucleotide, or another compound which inhibits expression of a novel MUCl 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 ofthe symptoms relating to disorders affected by expression or function of a novel MUCl 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 ofthe 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 ofthe 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 ofthe disease state, general health, age, weight and gender ofthe patient, diet, time and frequency of administration, other drugs being taken by the patient, and tolerance/response to the treatment.

Any or all analytical and mathematical operations involved in practicing the methods ofthe 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 MUCl 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 MUCl 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 ofthe invention are described in the following examples. Other embodiments within the scope ofthe claims herein will be apparent to one skilled in the art from consideration ofthe specification or practice ofthe invention as disclosed herein. It is intended that the specification, together with the examples, be considered exemplary only, with the scope and spirit ofthe invention being indicated by the claims which follow the examples.

EXAMPLES

The Examples herein are meant to exemplify the various aspects of carrying out the invention and are not intended to limit the scope ofthe 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 1 This example illustrates examination of various regions ofthe MUCl gene for polymoφhic sites.

Amplification of Target Regions

The following target regions were amplified using either the PCR primers represented below or 'tailed' PCR primers, each of which includes a universal sequence forming a noncomplementary 'tail' attached to the 5 ' end of each unique sequence in the PCR primer pairs. The universal 'tail' sequence for the forward PCR primers comprises the sequence 5 '-TGTAAAACGACGGCCAGT-3 ' (SEQ ID NO: 59) and the universal 'tail' sequence for the reverse PCR primers comprises the sequence 5 '-AGGAAACAGCTATGACCAT-3 ' (SEQ ID NO:60). The nucleotide positions ofthe first and last nucleotide ofthe forward and reverse primers for each region amplified are presented below and conespond to positions in SEQ ID NO:l (Figure 1).

PCR Primer Pairs

Fragment No. Forward Primer Reverse Primer PCR Product Fragment 1 485-505 complement of 1015-996 531 nt Fragment 2 800-822 complement of 1262-1240 463 nt Fragment 3 2056-2077 complement of 2625-2604 570 nt Fragment 4 2376-2399 complement of 2724-2705 349 nt Fragment 5 2579-2601 complement of 3047-3025 469 nt Fragment 6 2826-2848 complement of 3302-3281 477 nt Fragment 7 3019-3041 complement of 3530-3509 512 nt Fragment 8 4193-4215 complement of 4730-4710 538 nt Fragment 9 4413-4436 complement of 4988-4967 576 nt

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

Reaction volume 10 μl

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

100 ng of human genomic DNA l 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 6.6μl

Amplification profile: 97°C - 2 min. 1 cycle

97°C - 15 sec. 70°C - 45 sec. 10 cycles 72°C - 45 sec.

97°C - 15 sec. 64°C - 45 sec. 35 cycles 72°C - 45 sec.

Sequencing of PCR Products

The PCR products were purified using a Whatman/Polyfiltronics 100 μl 384 well unifilter plate essentially according to the manufacturers protocol. The purified DNA was eluted in 50 μl of distilled water. Sequencing reactions were set up using Applied Biosystems Big Dye Terminator chemistry essentially according to the manufacturers protocol. The purified PCR products were sequenced in both directions using either the primer sets represented below with the positions of their first and last nucleotide conesponding to positions in Figure 1, or the appropriate universal 'tail' sequence as a primer. Reaction products were purified by isopropanol precipitation, and run on an Applied Biosystems 3700 DNA Analyzer.

Sequencing Primer Pairs

Fragment No. Forward Primer Reverse Primer Fragment 1: Tailed Seq. Fragment 2 834-853 complement of 1221-1202 Fragment 3: Tailed Seq. Fragment 4: Tailed Seq. Fragment 5 2607-2626 complement of 3000-2981 Fragment 6 2864-2883 complement of 3258-3239 Fragment 7 3079-3099 complement of 3491-3472 Fragment 8 4253-4272 complement of 4695-4676 Fragment 9 4444-4463 complement of 4924-4905

Analysis of Sequences for Polymorphic Sites

Sequence information for a minimum of 80 humans was 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 MUCl reference genomic sequence (SEQ ID NO: 1) are listed in Table 2 below.

Table 2. Polymoφhic Sites Identified in the MUCl Gene

Polymoφhic Nucleotide Reference Variant CDS Variant AA

Site Number Polyld(a) Position Allele Allele Position Variant

PS1 22306318 718 C T

PS2 22306324 805 A T

PS3 19860821 917 G A

PS4 22305843 2511 T C

PS5 19861253 2714 C T

PS6 19861445 2797 G A 1009 V337M

PS7 19861541 3460 G A

PS8 19861826 4474 C T

PS9 19861922 . 4478 G A

PS10 19862018 4547 C T

PS11 19862305 4803 C T

(a) Polyld is a unique identifier assigned to each PS by Genaissance Pharmaceuticals, Inc.

EXAMPLE 2

This example illustrates analysis ofthe MUCl. polymoφhisms identified in the Index Repository for human genotypes and haplotypes. The different genotypes containing these polymoφhisms that were observed in unrelated members ofthe 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 were infened based on linkage disequilibrium and/or Mendelian inheritance.

Table 3(Part 1). Genotypes and Haplotype Pairs Observed for MUCl Gene

Genotype Polymoφhic Sites Number HAP Pair j PS1 PS2 PS3 PS4 PS5 PS6 PS7 PS8 PS9 PS10

1 9 9 1 C A G T C G G C G C

2 . 9 7 ^' ] C A G T C G G/A C G C

3 9 2 1 C A G/A T C G G C G C

4 9 10 i C A G T C/T G G C G C

5 9 5 1 C A G T/C C G G C G C

6 9 3 1 C A ■ G/A T C G G C G C/T

7 9 4 1 C A G/A T C G G C/T G C

8 9 12 | C/T A G T C G/A G C G C

9 9 8 1 C A G T. C G G C G/A C

10 1 9 13 j ^' C/T A G T C G G C G C

11 9 1 i C A G/A T C G G C G C

12 9 11 1 ¹ C A T G/A T C G G C G C

13 6 j C A G T C G/A G C G C

Table 3(Part 2). Genotypes and Haplotype Pairs Observed for MUCl Gene Genotype | | Polymoφhic Sites . Number | HAP Pair j PS11

1 1 9 9 1 C

2 1 9 1 C

3 9 2 1 C/T

4 1 9 10 j C

5 1 9 5 C

6 1 9 3 1 C

7 1 9 4 1 . C

8 1 9 12 j C

9 1 9 8 1 C

10 1 13 | C

11 1 ⁹ 1 i C

12 1 11 1 C

13 1 θ 1 C

The haplotype pairs shown in Table 3 were estimated from the unphased genotypes using a computer-implemented extension of Clark's algorithm (Clark, A.G. 1990 Mol Bio Evol 7, 111-122) for assigning haplotypes to unrelated individuals in a population sample, as described.in

PCT/US01/12831, filed April 18, 2001. In this method, haplotypes are assigned directly from individuals who are homozygous at all sites or heterozygous at no more than one ofthe variable sites. This list of haplotypes is then used to deconvolute the unphased genotypes in the remaining (multiply heterozygous) individuals. In the present analysis, the list of haplotypes was augmented with haplotypes obtained from two families (one three-generation Caucasian family and one two- generation African-American family).

By following this protocol, it was determined that the Index Repository examined herein and, by extension, the general population contains the 13 human MUCl haplotypes shown in Table 4 below.

An MUC 1 isogene defined by a full-haplotype shown in Table 4 below comprises the regions ofthe SEQ ID NOS indicated in Table 4, with their conesponding set of polymoφhic locations and identities, which are also set forth in Table 4.

Table 4(Part 1). Haplotypes ofthe MUCl gene.

Regions PS PS Haplotype Number(d)

Examined(a)No. (b) Position(c) 1 2 3 4 5 6 7 ^' 8 9 10

485-1262 1 718/30 C C C C C C C C C C

485-1262 2 805/150 A A A A A . A A A A A

485-1262 3 ^' 917/270 A A A A G G G G G G

2056-3530 4 2511/390 T T T T C T T T T T

2056-3530 5 2714/510 C C C C C C C C C T

2056-3530 6 2797/630 G G G G G A G G G G

2056-3530 7 3460/750 G G G G G G A G G G

4193-4988 8 4474/870 C C C T C C C C C C

4193-4988 9 4478/990 G G G G G G G A G G

4193-4988 10 4547/1110 C C T C C C C C C C

4193-4988 11 4803/1230 C T C C C C C C C C

Table 4(Part 2). Haplotypes ofthe MUCl gene.

Regions PS PS Haplotype Number(d)

Examined(a)No. (b) Position(c) 11 12 13

485-1262 1 718/30 C T T

485-1262 2 805/150 T A A

485-1262 3 917/270 A G G

2056-3530 4 2511/390 T T T

2056-3530 5 2714/510 C C C

2056-3530 6 2797/630 G A G

2056-3530 7 3460/750 . G G G

4193-4988 8 4474/870 C C C

4193-4988 9 4478/990 G G G

4193-4988 10 4547/1110 C C C

4193-4988 11 4803/1230 C C C

(a) Region examined represents the nucleotide positions defining the start and stop positions within SEQ ID NO:l ofthe regions sequenced;

(b) PS = polymoφhic site;

(c) Position of PS within the indicated SEQ ID NO, with the Imposition number referring to SEQ ID NO:l and the 2^nd position number referring to SEQ ID NO: 61, a modified version of SEQ JJD NO:l that comprises the context sequence of each polymoφhic site, PS1-PS11, to facilitate electronic searching-of the haplotypes;

(d) Alleles for MUCl haplotypes are presented 5' to 3' in each column.

SEQ ID NO:l refers to Figure 1, with the two alternative allelic variants of each polymoφhic site indicated by the appropriate nucleotide symbol. SEQ ID NO:61 is a modified version of SEQ ID NO:l that shows the context sequence of each of PS1-PS11 in a uniform format to facilitate electronic searching ofthe MUCl haplotypes. For each polymoφhic site, SEQ ID NO:61 contains a block of 60 bases ofthe nucleotide sequence encompassing the centrally-located polymoφhic site at the 30^th position, followed by 60 bases of unspecified sequence to represent that each polymoφhic site is separated by genomic sequence whose composition is defined elsewhere herein.

Table 5 below shows the percent of chromosomes characterized by a given MUCl haplotype for all unrelated individuals in the Index Repository for which haplotype data was obtained. The percent of these unrelated individuals who have a given MUCl haplotype pair is shown in Table 6. In Tables 5 and 6, the "Total" column shows this frequency data for all of these unrelated individuals, while the other columns show the frequency data for these unrelated individuals categorized according to their self-identified ethnogeographic origin. Abbreviations used in Tables 5 and 6 are AF = African Descent, AS = Asian, CA = Caucasian, HL = Hispanic-Latino, and AM = Native American. Table 5. Frequency of Observed MUC 1 Haplotypes In Unrelated Individuals

HAP No. . HAP ID Total CA AF AS HL AM

1 22466280 1.22 0.0 2.5 2.5 0.0 0.0

2 22466322 0.61 0.0. 0.0 2.5 0.0 0.0

3 22466317 0.61 0.0 2.5 0.0 0.0 0.0

4 22466308 0.61 2.38 0.0 0.0 0.0 0.0

5 22466299 0.61 2.38 0.0 0.0 0.0 0.0

6 22466271 1.83 0.0 5.0 0.0 2.78 0.0

7 ' 22466302 0.61 0.0 0.0 0.0 2.78 0.0

8 22466291 1.22 0.0 5.0, 0.0 0.0 0.0

9 22466251 ^' 88.41 95.24 75.0 90.0 91.67 100.0

10 22466286 1.22 0.0 0.0 5.0 0.0 0.0

11 22466313 0.61 0.0 2.5 0.0 0.0 0.0

12 22466283 0.61 0.0 2.5 0.0 0.0 0.0

13 22466266 1.83 0.0 5.0 0.0 2.78 0.0

Table 6. Frequency of Observed MUCl Haplotype Pairs In Unrelated

HAPl HAP2 Total CA AF AS HL AM

9 9 76.83 90.48 50.0 80.0 83.33 100.0

9 7 1.22 0.0 0.0 0.0 5.56 0.0

9 2 1.22 0.0 0.0 5.0 0.0 0.0

9 10 2.44 0.0 0.0 10.0 0.0 0.0

9 5 1.22 4.76 0.0 0.0 0.0 0.0

9 3 1.22 0.0 5.0 0.0 0.0 0.0

9 4 1.22 4.76 0.0 0.0 0.0 0.0

9 12 1.22 0.0 5.0 0.0 0.0 0.0

9 8 2.44 0.0 10.0 0.0 0.0 0.0

9 13 3.66 0.0 10.0 0.0 5.56 0.0

9 1 2.44 0.0 5.0 5.0 0.0 0.0

9 11 1.22 0.0 5.0 0.0 0.0 0.0

9 6 3.66 0.0 10.0 0.0 5.56 0.0 The size and composition ofthe Index Repository were chosen to represent the genetic diversity across and within four major population groups comprising the general United States population. For example, as described in Table 1 above, this repository contains approximately equal sample sizes of African-descent, Asian- American, European- American, and Hispanic-Latino population groups. Almost all individuals representing each group had all four grandparents with the same ethnogeographic background. The number of unrelated individuals in the Index Repository provides a sample size that is sufficient to detect SNPs and haplotypes that occur in the general population with high statistical certainty. For instance, a haplotype that occurs with a frequency of 5% in the general population has a probability higher than 99.9% of being observed in a sample of 80 individuals from the general population. Similarly, a haplotype that occurs with a frequency of 10% in a specific population group has a 99% probability of being observed in a sample of 20 individuals from that population group. In addition, the size and composition ofthe Index Repository means that the relative frequencies determined therein for the haplotypes and haplotype pairs ofthe MUCl gene are likely to be similar to the relative frequencies of these MUCl haplotypes and haplotype pairs in the general U.S. population and in the four population groups represented in the Index Repository. The genetic diversity observed for the three Native Americans is presented because it is of scientific interest, but due to the small sample size it lacks statistical significance.

In view ofthe above, it will be seen that the several advantages ofthe 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 ofthe 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 ofthe cited references.

Claims

What is Claimed is:

1. A method for haplotyping the mucin 1 , transmembrane (MUC 1 ) gene of an individual, which comprises determining which ofthe MUCl haplotypes shown in the table immediately below defines one copy ofthe individual's MUCl gene, wherein the determining step comprises identifying the phased sequence of nucleotides present at each of PS1-PS11 on at least one copy ofthe individual's MUCl gene, and wherein each ofthe MUCl haplotypes comprises a sequence of polymoφhisms whose positions and identities are set forth in the table immediately below:

PS PS Haplotype : Number(c) (Part i)

No.(a) Position(b) 1 2 3 4 5 6 7 8 9 10 1 718 C C C C C C C C C C

2 805 A A A A A A A A A A

3 917. A A A A. G G G G G G

4 2511 T T T T C T T T T T

5 2714 C C C C C C C C C T

6 2797 G G G G G A G G G G

7 3460 G G G G G G A G G G

8 4474 C C C T C C C C C C

9 4478 G G G G G G G A G G

10 4547 C C T C C C C C C C

11 4803 C T C C C C C C C C

PS PS Haplotype Number(c) (Part 2)

No.(a) ' Position(b) 11 12 13 1 718 C T T

2 805 T A A

3 917 A G G

4 2511 T T T

5 2714 C C C

6 2797 G A G

7 3460 G G G

8 4474 C C C

9 4478 G G G

10 4547 C C C

11 4803 C C C

(a) PS = polymoφhic site;

(b) Position of PS within SEQ ID NO:l;

(c) Alleles for haplotypes are presented 5 ' to 3 ' in each column.

A method for haplotyping the mucin 1, transmembrane (MUCl) gene of an individual, which comprises determining which ofthe MUCl haplotype pairs shown in the table immediately below defines both copies ofthe individual's MUCl gene, wherein the detennining step comprises identifying the phased sequence of nucleotides present at each of PS 1 -PS 11 on both copies ofthe individual's MUCl gene, and wherein each ofthe MUCl haplotype pairs consists of first and second haplotypes which comprise first and second sequences of . polymoφhisms whose positions and identities are set forth in the table immediately below:

PS . PS Haplotype Pair(c) (Part 1)

No.(a) Position(b) 9/9 9/7 9/2 9/10 9/5 9/3 9/4 9/12

1 718 C/C C/C C/C C/C C/C C/C C/C C/T

2 805 A/A A/A AA A/A A/A A/A A/A A/A

3 917 G/G G/G G/A G/G G/G G/A G/A G/G

4 2511 T/T T/T T/T T/T T/C T/T T/T T/T

5 2714 C/C C/C C/C C/T C/C C/C C/C C/C

6 2797 G/G G/G G/G G/G G/G G/G G/G . G/A

7 3460 • G/G G/A G/G G/G G/G G/G G/G G/G

8 4474 C/C C/C C/C C/C C/C C/C C/T C/C

9 4478 G/G G/G G/G G/G G/G G/G G/G G/G

10 .4547 C/C C/C C/C C/C C/C C/T C/C C/C

^■11 4803 C/C C/C C/T C/C C/C C/C C/C C/C

PS PS Haplotype Pair(c) (Part 2)

No.(a) Position(b) 9/8 9/13 9/1 9/11 9/6

1 718 C/C C/T C/C C/C C/C

2 ^' 805 A/A A/A A/A A/T ^' A/A

3 917 G/G G/G G/A G/A G/G

4 2511 T/T • T/T T/T T/T T/T

5 2714 C/C C/C C/C C/C C/C

6 2797 G/G G/G G/G G/G G/A

7 . 3460 G/G G/G G/G G/G G/G

8 4474 C/C C/C C/C C/C C/C

9 4478 G/A G/G G/G G/G G/G

10 4547 C/C C/C C/C C/C C/C

11 4803 C/C C/C C/C C/C C/C

(a) PS = polymoφhic site;

(b) Position of PS in SEQ ID NO: 1;

(c) Haplotype pairs are represented as 1^st haplotype/2^nd haplotype; with alleles of each haplotype shown 5 ' to 3 ' as 1^st polymoφhism/2^nd polymoφhism in each column.

A method for genotyping the mucin 1, transmembrane (MUCl) gene of an individual, comprising determining for the two copies ofthe MUCl gene present in the individual the identity ofthe nucleotide pair at one or more polymoφhic sites (PS) selected from the group consisting of PSl, PS2, PS3, PS4, PS5, PS6, PS7, PS8, PS9, PS10 and PSl 1, wherein the one or more polymoφhic sites (PS) have the position and alternative alleles shown in SEQ ID NO:l. The method of claim 3, wherein the determining step comprises:

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

(b) amplifying from the nucleic acid mixture a target region containing one ofthe selected polymoφhic sites;

(c) hybridizing a primer extension oligonucleotide to one allele ofthe amplified target region, wherein the oligonucleotide is designed for genotyping the selected polymoφhic site in the target region;

(d) performing a nucleic acid template-dependent, primer extension reaction on the hybridized oligonucleotide in the presence of at least one terminator ofthe reaction, wherein the terminator is complementary to one ofthe alternative nucleotides present at the selected polymoφhic site; and

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

5. The method of claim 3, which comprises determining for the two copies ofthe MUCl gene present in the individual the identity ofthe nucleotide pair at each of PS1-PS11.

6. A method for haplotyping the mucin 1 , transmembrane (MUC 1 ) gene of an individual which comprises determining, for one copy ofthe MUCl gene present in the individual, the identity ofthe nucleotide at two or more polymoφhic sites (PS) selected from the group consisting of PSl, PS2, PS3, PS4, PS5, PS6, PS7, PS8, PS9, PS10 and PSl 1, wherein the selected PS have the position and alternative alleles shown in SEQ ID NO:l.

7. The method of claim 6, wherein the determining step comprises:

(a) isolating from the individual a nucleic acid sample containing only one ofthe two copies . ofthe MUCl gene, or a fragment thereof, that is present in the individual;

(b) amplifying from the nucleic acid sample a target region containing one ofthe selected polymoφhic sites;

(c) hybridizing a primer extension oligonucleotide to one allele ofthe amplified target region, wherein the oligonucleotide is designed for haplotyping the selected polymoφhic site in the target region;

(d) performing a nucleic acid template-dependent, primer extension reaction on the hybridized oligonucleotide in the presence of at least one terminator ofthe reaction, wherein the terminator is complementary to one ofthe alternative nucleotides present at the selected polymoφhic site; and

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

8. A method for predicting a haplotype pair for the mucin 1, transmembrane (MUCl) gene of an individual comprising:

(a) identifying a MUCl genotype for the individual, wherein the genotype comprises the nucleotide pair at two or more polymoφhic sites (PS) selected from the group consisting of PSl, PS2, PS3, PS4, PS5, PS6, PS7, PS8, PS9, PS10 and PSll, wherein the selected

PS have the position and alternative alleles shown in SEQ ID NO: 1 ;

(b) comparing the genotype to the haplotype pair data set forth in the table immediately below; and

(c) determining which haplotype pair is consistent with the genotype ofthe individual and with the haplotype pair data PS PS Haplotype Pair(c) (Part 1)

No.(a) Position(b) 9/9 9/7 9/2 9/10 9/5 9/3 9/4 9/12

1 ^• 718 C/C C/C C/C C/C C/C C/C C/C C/T

2 805 A/A A/A A/A A/A A/A A/A A/A A/A

3 917 G/G G/G G/A G/G G/G G/A G/A G/G

4 2511 T/T T/T T/T T/T T/C T/T T/T T/T

5 2714 C/C C/C C/C C/T C/C C/C C/C C/C

6 2797 G/G G/G G/G G/G G/G G/G G/G G/A

7 3460 G/G G/A G/G G/G G/G G/G G/G G/G

8 4474 C/C C/C C/C C/C C/C C/C C/T C/C

9 4478 G/G G/G G/G G/G G/G G/G G/G G/G

10 4547 C/C C/C C/C C/C C/C C/T C/C ^' C/C

11 4803 C/C C/C C/T C/C C/C C/C C/C C/C

PS PS Haplotype Pair(c) (Part 2)

No.(a) Position(b) 9/8 9/13 9/1 9/11 9/6

1 718 C/C C/T C/C C/C C/C

2 805 A/A A/A A/A A/T A/A

3 917 G/G G/G G/A G/A G/G _'

4 2511 T/T T/T T/T T/T T/T

5 2714 C/C C/C C/C C/C C/C

6 2797 G/G G/G G/G G/G G/A

7 . 3460 G/G G/G G/G G/G G/G

8 4474 C/C . C/C C/C C/C C/C

9 4478 G/A G/G G/G G/G G/G

10 4547 C/C C/C C/C C/C C/C

11 4803 C/C C/C C/C C/C C/C

(a) PS = polymoφhic site;

(b) Position of PS in SEQ ID NO: 1;

(c) Haplotype pairs are represented as 1^st haplotype/2^nd haplotype; with alleles of each ' haplotype shown 5 ' to 3 ' as 1^st polymoφhism/2ⁿ polymoφhism in each column,

9. The method of claim 8, wherein the identified genotype of the individual comprises the nucleotide pair at each of PSl -PSl 1, which have the position and alternative alleles shown in SEQ ID NO:l.

10. A method for identifying an association between a trait and at least one haplotype or haplotype pair ofthe mucin 1, transmembrane (MUCl) gene which comprises comparing the frequency ofthe haplotype or haplotype pair in a population exhibiting the trait with the frequency ofthe haplotype or haplotype pair in a reference population, wherein the haplotype is selected from haplotypes 1-13 shown in the table presented, immediately below, wherein each ofthe haplotypes comprises a sequence of polymoφhisms whose positions and identities are set forth in the table immediately below:

..

PS PS Haplotype Number(c) (Part 1)

No.(a) Positionfb) 1 2 3 4 5 6 7 8 9 10

1 718 C C C C C C C C C . C

2 805 A A A A A A A A A A

3 917 A A A A G G G G G G

4 2511 T T T T C T T T T ^' T

5 2714 C C C C C C C C C T

6 2797 G G G G G A G G G G

7 3460 G G G G G G A G G G

8 4474 C C C T C C C C C C

9 4478 G G G G G G G A G G

10 4547 C C T C C C C C C C

11 4803 C T C C C C C C C C

PS PS Haplotype Number(c) (Part 2)

No.(a) Position(b) ^■ 11 12 13

1 718 C T T .

2 805 T A A

3 917 A G G

4 2511 T T T

5 2714 C C C

6 2797 G A G

7 3460 G G G

8 4474 C C C

9 4478 G G G

10 4547 C C C

11 4803 C C C

(a) PS = pdlymoφhic site;

(b) Position of PS within SEQ ID NO: 1 ;

(c) Alleles for haplotypes are presented 5 ' to 3 ' in each column; and wherein the haplotype pair is selected from the haplotype pairs shown in the table immediately below, wherein each ofthe MUCl haplotype pairs consists of first and second haplotypes which comprise first and second sequences of polymoφhisms whose positions in SEQ ID NO: 1 and identities are set forth in the table immediately below:

PS PS Haplotype Pair(c) (Part 1)

No.(a) Position(b) 9/9 9/7 9/2 9/10 9/5 9/3 9/4 9/12

1 718 C/C C/C C/C C/C C/C C/C C/C C/T

2 805 A/A A/A A/A A/A A/A A/A A/A A/A

3 917 G/G G/G G/A G/G G/G G/A G/A G/G

4 2511 T/T T/T T/T T/T T/C T/T T/T T/T

5 2714 C/C C/C C/C C/T C/C C/C C/C C/C

6 2797 G/G G/G G/G G/G G/G G/G G/G G/A

7 3460 G/G G/A G/G G/G G/G G/G G/G G/G

8 4474 C/C C/C C/C C/C C/C C/C C/T C/C

9 4478 G/G G/G G/G G/G G/G G/G G/G G/G

10 4547 C/C C/C C/C C/C C/C C/T C/C C/C

11 4803 C/C. C/C C/T C/C C/C C/C C/C C/C PS PS Haplotype Pair(c) (Part i) No.(a) Position(b) 9/8 9/13 9/1 9/11 9/6

1 718 C/C C/T C/C C/C C/C

2 805 A/A , A/A A/A AT A/A

3 917 G/G G/G G/A G/A G/G

4 2511 T/T T/T T/T T/T T/T

5 < 2714 C/C C/C C/C^' C/C C/C

6 2797 G/G G/G G/G G/G G/A

7 3460 G/G G/G G/G G/G G/G

8 4474 C/C C/C C/C C/C C/C

9 4478 G/A G/G G/G G/G G/G

10 4547 C/C C/C C/C C/C C/C

11 4803 C/C C/C ^'C/C C/C C/C

(a) PS = polymoφhic site;

(b) Position of PS in SEQ ID NO:l; (c) Haplotype pairs are represented as 1^st haplotype/2^nd haplotype; with alleles of each haplotype shown 5' to 3' as 1^st polymoφhism 2^nd polymoφhism in each column;

wherein a higher frequency ofthe haplotype or haplotype pair in the trait population than in the reference population indicates the trait is associated with the haplotype or haplotype pair.

11. The method of claim 10, wherein the trait is a clinical response to a drug targeting MUC 1 or to a drug for treating a condition or disease associated with MUC 1 activity.

12. An isolated oligonucleotide designed for detecting a polymoφhism in the mucin 1 , transmembrane (MUCl) gene at a polymoφhic site (PS) selected from the group consisting of PSl, PS2, PS3, PS4, PS5, PS6, PS7, PS8, PS9, PS10 and PSl 1, wherein the selected PS have the position and alternative alleles shown in SEQ ID NO: 1.

13. The isolated ohgonucleotide of claim 12, which is an allele-specific oligonucleotide that specifically hybridizes to an allele ofthe MUCl gene at a region containing the polymoφhic site.

14. The allele-specific oligonucleotide of claim 13, which comprises a nucleotide sequence selected from the group consisting of SEQ ID NOS:4-14, the complements of SEQ ID NOS:4- 14, and SEQ ID NOS: 15-36.

15. The isolated oligonucleotide of claim 12, which is a primer-extension oligonucleotide.

16. The primer-extension oligonucleotide of claim 15,whιch comprises a nucleotide sequence selected from the group consisting of SEQ ID NOS:37-58.

17. A kit for haplotyping or genotyping the mucin 1, transmembrane (MUCl) gene of an individual, which comprises a set of oligonucleotides designed to haplotype or genotype each of polymoφhic sites (PS) PSl, PS2, PS3, PS4, PS5, PS6, PS7, PS8, PS9, PS10 and PSl 1, wherein the selected PS have the position and alternative alleles shown in SEQ ID NO:l.

18. An isolated polynucleotide comprising a nucleotide sequence selected from the group consisting of: (a) a first nucleotide sequence which comprises a mucin 1, transmembrane (MUCl) isogene, wherein the MUCl isogene is selected from the group consisting of isogenes 1-8 and 10- 13 shown in the table immediately below and wherein each ofthe isogenes comprises the regions of SEQ ID NO: 1 shown in the table immediately below and wherein each ofthe isogenes 1-8 and 10-13 is further defined by the conesponding sequence of polymoφhisms whose positions and identities are set forth in the table immediately below; and

Region PS PS Isogene Number(d) (Part 1)

Examined(a ) No.(b) Position(c) 1 2 3 4 5 6 7 8 10

485-1262 1 718 C C C C C C C C C

485-1262 2 805 A A A A A A A A A

485-1262 3 917 A A A A G G G G G

2056-3530 4 2511 T T T T C T T T T

2056-3530 5 2714 C C C C C C C C T

2056-3530 6 2797 G G G G G A G G G

2056-3530 7 3460 G G G G G G A G G

4193-4988 8 4474 C C C T C C C C C

4193-4988 9 4478 G G G G G G G A G

4193-4988 10 4547. C C T C C C C C C

4193-4988 11 4803 C T C C C C C C C

Region PS PS Isogene Number(d) (Part 2)

Examined(a) No.fb) Position(c) 11 12 13

485-1262 1 718 C T T

485-1262 2 805 T A A

485-1262 ' 3 917 A • G G

2056-3530 4 2511 T T T

2056-3530 5 2714 C C C

2056-3530 6 2797 G A G

2056-3530 7 3460 G G G

4193-4988 8 4474 C C C

4193-4988 9 4478 G G G

4193-4988 10 4547 C C C

4193-4988 11 4803 C C C

(a) Region examined represents the nucleotide positions defining the start and stop positions within the 1^st SEQ ID NO ofthe sequenced region.

(b) PS = polymoφhic site;

(c) Position of PS in SEQ ID NO:l;

(d) Alleles for isogenes are presented 5' to 3' in each column;

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

19. The isolated polynucleotide of claim 18, 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.

20. A recombinant nonhuman organism transformed or transfected with the isolated polynucleotide of claim 19, wherein the organism expresses a MUCl protein that is encoded by the first nucleotide sequence.

21. The recombinant nonhuman organism of claim 20, which is a transgenic animal.

22. An isolated fragment of a mucin 1 , transmembrane (MUC 1) isogene, wherein the fragment comprises at least 10 nucleotides in one ofthe regions of SEQ ID NO: 1 shown in the table immediately below and wherein the fragment comprises one or more polymoφhisms selected from the group consisting of thymine at PSl, thymine at PS2, adenine at PS3, cytosine at PS4, thymine at PS5, adenine at PS6, adenine at PS7, thymine at PS8, adenine at PS9, thymine at PS 10 and thymine at PS 11 , wherein the selected polymoφhism has the position set forth in the table immediately below:

Region PS PS Isc )gene IS mmbei :(d) (P; art l)

Examined(a) No.(b) Position(c) 1 2 3 4 5 6 7 8 10

485-1262 1 718 C C C C C C C C C

485-1262 2 805 A A A A A A A A A

485-1262 3 917 A A A A G G G G G

2056-3530 4 2511 T T T T C T T T T

2056-3530 5 2714 C C C C C C C C T

2056-3530 6 2797 G G G G G A G G G

2056-3530 7 3460 G G G G G G A G G

4193-4988 8 4474 C C C T C C C C C

4193-4988 9 4478 G G G G G G G A G

4193-4988 10 4547 C C T C C C C C C

4193-4988 11 4803 C T C C C C C C C

Region PS - PS Isogene Number(d) (Part 2)

Examined(a) No.(b) Position(c) 11 12 13

485-1262 1 718 C T T

485-1262 2 805 T A A

485-1262 3 917 A G G

2056-3530 4 2511 T T T

2056-3530 5 ^' 2714 C C C

2056-3530 6 2797 G A G

2056-3530 7 3460 G G G

4193-4988 8 4474 C C C

4193-4988 9 4478 G G G

4193-4988 10 4547 C C C

4193-4988 11 4803 C C C

(a) Region examined represents the nucleotide positions defining the start and stop positions within SEQ ID NO:l ofthe regions sequenced;

(b) PS = polymoφhic site;

(c) Position of PS within SEQ ID NO: 1 ;

(d) Alleles for MUCl isogenes are presented 5' to 3' in each column.

23. An isolated polynucleotide comprising a MUCl coding sequence, wherein the coding sequence is selected from the group consisting of 6 and 12 shown in the table immediately below, and wherein each ofthe coding sequences comprises the regions of SEQ ID NO:2 that are defined by exons 1-7, except at each ofthe polymoφhic sites which have the positions in SEQ ID NO:2 and polymoφhisms set forth in the table immediately below: PS PS Isogene Coding Sequence Number(c)

No.(a) Position(b) 6c 12c

6 1009 A A

(a) PS = polymoφhic site;

(b) Position of PS in SEQ ID NO:2;

(c) Alleles for the isogene coding sequence are presented 5' to 3' in each column; the numerical portion ofthe isogene coding sequence number represents the number ofthe parent full MUCl isogene.

24. A recombinant nonhuman organism transformed or transfected with the isolated polynucleotide of claim 23, wherein the organism expresses a mucin 1, transmembrane (MUCl) protein that is encoded by the polymoφhic variant sequence.

25. The recombinant nonhuman organism of claim 24, which is a transgenic animal.

26. An isolated fragment of a MUC 1 cDNA, wherein the fragment comprises adenine at a position conesponding to nucleotide 1009 in SEQ ID NO:2.

27 An isolated polypeptide comprising an amino acid sequence which is a polymoφhic variant of a reference sequence for the mucin 1, transmembrane (MUCl) protein, wherein the reference sequence comprises SEQ ID NO:3 for the regions encoded by exons 1-7, except the polymoφhic variant comprises methionine at a position conesponding to amino acid position 337.

28. An isolated monoclonal antibody specific for and immunoreactive with the isolated polypeptide of claim 27.

29. A method for screening for drugs targeting the isolated polypeptide of claim 27 which comprises contacting the MUCl polymoφhic variant with a candidate agent and assaying for binding activity.

30. An isolated fragment ofthe MUCl polypeptide, wherein the fragment comprises methionine at a position conesponding to amino acid position 337 in SEQ ED NO:3.

31 A computer system for storing and analyzing polymoφhism data for the mucin 1 , transmembrane 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 any one or more ofthe haplotypes set forth in the table immediately below: PS PS Haplotype Number(c) (Part 1)

No.(a) Positionfb) 1 2 3 4 5 6 7 8 9 10 1 718 C C C C C C C C C C

2 805 A A A A A A A A A A

3 917 A A A A G G G G G G

4 2511 T T T T C T T T T T

5 . 2714 C C C C C C C C C T

6 2797 G G G G G A G G G G

7 3460 G G G G G G A G G G

8 4474 C C C T C C C C C C

9 4478 G G G G G G G . A G G

10 4547 C C T C C C C C C C

11 4803 C T C C C C C C C C

PS PS Haplotype Number(c) (Part 2)

No.(a) Position(b) 11 12 13

1 718 C T T

2 805 T A A

3 917 A G . G

4 2511 T T T

5 2714 C C C

6 2797 G A G ,

7 . 3460 G G G

8 4474 C C C

9 4478 G G G

10 4547 C C C

11 4803 C C C

(a) PS = polymoφhic site;

(b) Position of PS within SEQ ID NO:l;

(c) Alleles for haplotypes are presented 5 ' to 3 ' in each column; the haplotype pahs set forth in the table immediately below:

PS PS Haplotype ] Pair(c) (Part 1)

No.(a) Position(b) 9/9 9/7 9/2 9/10 9/5 9/3 9/4 9/12

1 718 C/C C/C C/C C/C C/C C/C C/C C/T

2 805 A/A A/A A/A A/A A/A A/A A/A A/A

3 917 G/G- G/G G/A G/G G/G G/A G/A G/G

4 2511 T/T T/T T/T T/C T/T T/T T/T

5 2714 C/C C/C C/C ^• C/T C/C C/C C/C C/C

6 2797 G/G G/G G/G G/G G/G G/G G/G G/A

7 3460 G/G G/A G/G G/G G/G G/G G/G G/G

8 4474 C/C C/C C/C ^■ C/C C/C C/C C/T C/C

9 4478 G/G G/G G/G G/G G/G G/G G/G G/G

10 4547 C/C C/C C/C C/C C/C C/T C/C C/C

11 4803 C/C C/C C/T . C/C C/C C/C C/C C/C PS PS Haplotype Pair(c) (Part 2)

No.(a) Position(b) 9/8 9/13 9/1 9/11 9/6

1 718 C/C C/T C/C- C/C C/C

2 805 . A/A A/A A/A A/T A/A

3 917 G/G G/G G/A G/A G/G

4 2511 T/T T/T T/T T/T T/T

5 2714 C/C C/C C/C C/C C/C

6 2797 G/G G/G G/G G/G G/A

7 3460 G/G G/G G/G G/G G/G

8 4474 c/c - C/C C/C C/C C/C

9 4478 G/A G/G G/G G/G G/G

10 4547 C/C C/C C/C C/C C/C

11 4803 C/C C/C C/C C/C C/C

(a) PS = polymoφhic site;

(b) Position of PS in SEQ ID NO:l; (c) Haplotype pairs are represented as 1 ^st haplotype/2^nd haplotype; with alleles of each haplotype shown 5 ' to 3 ' as 1^st polymoφhism/2^nd polymoφhism in each column;

and the frequency data in Tables 5 and 6. 32. A genome anthology for the mucin 1, transmembrane (MUCl) gene which comprises two or more MUCl isogenes selected from the group consisting of isogenes 1-13 shown in the table immediately below, and wherein each ofthe isogenes comprises the regions of SEQ ID NO: 1 shown in the table immediately below and wherein each ofthe isogenes 1-13 is further defined by the conesponding sequence of polymoφhisms whose positions and identities are set forth in the table immediately below:

Region PS PS Isogene Number(d) (Part 1)

Examined(a) No.(b) Position(c) 1 2 3 4 5 6 7 8 9 10

485-1262 1 718 C C C C C C C C C C

485-1262 2 805 A A A A A A A A A A

485-1262 3 917 A A A A G G G G G G

2056-3530 . 4 2511 T T T T C T T T T T

2056-3530 ' 5 2714 C C C C C C C C C T

2056-3530 6 2797 G G G G G A G G G G

2056-3530 7 3460 G G G G G G A G G G

4193-4988 8 4474 C C C T C C C C C C

4193-4988 . 9 4478 G G G G G G G A ^' G G

4193-4988 10 4547 C C T C C C C C C C

4193-4988 11 4803 C T C C C C C C C C Region PS PS Isogene IN Jumt

Examined(a) No.(b) Position(c) 11 12 13

485-1262 1 718 C T T

25 485-1262 2 805 T A A

485-1262 3 917 A G G

2056-3530 4 2511 T T T

2056-3530 5 2714 C C C

2056-3530 6 2797 G A G

30 2056-3530 7 3460 G G G

4193-4988 8 4474 C C C

4193-4988 9 4478 G G G

4193-4988 10 4547 C C C

4193-4988 11 4803 C C C

35

(a) Region examined represents the nucleotide positions defining the start and stop positions within SEQ JD NO:l ofthe regions sequenced;

(b) PS = polymoφhic site;

40. (c) Position of PS within SEQ ID NO: 1;

(d) Alleles for MUCl isogenes are presented 5' to 3' in each column.