WO2002038589A2

WO2002038589A2 - Haplotypes of the cyp2d6 gene

Info

Publication number: WO2002038589A2
Application number: PCT/US2001/047396
Authority: WO
Inventors: Alison E. Anastasio; Anne Chew; Julie Y. Choi; R. Rex Denton; Krishnan Nandabalan; Nathan Petersen; Eileen Rounds
Original assignee: Genaissance Pharmaceuticals, Inc.
Priority date: 2000-11-09
Filing date: 2001-11-09
Publication date: 2002-05-16
Also published as: AU2002227318A1; WO2002038589A3

Abstract

Novel genetic variants of the Cytochrome P450, Subfamily IID, Polypeptide 6 (CYP2D6) gene are described. Various genotypes, haplotypes, and haplotype pairs that exist in the general United States population are disclosed for the CYP2D6 gene. Compositions and methods for haplotyping and/or genotyping the CYP2D6 gene in an individual are also disclosed. Polynucleotides defined by the haplotypes disclosed herein are also described

Description

HAPLOTYPES OF THE CYP2D6 GENE

RELATED APPLICATIONS

This application claims the benefit of U.S. Provisional Application Serial No. 60/247,943 filed November 9, 2000.

FIELD OF THE INVENTION

This invention relates to variation in genes that encode pharmaceutically-important proteins. In particular, this invention provides genetic variants ofthe human Cytochrome P450, subfamily IID, Polypeptide 6 (CYP2D6) 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 absoφtion, 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 drag. 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 in the 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 ofthe 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; Kwok 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 J Respir Crit Care Med 161: 469-74) and drug response (Wolfe CR et al. 2000 BMJ 320:987-90; 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 RNJS 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 hypertension, atrial and ventricular arrhythmias, Parkinson's disease and drug-induced lupus syndrome is the Cytochrome P450, subfamily IID, Polypeptide 6 (CYP2D6) gene or its encoded product. CYP2D6 is an enzyme that belongs to the cytochrome P450 family, whose members are responsible for the detoxification of many drugs and environmental chemicals. CYP2D6 is involved in the metabolism of drugs such as antiarythmics, adrenoceptor antagonists and trycyclic antidepressants (SWISS-PROT:P 10635).

CYP2D6 was originally identified as the primary enzyme responsible for the hydroxylation of ' the hypertension drug, debrisoquine to its metabolite, 4-hydroxydebrisoquine. Clinically, patients exhibit wide variation in hypotensive response to treatment with debrisoquine, which has been attributed to polymorphisms in the CYP2D6 gene that alter the enzymes ability to metaboloize, ie, hydroxylate, this drag (Mahgoub et al., 1977, Lancet 2: 584-586). Clinically significant inherited variations of CYP2D6-mediated drag metabolism are characterized by two phenotypes: the extensive metabolizer (EM) and the poor metabolizer (PM). 5-10% of individuals in Caucasian populations are ^• ofthe PM phenotype and have deficient metabolism of debrisoquine and over 25 other drags (Kagimoto et si., J Biol Chem 1990 Oct 5;265(28): 17209-14). Lennard et al. (N. Engl. J Med 1982; 307:1558-1560) demonstrated that metabolism of metoprolol, a beta- 1 -selective adrenoceptor antagonist used for the treatment of angina, may be affected by CYP2D6 polymorphisms. In poor hydroxylators, a single daily dose of metoprolol may control angina, whereas in 'extensive hydroxylators,' 2 or 3 doses a day may be necessary, since plasma metoprolol concentrations may remain negligible 24 hours after dosing.

The antiarrhythmic agent propafenone, also metabolized by CYP2D6, is effective in the management of atrial and ventricular arrhythmias and has been shown to have variable efficacy as a beta-blocker (Lennard et al., 1983, Pharm. Int. 4: 61-65). Lee et al. (N. Engl. JMed 1990; 322:1764- 1768) presented evidence that genetically determined variations in the conversion of propafenone to its 5-hydroxy metabolite accounts for variations in the drag's beta-blocking action. Slow metabolizers showed greater beta-blockade than rapid metabolizers did at a lower drag dosage, with comparable responses seen with the higher doses.

The pathogenesis of Parkinson's disease may be influenced by genetic and environmental factors. Cytochrome P450 mono-oxygenases, such as CYP2D6, help to protect against toxic environmental compounds and individual variations in cytochrome P450 expression might, therefore, influence susceptibility to environmentally linked diseases (Smith et al., Lancet 1992; 339:1375- 1377). Studies show that significantly more parkinsonian than control subjects had partially or totally defective 4-hydroxylation of debrisoquine due to polymorphisms in the CYP2D6 (Barbeau et al., Lancet 1985; 2:1213-1216). The authors indicate that poor metabolizers of debrisoquine tended to have had earlier onset of disease.

CYP2D6 is also the major isozyme involved in the formation of Ν-hydroxyprocainamide, a metabolite potentially involved in the drug-induced lupus syndrome observed with procainamide (Lessard et al., Pharmacogenetics 1997; 7:381-390). The occurrence of lupus-like syndrome in a significant number of patients treated with procainamide has limited the clinical use of this antiarrhythmic drag. Further studies may show that a low CYP2D6 activity, either genetically determined or pharmacologically modulated, could prevent drag-induced lupus syndrome observed during chronic therapy with procainamide (Lessard et al., Pharmacogenetics 1999; 9:683-696). The Cytochrome P450, subfamily IID, Polypeptide 6 gene is located on chromosome 22ql3J and contains 9 exons that encode a 497 amino acid protein. A reference sequence for the CYP2D6 gene is shown in the contiguous lines of Figure 1 (Genaissance Reference No. 3578126; SEQ ID NO: 1). Reference sequences for the coding sequence (GenBank Accession No. NM_0001Q6.2) and protein are shown in Figures 2 (SEQ ID NO: 2) and 3 (SEQ ID NO: 3), respectively.

Thirteen polymorphisms have been reported in the CYP2D6 gene which are refered to herein as PS5, PS7, PS8, PS9, PS11, PS13, PS21, PS25, PS30, PS31, PS33, PS35, and PS41.

A polymorphism of guanine or adenine (PS5) at a position corresponding to nucleotide position 825 in Figure 1 has been reported in the NCBI SNP Database (rs# 1080993). A polymorphism of guanine or adenine (PS7) at a position corresponding to nucleotide position 1019 in Figure 1 which resutlts in the amino acid varaition of a valine or methionine at amino acid postion 7 in Figure 3 has been reported in the literature (Marez et al., Pharmacogenetics 1997; 7:193-202). A polymorphism of guanine or adenine (PS8) at a position corresponding to nucleotide position 1031 in Figure 1 that results in an amino acid variation of valine or methionine at a position corresponding to amino acid 11 has been identified (SWISS-PROT: P10635).

Kagimoto et al., (supra) identified a polymorphism of cytosine or thymine (PS9) at a position corresponding to nucleotide 1100 in Figure 1, which results in a variation of proline or serine at a position corresponding to amino acid 34 in Figure 3. A polymorphism of thymine or guanine (PSI 1) at a position corresponding to nucleotide position 1843 in Figure 1 has been reported in the NCBI SNP Database (rs# 769261). A polymorphism of a cytosine or adenine (PS13) and a polymorphism of an adenine or guanine (PS14) at nucleotide positions 1974 and 1984, respectively in Figure 1 have been reported in the literature (Marez et al., supra). These polymorphisms result in amino acid variations of leucine or methionine and histidine or arginine at amino acid positions 91 and 94, respectively in Figure 3.

A polymorphism of cytosine or thymine (PS21) at a position corresponding to nucleotide position 2039 in Figure 1 (NCBI SNP Database rs# 1081003) and a polymorphism of guanine or adenine (PS25) at a position corresponding to nucleotide position 2170 in Figure 1 (NCBI SNP Databse rs# 1081004) have been reported. A polymorphism of guanine ar cytosine at a position corresponding to nucleotide position 2661 in Figure 1 (PS30) has been reported in the NCBI SNP Database (rs# 1058164). This polymorphism results in a valine or isoleucine at a position corresponding to amino acid position 136 in Figure 3.

A polymorphism of cytosine or guanine (PS31) at a position corresponding to nucleotide position 2704 in Figure 1 has been reported in literature. This polymorphism results in the amin acid variation of of a glutamine or glutamate at amino acid position 151 in Figure 3 (Marez et al., supra). A polymorphisms of a guanine or adenine (PS33) at a position corresponding to nucleotide position 2846 in Figure has been reproted in the literature (Kagimoto et al., supra ).

A polymorphism of a thymine or cytosine (PS35) at a position corresponding to nucleotide position 3470 in Figure 1 has been reported in the NCBI SNP Database (rs# 1058169). A polymorphism of guanine or cytosine (PS41) at a position corresponding to nucleotide position 5180 in Figure 1, which causes an amino acid variation of serine or threonine at a position corresponding to amino acid 486 in Figure 3, was reported by (Yokota et al., Pharmacogenetics 1993; 3:256-263).

Because ofthe potential for variation in the CYP2D6 gene to affect the expression and function ofthe encoded protein, it would be useful to know whether additional polymorphisms exist in the CYP2D6 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 CYP2D6 as well as in identifying drags 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 29 novel polymorphic sites in the CYP2D6 gene. These polymorphic sites (PS) correspond to the following nucleotide positions in Figure 1: 636 (PSI), 678 (PS2), 769 (PS3), 776 (PS4), 915 (PS6), 1827 (PS10), 1966 (PS12), 1984 (PS14), 1997 (PS15), 2014 (PS16), 2022 (PS17), 2023 (PS18), 2028 (PS19), 2036 (PS20), 2062 (PS22), 2067 (PS23), 2118 (PS24), 2179 (PS26), 2611 (PS27), 2635 (PS28), 2659 (PS29), 2716 (PS32), 3292 (PS34), 4183 (PS36), 4201 (PS37), 4254 (PS38), 4384 (PS39), 4435 (PS40) and 5212 (PS42). The polymorphisms at these sites are guanine or adenine at PSI, thymine or cytosine at PS2, guanine or cytosine at PS3, adenine or guanine at PS4, thymine or cytosine at PS6, guanine or cytosine at PS 10, guanine or adenine at PS12, adenine or guanine at PSM, cytosine or guanine at PS15, thymine or cytosine at PS 16, adenine or thymine at PS 17, cytosine or thymine at PS 18, adenine or guanine at PS 19, thymine or cytosine at PS20, adenine or guanine at PS22, thymine or guanine at PS23, cytosine or thymine at PS24, guanine or cytosine at PS26, thymine or adenine at PS27, thymine or cytosine at PS28, guanine or adenine at PS29, guanine or adenine at PS32, guanine or adenine at PS34, guanine or adenine at PS36, cytosine or thymine at PS37, thymine or cytosine at PS38, adenine or cytosine at PS39, cytosine or adenine at PS40 and cytosine or thymine at PS42. In addition, the inventors have determined the identity ofthe alleles at these sites, as well as at the previously identified sites at nucleotide positions 825 (PS5), 1019 (PS7), 1031 (PS8), 1100 (PS9), 1843 (PS11), 1974 (PS13), 2039 (PS21), 2170 (PS25), 2661 (PS30), 2704 (PS31), 2846 (PS33), 3470 (PS35) and 5180 (PS41), 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-PS42 in the CYP2D6 gene, which are shown below in Tables 4 and 3, respectively. Each of these CYP2D6 haplotypes constitutes a code that defines the variant nucleotides that exist in the human population at this set of polymorphic sites in the CYP2D6 gene. Thus each CYP2D6 haplotype also represents a naturally-occurring isoform (also referred to herein as an "isogene") ofthe CYP2D6 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 CYP2D6 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 PSI, PS2, PS3, PS4, PS6, PS10, PS12, PSM, PS15, PS16- PS17, PS18, PS19, PS20, PS22, PS23, PS24, PS26, PS27, PS28, PS29, PS32, PS34, PS36, PS37, PS38, PS39, PS40 and PS42 in both copies ofthe CYP2D6 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 CYP2D6 polymorphic sites. A genotyping kit ofthe invention comprises a set of oligonucleotides designed to genotype each of these novel CYP2D6 polymorphic sites. In a preferred embodiment, the genotyping kit comprises a set of oligonucleotides designed to genotype each of PS1-PS42. The genotyping method, composition, and kit are useful in determining whether an individual has one ofthe haplotypes in Table 4 below or has one ofthe haplotype pairs in Table 3 below.

The invention also provides a method for haplotyping the CYP2D6 gene in an individual. In one embodiment, the haplotyping method comprises determining, for one copy ofthe CYP2D6 gene, the identity ofthe nucleotide at one or more polymorphic sites selected from the group consisting of PSI, PS2, PS3, PS4, PS6, PS10, PS12, PS14, PS15, PS16, PS17, PS18, PS19, PS20, PS22, PS23, PS24, PS26, PS27, PS28, PS29, PS32, PS34, PS36, PS37, PS38, PS39, PS40 and PS42. In another embodiment, the haplotyping method comprises determining whether one copy ofthe individual's CYP2D6 gene is defined by one ofthe CYP2D6 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 CYP2D6 gene are defined by one ofthe CYP2D6 haplotype pairs shown in Table 3 below, or a sub-haplotype pair thereof. Establishing the CYP2D6 haplotype or haplotype pair ofan individual is useful for improving the efficiency and reliability of several steps in the discovery and development of drags for treating diseases associated with CYP2D6 activity, e.g., hypertension, atrial and ventricular arrhythmias Parkinson's disease and drug-induced lupus syndrome.

For example, the haplotyping method can be used by the pharmaceutical research scientist to validate CYP2D6 as a candidate target for treating a specific condition or disease predicted to be associated with CYP2D6 activity. Determining for a particular population the frequency of one or more ofthe individual CYP2D6 haplotypes or haplotype pairs described herein will facilitate a decision on whether to pursue CYP2D6 as a target for treating the specific disease of interest. In particular, if variable CYP2D6 activity is associated with the disease, then one or more CYP2D6 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 CYP2D6 haplotypes are of similar frequencies in the disease and control groups, then it may be inferred that variable CYP2D6 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 CYP2D6 haplotype or haplotype pair, apply the information derived from detecting CYP2D6 haplotypes in an individual to decide whether modulating CYP2D6 activity would be useful in treating the disease.

The claimed invention is also useful in screening for compounds targeting CYP2D6 to treat a specific condition or disease predicted to be associated with CYP2D6 activity. For example, detecting which of the CYP2D6 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 CYP2D6 isoforms present in the disease population, or for only the most frequent CYP2D6 isoforms present in the disease population. Thus, without requiring any a priori knowledge ofthe phenotypic effect of any particular CYP2D6 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 CYP2D6 gene in an individual is also useful to control for genetically-based bias in the design of candidate drugs that target or are metabolized by CYP2D6. For example, for a lead compound that is metabolized by CYP2D6, the pharmaceutical scientist of ordinary skill would be concerned that a favorable efficacy and/or side effect profile shown in a Phase II or Phase III trial may not be replicated in the general population if a higher (or lower) percentage of patients in the treatment group, compared to the general population, have a form ofthe CYP2D6 gene that makes them genetically predisposed to metabolize the drag more efficiently than patients with other forms of the CYP2D6 gene. Similarly, this pharmaceutical scientist would recognize the potential for bias in the results of a Phase II or Phase III clinical trial of a drag targeting CYP2D6 that could be introduced if individuals whose CYP2D6 gene structure makes them genetically predisposed to respond well to the drag are present in a higher (or lower) frequency in the treatment group than in the control group (Bacanu et al., 2000, Am. J. Hum. Gen. 66J933-44; Pritchard et al., 2000, Am. J. Hum. Gen. 67: 170- 81).

The pharmaceutical scientist can immediately reduce this potential for genetically-base bias in the results of clinical trials of drugs metabolized by or targeting CYP2D6 by practicing the claimed invention. In particular, by determining which ofthe CYP2D6 haplotypes disclosed herein are present in individuals recruited to participate in a clinical trial of a drug metabolized by or targeting CYP2D6, the pharmaceutical scientist can then assign that individual to the treatment or control group as appropriate to ensure that approximately equal frequencies of different CYP2D6 haplotypes (or haplotype pairs) are represented in the two groups and/or the frequencies of different CYP2D6 haplotypes or haplotype pairs are similar to the frequencies in the general population. Thus, by practicing the claimed invention, the pharmaceutical scientist can more confidently rely on the information learned from the trial, without first determining the phenotypic effect of any CYP2D6 haplotype or haplotype pair.

In another embodiment, the invention provides a method for identifying an association between a trait and a CYP2D6 genotype, haplotype, or haplotype pair for one or more ofthe novel polymoφhic sites described herein. The method comprises comparing the frequency ofthe CYP2D6 genotype, haplotype, or haplotype pair in a population exhibiting the trait with the frequency ofthe CYP2D6 genotype or haplotype in a reference population. A higher frequency ofthe CYP2D6 genotype, haplotype, or haplotype pair in the trait population than in the reference population indicates the trait is associated with the CYP2D6 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 CYP2D6 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 hypertension, atrial and ventricular arrhythmias, Parkinson's disease and drug-induced lupus syndrome.

In yet another embodiment, the invention provides an isolated polynucleotide comprising a nucleotide sequence which is a polymoφhic variant of a reference sequence for the CYP2D6 gene or a fragment thereof. The reference sequence comprises the contiguous sequences shown in Figure 1 and the polymoφhic variant comprises at least one polymoφhism selected from the group consisting of adenine at PSI, cytosine at PS2, cytosine at PS3, guanine at PS4, cytosine at PS6, cytosine at PS 10, adenine at PS12, guanine at PS14, guanine at PS15, cytosine at PS16, thymine at PS17, thymine at PS18, guanine at PS19, cytosine at PS20, guanine at PS22, guanine at PS23, thymine at PS24, cytosine at PS26, adenine at PS27, cytosine at PS28, adenine at PS29, adenine at PS32, adenine at PS34, adenine at PS36, thymine at PS37, cytosine at PS38, cytosine at PS39, adenine at PS40 and thymine at PS42. In a preferred embodiment, the polymoφhic variant comprises one or more additional polymoφhisms selected from the group consisting of adenine at PS5, adenine at PS7, adenine at PS8, thymine at PS9, guanine at PSI 1, adenine at PS13, thymine at PS21, adenine at PS25, cytosine at PS30, guanine at PS31, adenine at PS33, cytosine at PS35 and cytosine at PS41.

A particularly preferred polymoφhic variant is an isogene ofthe CYP2D6 gene. A CYP2D6 isogene ofthe invention comprises guanine or adenine at PSI, thymine or cytosine at PS2, guanine or cytosine at PS3, adenine or guanine at PS4, guanine or adenine at PS5, thymine or cytosine at PS6, guanine or adenine at PS7, guanine or adenine at PS8, cytosine or thymine at PS9, guanine. The invention also provides a collection of CYP2D6 isogenes, referred to herein as a CYP2D6 genome anthology.

In another embodiment, the invention provides a polynucleotide comprising a polymoφhic variant of a reference sequence for a CYP2D6 cDNA or a fragment thereof. The reference sequence comprises SEQ ID NO:2 (Fig.2) and the polymoφhic cDNA comprises at least one polymoφhism selected from the group consisting of adenine at a position corresponding to nucleotide 263, guanine at a position corresponding to nucleotide 281, guanine at a position corresponding to nucleotide 294, cytosine at a position corresponding to nucleotide 311, thymine at a position corresponding to nucleotide 319, thymine at a position corresponding to nucleotide 320, guanine at a position corresponding to nucleotide 325, cytosine at a position corresponding to nucleotide 333, adenine at a position corresponding to nucleotide 358, cytosine at a position corresponding to nucleotide 382, adenine at a position corresponding to nucleotide 406, adenine at a position corresponding to ^• nucleotide 463, adenine at a position corresponding to nucleotide 1012, thymine at a position corresponding to nucleotide 1030, cytosine at a position corresponding to nucleotide 1083 and thymine at a position corresponding to nucleotide 1489. In a preferred embodiment, the polymoφhic variant comprises one or more additional polymoφhisms selected from the group consisting of adenine at a position corresponding to nucleotide 19, adenine at a position corresponding to nucleotide 31, thymine at a position corresponding to nucleotide 100, adenine at a position corresponding to nucleotide 271, thymine at a position corresponding to nucleotide 336, cytosine at a position corresponding to nucleotide 408, guanine at a position corresponding to nucleotide 451, cytosine at a position corresponding to nucleotide 696 and cytosine at a position corresponding to nucleotide 1457. A particularly preferred polymoφhic cDNA variant comprises the coding sequence of a CYP2D6 isogene defined by haplotypes 1-10, 13-16, 18, 19, 21, 22, and 24-34.

Polynucleotides complementary to these CYP2D6 genomic and cDNA variants are also provided by the invention. It is believed that polymoφhic variants ofthe CYP2D6 gene will be useful in studying the expression and function of CYP2D6, and in expressing CYP2D6 protein for use in screening for candidate drags to treat diseases related to CYP2D6 activity.

In other embodiments, the invention provides a recombinant expression vector comprising one ofthe polymoφhic 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 CYP2D6 for protein structure analysis and drag binding studies.

In yet another embodiment, the invention provides a polypeptide comprising a polymoφhic variant of a reference amino acid sequence for the CYP2D6 protein. The reference amino acid sequence comprises SEQ ID NO:3 (Fig.3) and the polymoφhic variant comprises at least one variant amino acid selected from the group consisting of histidine at a position corresponding to amino acid position 88, arginine at a position corresponding to amino acid position 94, alanine at a position corresponding to amino acid position 104, phenylalanine at a position corresponding to amino acid position 107, phenylalanine at a position corresponding to amino acid position 107, valine at a position corresponding to amino acid position 109, isoleucine at a position corresponding to amino acid position 120, arginine at a position corresponding to amino acid position 128, isoleucine at a position corresponding to amino acid position 136, lysine at a position corresponding to amino acid position 155, methionine at a position corresponding to amino acid position 338, termination codon at a position corresponding to amino acid position 344 and cysteine at a position corresponding to amino acid position 497. In some embodiments, the polymoφhic variant also comprises at least one variant amino acid selected from the group consisting of methionine at a position corresponding to amino acid position 7, methionine at a position corresponding to amino acid position 11, serine at a position corresponding to amino acid position 34, methionine at a position corresponding to amino acid position 91, isoleucine at a position corresponding to amino acid position 136, glutamic acid at a position corresponding to amino acid position 151 and threonine at a position corresponding to amino acid position 486. A polymoφhic variant of CYP2D6 is useful in studying the effect ofthe variation on the biological activity of CYP2D6 as well as on the binding affinity of candidate drags to CYP2D6, or studying the enzymatic properties of such CYP2D6 variants using these candidate drags as substrates. Herein, the term drug refers to a candidate drug or any of its metabolic derivatives.

The present invention also provides antibodies that recognize and bind to the above polymoφhic CYP2D6 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 CYP2D6 polymoφhic genomic variants described herein and methods for producing such animals. The transgenic animals are useful for studying expression ofthe CYP2D6 isogenes in vivo, for in vivo screening and testing of drugs targeted against CYP2D6 protein, and for testing the efficacy of therapeutic agents and compounds for hypertension, atrial and ventricular arrhythmias Parkinson's disease and drug-induced lupus syndrome in a biological system.

The present invention also provides a computer system for storing and displaying polymoφhism data determined for the CYP2D6 gene. The computer system comprises a computer processing unit; a display; and a database containing the polymoφhism data. The polymoφhism data includes one or more ofthe following: the polymoφhisms, the genotypes, the haplotypes, and the haplotype pairs identified for the CYP2D6 gene in a reference population. In a preferred embodiment, the computer system is capable of producing a display showing CYP2D6 haplotypes organized according to their evolutionary relationships.

BRIEF DESCRIPTION OF THE DRAWINGS

Figure 1 illustrates a reference sequence for the CYP2D6 gene (Genaissance Reference No.

3578126; 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 polymoφhic site(s) and polymoφhism(s) identified by Applicants in a reference population indicated by the variant nucleotide positioned below the polymoφhic site in the sequence. SEQ ID NO: 1 is equivalent to

Figure 1, with the two alternative allelic variants of each polymoφhic 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; WIPO standard ST.25). SEQ ID NO: 151 is a modified version of SEQ ID NOJ that shows the context sequence of each polymoφhic site, PS1-PS42, in a uniform format to facilitate electronic searching. For each polymoφhic site, SEQ ID NO: 151 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 PS is separated by genomic sequence whose composition is defined elsewhere herein.

Figure 2 illustrates a reference sequence for the CYP2D6 coding sequence (contiguous lines; SEQ ID NO:2), with the polymoφhic site(s) and polymoφhism(s) identified by Applicants in a reference population indicated by the variant nucleotide positioned below the polymoφhic site in the sequence.

Figure 3 illustrates a reference sequence for the CYP2D6 protein (contiguous lines; SEQ ID NO:3), with the variant amino acid(s) caused by the polymoφhism(s) of Figure 2 positioned below the polymoφhic site in the sequence.

DESCRIPTION OF THE PREFERRED EMBODIMENTS

The present invention is based on the discovery of novel variants ofthe CYP2D6 gene. As described in more detail below, the inventors herein discovered 34 isogenes ofthe CYP2D6 gene by characterizing the CYP2D6 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 unrelated 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 CYP2D6 isogenes present in the human reference population are defined by haplotypes for 42 polymoφhic sites in the CYP2D6 gene, 29 of which are believed to be novel. The CYP2D6 polymoφhic sites identified by the inventors are referred to as PS1-PS42 to designate the order in which they are located in the gene (see Table 2 below), with the novel polymoφhic sites referred to as PSI, PS2, PS3, PS4, PS6, PS10, PS12, PS14, PS15, PS16, PS17, PS18, PS19, PS20, PS22, PS23, PS24, PS26, PS27, PS28, PS29, PS32, PS34, PS36, PS37, PS38, PS39, PS40 and PS42. Using the genotypes identified in the Index Repository for PS1-PS42 and the methodology described in the Examples below, the inventors herein also determined the pair of haplotypes for the CYP2D6 gene present in individual human members of this repository. The human genotypes and haplotypes found in the repository for the CYP2D6 gene include those shown in Tables 3 and 4, respectively. The polymoφhism and haplotype data disclosed herein are useful for validating whether CYP2D6 is a suitable target for drags to treat hypertension, atrial and ventricular arrhythmias Parkinson's disease and drug-induced lupus syndrome, screening for such drags and reducing bias in clinical trials of such drags.

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 polymoφhic sites in a locus on a pair of homologous chromosomes in an individual. As used herein, genotype includes a full-genotype and/or a sub-genotype as described below.

Full-genotype - The unphased 5' to 3' sequence of nucleotide pairs found at all polymoφhic 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 of the polymoφhic sites examined herein in a locus on a pair of homologous chromosomes in a single individual.

Genotyping - A process for determining a genotype ofan individual.

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

Full-haplotype - The 5' to 3' sequence of nucleotides found at all polymoφhic 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 polymoφhic 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.

Isoform - A particular form of a gene, mRNA, cDNA, coding sequence 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 of the polymoφhisms 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 ofthe 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 polymoφhic 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 polymoφhic site on the two copies of a chromosome from an individual.

Phased - As applied to a sequence of nucleotide pairs for two or more polymoφhic sites in a locus, phased means the combination of nucleotides present at those polymoφhic sites on a single copy 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 (or variant)- A gene, mRNA, cDNA, polypeptide, protein or peptide whose nucleotide or amino acid sequence varies from a reference sequence due to the presence of a polymoφhism in the gene.

Polymorphism - The sequence variation observed in an individual at a polymoφhic site. Polymoφhisms include nucleotide substitutions, insertions, deletions and microsatellites and may, but need not, result in detectable differences in gene expression or protein function.

Polymorphism data - Information concerning one or more ofthe following for a specific gene: location of polymoφhic sites; sequence variation at those sites; frequency of polymoφhisms in one or more populations; the different genotypes and/or haplotypes determined for the gene; frequency of one or more of these genotypes and/or haplotypes in one or more populations; any known association(s) between a trait and a genotype or a haplotype for the gene.

Polymorphism Database - A collection of polymoφhism data arranged in a systematic or methodical way and capable of being individually accessed by electronic or other means.

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

Population Group - A group of individuals sharing a common ethnogeographic origin.

Reference Population - A group of subjects or individuals who are predicted to be representative 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 polymoφhic site. In rare cases, three or four nucleotides may be found.

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

Treatment - A stimulus administered internally or externally to a subject.

Unphased - As applied to a sequence of nucleotide pairs for two or more polymoφhic sites in a locus, unphased means the combination of nucleotides present at those polymoφhic sites on a single copy ofthe locus is not known.

As discussed above, information on the identity of genotypes and haplotypes for the CYP2D6 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 drag discovery and development applications. Thus, the invention also provides compositions and methods for detecting the novel CYP2D6 polymoφhisms, 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 CYP2D6 polymoφhic site in one copy or two copies ofthe CYP2D6 gene. Such oligonucleotides are referred to herein as CYP2D6 haplotyping oligonucleotides or genotyping oligonucleotides, respectively, and collectively as CYP2D6 oligonucleotides. In one embodiment, a CYP2D6 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 of the novel polymoφhic sites described herein.

As used herein, the term "oligonucleotide" refers to a polynucleotide molecule having less than about 100 nucleotides. A 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 oligonucleotide may be comprised of any phosphorylation state of ribonucleotides, deoxyribonucleotides, and acyclic nucleotide derivatives, and other functionally equivalent derivatives. Alternatively, oligonucleotides may have a phosphate-free backbone, which may be comprised of linkages such as carboxymethyl, acetamidate, carbamate, polyamide (peptide nucleic acid (PNA)) and the like (Varma, R. in Molecular Biology and Biotechnology, A Comprehensive Desk Reference, Ed. R. Meyers, VCH Publishers, Inc. (1995), pages 617-620). Oligonucleotides 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 CYP2D6 polynucleotide. Preferably, the target region is located in a CYP2D6 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 CYP2D6 polynucleotide or with a non-CYP2D6 polynucleotide under the same hybridizing conditions. Preferably, the oligonucleotide specifically hybridizes to the target region under conventional high stringency conditions. The skilled artisan can readily design and test oligonucleotide probes and primers suitable for detecting polymoφhisms in the CYP2D6 gene using the polymoφhism information provided herein in conjunction with the known sequence information for the CYP2D6 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, IRL 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 of the 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; WIPO 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 CYP2D6 gene polymoφhisms comprises a nucleotide sequence, listed 5 ' to 3 ', selected from the group consisting of:

GATGGCCRGGTCCAC (SEQ ID NO :4) and its com lement ,

TGCAGGCYTCAGGAG (SEQ ID NO :5) and : LtS complement,

GAAGCAGSGGCAAGA (SEQ ID NO 6) and its complement,

GGGCAAGRACCTCTG (SEQ ID NO 7) and its complement ,

GGTGTGCYGAGAGTG (SEQ ID NO :8) and its complement,

GGACTAGSACCTGTA (SEQ ID NO :9) and its complement,

GCCGTGCRCGAGGCG (SEQ ID NO 10) and its complement

GTGACCCRCGGCGAG SEQ ID NO ID and its complement

AGGACACSGCCGACC .SEQ ID NO 12) and its complement

CCGCCTGYGCCCATC (SEQ ID NO 13) and its complement

GCCCATC CCCAGAT (SEQ ID NO .14) and its complement

CCCATCAYCCAGATC (SEQ ID NO 15) and its complement

CACCCAGRTCCTGGG SEQ ID NO 16) and its complement

TCCTGGGYTTCGGGC SEQ ID NO 17) and its complement

GGCAAGCRGCGGTGG SEQ ID NO 18) and its complement

GCAGCGGKGGGGACA SEQ ID NO 19) and its complement

CGTAGTCYGAGCTGG SEQ ID NO 20) and its complement

GGACAGCSGGCCAAG SEQ ID NO 21) and its complement

AGGGGTGWTCCTGGC SEQ ID NO 22) and its complement

GCCCGCGYGGCGCGA SEQ ID NO 23) and its complement

CTTCTCCRTGTCCAC SEQ ID NO 24) and its complement

GGTGACCRAGGAGGC SEQ ID NO 25) and its complement

AGAGAGGRTGGAGGC < SEQ ID NO 26) and its complement

CGACGACRTGATAGG SEQ ID NO 27) and its complement

GGTGCGGYGACCAGA SEQ ID NO 28) and its complement

TGATTCAYGAGGTGC SEQ ID NO 29) and its complement

CACCAGCMCCTGGTG ( SEQ ID NO 30) and its complement

CTAGGAA CCTGGCC ( SEQ ID NO- 31) and its complement and

TGTGCCCYGCTAGAA ( SEQ ID NO 32) and its complement

A preferred ASO primer for detecting CYP2D6 gene polymoφhisms comprises a nucleotide sequence, listed 5' to 3', selected from the group consisting of: GAGGTGGATGGCCRG .SEQ ID NO 33) ^• GTTTCAGTGGACCYG iSEQ ID NO 34);

AGGCTTTGCAGGCYT SEQ ID NO 35) ^• TCCAAGCTCCTGARG iSEQ ID NO 36)

GAGCAGGAAGCAGSG SEQ ID NO 37) ^• AGAGGTTCTTGCCSC SEQ ID NO 38)

AAGCAGGGGCAAGRA SEQ ID NO 39) ^• CTGCTCCAGAGGTYC SEQ ID NO 40)

GCGCTCGGTGTGCYG SEQ ID NO 41) ^• GCAGGACACTCTCRG (SEQ ID NO 42)

CAAATAGGACTAGSA SEQ ID NO 43) ^• CCAGACTACAGGTSC SEQ ID NO 44)

CTGGCGGCCGTGCRC SEQ ID NO 45) ^• CACCAGCGCCTCGYG SEQ ID NO 46)

GCGCTGGTGACCCRC .SEQ ID NO 47) ^• GGTGTCCTCGCCGYG .SEQ ID NO 48)

ACGGCGAGGACACSG SEQ ID NO 49) ^• GCGGGCGGTCGGCSG (SEQ ID NO 50)

GACCGCCCGCCTGYG SEQ ID NO 51) ^■ CTGGGTGATGGGCRC ^rSEQ ID NO 52)

GCCTGTGCCCATC C SEQ ID NO 53) ^• CCCAGGATCTGGG G SEQ ID NO 54)

CCTGTGCCCATCAYC SEQ ID NO 55) ^• ACCCAGGATCTGGRT (SEQ ID NO 56)

GCCCATCACCCAGRT SEQ ID NO 57) ^• CCGAAACCCAGGAYC [SEQ ID NO 58)

CCCAGATCCTGGGYT SEQ ID NO 59) AACGCGGCCCGAARC SEQ ID NO 60)

TCCCAAGGCAAGCRG SEQ ID NO 61) CTGTCCCCACCGCYG SEQ ID NO 62)

AGGCAAGCAGCGGKG SEQ ID NO 63) TGTCTCTGTCCCC C SEQ ID NO 64)

GATGACCGTAGTCYG SEQ ID NO 65) CTCTGCCCAGCTCRG SEQ ID NO 66)

GAGTGGGGACAGCSG SEQ ID NO 67) TGGTTTCTTGGCCSG SEQ ID NO 68)

ACCCCCAGGGGTGWT I SEQ ID NO 69) TAGCGCGCCAGGAWC ( SEQ ID NO 70)

CTATGGGCCCGCGYG SEQ ID NO 71) CTCTGCTCGCGCCRC SEQ ID NO 72)

GAGGCGCTTCTCCRT SEQ ID NO 73) CGCAAGGTGGACAYG SEQ ID NO 74)

GCAGTGGGTGACCRA SEQ ID NO 75) CAGGCGGCCTCCTYG ( SEQ ID NO 76),

GCAAGGAGAGAGGRT SEQ ID NO 77) GTGCCAGCCTCCAYC SEQ ID NO 78)

GGAGATCGACGACRT SEQ ID NO 79) ACCTGCCCTATCAYG SEQ ID NO 80)

AGGGCAGGTGCGGYG ( SEQ ID NO 81) CCCATCTCTGGTCRC < SEQ ID NO 82)

CTGCCGTGATTCAYG ( SEQ ID NO 83) , AGCGCTGCACCTCRT ( SEQ ID NO 84) ,

GCTCAGCACCAGCMC SEQ ID NO 85) GGCTATCACCAGGKG SEQ ID NO 86)

CCCACTCTAGGAAMC ( SEQ ID NO 87) CTAGGTGGCCAGGKT SEQ ID NO 88) ,

TTGTGCTGTGCCCYG ( SEQ ID NO 89) and ACCCCATTCTAGCF -G (SEQ ID NO: 90)

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 ofthe 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 CYP2D6 gene polymoφhisms by primer extension terminates in a nucleotide sequence, listed 5' to 3', selected from the group consisting of:

GTGGATGGCC (SEQ ID NO: 91) TCAGTGGACC (SEQ ID NO: 92)

CTTTGCAGGC (SEQ ID NO: 93) AAGCTCCTGA (SEQ ID NO: 94)

CAGGAAGCAG (SEQ ID NO: 95) GGTTCTTGCC (SEQ ID NO: 96)

CAGGGGCAAG (SEQ ID NO: 97) CTCCAGAGGT (SEQ ID NO: 98)

CTCGGTGTGC (SEQ ID NO: 99) GGACACTCTC (SEQ ID NO: 100);

ATAGGACTAG (SEQ ID NO: 101) GACTACAGGT (SEQ ,ID NO: 102)

GCGGCCGTGC (SEQ ID NO: 103) CAGCGCCTCG (SEQ ID NO: 104)

CTGGTGACCC (SEQ ID NO: 105) GTCCTCGCCG (SEQ ID NO: 106)

GCGAGGACAC (SEQ ID NO: 107) GGCGGTCGGC (SEQ ID NO: 108) CGCCCGCCTG SEQ ID NO 109) GGTGATGGGC SEQ ID NO 110)

TGTGCCCATC SEQ ID NO 111) AGGATCTGGG SEQ ID NO 112)

GTGCCCATCA SEQ ID NO 113) CAGGATCTGG SEQ ID NO 114)

CATCACCCAG SEQ ID NO 115) AAACCCAGGA SEQ ID NO 116)

AGATCCTGGG SEQ ID NO 117) GCGGCCCGAA SEQ ID NO 118)

CAAGGCAAGC SEQ ID NO 119) TCCCCACCGC SEQ ID NO 120)

CAAGCAGCGG SEQ ID NO 121) CTCTGTCCCC SEQ ID NO 122)

GACCGTAGTC SEQ ID NO 123) TGCCCAGCTC SEQ ID NO 124)

TGGGGACAGC SEQ ID NO 125) TTTCTTGGCC SEQ ID NO 126)

CCCAGGGGTG SEQ ID NO 127) CGCGCCAGGA SEQ ID NO 128)

TGGGCCCGCG SEQ ID NO 129) TGCTCGCGCC SEQ ID NO 130)

GCGCTTCTCC SEQ ID NO 131) AAGGTGGACA SEQ ID NO 132)

GTGGGTGACC SEQ ID NO 133) GCGGCCTCCT SEQ ID NO 134)

AGGAGAGAGG SEQ ID NO 135) CCAGCCTCCA SEQ ID NO 136)

GATCGACGAC SEQ ID NO 137) TGCCCTATCA SEQ ID NO 138)

GCAGGTGCGG SEQ ID NO 139) ATCTCTGGTC SEQ ID NO 140)

CCGTGATTCA SEQ ID NO 141) GCTGCACCTC SEQ ID NO 142)

CAGCACCAGC SEQ ID NO 143) TATCACCAGG SEQ ID NO 144)

ACTCTAGGAA SEQ ID NO 145) GGTGGCCAGG SEQ ID NO 146)

TGCTGTGCCC SEQ ID NO 147) and CCATTCTAGC (SEQ ID NO:148) .

In some embodiments, a composition contains two or more differently labeled CYP2D6 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.

CYP2D6 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 CYP2D6 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 CYP2D6 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 CYP2D6 gene in an individual. As used herein, the terms "CYP2D6 genotype" and "CYP2D6 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 CYP2D6 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 CYP2D6 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 PSI, PS2, PS3, PS4, PS6, PS10, PS12, PS14, PS15, PS16, PS17, PS18, PS19, PS20, PS22, PS23, PS24, PS26, PS27, PS28, PS29, PS32, PS34, PS36, PS37, PS38, PS39, PS40 and PS42 in the two copies to assign a CYP2D6 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 CYP2D6 molecules) in an individual may be the same allele or may be different alleles. In a preferred embodiment ofthe method for assigning a CYP2D6 genotype, the identity ofthe nucleotide pair at one or more ofthe polymoφhic sites selected from the group consisting of PS5, PS7, PS8, PS9, PS11, PS13, PS21, PS25, PS30, PS31, PS33, PS35 and PS41 is also determined. In another embodiment, a genotyping method ofthe invention comprises determining the identity ofthe nucleotide pair at each of PS1-PS42.

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 CYP2D6 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 CYP2D6 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 CYP2D6 gene, mRNA or cDNA, or a fragment Of such CYP2D6 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 PSI, PS2, PS3, PS4, PS6, PS10, PS12, PS14, PS15, PS16, PS17, PS18, PS19, PS20, PS22, PS23, PS24, PS26, PS27, PS28, PS29, PS32, PS34, PS36, PS37, PS38, PS39, PS40 and PS42 in that copy to assign a CYP2D6 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 CYP2D6 gene or fragment such as one ofthe methods described above for preparing CYP2D6 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 CYP2D6 gene copies present in an individual. If haplotype information is desired for the individual's other copy, additional CYP2D6 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 of the CYP2D6 gene in an individual. In some cases, however, once the haplotype for one CYP2D6 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 group is known. In some embodiments, the CYP2D6 haplotype is assigned to the individual by also identifying the nucleotide at one or more polymoφhic sites selected from the group consisting of PS5, PS7, PS8, PS9, PS11, PS13, PS21, PS25, PS30, PS31, PS33, PS35 and PS41. In a particularly preferred embodiment, the nucleotide at each of PS1-PS42 is identified.

In another embodiment, the haplotyping method comprises determining whether an individual has one or more of the CYP2D6 haplotypes shown in Table 4. This can be accomplished by identifying, for one or both copies ofthe individual's CYP2D6 gene, the phased sequence of nucleotides present at each of PS1-PS42. This identifying step does not necessarily require that each of PS1-PS42 be directly examined. Typically only a subset of PS1-PS42 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 CYP2D6 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 PSI, PS2, PS3, PS4, PS6, PS10, PS12, PS14, PS15, PS16, PS17, PS18, PS19, PS20, PS22, PS23, PS24, PS26, PS27, PS28, PS29, PS32, PS34, PS36, PS37, PS38, PS39, PS40 and PS42 in each copy ofthe CYP2D6 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-PS42 in each copy ofthe CYP2D6 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 ofthe 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 CYP2D6 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 guanine/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 of the allele-specific oligonucleotide or target nucleic acid.

The genotype or haplotype for the CYP2D6 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., Genomics 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 ofthe gene or in other genomic regions not examined herein. Detection ofthe allele(s) present at a polymoφhic site in linkage disequilibrium with the novel polymoφhic sites described herein may be performed by, but is not limited to, any of the above-mentioned methods for detecting the identity ofthe allele at a polymoφhic site. In another aspect ofthe invention, an individual's CYP2D6 haplotype pair is predicted from its CYP2D6 genotype using information on haplotype pairs known to exist in a reference population.

In its broadest embodiment, the haplotyping prediction method comprises identifying a CYP2D6 genotype for the individual at two or more CYP2D6 polymoφhic sites described herein, accessing data containing CYP2D6 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 CYP2D6 haplotype pairs shown in Table 3. The CYP2D6 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, the comparing step 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, 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, for example by consulting Table 6. If a particular CYP2D6 haplotype pair 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 CYP2D6 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, I H₂ is equal to p_H__w(H, IH₂) = 2p(H_{)p(H₂) if H, ≠ H₂ and p_H__w(H IH₂) = p(H )p(H₂) if H. = H₂ .

A statistically significant difference between the observed and expected haplotype frequencies could be due to one or more factors including significant inbreeding in the population group, strong selective pressure on the gene, sampling bias, and/or 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 CYP2D6 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 >/Rto Evσ/ 7:l l l-22; copending PCT/US01/12831 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 CYP2D6 genotype, haplotype, or haplotype pair in a population. The method comprises, for each member ofthe population, determining the genotype or the haplotype pair for the novel CYP2D6 polymoφhic sites described herein, and calculating the frequency any particular genotype, haplotype, or haplotype pair 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 of the invention, frequency data for CYP2D6 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 CYP2D6 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 of the 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 preferred embodiment, the frequencies of all genotypes, haplotypes, and/or haplotype pairs observed in the populations are compared. If a particular CYP2D6 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 CYP2D6 genotype, haplotype or haplotype pair. Preferably, the CYP2D6 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. Sub-genotypes useful in the invention preferably do not include sub-genotypes solely for any one of PS5, PS7, PS8, PS9, PSI 1, PS13, PS21, PS25, PS30, PS31, PS33, PS35 and PS41 or for any combination thereof.

In a preferred embodiment ofthe method, the trait of interest is a clinical response exhibited by a patient to some therapeutic treatment, for example, response to a drag targeting CYP2D6 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 correlation between clinical response to a treatment and a CYP2D6 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 ran 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 III clinical trials. Standard methods are used to define the patient population and to enroll subjects.

It is preferred 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 correlation 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 correlation 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 CYP2D6 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, correlations between individual response and CYP2D6 genotype or haplotype content are created. Correlations may be produced in several ways. In one method, individuals are grouped by their CYP2D6 genotype or haplotype (or haplotype pair) (also referred 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 CYP2D6 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 correlations between CYP2D6 haplotype content and clinical responses uses predictive models based on error-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 correlation is found using a genetic algorithm approach as described in WO 01/01218.

Correlations 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 CYP2D6 gene. As described in WO 01/01218, ANOVA is used to test hypotheses about whether a response variable is caused by or correlated 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 CYP2D6 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 CYP2D6 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 drag. 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 CYP2D6 gene), a serological test, or a physical exam measurement. The only requirement is that there be a good correlation between the diagnostic test results and the underlying CYP2D6 genotype or haplotype that is in rum correlated with the clinical response. In a preferred 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 CYP2D6 gene or a fragment ofthe gene which contains at least one ofthe novel polymoφhic sites described herein. The nucleotide sequence of a variant CYP2D6 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 PSI, PS2, PS3, PS4, PS6, PS10, PS12, PS14, PS15, PS16, PS17, PS18, PS19,

PS20, PS22, PS23, PS24, PS26, PS27, PS28, PS29, PS32, PS34, PS36, PS37, PS38, PS39, PS40 and

PS42, and may also comprise one or more additional polymoφhisms selected from the group consisting of adenine at PS5, adenine at PS7, adenine at PS8, thymine at PS9, guanine at PSI 1, adenine at PS13, thymine at PS21, adenine at PS25, cytosine at PS30, guanine at PS31, adenine at

PS33, cytosine at PS35 and cytosine at PS41. Similarly, the nucleotide sequence of a variant fragment ofthe CYP2D6 gene is identical to the corresponding 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 CYP2D6 gene (or other reported CYP2D6 sequences) or to portions ofthe reference sequence (or other reported CYP2D6 sequences), except for the haplotyping and genotyping oligonucleotides described above.

The location of a polymoφhism in a variant CYP2D6 gene or fragment is preferably identified by aligning its sequence against SEQ ID NO: 1. The polymoφhism is selected from the group consisting of adenine at PSI, cytosine at PS2, cytosine at PS3, guanine at PS4, cytosine at PS6, cytosine at PS10, adenine at PS12, guanine at PS14, guanine at PS15, cytosine at PS16, thymine at PS 17, thymine at PS 18, guanine at PS 19, cytosine at PS20, guanine at PS22, guanine at PS23, thymine at PS24, cytosine at PS26, adenine at PS27, cytosine at PS28, adenine at PS29, adenine at PS32, adenine at PS34, adenine at PS36, thymine at PS37, cytosine at PS38, cytosine at PS39, adenine at PS40 and thymine at PS42. In a preferred embodiment, the polymoφhic variant comprises a naturally-occurring isogene ofthe CYP2D6 gene which is defined by any one of haplotypes 1-34 shown in Table 4 below.

Polymoφhic variants ofthe invention may be prepared by isolating a clone containing the CYP2D6 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 CYP2D6 variant or fragment thereof may also be prepared using synthetic or semi-synthetic methods known in the art.

CYP2D6 isogenes, or fragments thereof, may be isolated using any method that allows separation ofthe two "copies" ofthe CYP2D6 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._s 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 CYP2D6 genome anthologies, which are collections of at least two CYP2D6 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 CYP2D6 genome anthology may comprise individual CYP2D6 isogenes stored in separate containers such as microtest tubes, separate wells of a microtitre plate and the like. Alternatively, two or more groups ofthe CYP2D6 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 preferred CYP2D6 genome anthology of the invention comprises a set of isogenes defined by the haplotypes shown in Table 4 below.

An isolated polynucleotide containing a polymoφhic variant nucleotide sequence 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 CYP2D6 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, retrovirases, or SV40. Other regulatory elements include, but are not limited to, appropriate leader sequences, termination codons, polyadenylation signals, and other sequences required for the appropriate transcription and subsequent translation of the nucleic acid sequence in a given host cell. Of course, the correct combinations of expression regulatory elements will depend on the host system used. In addition, it is understood that the expression vector contains any additional elements necessary for its transfer to and subsequent replication in the host cell. Examples of such elements include, but are not limited to, origins of replication and selectable markers. Such expression vectors are commercially available or are readily constructed using methods known to those in the art (e.g., F. Ausubel et al., 1987, in "Current Protocols in Molecular Biology", John Wiley and Sons, New York, New York). Host cells which may be used to express the variant CYP2D6 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 preferred aspect, eukaryotic expression vectors that function in eukaryotic cells, and preferably mammalian cells, are used. Non-limiting examples of such vectors include vaccinia virus vectors, adenovirus vectors, heφes virus vectors, and baculovirus transfer vectors. Preferred eukaryotic cell lines include COS cells, CHO cells, HeLa cells, NIH/3T3 cells, and embryonic stem cells (Thomson, J. A. et al., 1998 Science 282: 1145-1147). Particularly preferred host cells are mammalian cells.

As will be readily recognized by the skilled artisan, expression of polymoφhic variants ofthe

CYP2D6 gene will produce CYP2D6 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 CYP2D6 cDNA comprising a nucleotide sequence which is a polymoφhic variant of the CYP2D6 reference coding sequence shown in Figure 2. Thus, the invention also provides CYP2D6 mRNAs and corresponding cDNAs which comprise a nucleotide sequence that is identical to SEQ ID NO:2 (Fig. 2) (or its corresponding RNA sequence) for those regions of SEQ ID NO:2 that correspond to the examined portions ofthe CYP2D6 gene (as described in the Examples below), except for having one or more polymoφhisms selected from the group consisting of adenine at a position corresponding to nucleotide 263, guanine at a position corresponding to nucleotide 281, guanine at a position corresponding to nucleotide 294, cytosine at a position corresponding to nucleotide 311, thymine at a position corresponding to nucleotide 319, thymine at a position corresponding to nucleotide 320, guanine at a position corresponding to nucleotide 325, cytosine at a position corresponding to nucleotide 333, adenine at a position corresponding to nucleotide 358, cytosine at a position corresponding to nucleotide 382, adenine at a position corresponding to nucleotide 406, adenine at a position corresponding to nucleotide 463, adenine at a position corresponding to nucleotide 1012, thymine at a position corresponding to nucleotide 1030, cytosine at a position corresponding to nucleotide 1083 and thymine at a position corresponding to nucleotide 1489, and may also comprise one or more additional polymoφhisms selected from the group consisting of adenine at a position corresponding to nucleotide 19, adenine at a position corresponding to nucleotide 31, thymine at a position corresponding to nucleotide 100, adenine at a position corresponding to nucleotide 271, thymine at a position corresponding to nucleotide 336, cytosine at a position corresponding to nucleotide 408, guanine at a position corresponding to nucleotide 451, cytosine at a position corresponding to nucleotide 696 and cytosine at a position corresponding to nucleotide 1457. A particularly preferred polymoφhic cDNA variant comprises the coding sequence of a CYP2D6 isogene defined by any one of haplotypes 1-10, 13-16, 18, 19, 21, 22, and 24-34. Fragments of these variant mRNAs and cDNAs are included in the scope of the invention, provided they contain one or more ofthe novel polymoφhisms described herein. The invention specifically excludes polynucleotides identical to previously identified CYP2D6 mRNAs, cDNAs, or previously described fragments thereof. Polynucleotides comprising a variant CYP2D6 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 CYP2D6 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 CYP2D6 polymoφhic sites identified herein, reference is made to the sense strand of the gene for convenience. However, as recognized by the skilled artisan, nucleic acid molecules containing the CYP2D6 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 corresponding site on the complementary antisense strand. Thus, reference may be made to the same polymoφhic site on either strand and an oligonucleotide may be designed to hybridize specifically to either strand at a target region containing the polymoφhic site. Thus, the invention also includes single-stranded polynucleotides which are complementary to the sense strand ofthe CYP2D6 genomic, mRNA and cDNA variants described herein.

Polynucleotides comprising a polymoφhic gene variant or fragment of the invention may be useful for therapeutic puφoses. For example, where a patient could benefit from expression, or increased expression, of a particular CYP2D6 protein isoform, an expression vector encoding the isoform may be administered to the patient. The patient may be one who lacks the CYP2D6 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 CYP2D6 isogene. Expression of a CYP2D6 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 preferred. 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. Carr, Molecular and Immunologic Approaches, Futura Publishing Co., Mt. Kisco, N.Y., 1994). Antisense oligonucleotides may also be designed to block translation of CYP2D6 mRNA transcribed from a particular isogene. It is also contemplated that ribozymes may be designed that can catalyze the specific cleavage of CYP2D6 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-, thio-, and similarly modified forms of adenine, cytosine, guanine, thymine, and uracil which are not as easily recognized by endogenous nucleases.

The invention also provides an isolated polypeptide comprising a polymoφhic variant of (a) the reference CYP2D6 amino acid sequence shown in Figure 3 or (b) a fragment of this reference sequence. The location of a variant amino acid in a CYP2D6 polypeptide or fragment ofthe invention is identified by aligning its sequence against SEQ ID NO:3 (Fig. 3). A CYP2D6 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 CYP2D6 gene (as described in the Examples below), except for having one or more variant amino acids selected from the group consisting ofhistidine at a position corresponding to amino acid position 88, arginine at a position corresponding to amino acid position 94, alanine at a position corresponding to amino acid position 104, phenylalanine at a position corresponding to amino acid position 107, phenylalanine at a position corresponding to amino acid position 107, valine at a position corresponding to amino acid position 109, isoleucine at a position corresponding to amino acid position 120, arginine at a position corresponding to amino acid position 128, isoleucine at a position corresponding to amino acid position 136, lysine at a position corresponding to amino acid position 155, methionine at a position corresponding to amino acid position 338, termination codon at a position corresponding to amino acid position 344 and cysteine at a position corresponding to amino acid position 497, and may also comprise one or more additional variant amino acids selected from the group consisting of methionine at a position corresponding to amino acid position 7, methionine at a position corresponding to amino acid position 11, serine at a position corresponding to amino acid position 34, methionine at a position corresponding to amino acid position 91, isoleucine at a position corresponding to amino acid position 136, glutamic acid at a position corresponding to amino acid position 151 and threonine at a position corresponding to amino acid position 486. Thus, a CYP2D6 fragment of the invention, also referred to herein as a CYP2D6 peptide variant, is any fragment of a CYP2D6 protein variant that contains one or more ofthe amino acid variations described herein. The invention specifically excludes amino acid sequences identical to those previously identified for CYP2D6, including SEQ ID NO:3, and previously described fragments thereof. CYP2D6 protein variants included within the invention comprise all amino acid sequences based on SEQ ID NO: 3 and having any combination of amino acid variations described herein. In preferred embodiments, a CYP2D6 protein variant ofthe invention is encoded by an isogene defined by one ofthe observed haplotypes, 1-10, 13-16, 18, 19, 21, 22, and 24- 34, shown in Table 4.

A CYP2D6 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 CYP2D6 peptide variants may be useful as antigens to generate antibodies specific for one ofthe above CYP2D6 isoforms. In addition, the CYP2D6 peptide variants may be useful in drug screening assays.

A CYP2D6 variant protein or peptide ofthe invention may be prepared by chemical synthesis or by expressing an appropriate variant CYP2D6 genomic or cDNA sequence described above.

Alternatively, the CYP2D6 protein variant may be isolated from a biological sample of an individual having a CYP2D6 isogene which encodes the variant protein. Where the sample contains two different CYP2D6 isoforms (i.e., the individual has different CYP2D6 isogenes), a particular CYP2D6 isoform ofthe invention can be isolated by immunoaffinity chromatography using an antibody which specifically binds to that particular CYP2D6 isoform but does not bind to the other CYP2D6 isoform.

The expressed or isolated CYP2D6 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 CYP2D6 protein or peptide as discussed further below. CYP2D6 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 CYP2D6 gene of the invention may also be fused in frame with a heterologous sequence to encode a chimeric CYP2D6 protein. The non-CYP2D6 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 CYP2D6 and non- CYP2D6 portions so that the CYP2D6 protein may be cleaved and purified away from the non- CYP2D6 portion.

An additional embodiment ofthe invention relates to using a novel CYP2D6 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 CYP2D6 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 CYP2D6 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 CYP2D6 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 CYP2D6 protein(s) of interest and then washed. Bound CYP2D6 protein(s) are then detected using methods well-known in the art.

In another embodiment, a novel CYP2D6 protein isoform may be used in assays to measure the binding affinities of one or more candidate drugs targeting the CYP2D6 protein or to measure the enzymatic activity of CYP2D6 when using one or more candidate drugs as substrates.

In yet another embodiment, when a particular CYP2D6 haplotype or group of CYP2D6 haplotypes encodes a CYP2D6 protein variant with an amino acid sequence distinct from that of CYP2D6 protein isoforms encoded by other CYP2D6 haplotypes, then detection of that particular CYP2D6 haplotype or group of CYP2D6 haplotypes may be accomplished by detecting expression of the encoded CYP2D6 protein variant using any ofthe 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 CYP2D6 variant proteins described herein. The antibodies may be either monoclonal or polyclonal in origin. The CYP2D6 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 CYP2D6 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. D.P. Stites, and A.I. Terr, Appleton and Lange, Norwalk Connecticut, San Mateo, California).

In one embodiment, an antibody specifically immunoreactive with one ofthe novel protein isoforms described herein is administered to an individual to neutralize activity of the CYP2D6 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 CYP2D6 protein variant from solution as well as react with CYP2D6 protein isoforms on Western or immunoblots of polyacrylamide gels on membrane supports or substrates. In another preferred embodiment, the antibodies will detect CYP2D6 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 ofthe novel CYP2D6 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 CYP2D6 protein variant and the antibody is detected. As described, suitable immunoassays include radioimmunoassay, Western blot assay, immunofluorescent assay, enzyme linked immunoassay (ELISA), chemiluminescent assay, immunohistochemical assay, immunocytochemical assay, and the like (see, e.g., Principles and Practice of Immunoassay, 1991, Eds. Christopher P. Price and David J. Neoman, Stockton Press, New York, New York; Current Protocols in Molecular Biology, 1987, Eds. Ausubel et al., John Wiley and Sons, New York, New York). Standard techniques known in the art for ELISA are described in Methods in Immunodiagnosis, 2nd Ed., Eds. Rose and Bigazzi, John Wiley and Sons, New York 1980; and Campbell et al., 1984, Methods in Immunology, W.A. Benjamin, Inc.). Such assays may be direct, indirect, competitive, or noncompetitive as described in the art (see, e.g., Principles and Practice of Immunoassay, 1991, Eds. Christopher P. Price and David J. Neoman, Stockton Pres, NY, NY; and Oellirich, M., 1984, J. Clin. Chem. Clin. Biochem., 22:895-904). Proteins may be isolated from test specimens and biological samples by conventional methods, as described in Current 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 CYP2D6 may be investigated by various means known in the art, such as by in vitro translation of mRNA transcripts of the CYP2D6 gene, cDNA orfragment thereof, or by preparing recombinant cells and/or nonhuman recombinant organisms, preferably recombinant animals, containing a polymoφhic variant of the CYP2D6 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 of the mature mRNA(s) into CYP2D6 protein(s) (including effects of polymoφhihsms on codon usage and tRNA availability); and glycosylation and/or other modifications ofthe translation product, if required for proper expression and function.

To prepare a recombinant cell ofthe invention, the desired CYP2D6 isogene, cDNA or coding sequence may be introduced into the cell in a vector such that the isogene, cDNA or coding sequence remains extrachromosomal. In such a situation, the gene will be expressed by the cell from the extrachromosomal location. In a preferred embodiment, the CYP2D6 isogene, cDNA or coding sequence is introduced into a cell in such a way that it recombines with the endogenous CYP2D6 gene present in the cell. Such recombination requires the occurrence of a double recombination event, thereby resulting in the desired CYP2D6 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 CYP2D6 isogene, cDNA or coding sequence may be introduced include, but are not limited to, continuous culture cells, such as COS, CHO, NIH/3T3, and primary or culture cells ofthe relevant tissue type, i.e., they express the CYP2D6 isogene, cDNA or coding sequence. 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 CYP2D6 gene, cDNA or coding sequence are prepared using standard procedures known in the art. Preferably, a construct comprising the variant gene, cDNA or coding sequence 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 retroviras constracted to contain one or more insulator elements, a gene or genes (or cDNA or coding sequence) 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 CYP2D6 isogene, cDNA or coding sequences 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 CYP2D6 isogene, cDNA or coding sequence and producing the encoded human CYP2D6 protein can be used as biological models for studying diseases related to abnormal CYP2D6 expression and/or activity, and for screening and assaying various candidate drags, 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 CYP2D6 isogene described herein. The pharmaceutical composition may comprise any ofthe following active ingredients: a polynucleotide comprising one of these novel CYP2D6 isogenes (or cDNAs or coding sequences); an antisense oligonucleotide directed against one ofthe novel CYP2D6 isogenes, a polynucleotide encoding such an antisense oligonucleotide, or another compound which inhibits expression of a novel CYP2D6 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 CYP2D6 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 CYP2D6 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 CYP2D6 polymoφhism data described herein may be stored as part of a relational database (e.g., an instance ofan 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.

Preferred 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 of the CYP2D6 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: 149) and the universal 'tail' sequence for the reverse PCR primers comprises the sequence 5 '-AGGAAACAGCTATGACCAT-3 ' (SEQ ID NO: 150). The nucleotide positions of the first and last nucleotide ofthe forward and reverse primers for each region amplified are presented below and correspond to positions in SEQ IDNOJ (Figure 1).

PCR Primer Pairs

Fragment No. Forward Primer Reverse Primer PCR Product Fragment 1 378-400 complement of 934-913 557 nt Fragment 2 645-667 complement bf 1184-1163 540 nt Fragment 3 833-855 complement of 1363-1343 531 nt Fragment 4 1701-1723 complement of 2203-2182 503 nt Fragment 5 2342-2364 complement of 2942-2922 601 nt Fragment 6 2652-2671 complement of 3244-3220 593 nt Fragment 7 3213-3235 complement of 3794-3773 582 nt Fragment 8 3604-3627 complement of 4184-4164 581 nt Fragment 9 4008-4028 complement of 4555-4533 548 nt Fragment 10 4651-4673 complement of 5094-5072 444 nt Fragment 11 4867-4886 complement of 5297-5275 431 nt Fragment 12 4968-4987 complement of 5435-5413 468 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 JO μl

10 x Advantage 2 Polymerase reaction buffer (Clontech) = 1 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 corresponding to positions in Figure 1, or the appropriate universal 'tail' sequence as a primer. Reaction products were purified by isopropanol precipitation, and ran on an Applied Biosystems 3700 DNA Analyzer.

Sequencing Primer Pairs

Fragment No. Forward Primer Reverse Primer Fragment 1 Tailed sequence Fragment 2 778-797 complement of 1 155-1136 Fragment 3 Tailed sequence Fragment 4 Tailed sequence Fragment 5 2471-2490 complement of 2890-2871 Fragment 6 2687-2706 complement of 3133-3113 Fragment 7 Tailed sequence Fragment 8 3688-3707 complement of 4079-4058 Fragment 9 4036-4055 complement of 4469-4450 Fragment 10 Tailed sequence Fragment 11 4915-4934 complement of 5260-5241 Fragment 12 5070-5089 complement of 5412-5392

Analysis of Sequences for Polymoφhic Sites

Sequence information for a minimum of 80 humans was analyzed for the presence of polymoφhisms using the Polypi-red 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 CYP2D6 reference genomic sequence (SEQ ID NOJ) are listed in Table 2 below. Table 2. Polymoφhic Sites Identified in the CYP2D6 Gene

Polymoφhic Nucleotide Reference Variant CDS Variant AA

Site Number Polyld(a) Position Allele Allele Position Variant

PSI 3578169 636 G A

PS2 3578173 678 T C

PS3 3578177 769 G C

PS4 3578179 776 A G

PS5(R) 3578181 825 G A

PS6 3578183 915 T C

PS7(R) 3578185 1019 G A 19 V7M

PS8(R) 3578187 1031 G A 31 V11M

PS9(R) 3578189 1100 C T 100 P34S

PS10 8552536 1827 G C

PS11(R) 6823986 1843 T G

PS12 8552444 1966 G A 263 R88H

PS13(R) 8060758 1974 C A 271 L91M

PS14 8060761 1984 A G 281 H94R

PS15 8060764 1997 C G 294 T98T

PS16 8552352 2014 T C 311 VI04A

PS17 8552259 2022 A T 319 T107F

PS18 8060767 ' 2023 C T 320 T107F

PS19 8552166 2028 A G 325 1109V

PS20 8552073 2036 T C 333 G111G

PS21(R) 8060770 2039 C T 336 F112F

PS22 8551980 2062 A G

PS23 8551887 2067 T G

PS24 8551795 2118 C T

PS25(R) 8551703 2170 G A

PS26 8551610 2179 G C

PS27 3578191 2611 T A 358 F120I

PS28 3578193 2635 T C 382 W128R

PS29 3578195 2659 G A 406 V136I

PS30(R) 3578199 2661 G C 408 V136I

PS31(R) 3578201 2704 C G 451 Q151E

PS32 3578203 2716 G A 463 E155K

PS33(R) 3578210 2846 G A

PS34 3578212 3292 G A

PS35(R) 3578214 3470 T C 696 H232H

PS36 3578221 4183 G A 1012 V338M

PS37 3578223 4201 C T 1030 R344!

PS38 3578229 4254 T C 1083 H361H

PS39 3578235 4384 A C

PS40 3578241 4435 C A

PS41(R) 3578249 5180 G C 1457 S486T

PS42 3578251 5212 C T 1489 R497C

(a)PolyId is a unique identifier assigned to each PS by Genaissance Pharmaceuticals, Inc. (R)Reported previously EXAMPLE 2

This example illustrates analysis ofthe CYP2D6 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 inferred based on linkage disequilibrium and/or Mendelian inheritance.

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Table 3 (Part 5). Genotypes and Haplotype Pairs Observed for CYP2D6 Gene

Genotype Polymoφhic Sites

Number HAP Pair PS41 PS42

1 15 15 C C

2 19 19 C C

3 32 32 C C

4 7 7 C C

5 15 20 C/G C

6 15 19 C C

7 23 33 G/C C

8 22 20 C/G C

9 23 24 G/C C

10 23 25 G/C C

11 15 9 C C

12 32 21 C/G C

13 23 16 G/C C

14 20 28 G/C C

15 32 13 C C

16 32 26 C C

17 23 1 G/C C

18 32 20 C/G C

19 15 12 C/G C

20 23 26 G/C C

21 23 18 G/C C

22 23 27 G/C C

23 32 2 C C

24 15 34 C/G C

25 15 14 C C

26 23 8 G/C C

27 23 28 G/C C

28 15 7 C C

29 23 10 G/C C

30 23 5 G/C C

31 32 17 C/G C

32 15 26 C C

33 15 11 C/G C

34 32 4 C C

35 26 19 C C

36 23 4 G/C C

37 32 12 C/G C

38 30 29 C C

39 23 6 G/C C

40 23 32 G/C C

41 23 15 G/C C

42 15 3 C C

43 26 2 C C

44 15 32 C C

45 23 22 G/C C

46 4 31 C C

47 15 31 C C

48 15 4 C 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/USOl/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 34 human CYP2D6 haplotypes shown in Table 4 below.

A CYP2D6 isogene defined by a full-haplotype shown in Table 4 below comprises the regions ofthe SEQ ID NOS indicated in Table 4, with their corresponding set of polymoφhic locations and identities, which are also set forth in Table 4.

Table 4 (Part 1). Haplotypes ofthe CYP2D6 gene.

Regions PS PS Haplotype Number(d)

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

378-1363 1 636/30 A G G G G G G G G G

378-1363 2 678/150 T C T T T T T T T T

378-1363 3 769/270 G G C G G G G G G G

378-1363 4 776/390 A A G A A A A A A A

378-1363 5 825/510 G G G A G G G G G G

378-1363 6 915/630 T T T T C T T T T T

378-1363 7 1019/750 G G G G G A G G G G

378-1363 8 1031/870 G G G G G G A A G G

378-1363 9 1100/990 C C T C C C C C C C

1701-2203. 10 1827/1110 G G G G G G G G C G

1701-2203 11 1843/1230 T G G G T G G G G G

1701-2203 12 1966/1350 G G G G G G G G G A

1701-2203 13 1974/1470 C C C C C C C C C C

1701-2203 14 1984/1590 A A A A A A A A A A

1701-2203 15 1997/1710 C C C C C C C C C C

1701-2203 16 2014/1830 T T T T T T T T T T

1701-2203 17 2022/1950 A A A A A A A A A A

1701-2203 18 2023/2070 C C C C C C C C T C

1701-2203 19 2028/2190 A A A A A A A A A A

1701-2203 20 2036/2310 T T T T T T T T T T

1701-2203 21 2039/2430 C C T C C C C C C C

1701-2203 22 2062/2550 A A A A A A A A A A

1701-2203 23 2067/2670 T T T T T T T T T T

1701-2203 24 2118/2790 C C C C C C C C C C

1701-2203 25 2170/2910 G G G G G G G G G G

1701-2203 26 2179/3030 G G G G G G G G G G

2342-4555 27 2611/3150 T T T T T T T T T T

2342-4555 28 2635/3270 T T T T T T T T C T

2342-4555 29 2659/3390 G G G A G G G G G G

2342-4555 30 2661/3510 G C C C G C C G C C

2342-4555 31 2704/3630 C C C C C G C C C C

2342-4555 32 2716/3750 G G G G G G G G G G

2342-4555 33 2846/3870 G G G G G G G G G G

2342-4555 34 3292/3990 G G G A G G G G G G

2342-4555 35 3470/4110 T T T T T T T T T T

2342-4555 36 4183/4230 G G G A G G G G G G

2342-4555 37 4201/4350 C C C C C C C C C C

2342-4555 38 4254/4470 T T T T T T T T T T

2342-4555 39 4384/4590 A C C C A C C C C C

2342-4555 40 4435/4710 C C C C C C C C C C

4651-5435 41 5180/4830 C C C C C C C C C C

4651-5435 42 5212/4950 C C C C C C C C C C

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Table 4 (Part 3). Haplotypes ofthe CYP2D6 gene.

Regions PS PS Haplotype Number(d)

Examined(a) No.(b) Position(c) 21 22 23 24 25 26 27 28 29 30

378-1363 1 636/30 G G G G G G G G G G

378-1363 2 678/150 T T T T T T T T T T

378-1363 3 769/270 G G G G G G G G G G

378-1363 4 776/390 A A A A A A A A A A

378-1363 5 825/510 G G G G G G G G G G

378-1363 6 915/630 T T T T T T T T T T

378-1363 7 1019/750 G G G G G G G G G G

378-1363 8 1031/870 G G G G G G G G G G

378-1363 9 1100/990 C C C C T T T T T T

1701-2203 10 1827/1110 G G G G G G G G G G

1701-2203 11 1843/1230 T T T T G G G G G G

1701-2203 12 1966/1350 G G G G G G G G G G

1701-2203 13 1974/1470 C C C C A A A A A A

1701-2203 14 1984/1590 A A A A A A A A G G

1701-2203 15 1997/1710 C C C C C G G G G G

1701-2203 16 2014/1830 T T T T T T T T T T

1701-2203 17 2022/1950 A A A A A A A A A A

1701-2203 18 2023/2070 C C C C C C C C C C

1701-2203 19 2028/2190 A A A A A A A A A A

1701-2203 20 2036/2310 T T T T T T T T T T

1701-2203 21 2039/2430 C C C C C C C C C C

1701-2203 22 2062/2550 A A A A A A A A A A

1701-2203 23 2067/2670 T T T T T T T T T T

1701-2203 24 2118/2790 C C C T C C C C C C

1701-2203 25 2170/2910 G G G G G G G G G G

1701-2203 26 2179/3030 G G G G G G G G G G

2342-4555 27 2611/3150 T T T T T T T T T T

2342-4555 28 2635/3270 T T T T T T T T T T

2342-4555 29 2659/3390 G G G G G G G G G G

2342-4555 30 2661/3510 C G G G C C C C C C

2342-4555 31 2704/3630 C C C C C C C C C C

2342-4555 32 2716/3750 G G G G G G G G G G

2342-4555 33 2846/3870 G G G G G A G G A G

2342-4555 34 3292/3990 G G G G G G G G G G

2342-4555 35 3470/4110 T T T T T T T T T T

2342-4555 36 4183/4230 G G G G G G G G G G

2342-4555 37 4201/4350 C C C C C C C C C C

2342-4555 38 4254/4470 T T T T T T T T T T

2342-4555 39 4384/4590 A A A A C C C C C C

2342-4555 40 4435/4710 C C C C C C A C C A

4651-5435 41 5180/4830 G C G C C C C C C C

4651-5435 42 5212/4950 C C C C C C C C C C Table 4 (Part 4). Haplotypes ofthe CYP2D6 gene.

Regions PS PS Haplotype Number(d)

Examined(a) No.(b) Position(c) 31 32 33 34

378-1363 1 636/30 G G G G

378-1363 2 678/150 T T T T

378-1363 3 769/270 G G G G

378-1363 4 776/390 A A A A

378-1363 5 825/510 G G G G

378-1363 6 915/630 T T T T

378-1363 7 1019/750 G G G G

378-1363 8 1031/870 G G G G

378-1363 9 1100/990 T T T T

1701-2203 ^ 10 1827/1110 G G G G

1701-2203 11 1843/1230 G G G T

1701-2203 12 1966/1350 G G G G

1701-2203 13 1974/1470 C C C A

1701-2203 14 1984/1590 A A A A

1701-2203 15 1997/1710 C C C G

1701-2203 16 2014/1830 T T T T

1701-2203 17 2022/1950 A A A A

1701-2203 18 2023/2070 C C C C

1701-2203 19 2028/2190 A A A A

1701-2203 20 2036/2310 T T T T

1701-2203 21 2039/2430 T T T C

1701-2203 22 2062/2550 A A A ^■ A

1701-2203 23 2067/2670 T T T T

1701-2203 24 2118/2790 C C C C

1701-2203 25 2170/2910 G G G G

1701-2203 26 2179/3030 G G G G

2342-4555 27 2611/3150 T T T T

2342-4555 28 2635/3270 T T T T

2342-4555 29 2659/3390 G G G G

2342-4555 30 2661/3510 C C C C

2342-4555 31 2704/3630 C C C C

2342-4555 32 2716/3750 G G G G

2342-4555 33 2846/3870 A G G A

2342-4555 34 3292/3990 G G G G

2342-4555 35 3470/4110 T T T T

2342-4555 36 4183/4230 G G G G

2342-4555 37 4201/4350 C C T C

2342-4555 38 4254/4470 T T T T

2342-4555 39 4384/4590 C C C A

2342-4555 40 4435/4710 C C C C

4651-5435 41 5180/4830 C C C G

4651-5435 42 5212/4950 C C C C

(a) Region examined represents the nucleotide positions defining the start and stop positions within SEQ ID NOJ 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 NOJ and the 2^nd position number referring to SEQ ID NOJ51, a modified version of SEQ ID NOJ that comprises the context sequence of each polymoφhic site, PS1-PS42, to facilitate electronic searching ofthe haplotypes;

(d) Alleles for CYP2D6 haplotypes are presented 5 ' to 3 ' in each column. SEQ ID NO: 1 refers to Figure 1, with the two alternative allelic variants of each polymoφhic site indicated by the appropriate nucleotide symbol. SEQ ID NO: 151 is a modified version of SEQ ID NOJ that shows the context sequence of each of PS1-PS42 in a uniform format to facilitate electronic searching of the CYP2D6 haplotypes. For each polymoφhic site, SEQ ID NO: 151 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 CYP2D6 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 CYP2D6 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.

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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 CYP2D6 gene are likely to be similar to the relative frequencies of these CYP2D6 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 Cytochrome P450, subfamily IID, Polypeptide 6 (CYP2D6) gene ofan individual, which comprises determining which ofthe CYP2D6 haplotypes shown in the table immediately below defines one copy ofthe individual's CYP2D6 gene, wherein the determining step comprises identifying the phased sequence of nucleotides present at each of PS1-PS42 on at least one copy ofthe individual's CYP2D6 gene, and wherein each ofthe CYP2D6 haplotypes comprises a sequence of polymoφhisms whose positions and identities are set forth in the table immediately below:

PS PS Haplotype Number(c) (Part V)

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

1 636 A G G G G G G G G G

2 678 T C T T T T T T T T

3 769 G G C G G G G G G G

4 776 A A G A A A A A A A

5 825 G G G A G G G G G G

6 915 T T T T C T T T T T

7 1019 G G G G G A G G G G

8 1031 G G G G G G A A G G

9 1100 C C T C C C C C C C

10 1827 G G G G G G G G C G

11 1843 T G G G T G G G G G

12 1966 G G G G G G G G G A

13 1974 C C C C C C C C C C

14 1984 A A A A A A A A A A

15 1997 C C C C C C C C C C

16 2014 T T T T T T T T T T

17 2022 A A A A A A A A A A

18 2023 C C C C C C C C T C

19 2028 A A A A A A A A A A

20 2036 T T T T T T T T T T

21 2039 C C T C C C C C C C

22 2062 A A A A A A A A A A

23 2067 T T T T T T T T T T

24 2118 C C C C C C C C C C

25 2170 G G G G G G G G G G

26 2179 G G G G G G G G G G

27 2611 T T T T T T T T T T

28 2635 T T T T T T T T C T

29 2659 G G G A G G G G G G

30 2661 G C C C G C C G C C

31 2704 C C C C C G C C C C

32 2716 G G G G G G G G G G

33 2846 G G G G G G G G G G

34 3292 G G G A G G G G G G

35 3470 T T T T T T T T T T

36 4183 G G G A G G G G G G

37 4201 C C C C C C C C C C

38 4254 T T T T T T T T T T

39 4384 A C C C A C C C C C

40 4435 C C C C C C C C C C 1 5180 C C C C C C C C C C 2 5212 C C C C C C C C C C ji i t >-

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PS PS Haplotype Number(c) (Part 3)

No.(a) Position(b) 21 22 23 24 25 26 27 28 29 30

1 636 G G G G G G G G G G

2 678 T T T T T T T T T T

3 769 G G G G G G G G G G

4 776 A A A A A A A A A A

5 825 G G G G G G G G G G

6 915 T T T T T T T T T T

7 1019 G G G G G G G G G G

8 1031 G G G G G G G G G G

9 1100 C C C C T T T T T T

10 1827 G G G G G G G G G G

11 1843 T T T T G G G G G G

12 1966 G G G G G G G G G G

13 1974 C C C C A A A A A A

14 1984 A A A A A A A A G G

15 1997 C C C C C G G G G G

16 2014 T T T T T T T T T T

17 2022 A A A A A A A A A A

18 2023 C C C C C C C C C C

19 2028 A A A A A A A A A A

20 2036 T T T T T T T T T T

21 2039 C C C C C C C C C C

22 2062 A A A A A A A A A A

23 2067 T T T T T T T T T T

24 2118 C C C T C C C C C C

25 2170 G G G G G G G G G G

26 2179 G G G G G G G G G G

27 2611 T T T T T T T T T T

28 2635 T T T T T T T T T T

29 2659 G G G G G G G G G G

30 2661 C G G G C C C C C C

31 2704 C C C C C C C C C C

32 2716 G G G G G G G G G G

33 2846 G G G G G A G G A G

34 3292 G G G G G G G G G G

35 3470 T T T T T T T T T T

36 4183 G G G G G G G G G G

37 4201 C C C C C C C C C C

38 4254 T T T T T T T T T T

39 4384 A A A A C C C C C C

40 4435 C C C C C C A C C A

41 5180 G C G C C C C C C C

42 5212 C C C C C C C C C C PS PS Haplotype Number(c) (Part 4)

No.(a) Position(b) 31 32 33 34

1 636 G G G G

2 678 T T T T

3 769 G G G G

4 776 A A A A

5 825 G G G G

6 915 T T T T

7 1019 G G G G

8 1031 G G G G

9 1100 T T T T

10 1827 G G G G

11 1843 G G G T

12 1966 G G G G

13 1974 C C C A

14 1984 A A A A

15 1997 C C C G

16 2014 T T T T

17 2022 A A A A

18 2023 C C C C

19 2028 A A A A

20 2036 T T T T

21 2039 T T T C

22 2062 A A A A

23 2067 T T T T

24 2118 C C C C

25 2170 G G G G

26 2179 G G G G

27 2611 T T T T

28 2635 T T T T

29 2659 G G G G

30 2661 C C C C

31 2704 C C C C

32 2716 G G G G

33 2846 A G G A

34 3292 G G G G

35 3470 T T T T

36 4183 G G G G

37 4201 C C T C

38 4254 T T T T

39 4384 C C C A

40 4435 C C C C

41 5180 C C C G

42 5212 C C C C

(a) PS = polymoφhic site;

(b) Position of PS within SEQ ID NOJ;

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

A method for haplotyping the Cytochrome P450, subfamily IID, Polypeptide 6 (CYP2D6) gene ofan individual, which comprises determining which ofthe CYP2D6 haplotype pairs shown in the table immediately below defines both copies ofthe individual's CYP2D6 gene, wherein the determining step comprises identifying the phased sequence of nucleotides present at each of PS1-PS42 on both copies ofthe individual's CYP2D6 gene, and wherein each ofthe CYP2D6 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) 15/15 19/19 32/32 7/7 15/20 15/19 23/33 22/20

1 636 G/G G/G G/G G/G G/G G/G G/G G/G

2 678 T/T T/T T/T T/T T/T T/T T/T T/T

3 769 G/G G/G G/G G/G G/G G/G G/G G/G

4 776 A/A A/A A/A A/A A/A A/A A/A A/A

5 825 G/G G/G G/G G/G G/G G/G G/G G/G

6 915 T/T T/T T/T T/T T/T T/T T/T T/T

7 1019 G/G G/G G/G G/G G/G G/G G/G G/G

8 1031 G/G G/G G/G AA G/G G/G G/G G/G

9 1100 C/C C/C T/T C/C C/C C/C C/T C/C

10 1827 G/G G/G G/G G/G G/G G/G G/G G/G

11 1843 G/G G/G G/G G/G G/T G/G T/G T/T

12 1966 G/G G/G G/G G/G G/G G/G G/G G/G

13 1974 C/C C/C C/C C/C C/C C/C C/C C/C

14 1984 A/A A/A A/A AA A/A A/A A/A A/A

15 1997 C/C C/C C/C C/C C/C C/C C/C C/C

16 2014 T/T T/T T/T T/T T/T T/T T/T T/T

17 2022 AA A/A A/A A/A A/A A/A A/A A/A

18 2023 C/C T/T 'C/C C/C C/C C/T C/C C/C

19 2028 A/A A/A A/A A/A A/A A/A A/A A/A

20 2036 T/T' T/T T/T T/T T/T T/T T/T T/T

21 2039 C/C C/C T/T C/C C/C C/C C/T C/C

22 2062 A/A A/A A/A A/A A/A A/A A/A A/A

23 2067 T/T T/T T/T T/T T/T T/T T/T T/T

24 2118 C/C C/C C/C C/C C/C C/C C/C C/C

25 2170 G/G G/G G/G G/G G/A . G/G G/G G/A

26 2179 G/G G/G G/G G/G G/G G/G G/G G/G

27 2611 T/T T/T T/T T/T T/T T/T T/T T/T

28 2635 T/T T/T T/T T/T T/T T/T T/T T/T

29 2659 G/G G/G G/G G/G G/G G/G G/G G/G

30 2661 C/C C/C C/C C/C C/G C/C G/C G/G

31 2704 C/C C/C C/C C/C C/C C/C C/C C/C

32 2716 G/G G/G G/G G/G G/G G/G G/G G/G

33 2846 G/G G/G G/G G/G G/G G/G G/G G/G

34 3292 G/G G/G G/G G/G G/G G/G G/G G/G

35 3470 T/T T/T T/T T/T T/T T/T T/T T/T

36 4183 G/G G/G G/G G/G G/G G/G G/G G/G

37 4201 C/C C/C C/C C/C C/C C/C C/T C/C

38 4254 T/T T/T T/T T/T T/T T/T T/T T/T

39 4384 C/C C/C C/C C/C C/A C/C A/C A/A

40 4435 C/C C/C C/C C/C C/C C/C C/C C/C

41 5180 C/C C/C C/C C/C C/G C/C G/C C/G

42 5212 C/C C/C C/C C/C C/C C/C C/C C/C PS PS Haplotype Pair(c) (Part 2)

No.(a) Position(b) 23/24 23/25 15/9 32/21 23/16 20/28 32/13 32/26

1 636 G/G G/G G/G G/G G/G G/G G/G G/G

2 678 T/T T/T T/T T/T T/T T/T T/T T/T

3 769 G/G G/G G/G G/G G/G G/G G/G G/G

4 776 A/A A/A A/A A/A A/A A/A A/A A/A

5 825 G/G G/G G/G G/G G/G G/G G/G G/G

6 915 T/T T/T T/T T/T T/T T/T T/T T/T

7 1019 G/G G/G G/G G/G G/G G/G G/G G/G

8 1031 G/G G/G G/G G/G G/G G/G G/G G/G

9 1100 C/C C/T C/C T/C C/C C/T T/C T/T

10 1827 G/G G/G G/C G/G G/G G/G G/G G/G

11 1843 t/t t/g g/g g/t t g t g g/g g/g

12 1966 G/G G/G G/G G/G G/G G/G G/G G/G

13 1974 C/C C/A C/C C/C C/C C/A C/C C/A

14 1984 A/A A/A A/A A/A A/A A/A A/A A/A

15- 1997 C/C C/C C/C C/C C/C C/G C/C C/G

16 2014 T/T T/T T/T T/T T/T T/T T/T T/T

17 2022 A/A A/A A/A A/A A/A A A A/A A/A

18 2023 C/C C/C C/T C/C C/C C/C C/C C/C

19 2028 A/A A/A A/A A/A A A A/A A/A A/A

20 2036 T/T T/T T/T T/T T/T T/T T/T T/T

21 2039 C/C C/C C/C T/C C/C C/C T/C T/C

22 2062 A/A A/A A/A A/A A/A A/A A/A A/A

23 2067 T/T T/T T/T T/T T/T T/T T/T T/T

24 2118 C/T C/C C/C C/C C/C C/C C/C C/C

25 2170 G/G G/G G/G G/G G/G A/G G/G G/G

26 2179 G/G G/G G/G G/G G/G G/G G/G G/G

27 2611 T/T T/T T/T T/T T/T T/T T/A T/T

28 2635 T/T T/T T/C T/T T/T T/T T/T T/T

29 2659 G/G G/G G/G G/G G/G G/G G/G G/G

30 2661 G/G G/C C/C C/C G/G G/C C/C C/C

31 2704 C/C C/C C/C C/C C/C C/C C/C C/C

32 2716 G/G G/G G/G G/G G/G G/G G/G G/G

33 2846 G/G G/G G/G G/G G/G G/G G/G G/A

34 3292 G/G G/G G/G G/G G/G G/G G/G G/G

35 3470 T/T T/T T/T T/T T/T T/T T/T T/T

36 4183 G/G G/G G/G G/G G/G G/G G/G G/G

37 4201 C/C C/C C/C C/C C/C C/C C/C C/C

38 4254 T/T T/T T/T T/T T/T T/T T/T T/T

39 4384 A/A A C C/C C/A A/A A/C C/C C/C

40 4435 C/C C/C C/C C/C C/C C/C C/C C/C

41 5180 G/C G/C C/C C/G G/C G/C C/C C/C

42 5212 C/C C/C C/C C/C C/C C/C C/C C/C PS PS Haplotype Pair(c) (Part 3)

No.(a) Position(b) 23/1 32/20 15/12 23/26 23/18 23/27 32/2 15/34

1 636 G/A G/G G/G G/G G/G G/G G/G G/G

2 678 T/T T/T T/T T/T T/T T/T T/C T/T

3 769 G/G G/G G/G G/G G/G G/G G/G G/G

4 776 A/A A/A A/A A/A A/A A/A A/A A/A

5 825 G/G G/G G/G G/G G/G G/G G/G G/G

6 915 T/T T/T T/T T/T T/T T/T T/T T/T

7 1019 G/G G/G G/G G/G G/G G/G G/G G/G

8 1031 G/G G/G G/G G/G G/G G/G G/G G/G

9 1100 C/C T/C C/C C/T C/C C/T T/C C/T

10 1827 G/G G/G G/G G/G G/G G/G G/G G/G

11 1843 T/T G/T G/G T/G T/G T/G G/G G/T

12 1966 G/G G/G G/G G/G G/G G/G G/G G/G

13 1974 C/C C/C C/C C/A C/C C/A C/C C/A

14 1984 A/A A/A A/A A/A A/A A/A A/A A/A

15 1997 C/C C/C C/C C/G C/C C/G C/C C/G

16 2014 T/T T/T T/T T/T T/T T/T T/T T/T

17 2022 A/A A/A A/A A/A A/A A/A A/A A/A

18 2023 C/C C/C C/C C/C C/T C/C C/C C/C

19 2028 A/A A/A A/A A/A A/A A/A A/A A/A

20 2036 T/T T/T T/T T/T T/T T/T T/T T/T

21 2039 C/C T/C C/C C/C C/C C/C T/C C/C

22 2062 A/A A/A A/A A/A A/A A/A A/A A/A

23 2067 T/T T/T T/G T/T T/T T/T T/T T/T

24 2118 C/C C/C C/C C/C C/C C/C C/C C/C

25 2170 G/G G/A G/G G/G G/G G/G G/G G/G

26 2179 G/G G/G G/G G/G G/G G/G G/G G/G

27 2611 T/T T/T T/T T/T T/T T/T T/T T/T

28 2635 T/T T/T T/T T/T T/T T/T T/T T/T

29 2659 G/G G/G G/G G/G G/G G/G G/G G/G

30 2661 G/G C/G C/G G/C G/C G/C C/C C/C

31 2704 C/C C/C C/C C/C C/C C/C C/C C/C

32 2716 G/G G/G G/G G/G G/G G/G G/G G/G

33 2846 G/G G/G G/G G/A G/G G/G G/G G/A

34 3292 G/G G/G G/G G/G G/G G/G G/G G/G

35 3470 T/T T/T T/T T/T T/C T/T T/T T/T

36 4183 G/G G/G G/G G/G G/G G/G G/G G/G

37 4201 C/C C/C C/C C/C C/C C/C C/C C/C

38 4254 T/T T/T T/T T/T T/T T/T T/T T/T

39 4384 A/A C/A C/A A/C A/C AC C/C C/A

40 4435 C/C C/C C/C C/C C/C C/A C/C C/C

41 5180 G/C C/G C/G G/C G/C G/C C/C C/G

42 5212 C/C C/C C/C C/C C/C C/C C/C C/C PS PS Haplotype Pair(c) (Part 4)

No.(a) Position(b) 15/14 23/8 23/28 15/7 23/10 23/5 32/17 15/26

1 636 G/G G/G G/G G/G G/G G/G G/G G/G

2 678 T/T T/T T/T T/T T/T T/T T/T T/T

3 769 G/G G/G G/G G/G G/G G/G G/G G/G

4 776 A/A A/A A/A A/A A/A A/A A/A A/A

5 825 G/G G/G G/G G/G G/G G/G G/G G/G

6 915 T/T T/T T/T T/T T/T T/C T/T T/T

7 1019 G/G G/G G/G G/G G/G G/G G/G G/G

8 1031 G/G G/A G/G G/A G/G G/G G/G G/G

9 1100 C/C C/C C/T C/C C/C C/C T/C C/T

10 1827 G/G G/G G/G G/G G/G G/G G/G G/G

11 1843 G/G T/G T/G G/G T/G T/T G/G G/G

12 1966 G/G G/G G/G G/G G/A G/G G/G G/G

13 1974 C/C C/C C/A C/C C/C C/C C/C C/A

14 1984 A/A A/A A/A A/A A/A A/A A/A A/A

15 1997 C/C C/C C/G C/C C/C C/C C/C C/G

16 2014 T/T T/T T/T T/T T/T T/T T/T T/T

17 2022 A/A A/A A/A A/A A/A A/A A/A A/A

18 2023 C/C C/C C/C C/C C/C C/C C/C C/C

19 2028 AA A/A A/A A/A A/A A/A A/A A/A

20 2036 T/T T/T T/T T/T T/T T/T T/T T/T

21 2039 C/C C/C C/C C/C C/C C/C T/C C/C

22 2062 A/A A/A A/A A/A A/A A/A A/A A/A

23 2067 T/T T/T T/T T/T T/T T/T T/T T/T

24 2118 C/C C/C C/C C/C C/C C/C C/C C/C

25 2170 G/G G/G G/G G/G G/G G/G G/G G/G

26 2179 G/G G/G G/G G/G G/G G/G G/G G/G

27 2611 T/T T/T T/T T/T T/T T/T T/T T/T

28 2635 T/T T/T T/T T/T T/T T/T T/T T/T

29 2659 G/G G/G G/G G/G G/G G/G G/G G/G

30 2661 C/C G/G G/C C/C G/C G/G C/G C/C

31 2704 C/C C/C C/C C/C C/C C/C C/C C/C

32 2716 G/A G/G G/G G/G G/G G/G G/G G/G

33 2846 G/G G/G G/G G/G G/G G/G G/G G/A

34 3292 G/G G/G G/G G/G G/G G/G G/G G/G

35 3470 T/T T/T T/T T/T T/T T/T T/T T/T

36 4183 G/G G/G G/G G/G G/G G/G G/G G/G

37 4201 C/C C/C C/C C/C C/C C/C C/C C/C

38 4254 T/T T/T T/T T/T T/T T/T T/T T/T

39 4384 C/C A/C A/C C/C A/C A/A C/A C/C

40 4435 C/C C/C C/C C/C C/C C/C C/C C/C

41 5180 C/C G/C G/C C/C G/C G/C C/G C/C 2 5212 C/C C/C C/C C/C C/C C/C C/C C/C PS PS Haplotype Pair(c) (Part 5)

No.(a) Position(b) 15/11 32/4 26/19 23/4 32/12 30/29 23/6 23/32

1 636 G/G G/G G/G G/G G/G G/G G/G G/G

2 678 T/T T/T T/T T/T T/T T/T T/T T/T

3 769 G/G G/G G/G G/G G/G G/G G/G G/G

4 776 A/A A/A A/A A/A A/A A/A A/A A/A

5 825 G/G G/A G/G G/A G/G G/G G/G G/G

6 915 T/T T/T T/T T/T T/T T/T T/T T/T

7 1019 G/G G/G G/G G/G G/G G/G G/A G/G

8 1031 G/G G/G G/G G/G G/G G/G G/G G/G

9 1100 C/C T/C T/C C/C T/C T/T C/C C/T

10 1827 G/G G/G G/G G/G G/G G/G G/G G/G

11 1843 G/G G/G G/G T/G G/G G/G T/G T/G

12 1966 G/G G/G G/G G/G G/G G/G G/G G/G

13 1974 C/C C/C A/C C/C C/C A/A C/C C/C

14 1984 A/A AA A/A A/A A/A G/G A/A A/A

15 1997 C/C C/C G/C C/C C/C G/G C/C C/C

16 2014 T/T T/T T/T T/T T/T T/T T/T T/T

17 2022 A/A A/A A/A A/A A/A A/A AA A/A

18 2023 C/C C/C C/T C/C C/C C/C C/C C/C

19 2028 A/A A/A A/A A/A A/A A/A A/A A/A

20 2036 T/T T/T T/T T/T T/T T/T T/T T/T

21 2039 C/C T/C C/C C/C T/C C/C C/C C/T

22 2062 A/A A/A A/A A/A A/A A/A A/A A/A

23 2067 T/G T/T T/T T/T T/G T/T T/T T/T

24 2118 C/C C/C C/C C/C C/C C/C C/C C/C

25 2170 G/G G/G G/G G/G G/G G/G G/G G/G

26 2179 G/C G/G G/G G/G G/G G/G G/G G/G

27 2611 T/T T/T T/T T/T T/T T/T T/T T/T

28 2635 T/T T/T T/T T/T T/T T/T T/T T/T

29 - 2659 G/G G/A G/G G/A G/G G/G G/G G/G

30 2661 C/G C/C C/C G/C C/G C/C G/C G/C

31 2704 C/C C/C C/C C/C C/C C/C C/G C/C

32 2716 G/G G/G G/G G/G G/G G/G G/G G/G

33 2846 G/G G/G A/G G/G G/G G/A G/G G/G

34 3292 G/G G/A G/G G/A G/G G/G G/G G/G

35 3470 T/T T/T T/T T/T T/T T/T T/T T/T

36 4183 G/G G/A G/G G/A G/G G/G G/G G/G

37 4201 C/C C/C C/C C/C C/C C/C C/C C/C

38 4254 T/T T/T T/T T/T T/T T/T T/T T/T

39 4384 C/A C/C C/C A/C C/A C/C A/C A/C

40 4435 C/C C/C C/C C/C C/C A/C C/C C/C

41 5180 C/G C/C C/C G/C C/G C/C G/C G/C

42 5212 C/C C/C C/C C/C C/C C/C C/C C/C PS PS Haplotype Pair(c) (Part 6)

No.(a) Position(b) 23/15 15/3 26/2 15/32 23/22 4/31 15/31 15/4

1 636 G/G G/G G/G G/G G/G G/G G/G G/G 2 678 T/T T/T T/C T/T T/T T/T T/T T/T 3 769 G/G G/C G/G G/G G/G G/G G/G G/G 4 776 A/A A/G A/A A/A A/A A/A A/A A/A 5 825 G/G G/G G/G G/G G/G A/G G/G G/A 6 915 T/T T/T T/T T/T T/T T/T T/T T/T 7 1019 G/G G/G G/G G/G G/G G/G G/G G/G

1031 G/G G/G G/G G/G G/G G/G G/G G/G

9 1100 C/C C/T T/C C/T C/C C/T C/T C/C

10 1827 G/G G/G G/G G/G G/G G/G G/G G/G

11 1843 T/G G/G G/G G/G T/T G/G G/G G/G

12 1966 G/G G/G G/G G/G G/G G/G G/G G/G

13 1974 C/C C/C A/C C/C C/C C/C C/C C/C

14 1984 A/A A/A A/A A/A A/A A/A A/A A/A

15 1997 C/C C/C G/C C/C C/C C/C C/C C/C

16 2014 T/T T/T T/T T/T T/T T/T T/T T/T

17 2022 A/A AA A/A A/A A/A A/A A/A A/A

18 2023 C/C C/C C/C C/C C/C C/C C/C C/C

19 2028 A/A A/A A/A A/A A/A A/A A/A A/A

20 2036 T/T T/T T/T T/T T/T T/T T/T T/T

21 2039 C/C C/T C/C C/T C/C C/T C/T C/C

22 2062 A/A A/A A/A A/A A/A A/A A/A A/A

23 2067 T/T T/T T/T T/T T/T T/T T/T T/T

24 2118 C/C C/C C/C C/C C/C C/C C/C C/C

25 2170 G/G G/G G/G G/G G/G G/G G/G G/G

26 2179 G/G G/G G/G G/G G/G G/G G/G G/G

27 2611 T/T T/T T/T T/T T/T T/T T/T T/T

28 2635 T/T T/T T/T T/T T/T T/T T/T T/T

29 2659 G/G G/G G/G G/G G/G A/G G/G G/A

30 2661 G/C C/C C/C C/C G/G C/C C/C C/C

31 2704 C/C C/C C/C C/C C/C C/C C/C C/C

32 2716 G/G G/G G/G G/G G/G G/G G/G G/G

33 2846 G/G G/G A/G G/G G/G G/A G/A G/G

34 3292 G/G G/G G/G G/G G/G A/G G/G G/A

35 3470 T/T T/T T/T T/T T/T T/T T/T T/T

36 4183 G/G G/G G/G G/G G/G A/G G/G G/A

37 4201 C/C C/C C/C C/C C/C C/C C/C C/C

38 4254 T/T T/T T/T T/T T/T T/T T/T T/T

39 4384 A/C C/C C/C C/C A/A C/C C/C C/C

40 4435 C/C C/C C/C C/C C/C C/C C/C C/C

41 5180 G/C C/C C/C C/C G/C C/C C/C C/C

42 5212 C/C C/C C/C C/C C/C C/C C/C C/C

(a) PS = polymoφhic site;

(b)Position of PS in SEQ ID NOJ;

(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.

3. A method for genotyping the Cytochrome P450, subfamily IID, Polypeptide 6 (CYP2D6) gene of an individual, comprising determining for the two copies of the CYP2D6 gene present in the individual the identity ofthe nucleotide pair at one or more polymoφhic sites (PS) selected from the group consisting of PSI, PS2, PS3, PS4, PS6, PS10, PS12, PSM, PS15, PS16, PS17, PS18, PS19, PS20, PS22, PS23, PS24, PS26, PS27, PS28, PS29, PS32, PS34, PS36, PS37, PS38, PS39, PS40 and PS42, wherein the one or more polymoφhic sites (PS) have the position and alternative alleles shown in SEQ ID NOJ.

4. The method of claim 3, wherein the determining step comprises:

(a) isolating from the individual a nucleic acid mixture comprising both copies ofthe CYP2D6 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 CYP2D6 gene present in the individual the identity ofthe nucleotide pair at each of PS1-PS42.

6. A method for haplotyping the Cytochrome P450, subfamily IID, Polypeptide 6 (CYP2D6) gene of an individual which comprises determining, for one copy of the CYP2D6 gene present in the individual, the identity ofthe nucleotide at two or more polymoφhic sites (PS) selected from the group consisting of PSI, PS2, PS3, PS4, PS6, PS10, PS12, PSM, PS15, PS16, PS17, PS18, PS19, PS20, PS22, PS23, PS24, PS26, PS27, PS28, PS29, PS32, PS34, PS36, PS37, PS38, PS39, PS40 and PS42, wherein the selected PS have the position and alternative alleles shown in SEQ ID NOJ.

7. The method of claim 6, further comprising determining the identity ofthe nucleotide at one or more polymoφhic sites selected from the group consisting of PS5, PS7, PS8, PS9, PSI 1, PS 13, PS21, PS25, PS30, PS31, PS33, PS35 and PS41, wherein the one or more polymoφhic sites (PS) have the position and alternative alleles shown in SEQ ID NOJ.

8. 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 CYP2D6 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;

A method for predicting a haplotype pair for the Cytochrome P450, subfamily IID, Polypeptide 6 (CYP2D6) gene ofan individual comprising:

(a) identifying a CYP2D6 genotype for the individual, wherein the genotype comprises the nucleotide pair at two or more polymoφhic sites (PS) selected from the group consisting of PSI, PS2, PS3, PS4, PS6, PS10, PS12, PSM, PS15, PS16, PS17, PS18, PS19, PS20, PS22, PS23, PS24, PS26, PS27, PS28, PS29, PS32, PS34, PS36, PS37, PS38, PS39, PS40 and PS42, wherein the selected PS have the position and alternative alleles shown in SEQ ID NOJ;

(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) 15/15 19/19 32/32 7/7 15/20 15/19 23/33 22/2C

1 636 G/G G/G G/G G/G G/G G/G G/G G/G

2 678 T/T T/T T/T T/T T/T T/T T/T T/T

3 769 G/G G/G G/G G/G G/G G/G G/G G/G

4 776 A/A A/A A/A A/A A/A A/A A/A A/A

5 825 G/G G/G G/G G/G G/G G/G G/G G/G

6 915 T/T T/T T/T T/T T/T T/T T/T T/T

7 1019 G/G G/G G/G G/G G/G G/G G/G G/G

8 1031 G/G G/G G/G A/A G/G G/G G/G G/G

9 1100 C/C C/C T/T C/C C/C C/C C/T C/C

10 1827 G/G G/G G/G G/G G/G G/G G/G G/G

11 1843 G/G G/G G/G G/G G/T G/G T/G T/T

12 1966 G/G G/G G/G G/G G/G G/G G/G G/G

13 1974 C/C C/C C/C C/C C/C C/C C/C C/C

14 1984 A/A A/A A/A A/A A/A A/A A/A A/A

15 1997 C/C C/C C/C C/C C/C C/C C/C C/C

16 2014 T/T T/T T/T T/T T/T T/T T/T T/T

17 2022 A/A A/A A/A A/A A/A A/A A/A A/A

18 2023 C/C T/T C/C C/C C/C C/T C/C C/C

19 2028 A/A A/A A/A A/A A/A A/A A/A A/A

20 2036 T/T T/T T/T T/T T/T T/T T/T T/T

21 2039 C/C C/C T/T C/C C/C C/C C/T C/C

22 2062 A/A A/A A/A A/A A/A A/A A/A A/A

23 2067 T/T T/T T/T T/T T/T T/T T/T T/T

24 2118 C/C C/C C/C C/C C/C C/C C/C C/C

25 2170 G/G G/G G/G G/G G/A G/G G/G G/A

26 2179 G/G G/G G/G G/G G/G G/G G/G G/G

27 2611 T/T T/T T/T T/T T/T T/T T/T T/T

28 2635 T/T T/T T/T T/T T/T T/T T/T T/T

29 2659 G/G G/G G/G G/G G/G G/G G/G G/G

30 2661 C/C C/C C/C C/C C/G C/C G/C G/G

31 2704 C/C C/C C/C C/C C/C C/C C/C C/C

32 2716 G/G G/G G/G G/G G/G G/G G/G G/G

33 2846 G/G G/G G/G G/G G/G G/G G/G G/G

34 3292 G/G G/G G/G G/G G/G G/G G/G G/G

35 3470 T/T T/T T/T T/T T/T T/T T/T T/T

36 4183 G/G G/G G/G G/G G/G G/G G/G G/G

37 4201 C/C C/C C/C C/C C/C C/C C/T C/C

38 4254 T/T T/T T/T T/T T/T T/T T/T T/T

39 4384 C/C C/C C/C C/C C/A C/C A/C A/A

40 4435 C/C C/C C/C C/C C/C C/C C/C C/C

41 5180 C/C C/C C/C C/C C/G C/C G/C C/G

42 5212 C/C C/C C/C C/C C/C C/C C/C C/C PS PS Haplotype Pair(c) (Part 2)

No.(a) Position(b) 23/24 23/25 15/9 32/21 23/16 20/28 32/13 32/26

1 636 G/G G/G G/G G/G G/G G/G G/G G/G

2 678 T/T T/T T/T T/T T/T T/T T/T T/T

3 769 G/G G/G G/G G/G G/G G/G G/G G/G

4 776 A/A A/A A/A A/A A/A A/A A/A A/A

5 825 G/G G/G G/G G/G G/G G/G G/G G/G

6 915 T/T T/T T/T T/T T/T T/T T/T T/T

7 1019 G/G G/G G/G G/G G/G G/G G/G G/G

8 1031 G/G G/G G/G G/G G/G G/G G/G G/G

9 1100 C/C C/T C/C T/C C/C C/T T/C T/T

10 1827 G/G G/G G/C G/G G/G G/G G/G G/G

11 1843 T/T T/G G/G G/T T/G T/G G/G G/G

12 1966 G/G G/G G/G G/G G/G G/G G/G G/G

13 1974 C/C C/A C/C C/C C/C C/A C/C C/A

14 1984 A/A A/A A/A A/A A/A A/A A/A A/A

15 1997 C/C C/C C/C C/C C/C C/G C/C C/G

16 2014 T/T T/T T/T T/T T/T T/T T/T T/T

17 2022 A/A A/A A/A A/A A/A A/A A/A A/A

18 2023 C/C C/C C/T C/C C/C C/C C/C C/C

19 2028 A/A A/A A/A A/A A/A A/A A/A A/A

20 2036 T/T T/T T/T T/T T/T T/T T/T T/T

21 2039 C/C C/C C/C T/C C/C C/C T/C T/C

22 2062 A/A A/A A/A A/A A/A A/A A/A A/A

23 2067 T/T T/T T/T T/T T/T T/T T/T T/T

24 2118 C/T C/C C/C C/C C/C C/C C/C C/C

25 2170 G/G G/G G/G G/G G/G A/G G/G G/G

26 2179 G/G G/G G/G G/G G/G G/G G/G G/G

27 2611 T/T T/T T/T T/T T/T T/T T/A T/T

28 2635 T/T T/T T/C T/T T/T T/T T/T T/T

29 2659 G/G G/G G/G G/G G/G G/G G/G G/G

30 2661 G/G G/C C/C C/C G/G G/C C/C C/C

31 2704 C/C C/C C/C C/C C/C C/C C/C C/C

32 2716 G/G G/G G/G G/G G/G G/G G/G G/G

33 2846 G/G G/G G/G G/G G/G G/G G/G G/A

34 3292 G/G G/G G/G G/G G/G G/G G/G G/G

35 3470 T/T T/T T/T T/T T/T T/T T/T T/T

36 4183 G/G G/G G/G G/G G/G G/G G/G G/G

37 4201 C/C C/C C/C C/C C/C C/C C/C C/C

38 4254 T/T T/T T/T T/T T/T T/T T/T T/T

39 4384 A/A A/C C/C C/A A/A A/C C/C C/C

40 4435 C/C C/C C/C C/C C/C C/C C/C C/C

41 5180 G/C G/C C/C C/G G/C G/C C/C C/C

42 5212 C/C C/C C/C C/C C/C C/C C/C C/C PS PS Haplotype Pair(c) (Part 3)

No.(a) Position(b) 23/1 32/20 15/12 23/26 23/18 23/27 32/2 15/34

1 636 G/A G/G G/G G/G G/G G/G G/G G/G

2 678 T/T T/T T/T T/T T/T T/T T/C T/T

3 769 G/G G/G G/G G/G G/G G/G G/G G/G

4 776 A/A A/A A/A A/A A/A A/A A/A A/A

5 825 G/G G/G G/G G/G G/G G/G G/G G/G

6 915 T/T T/T T/T T/T T/T T/T T/T T/T

7 1019 G/G G/G G/G G/G G/G G/G G/G G/G

8 1031 G/G G/G G/G G/G G/G G/G G/G G/G

9 1100 C/C T/C C/C C/T C/C C/T T/C C/T

10 1827 G/G G/G G/G G/G G/G G/G G/G G/G

11 1843 T/T G/T G/G T/G T/G T/G G/G G/T

12 1966 G/G G/G G/G G/G G/G G/G G/G G/G

13 1974 C/C C/C C/C C/A C/C C/A C/C C/A

14 1984 A/A A/A A/A A/A A/A A/A A/A A/A

15 1997 C/C C/C C/C C/G C/C C/G C/C C/G

16 2014 T/T T/T T/T T/T T/T T/T T/T T/T

17 2022 A/A A/A A/A A/A A/A A/A A/A A/A

18 2023 C/C C/C C/C C/C C/T C/C C/C C/C

19 2028 A/A A/A A/A A/A A A A/A A/A A/A

20 2036 T/T T/T T/T T/T T/T T/T T/T T/T

21 2039 C/C T/C C/C C/C C/C C/C T/C C/C

22 2062 A/A A/A A/A A/A A/A A/A A/A A/A

23 2067 T/T T/T T/G T/T T/T T/T T/T T/T

24 2118 C/C C/C C/C C/C C/C C/C C/C C/C

25 2170 G/G G/A G/G G/G G/G G/G G/G G/G

26 2179 G/G G/G G/G G/G G/G G/G G/G G/G

27 2611 T/T T/T T/T T/T T/T T/T T/T T/T

28 2635 T/T T/T T/T T/T T/T T/T T/T T/T

29 2659 G/G G/G G/G G/G G/G G/G G/G G/G

30 2661 G/G C/G C/G G/C G/C G/C C/C C/C

31 2704 C/C C/C C/C C/C C/C C/C C/C C/C

32 2716 G/G G/G G/G G/G G/G G/G G/G G/G

33 2846 G/G G/G G/G G/A G/G G/G G/G G/A

34 3292 G/G G/G G/G G/G G/G G/G G/G G/G

35 3470 T/T T/T T/T T/T T/C T/T T/T T/T

36 4183 G/G G/G G/G G/G G/G G/G G/G G/G

37 4201 C/C C/C C/C C/C C/C C/C C/C C/C

38 4254 T/T T/T T/T T/T T/T T/T T/T T/T

39 4384 A/A C/A C/A A/C A/C A/C C/C C/A

40 4435 C/C C/C C/C C/C C/C C/A C/C C/C

41 5180 G/C C/G C/G G/C G/C G/C C/C C/G

42 5212 C/C C/C C/C C/C C/C C/C C/C C/C 4- to

W tJ t

O O O O H O O O O O O O O H H O O H _> Q H |> Ω 1> o ;> Ω Q Q o o o ^o o on o o o o H Ω O o o > ooo H H O O Ω H > Ω H > Ω > o > o O O O o o o > o o

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OJ Ω Ω Ω~ Ω H O O H^" O O C5 O H H O O O > o H > > H Ω > Ω O O C5 o o > o o ^ -34-

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PS PS Haplotype Pair(c) (Part 5)

No.(a) Position(b) 15/11 32/4 26/19 23/4 32/12 30/29 23/6 23/32

1 636 G/G G/G G/G G/G G/G G/G G/G G/G

2 678 T/T T/T T/T T/T T/T T/T T/T T/T

3 769 G/G G/G G/G G/G G/G G/G G/G G/G

4 776 A/A A/A A/A A/A A/A A/A A/A A/A

5 825 G/G G/A G/G G/A G/G G/G G/G G/G

6 915 T/T T/T T/T T/T T/T T/T T/T T/T

7 1019 G/G G/G G/G G/G G/G G/G G/A G/G

8 1031 G/G G/G G/G G/G G/G G/G G/G G/G

9 1100 C/C T/C T/C C/C T/C T/T C/C C/T

10 1827 G/G G/G G/G G/G G/G G/G G/G G/G

11 1843 G/G G/G G/G T/G G/G G/G T/G T/G

12 1966 G/G G/G G/G G/G G/G G/G G/G G/G

13 1974 C/C C/C A/C C/C C/C A/A C/C C/C

14 1984 A/A A/A A/A A/A A/A G/G A/A A/A

15 1997 C/C C/C G/C C/C C/C G/G C/C C/C

16 2014 T/T T/T T/T T/T T/T T/T T/T T/T

17 2022 A/A A/A A/A A/A A/A A/A A/A A/A

18 2023 C/C C/C C/T C/C C/C C/C C/C C/C

19 2028 A/A A/A A/A A/A A/A A/A A/A A/A

20 2036 T/T T/T T/T T/T T/T T/T T/T T/T

21 2039 C/C T/C C/C C/C T/C C/C C/C C/T

22 2062 A/A A/A A/A A/A A/A A/A A/A A/A

23 2067 T/G T/T T/T T/T T/G T/T T/T T/T

24 2118 C/C C/C C/C C/C C/C C/C C/C C/C

25 2170 G/G G/G G/G G/G G/G G/G G/G G/G

26 2179 G/C G/G G/G G/G G/G G/G G/G G/G

27 2611 T/T T/T T/T T/T T/T T/T T/T T/T

28 2635 T/T T/T T/T T/T T/T T/T T/T T/T

29 2659 G/G G/A G/G G/A G/G G/G G/G G/G

30 2661 C/G C/C C/C G/C C/G C/C G/C G/C

31 2704 C/C C/C C/C C/C C/C C/C C/G C/C

32 2716 G/G G/G G/G G/G G/G G/G G/G G/G

33 2846 G/G G/G A/G G/G G/G G/A G/G G/G

34 3292 G/G G/A G/G G/A G/G G/G G/G G/G

35 3470 T/T T/T T/T T/T T/T T/T T/T T/T

36 4183 G/G G/A G/G G/A G/G G/G G/G G/G

37 4201 C/C C/C C/C C/C C/C C/C C/C C/C

38 4254 T/T T/T T/T T/T T/T T/T T/T T/T

39 4384 C/A C/C C/C A/C C/A C/C A/C A/C

40 4435 C/C C/C C/C C/C C/C A/C C/C C/C

41 5180 C/G C/C C/C G/C C/G C/C G/C G/C 2 5212 C/C C/C C/C C/C C/C C/C C/C C/C PS PS Haplotype Pair(c) (Part 6)

No.(a) Position(b) 23/15 15/3 26/2 15/32 23/22 4/31 15/31 15/4

1 636 G/G G/G G/G G/G G/G G/G G/G G/G

2 678 T/T T/T T/C T/T T/T T/T ^■T/T T/T

3 769 G/G G/C G/G G/G G/G G/G G/G G/G

4 776 A/A A/G A/A A/A A/A A/A A/A A/A

5 825 G/G G/G G/G G/G G/G A/G G/G G/A

6 915 T/T T/T T/T T/T T/T T/T T/T T/T

7 1019 G/G G/G G/G G/G G/G G/G G/G G/G

8 1031 G/G G/G G/G G/G G/G G/G G/G G/G

9 1100 C/C C/T T/C C/T C/C C/T C/T C/C

10 1827 G/G G/G G/G G/G G/G G/G G/G G/G

11 1843 T/G G/G G/G G/G T/T G/G G/G G/G

12 1966 G/G G/G G/G G/G G/G G/G G/G G/G

13 1974 C/C C/C A/C C/C C/C C/C C/C C/C

14 1984 A/A A/A A/A A/A A/A A/A A/A A/A

15 1997 C/C C/C G/C C/C C/C C/C C/C C/C

16 2014 T/T T/T T/T T/T T/T T/T T/T T/T

17 2022 A/A A/A A/A A/A A/A A/A A/A A/A

18 2023 C/C C/C C/C C/C C/C C/C C/C C/C

19 2028 A/A A/A A/A A/A A/A A/A A/A A/A

20 2036 T/T T/T T/T T/T T/T T/T T/T T/T

21 2039 C/C C/T C/C C/T C/C C/T C/T C/C

22 2062 A/A A/A A/A A/A A/A A/A A/A A/A

23 2067 T/T T/T T/T T/T T/T T/T T/T T/T

24 2118 C/C ^•C/C C/C C/C C/C C/C C/C C/C

25 2170 G/G G/G G/G G/G G/G G/G G/G G/G

26 2179 G/G G/G G/G G/G G/G G/G G/G G/G

27 2611 T/T T/T T/T T/T T/T T/T T/T T/T

28 2635 T/T T/T T/T T/T T/T T/T T/T T/T

29 2659 G/G G/G G/G G/G G/G A/G G/G G/A

30 2661 G/C C/C C/C C/C G/G C/C C/C C/C

31 2704 C/C C/C C/C C/C C/C C/C C/C C/C

32 2716 G/G G/G G/G G/G G/G G/G G/G G/G

33 2846 G/G G/G A/G G/G G/G G/A G/A G/G

34 3292 G/G G/G G/G G/G G/G A/G G/G G/A

35 3470 T/T T/T T/T T/T T/T T/T T/T T/T

36 4183 G/G G/G G/G G/G G/G A/G G/G G/A

37 4201 C/C C/C C/C C/C C/C C/C C/C C/C

38 4254 T/T T/T T/T T/T T/T T/T T/T T/T

39 4384 A/C C/C C/C C/C A/A C/C C/C C/C

40 4435 C/C C/C C/C C/C C/C C/C C/C C/C

41 5180 G/C C/C C/C C/C G/C C/C C/C C/C

42 5212 C/C C/C C/C C/C C/C C/C C/C C/C

(a) PS = polymoφhic site;

(b) Position of PS in SEQ ID NOJ;

(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.

10. The method of claim 9, wherein the identified genotype ofthe individual comprises the nucleotide pair at each of PS1-PS42, which have the position and alternative alleles shown in

SEQ ID NOJ.

1. A method for identifying an association between a trait and at least one haplotype or haplotype pair ofthe Cytochrome P450, subfamily IID, Polypeptide 6 (CYP2D6) 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 1-34 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:

-J. tO

on t to

ΩΩΩ>HΩOHOOOΩOOHHOOOH ΩH Ω>HΩ>ΩOHOΩOOHO>OH>_'-

OΩΩΩHΩOHOOOΩΩOHHOOΩH ΩH Ω>HΩ ΩOOOΩOOHO>OΩOM

TJ

ΩΩΩΩHΩOHOOOΩΩOHHθOΩH ΩH>Ω HΩ>ΩOOOΩ>OHO θHθ-J^

OΩΩΩHΩOHOOOΩOOHHOOΩH ΩH Ω>HΩ>ΩOOOΩ OHO>OHO∞

Ω Ω Ω-Ω HΩOHOOOΩΩOΩHθOΩH ΩH>H>HΩ>ΩOOΩΩOOHO>θHθ^>

OΩΩΩHΩOHOOOΩΩOHHOOΩH>ΩH Ω>HΩ>Ω>OOΩOOHO>OH03

-^ -^ -ji w w ω ω wj w w ω w w io t t to to to t to to to i-' f- i-' ^ h- f- so oo -~4 0s on -t-. OJ t to >— ' θ Vθ oo -o σs θn -1-. θJ tθ ⁾— ' © so oo _^o os on 4-. oj to .-> o so oo --i ON On 4- ω to O 2 TJ o ∞

W t^{O h}- oo

M O

ΩOΩ>HΩOHOOOΩOOHHΩOΩO>ΩH>Ω HΩ>ΩOOOΩOOHO>OHO^:

ΩOΩ>HΩOHOO ΩOOHHOOΩO>ΩH>Ω>HΩ>ΩOOOΩOOHO OHO^

ΩOΩ>HΩOHOOOΩOOHHOOΩH>ΩH>Ω>HΩ ΩΩOOΩOΘHO>OHΘ!^S_IJ to ΩΩΩΩHΩOOOOOOΩOHHOOOH>ΩH>H;>HΩ>ΩOOOOOOHO;>OHΩ£.

ΩΩΩΩHΩOHOOOΩΩOHHOOΩH>ΩH>H>HΩ>ΩOOOΩOθHO>OHθS

ΩOΩ>HΩOHOOOOOOHHO>ΩH>ΩH Ω HΩ>ΩOHOΩOOHO>OHOS

Ψ

W w *-o Jwⁱ

NOlΛ

ΩOΩ>HΩOHOOOΩΩOHHOOOH>ΩH>Ω HΩ ΩOHOΩOΩHO>OHO to

ΩΩΩ>HΩOHOOOΩOOHHOOOH>ΩH>Ω>HΩ>ΩOHOΩOOHO OHOK

SO

OΩ>ΩHΩOHOOOΩΩOHHOOΩH>ΩH>Ω HO>>OOOHOOHO OHO^^

OJ

ΩΩOΩHΩθHθOOΩΩOHHOOΩH ΩH>Ω HO>>OOOHOθHO>OHOc^

ΩΩΩΩHΩ^QHθ>OΩΩΩHHOOΩH>ΩH>Ω>HOO>OΩOHOΩHO> HOS

ΩΩ>ΩHΩOHOOOΩΩOHHOOΩH>ΩH Ω HOO>OOOHOOHO>ΩHOo

PS PS Haplotype Number(c) (Part 4)

No.(a) Position(b) 31 32 33 34

1 636 G G G G

2 678 T T T T

3 769 G G G G

4 776 A A A A

5 825 G G G G

6 915 T T T T

7 1019 G G G G

8 1031 G G G G

9 1100 T T T T

10 1827 G G G G

11 1843 G G G T

12 1966 G G G G

13 1974 C C C A

14 1984 A A A A

15 1997 C C C G

16 2014 T T T T

17 2022 A A A A

18 2023 C C C C

19 2028 A A A A

20 2036 T T T T

21 2039 T T T C

22 2062 A A A A

23 2067 T T T T

24 2118 C C C C

25 2170 G G G G

26 2179 G G G G

27 2611 T T T T

28 2635 T T T T

29 2659 G G G G

30 2661 C C C C

31 2704 C C C C

32 2716 G G G G

33 2846 A G G A

34 3292 G G G G

35 3470 T T T T

36 4183 G G G G

37 4201 C C T C

38 4254 T T T T

39 4384 C C C A

40 4435 C C C C

41 5180 C C C G

42 5212 C C C C

(a) PS = polymoφhic site;

(b) Position of PS within SEQ ID NOJ;

(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 CYP2D6 haplotype pairs consists of first and second haplotypes which comprise first and second sequences of polymoφhisms whose positions in 4-. 4- tθ

ΩΩΩΩHΩ |Hθ Ω _!HHQQΩH- Ω_!H^Ω^H ^ QOQΩQQ|H ^ ^Q^ ΩΩ~ΩΩ^~H^'OOHOOOΩΩ~OHHOO~ΩH>ΩH>Ω>H^'Ω>OΩOOOOOHO 0^ ^C^~-

ΩΩ ΩH_ΩQH^QQΩΩQH_H_^QQΩH. H_;>!-I ΩΓ5Ω?5^ΩOHOOOΩΓ5OHHOOΩH ΩH>H >HΩ>ΩOOOΩOOHO>OH s

ΩΩ ;>HΩ H_OQQΩQQH_^HQQΩH - Ω ;H J> Ω > H Ω ΩOHQOQOHO 0 oK Ω^Ω>^ΩOHOOOΓ5C5OHHO ^:ΩH > Ω H > Ω j H^" ?5 ΩOHθfiθOHC5>^0 o to

©

PS PS Haplotype Pair(c) (Part 2)

No.(a) Position(b) 23/24 23/25 15/9 32/21 23/16 20/28 32/13 32/26

1 636 G/G G/G G/G G/G G/G G/G G/G G/G

2 678 T/T T/T T/T T/T T/T T/T T/T T/T

3 769 G/G G/G G/G G/G G/G G/G G/G G/G

4 776 A/A A/A A/A A/A A/A A/A A/A A/A

5 825 G/G G/G G/G G/G G/G G/G G/G G/G

6 915 T/T T/T T/T T/T T/T T/T T/T T/T

7 1019 G/G G/G G/G G/G G/G G/G G/G G/G

8 1031 G/G G/G G/G G/G G/G G/G G/G G/G

9 1100 C/C C/T C/C T/C C/C C/T T/C T/T

10 1827 G/G G/G G/C G/G G/G G/G G/G G/G

11 1843 T/T T/G G/G G/T T/G T/G G/G G/G

12 1966 G/G G/G G/G G/G G/G G/G G/G G/G

13 1974 C/C C/A C/C C/C C/C C/A C/C C/A

14 1984 A/A A/A A/A A/A A/A A/A A/A A/A

15 1997 C/C C/C C/C C/C C/C C/G C/C C/G

16 2014 T/T T/T T/T T/T T/T T/T T/T T/T

17 2022 A/A A/A A/A A/A A/A A/A A/A A/A

18 2023 C/C C/C C/T C/C C/C C/C C/C C/C

19 2028 A/A A/A AA A/A A/A A/A A/A A/A

20 2036 T/T T/T T/T T/T T/T T/T T/T T/T

21 2039 C/C C/C C/C T/C C/C C/C T/C T/C

22 2062 A/A A/A A/A A/A A/A A/A A/A A/A

23 2067 T/T T/T T/T T/T T/T T/T T/T T/T

24 2118 C/T C/C C/C C/C C/C C/C C/C C/C

25 2170 G/G G/G G/G G/G G/G A/G G/G G/G

26 2179 G/G G/G G/G G/G G/G G/G G/G G/G

27 2611 T/T T/T T/T T/T T/T T/T T/A T/T

28 2635 T/T T/T T/C T/T T/T T/T T/T T/T

29 2659 G/G G/G G/G G/G G/G G/G G/G G/G

30 2661 G/G G/C C/C C/C G/G G/C C/C C/C

31 2704 C/C C/C C/C C/C C/C C/C C/C C/C

32 2716 G/G G/G G/G G/G G/G G/G G/G G/G

33 2846 G/G G/G G/G G/G G/G G/G G/G G/A

34 3292 G/G G/G G/G G/G G/G G/G G/G G/G

35 3470 T/T T/T T/T T/T T/T T/T T/T T/T

36 4183 G/G G/G G/G G/G G/G G/G G/G G/G

37 4201 C/C C/C C/C C/C C/C C/C C/C C/C

38 4254 T/T T/T T/T T/T T/T T/T T/T T/T

39 4384 A/A A/C C/C C/A A/A A/C C/C C/C

40 4435 C/C C/C C/C C/C C/C C/C C/C C/C

41 5180 G/C G/C C/C C/G G/C G/C C/C C/C

42 5212 C/C C/C C/C C/C C/C C/C C/C C/C

* t H- 4. «) W t O n

Ωr5Ω>HΩOHOOOΩOOHHOOΩH ΩH>Ω H?5>?5dHOΩOO^O>OH ^ QQ ^ ^QQ Q Q^^ QQ^^^^r>!H ^ΩQθθHθθHθ θHθi

ΩOΩ>HΩOHOOOΩOOHHO>ΩH ΩH fi H^>ΩOHC5ΩC5θ^O>OHO^

Ω ΩΩH O^OQOΩΩOiH^QQΩ^^H^Ω^H ^ΩQO^OO^O^O^O^ ΩΩ~ΩOH^"Ωd^~HOO~0~ΩOOHH^"θδ~ΩH ΩH Ω^~ HΩ>00 ^ 5^ 5$QQ^^ ^ πH n Hθ ΩθθQnΘθ^o oβoc; Ω OΩ > H ΩOHO > OΩ ΩO H H OO Ω H >Ω^> Ω > H O ^OH OHO 5H O O H O ^

4s. 4^ 4i. OJ OJ OJ OJ OJ OJ J OJ OJ OJ t tO tO tO tO t tO tO lO tO >— ►— >— . t—J i-^J r-J r^ VO OO -J O\ J- W t to »— o so oo -o σs on -ii>- θJ to >— ' O O oo ---j Os on -i-. oJ to i— ' © so oo ~-j σs on -i->. oj to Z ^ o ∞

ΩΩ ΩHΩ ^O_ ΩΩ |H|HθOΩ_!H- H^Ω^HΩ^Ω θΩ |HQ^Q|^ on Ω~ΩΩ^"ΩH^"θΩHOO.>ΩθdHHΩOΩH>ΩH Ω>HΩ OQ^ΩQ^ QQ ^i ^OOΩ^ΩH^ ^HO^ QHOΩQ ^ ^Q^ K ~ΩΩ^~ΩHOOHOOΩΩO~OHHOOΩH>ΩH>Ω HΩ

OJ

QΩΩΩHΩ0H O0HH00ΩH^;HHj Ω HΩ^Ω000!H00H0^ |^0 to ΩO?5 HΩOHOOOΩOOHHOOΩH>ΩH Ω^HΩ ΩOOOΩOOHO>OHO -J

ΩΩQΩHΩ ^ Q ΩO^HθOOH^ΩH-^Ω^!HΩ Ω OΩΩθ !Hθ>θ!H on <^ΩΩΩHOOHO. OΩOOHHOOΩH ΩH>0> to σs

4-. -l-. to »-.

υι αι t0 t-

»— oo to ©

ΩΩ Ω iH ΩQH OOO ΩΩ H H O Ω ^^Ω H ^Ω ^ H Ω ^Ω O Ω O iH Q^ H Q n ΩO Ω > H ΩO^OO Ω ΩO O H H Ω θr5θ Ω H Ω > ^Ω >Ω O ^O Ω O

ΩΩΩ Ω H_^Ω H O OOΩΩ H H_^QO Ω H ^H tH ^Ω ^HΩ ^Ω O OO H Q iH O ^O H ^ ΩΩΩ Ω H O^H ;> cSdΩθ ; H H ddΩ H Ω H Ω

O Ω Ω Ω H Q O_ H_ ;> Ω Ω Ω H_ H O O Ω H^ Ω H^ ;> Ω ,> H_ 0 ΩΩΩ~Ω H O O H^"θO OΩθdH H Ω ΩΩ H >Ω H ^H > H Ω > Ω

ΩO O J |H Ω O H OOO ΩO O H !H OΩ H - Ω !H ^ Ω Ϊ> H Ω > Ω O H O Ω O O H O ^O H oo n ΩΩ O Ω H Ω ^H ^OO ΩΩ ^ H H O OΩ H^" Ω H Ω > H Ω ^O Ω OOO O O

Ω Ω Ω Ω H Ω O H O O O O Ω O H H Ω O O !H J H H > Ω ;> H Ω > Ω O Ω Ω H_ O O H O _I> O H Ω Ω OΩ > H Ω O H ^OO ΩO O H H O O ΩO >Ω H ^Ω > H Ω^Ω^OOΩ O O H O >O H

ΩΩ ^Ω;H Ω Q|H θO O ΩΩ Q^H θ θ Ω !H ^Ω H ^Ω ^!H θ ^ θ H |H ^ HQ

ΩΩΩΩHO ~H^"O.>OΩOOHHOOΩH>ΩH O>H^"OO>

ΩOΩ>H_ΩΩHOΩOΩΩOHH_ QOH;>ΩH_;>Ω>HΩ;>ΩO!HΩOOΩHO. OHΩ_ _J'

ΩΩΩΩH^"ΩOHOOOOOOHHOOΩH ΩH>Ω:

Ω O Ω ^ IH Ω JH O O O Ω O O H H O Ω JH ^ Ω JH ^ Ω ^ H Ω ^ Ω O IH O Ω H Ω ^ O H O w ΩΩ Ω Ω H O O H ΩO~Ω~ΩO O H H Ω OΩ H >H H ^Ω > HΩ >00 ^Hθ£

^{//923/4321230/22619} ^{pyp() ()}o^tacIart ⁵ H^{a le Fir} ^' ^' PS PS Hapilotype Pair(c) (Part 6)

No.(a) Position(b) 23/15 15/3 26/2 15/32 23/22 4/31 15/31 15/4

1 636 G/G G/G G/G G/G G/G G/G G/G G/G

2 678 T/T T/T T/C T/T T/T T/T T/T T/T

3 769 G/G G/C G/G G/G G/G G/G G/G G/G

4 776 A/A A/G A/A A/A AA A/A A/A A/A

5 825 G/G G/G G/G G/G G/G A/G G/G G/A

6 915 T/T T/T T/T T/T T/T T/T T/T T/T

7 1019 G/G G/G G/G G/G G/G G/G G/G G/G

8 1031 G/G G/G G/G G/G G/G G/G G/G G/G

9 1100 C/C C/T T/C C/T C/C C/T C/T C/C

10 1827 G/G G/G G/G G/G G/G G/G G/G G/G

11 1843 T/G G/G G/G G/G T/T G/G G/G G/G

12 1966 GIG G/G G/G G/G G/G G/G G/G G/G

13 1974 C/C C/C A/C C/C C/C C/C C/C C/C

14 1984 A/A A/A A/A A/A A/A A/A A/A A/A

15 1997 C/C C/C G/C C/C C/C C/C C/C C/C

16 2014 T/T T/T T/T T/T T/T T/T T/T T/T

17 2022 A/A A/A A/A A/A A/A A/A A/A A/A

18 2023 C/C C/C C/C C/C C/C C/C C/C C/C

19 2028 A/A A/A AA A/A A/A A/A A/A A/A

20 2036 T/T T/T T/T T/T T/T T/T T/T T/T

21 2039 C/C C/T C/C C/T C/C C/T C/T C/C

22 2062 A/A A/A A/A A/A A/A A/A A/A A/A

23 2067 T/T T/T T/T T/T T/T T/T T/T T/T

24 2118 C/C C/C C/C C/C C/C C/C C/C C/C

25 2170 G/G G/G G/G G/G G/G G/G G/G G/G

26 2179 G/G G/G G/G G/G G/G G/G G/G G/G

27 2611 T/T T/T T/T T/T T/T T/T T/T T/T

28 2635 T/T T/T T/T T/T T/T T/T T/T T/T

29 2659 G/G G/G G/G G/G G/G A/G G/G G/A

30 2661 G/C C/C C/C C/C G/G C/C C/C C/C

31 2704 C/C C/C C/C C/C C/C C/C C/C C/C

32 2716 G/G G/G G/G G/G G/G G/G G/G G/G

33 2846 G/G G/G A/G G/G G/G G/A G/A G/G

34 3292 G/G G/G G/G G/G G/G A/G G/G G/A

35 3470 T/T T/T T/T T/T T/T T/T T/T T/T

36 4183 G/G G/G G/G G/G G/G A/G G/G G/A

37 4201 C/C C/C C/C C/C C/C C/C C/C C/C

38 4254 T/T T/T T/T T/T T/T T/T T/T T/T

39 4384 A/C C/C C/C C/C A/A C/C C/C C/C

40 4435 C/C C/C C/C C/C C/C C/C C/C C/C

41 5180 G/C C/C C/C C/C G/C C/C C/C C/C

42 5212 C/C C/C C/C C/C C/C C/C C/C C/C

(a) PS = polymoφhic site;

(b) Position of PS in SEQ ID NOJ;

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

12. The method of claim 11, wherein the trait is a clinical response to a drug targeting or metabolized by CYP2D6 or to a drug for treating a condition or disease associated with CYP2D6 activity.

13. An isolated oligonucleotide designed for detecting a polymoφhism in the Cytochrome P450, subfamily IID, Polypeptide 6 (CYP2D6) gene at a polymoφhic site (PS) selected from the group consisting of PSI, PS2, PS3, PS4, PS6, PS 10, PS 12, PSM, PS 15, PS 16, PS 17, PS 18, PS 19, PS20, PS22, PS23, PS24, PS26, PS27, PS28, PS29, PS32, PS34, PS36, PS37, PS38, PS39, PS40 and PS42, wherein the selected PS have the position and alternative alleles shown in SEQ ID NOJ.

14. The isolated oligonucleotide of claim 13, which is an allele-specific oligonucleotide that specifically hybridizes to an allele ofthe CYP2D6 gene at a region containing the polymoφhic site.

15. The allele-specific oligonucleotide of claim 14, which comprises a nucleotide sequence selected from the group consisting of SEQ ID NOS:4-32, the complements of SEQ ID NOS:4-32, and SEQ ID NOS:33-90.

16. The isolated oligonucleotide of claim 13, which is a primer-extension oligonucleotide.

17. The primer-extension oligonucleotide of claim 16,which comprises a nucleotide sequence selected from the group consisting of SEQ ID NOS:91-M8.

18. A kit for haplotyping or genotyping the Cytochrome P450, subfamily IID, Polypeptide 6 (CYP2D6) gene of an individual, which comprises a set of oligonucleotides designed to haplotype or genotype each of polymoφhic sites (PS) PSI, PS2, PS3, PS4, PS6, PS10, PS12, PSM, PS15, PS16, PS17, PS18, PS19, PS20, PS22, PS23, PS24, PS26, PS27, PS28, PS29, PS32, PS34, PS36, PS37, PS38, PS39, PS40 and PS42, wherein the selected PS have the position and alternative alleles shown in SEQ ID NOJ.

19. The kit of claim 18, which further comprises oligonucleotides designed to genotype or haplotype each of PS5, PS7, PS8, PS9, PS11, PS13, PS21, PS25, PS30, PS31, PS33, PS35 and PS41, wherein the selected PS have the position and alternative alleles shown in SEQ ID NOJ.

20. An isolated polynucleotide comprising a nucleotide sequence selected from the group consisting of:

(a) a first nucleotide sequence which comprises a Cytochrome P450, subfamily IID, Polypeptide 6 (CYP2D6) isogene, wherein the CYP2D6 isogene is selected from the group consisting of isogenes 1-34 shown in the table immediately below and wherein each ofthe isogenes comprises the regions of SEQ ID NOJ shown in the table immediately below and wherein each ofthe isogenes 1-34 is further defined by the corresponding sequence of polymoφhisms whose positions and identities are set forth in the table immediately below; and -^ -fc tJ M W t td M i t t ι M M t tθ M H h- M h- M i-^» H M ω ω ω ω ι ω ω w ω w M Φ α w ω w ω w w w w ω w wJ w w w Ni i vj ^ v) --ι --ι -j vj --i i -j si i j -j i i i i ~-j i ~-i vi -i j ^ .

On n 4^ 4^ 4^ 4^ 4^ 4^ 4^ 4^ 4^ ^ 4^ ^ 4^ 4^ 0 © © © 0 © © 0 © © 00 © © O O O C>O Oo OO OO OO OO OO OO Go £ <jQ t— tO M | W N tO | M t t t td M | | M H H l|- H H l- M -. -. H M ^ I- ^ ^ ^ ^ ^ ^ ^ ^ ^ a -• tln ό i^ ^ ^ Φ' ^ ^ ^ ^ - ^ ^ i^ ^ ^ t t to to t t to to to

4^ 4^ on on on on on on on on on on on on on on to to to to to to to to to to to to to t to to to σs <Λ σs σN σs σs σs Λ σs 5 J θJ θn on on on on on on on on on on on on on © o o © © © © © 00 © © © O O O O θJ θJ θJ θJ θJ θJ θJ θJ θJ S on OΛ On on on on on on on on on on on on on on o oJ OJ OJ OJ OJ OJ OJ OJ OJ OJ OJ OJ OJ OJ OJ OJ ,ϋ;

4- i TI t G

u j- j-

H- o ω oo N θ tΛ j.

O ΩΩ> H Ω0 H 000 Ω 00 H H 00 Ω H Ω H > Ω > H Ω > Ω 0 H 0 Ω00 H 0 0H >'- ι-_l o

_ΩΩΩΩH_Ω0_H000_ΩΩ0HH00_{ΩH ΩH Ω H}Ω>_Ω000Ω00HO 0_O0^s

O_ΩΩ_ΩH_Ω0_H0000Ω0HH00ΩH>ΩH>Ω HΩ>Ω000Ω0>H0 0H0σs

ΩΩΩΩHΩ0H000ΩΩ0HH00OH>ΩH>Ω>HΩ>Ω000Ω>0H0 0H0--J

ΩΩΩΩHΩOHOOOΩOOHHOOOH>ΩH>Ω HΩ ΩOOOΩ>OHO OHO∞ ΩΩΩΩHΩ0H000ΩΩ0ΩH00ΩH>ΩH>H>HΩ>Ω00ΩΩ00H0>0H0^0

OΩΩΩHΩOHOOOΩΩOHHOOΩH>ΩH>Ω HΩ Ω OOΩOOHO OH03

w υ> 4. to * t) θo w tzι ι o u

Ω 0 Ω H Ω 0 H 000 O00 H H Ω 0Ω0 Ω H > Ω H Ω Ω000 ΩO0 H 0 0 H 0 ^: vc-n-_l o

Ω0Ω HΩ0H000Ω00HH00Ω0>ΩH Ω>HΩ>Ω000Ω00H0>0H0t S

ΩΩΩ>HΩ0H000O00HH00ΩH>ΩH Ω>HΩ Ω000Ω00H0 0H0S O0Ω>HΩ0H000Ω00HH00ΩH ΩH>Ω>HΩ>Ω000Ω00H0 0H0 -i OΩΩΩHΩOOOOOOΩOHHOOOH ΩH>H>HΩ>ΩOΩΩOΩΩHΩ>ΩHO_∞

ΩΩΩΩHΩ0H000ΩΩ0HH00OH>ΩH>H>HΩ>Ω00ΩΩΩ0H0 0HΩS ΩOΩ HΩOHOOOΩOOHHO>ΩH ΩH>Ω>HΩ>ΩθHOΩΩOHO>OHOo

ΩΩΩΩHΩθHO ΩΩΩOHHOOΩH ΩH>Ω>HO >OOOHOOHO OHOo^

ΩΩ>ΩHΩθHOOOΩΩOHHOOΩH>ΩH>Ω>HO> OΩOHOθHO OHO-^

OOOOHΩOHOOOΩΩOHHOOΩH>ΩH>Ω>HO>>ΩOOHOOHO>OHO^

ΩΩ>ΩHΩOHOOOΩΩOHHOOΩH ΩH>Ω>HOO>OOOHOOHO>ΩHOO

Region PS PS Isogene Number(d) (Part 4)

Examined(a) No.(b) Position(c) 31 32 33 34

378-1363 1 636 G G G G

378-1363 2 678 T T T T

378-1363 3 769 G G G G

378-1363 4 776 A A A A

378-1363 5 825 G G G G

378-1363 6 915 T T T T

378-1363 7 1019 G G G G

378-1363 8 1031 G G G G

378-1363 9 1100 T T T T

1701-2203 10 1827 G G G G

1701-2203 11 1843 G G G T

1701-2203 12 1966 G G G G

1701-2203 13 1974 C C C A

1701-2203 14 1984 A A A A

1701-2203 15 1997 C C C G

1701-2203 16 2014 T T T T

1701-2203 17 2022 A A A A

1701-2203 18 2023 C C C C

1701-2203 19 2028 A A A A

1701-2203 20 2036 T T T T

1701-2203 21 2039 T T T C

1701-2203 22 2062 A A A A

1701-2203 23 2067 T T T T

1701-2203 24 2118 C C C C

1701-2203 25 ' 2170 G G G G

1701-2203 26 2179 G G G G

2342-4555 27 2611 T T T T

2342-4555 28 2635 T T T T

2342-4555 29 2659 G G G G

2342-4555 30 2661 C C C C

2342-4555 31 2704 C C C C

2342-4555 32 2716 G G G G

2342-4555 33 2846 A G G A

2342-4555 34 3292 G G G G

2342-4555 35 3470 T T T T

2342-4555 36 4183 G G G G

2342-4555 37 4201 C C T C

2342-4555 38 4254 T T T T

2342-4555 39 4384 C C C A

2342-4555 40 4435 C C C C

4651-5435 41 5180 C C C G

4651-5435 42 5212 C C C C

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

(b) PS = polymoφhic site;

(c) Position of PS in SEQ ID NOJ;

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

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

21. The isolated polynucleotide of claim 20, 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.

22. A recombinant nonhuman organism transformed or transfected with the isolated polynucleotide of claim 21, wherein the organism expresses a CYP2D6 protein that is encoded by the first nucleotide sequence.

23. The recombinant nonhuman organism of claim 22, which is a transgenic animal.

24. An isolated fragment of a Cytochrome P450, subfamily IID, Polypeptide 6 (CYP2D6) isogene, wherein the fragment comprises at least 10 nucleotides in one ofthe regions of SEQ ID NOJ shown in the table immediately below and wherein the fragment comprises one or more polymoφhisms selected from the group consisting of adenine at PSI, cytosine at PS2, cytosine at PS3, guanine at PS4, cytosine at PS6, cytosine at PS10, adenine at PS12, guanine at PSM, guanine at PS 15, cytosine at PS 16, thymine at PS 17, thymine at PS 18, guanine at PS 19, cytosine at PS20, guanine at PS22, guanine at PS23, thymine at PS24, cytosine at PS26, adenine at PS27, cytosine at PS28, adenine at PS29, adenine at PS32, adenine at PS34, adenine at PS36, thymine at PS37, cytosine at PS38, cytosine at PS39, adenine at PS40 and thymine at PS42, wherein the selected polymoφhism has the position set forth in the table immediately below:

j. j- M i io t w i t w to M i M M i H i-^r M h- H i-' M M H W w ω ω w u ω ω ω M σs σs 0J θJ 0 0J 0J 0J J 0J 0J θ 0J 0J 0J 0J ---j ^ ^ ^ -o t ^ t ι ^ ^ ^ ^ ι ι ι ^ ^ ^ ^ ^ ^ ^ ^ --J -0 <i fζ t-n on 4-. 4-^ 4^ 4^ 4^ 4^ 4^ 4^ 4^ 4-. 4-- 4-. 4^ 4^ 0 0 © © © © © © 0 0 0 © © © © © © Oθ ∞ OO OO CO OO Oθ OO Oθ <γo l M t t t tO t t t t W M M t i-' t- H. w i-. h- ^ ^ l _^ l I I i I 5 — •

On n 4^ 4^ 4^ 4^ 4^ 4^ 4^ 4^ 4^ 4^ 4^ 4^ 4^ - tO tO tO l tO t t t tO

4^ 4^ on on on on on on on on on on on on on on to to to to to to to to to to to to t to to to to os os os Os Os Os Os Os Os S oJ OJ On on on on on on on on on on on on on on © © © © © © © o o o © o © © © © © OJ OJ OJ OJ OJ OJ OJ OJ OJ >S on on on on on on on on on on on on on on on on OJ OJ OJ OJ OJ OJ OJ OJ OJ OJ OJ OJ OJ OJ OJ OJ OJ ,u;

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N θ « o θ Φ iΛ j- ω t f- o ϋ oo vj

on on

IO _{θ w}TJ to o

ΩΩΩΩHΩOHOOOOΩOHHOOΩH>ΩH Ω>HΩ ΩOOOΩO HO>OHOσs

ΩΩΩΩHΩθHΩOOΩΩOHHOOΩH>ΩH>Ω HΩ ΩOOQΩ>ΩHΩ>OHO--J ΩΩΩΩHΩOHOOOΩOOHHOOΩH ΩH>Ω HΩ>ΩOOOO>OHO>OHO∞

ΩΩΩΩHΩOHOOOΩΩOHHOOΩH ΩH>Ω>HΩ>Ω>OOΩOOHO>OH05

-t. -i- to to to to to to to io to to io to io to >-' »— ^ ►— ,— -— -— K-. ►— — . -— ►— H^ h— r-^j r^ ~J w w ω ω w w ω w ω w w os Os OJ J OJ OJ J OJ O OJ OJ O OJ OJ OJ ^j ^ ^ ^ i ^ ^ ---3 ^ ^ ---o ^ ^ -o ^ ^ ^ ^ '-o ^ ^ ^ '~j ~-i ^--i -^-i -o ><' π>

Ui U > 4. - * -!i -|i ^ ^ 4s - -ti - J- O O O O O O O O O O O O O O O O O C0 00 00 00 00 00 00 Ki 00 |ii tfc

►— i— ' tO tO tO tO tO tO tO tO tO tO tO tO tO tO — . ►— -— ►— ►—. -— ►— -_ ' t- H i— ^■ —^■ ►_. -— -— ■ a "-3. t-Λι On 4^ 4^ 4^ 4^ 4^ 4^ 4^ 4^ 4^ 4^ 4^ 4^ 4^ 4^ tO tO tJ tO tO t lO tO tJ tO tO O tO t OJ OJ OJ O OJ OJ J O OJ e- 3 -^ 4^ on on on on on on on on on on on on on on to to to to to to to to to to to to to to to to to os Os ON Os Os ON OS ON Os 5 J θJ n on on on on on on on on on on on on ι-Λ © © © o © © © © © © © o θ © © © © θJ θJ θJ θJ θJ θJ θJ θJ θJ i; on on on on on on on on on on on on on on on on o oJ OJ OJ OJ OJ OJ OJ OJ OJ OJ OJ OJ OJ OJ OJ OJ ,ϋ;

^ 4. ^ ω ω w ω ω w w ω ω w M i t M i N M M S) t H -- H H h. M -- H -' p 2; J t O ^ oo -o σ^ w -ii w t M O ^ oo i a w -i- w M O vo i vj α tΛ ψ w iO O ^ ^ ^ ^ ^ ^ ^ ^ ^ ai

i * s Ji 4s W W t tO to ►— ^j o^j to to >— ji. to oo -o TJ .— oo oJ Oo on © oo -o so -t- >— M to © n *. 4. >— OJ © to σs Os

SO

ΩΩΩ>HΩ0H000O00HH00ΩH>ΩH Ω HΩ>Ω000Ω00H0 0H0σ

Ω0Ω>HΩ0H000Ω00HH00ΩH>ΩH>Ω>HΩ>Ω000O00H0>0H0 .

ΩΩΩΩHΩOΩOOOΩΩOHHOOΩH>ΩH H>HΩ>ΩOOOΩOOHO>OHθoo ΩΩΩΩHΩθHOOOΩΩOHHOOΩH>ΩH>H>HΩ>ΩOOOΩOOHO OHO o

4^ -t tO tO tO tO tO tO tO tO t tO tO tO tO tO >— — - ►— _ -— -— _ ►— -_, -_. H- — ' >— »— >— -— ►— OJ OJ OJ OJ OJ OJ OJ OJ OJ t_Tj W σs σs θJ θJ J θo oJ θJ θJ θ θ θJ J θj ^ ^ -o ^ -^ ^ ^ ^ ^ ^ ι t ι ^ '^ ^ ^ ^ ι ι ^ ^ ^ -^ -^ -^ χ h>

W Uι -|i -l- -l- 4s 4i ^ ^ -|i -|i * Ji * 4i * O O O O O O O O O O O O O O O O O M OO OO OO (» CO OO OO (» S (m r- H t M t tO M t M M M I M t-) tO t M -- H. -Η f- l- M H l I 1 I 3 W •

I I I I I I t 1 I I I I I I I 1 1 1 I I I I I I I I I I I I I i i ■— ι — ' i — ' ' — ' •— ^» i — ^l — ^J *— . *— ' 3 O w j- 4- ^ 4s -ii 4s -^ -i- -^ 4s 4> -i- 4. i io to to M io to ιo ιo to to to to to w to M to w ω ω w ω w ^ 4^ on on on on on on on on on on on on on on to to to to to tJ to to to to to to to to to to to os Os Os os Os Os <3s ON Os S OJ OJ on on on on on on on on on on on on on on © © © © © o © © © © © © © © © © © OJ OJ OJ OJ OJ OJ OJ OJ OJ _f? on on on on on on on on on on on on on on on on oJ OJ OJ OJ OJ OJ OJ OJ O OJ OJ OJ OJ OJ OJ OJ OJ =t

£s >jj [Λ

On n _ to O—O ^■ _I T_zJ_l to o

Ω0Ω HΩ0H000OΩ0HH00ΩH>ΩH>Ω HΩ Ω0H0Ω00H0 OH0 --.

O era

ΩΩΩ HΩOHΩOOΩOOHHOOΩH>ΩH Ω>HΩ>ΩOHOΩOOHO OHθKS

ΩΩΩΩHΩOHO>OΩΩOHHOOΩH>ΩH Ω>HO OOOHθOHO>OHOσ^

ΩΩ>ΩHΩ0H000OΩ0HH00ΩH>ΩH>Ω H0>>00ΩH00H0>0H0---J

ΩΩΩΩHΩOHOOOΩΩOHHOOΩH>ΩH Ω HO>>OOOHOOHO>OHOO^

ΩΩΩΩHΩ0H0 0ΩΩ0HH00ΩH>ΩH>Ω>H00>000H00H0>0H05o

ΩΩ ΩHΩOHOOOΩΩOHHOOΩH>OH Ω HOO>OOθHθOHO>OHθo

Region PS PS Isogene Number(d) (Part 4)

Examined(a) No.(b) Position(c) 31 32 33 34

378-1363 1 636 G G G G

378-1363 2 678 T T T T

378-1363 3 769 G G G G

378-1363 4 776 A A A A

378-1363 5 825 G G G G

378-1363 6 915 T T T T

378-1363 7 1019 G G G G

378-1363 8 1031 G G G G

378-1363 9 1100 T T T T

1701-2203 10 1827 G G G G

1701-2203 11 1843 G G G T

1701-2203 12 1966 G G G G

1701-2203 13 1974 C C C A

1701-2203 14 1984 A A A A

1701-2203 15 1997 C C C G

1701-2203 16 2014 T T T T

1701-2203 17 2022 A A A A

1701-2203 18 2023 C C C C

1701-2203 19 2028 A A A A

1701-2203 20 2036 T T T T

1701-2203 21 2039 T T T C

1701-2203 22 2062 A A A A

1701-2203 23 2067 T T T T

1701-2203 24 2118 C C C C

1701-2203 25 2170 G G G G

1701-2203 26 2179 G G G G

2342-4555 27 2611 T T T T

2342-4555 28 2635 T T T T

2342-4555 29 2659 G G G G

2342-4555 30 2661 C C C C

2342-4555 31 2704 C C C C

2342-4555 32 2716 G G G G

2342-4555 33 2846 A G G A

2342-4555 34 3292 G G G G

2342-4555 35 3470 T T T T

2342-4555 36 4183 G G G G

2342-4555 37 4201 C C T C

2342-4555 38 4254 T T T T

2342-4555 39 4384 C C C A

2342-4555 40 4435 C C C C

4651-5435 41 5180 C C C G

4651-5435 42 5212 C C C C

(b) PS = polymoφhic site;

(c) Position of PS within SEQ ID NOJ;

(d) Alleles for CYP2D6 isogenes are presented 5' to 3' in each column.

25. An isolated polynucleotide comprising a coding sequence of a CYP2D6 isogene, wherein the coding sequence comprises the regions of SEQ ID NO: 2 that are defined by exons 1-9, except at — . so oo d

toos o ^ T' p-. ^ 3

ΩΩHΩOHOΩOOHHΩH Ω HΩ ΩOΩ 0°ϊ³

ΩΩHΩOHOΩΩOΩHΩH H>HΩ>ΩOΩOO_c?

. J>- OJ OJ OJ OJ OJ OJ J tO tO t tO tO — ' >— — ' — ' ►— so oo -o ₄-^wωwωωww_{t M} i _{t t}θH.Mi- _' Mh- so oo -j tO — ' 00 O 0\ Ul tO M © SO OO -J i— © SO OO -O ON tΛ J OJ to _Z, TI O C to t— oo -j σs on to — _' © so oo ^j — _' © so oo--α σs on -!-. oj to 2; o

P

TJ TJ o o

^ ^ ^ T' T* os ^ 4^ 4^ 4^ J J OJ OJ to tO tO tO i—> -_J, -__J J-V

£ ft§ S S so σs © © ooo o o to o .— >— so oo ^ σ- © „ rϊ -- TI ^i_jgS_Q^3σs θJ _>- oo σ to oo σ o o oso _l— j>i— '- j ©^|-^{- o} GO M lΛ M S 2 ^{IO Λ 0}0 <» υι W ^W N N ^ ^>- ^ ∞ 00^\ 0 ^ n'

3 S j ω o to °^{l W M W M 00} ^ ^{w o φ} -^{,:i ω o} ° cr r

ΩΩHΩOHΩΩΩOHHΩH Ω HO> OHOO o-^ ΩΩHΩOHOΩOOHHΩH>Ω>HΩ>ΩΩOΩO^

OΩHΩOHOΩΩOHHΩH>Ω>HΩ>>OHOO^

(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 CYP2D6 isogene.

26. A recombinant nonhuman organism transformed or transfected with the isolated polynucleotide of claim 25, wherein the organism expresses a Cytochrome P450, subfamily IID, Polypeptide 6 (CYP2D6) protein that is encoded by the polymoφhic variant sequence.

27. The recombinant nonhuman organism of claim 26, which is a transgenic animal.

28. An isolated fragment of a CYP2D6 coding sequence, wherein the fragment comprises one or more polymoφhisms selected from the group consisting of adenine at a position corresponding to nucleotide 263, guanine at a position corresponding to nucleotide 281, guanine at a position corresponding to nucleotide 294, cytosine at a position corresponding to nucleotide 311, thymine at a position corresponding to nucleotide 319, thymine at a position corresponding to nucleotide 320, guanine at a position corresponding to nucleotide 325, cytosine at a position corresponding to nucleotide 333, adenine at a position corresponding to nucleotide 358, cytosine at a position corresponding to nucleotide 382, adenine at a position corresponding to nucleotide 406, adenine at a position corresponding to nucleotide 463, adenine at a position corresponding to nucleotide 1012, thymine at a position corresponding to nucleotide 1030, cytosine at a position corresponding to nucleotide 1083 and thymine at a position corresponding to nucleotide 1489 in SEQ ID NO:2.

29 An isolated polypeptide comprising an amino acid sequence which is a polymoφhic variant of a reference sequence for the Cytochrome P450, subfamily IID, Polypeptide 6 (CYP2D6) protein, wherein the reference sequence comprises SEQ ID NO:3 for the regions encoded by exons 1-9, except the polymoφhic variant comprises one or more variant amino acids selected from the group consisting of histidine at a position corresponding to amino acid position 88, arginine at a position corresponding to amino acid position 94, alanine at a position corresponding to amino acid position 104, phenylalanine at a position corresponding to amino acid position 107, phenylalanine at a position corresponding to amino acid position 107, valine at a position corresponding to amino acid position 109, isoleucine at a position corresponding to amino acid position 120, arginine at a position corresponding to amino acid position 128, isoleucine at a position corresponding to amino acid position 136, lysine at a position corresponding to amino acid position 155, methionine at a position corresponding to amino acid position 338, termination codon at a position corresponding to amino acid position 344 and cysteine at a position corresponding to amino acid position 497.

30. An isolated monoclonal antibody specific for and immunoreactive with the isolated polypeptide of claim 29.

31. A method for screening for drugs, or other chemical compounds, that bind to or are enzymatic substrates for the isolated polypeptide of claim 29 which comprises contacting the CYP2D6 polymoφhic variant with a candidate agent and assaying for binding activity.

32. An isolated fragment of a CYP2D6 protein, wherein the fragment comprises one or more variant amino acids selected from the group consisting of histidine at a position corresponding to amino acid position 88, arginine at a position corresponding to amino acid position 94, alanine at a position corresponding to amino acid position 104, phenylalanine at a position corresponding to amino acid position 107, phenylalanine at a position corresponding to amino acid position 107, valine at a position corresponding to amino acid position 109, isoleucine at a position corresponding to amino acid position 120, arginine at a position corresponding to amino acid position 128, isoleucine at a position corresponding to amino acid position 136, lysine at a position corresponding to amino acid position 155, methionine at a position corresponding to amino acid position 338, termination codon at a position corresponding to amino acid position 344 and cysteine at a position corresponding to amino acid position 497 in SEQ ID NO:3.

33. A computer system for storing and analyzing polymoφhism data for the Cytochrome P450, subfamily IID, Polypeptide 6 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:

4-. -fc- 4i- OJ OJ OJ to —- o so oo -4

tΛ -J-

|θ 4-

ΩΩΩ>HΩOHOOOΩOOHHOOΩH ΩH Ω>HΩ ΩΩHOΩOOHO>ΩH>'- X

TJ

ΩΩΩΩHΩOHOOOOΩOHHOOΩH>ΩH Ω>HΩ>ΩOOOΩOOHO>OΩOW_<

ΩΩΩ>HΩOHOOOΩOOHHOOΩH>ΩH Ω>HΩ ΩOHOΩOOΩO>OHOW^ ΩΩΩΩHΩ0H0000Ω0HH00ΩH>ΩH Ω>HΩ Ω000ΩΩ>HO>0H0σs

ΩΩΩΩ HΩOHOOOΩΩOH H OOΩH ΩH>Ω >HΩ ΩOOOΩ OHO>ΩHO -~J

ΩΩΩΩHΩOHOOOOOOHHOOΩH>ΩH>Ω>HΩ ΩOOOO>OHO>OHO∞

ΩΩΩΩHΩOHOOO_ΩΩOΩHOOΩH>ΩH>H>HΩ>ΩOOΩΩOOHO>θHO^o

ΩΩΩΩHΩOHOOOΩΩOHHOOΩH>ΩH Ω>HΩ>Ω>OOOOOHO>OHO

4-. - - to — '

W tO t—

Mθo too

OΩΩ>HΩOHOOOΩOOHHOOΩH>ΩH>Ω>HΩ>ΩOOOΩOOHO OHO σs

ΩOΩ HΩOHOOOΩOOHHOOΩH>ΩH>Ω HΩ>ΩOOOΩOOHO>ΩHO . OΩΩΩHΩΩΩOOOΩΩOHHOΩOH ΩH H>HΩ>ΩOOOOOθHO>ΩHΩ_∞

ΩΩΩΩHΩOHOOΩΩΩOHHOOΩH>ΩH H HΩ>ΩOOOΩOθHO θHO o

ΩOΩ HΩOHOOOΩOOHHO>ΩH ΩH>Ω HΩ>ΩOHOΩOOHO>OHOS

4-. to

Ω0Ω>HΩ0H000O00HH00ΩH>ΩH Ω>HΩ Ω0H0Ω00H0>OHO i ' cr

ΩΩΩ>HΩOHOOOΩOOHHOOHH>ΩH>Ω HΩ ΩOHOΩOOHO>OHO t

O Ω ΩΩ H Ω O H OO O Ω ΩO H H O OΩ H >Ω H Ω H Ω > O ΩO HOO H O > O H O ^ ^ o 00 OJ

ΩΩΩΩHΩOHO OΩΩθHHOOΩH>ΩH Ω Hθ> OOθHθOHO>OHOσ^

ΩΩ ΩHΩOHOOOΩΩOHHOOΩH>ΩH Ω>Hθ>>OOOHOOHO>OHθ!-3

ΩΩΩΩHΩOHOOOΩΩOHHOOΩH>ΩH>Ω HO>>OOOHOOHO>OHOO^ ΩΩΩΩHΩOHO>OΩΩOHHOOΩH>ΩH Ω HθO>OOθHθOHO>OHO^

ΩΩ>ΩHΩOHOOOOΩOHHOOΩH>ΩH>Ω HOO OOOHΩOHO>OHO^

. — ' — ' SO 00 -o as on .(-- OJ to Γ CΛ

-o -o σs σs O-J TI ^{oo w}

J 4a- 4i. OJ J J J J OJ OJ J J OJ t tO tO tO tO tO t tO tO t >— >— ►— ►— — ' i— i— ' »— so oo -o σs on 4i. θJ tθ ι— • 25 TJ o t— o so oo -o σs on 4i. θJ tθ — o so oo -j os on 4i. θJ to »— o so oo _^j σs on 4^ oj to o c

(a

TI O on on 4*. -fe. *. 4 4 oj oj to to to to to to to to to to to to to to to to to to t — ■ 4_, ) tO tO — ' J- tO OO O O Os ON Os Oi — I-- O O O O O O O O so so so so oo oo - © © i≤ °° -J _J σs g5 TJ

>— oo OJ oo on o ~ 00 i φ 4s i- © σs on oj «— -j -o ►— σs σs oJ OJ to to tO f— so oo -^j σs 4^ t © oo ι— r^ ^ i^J g PS ^ GO to © on J 4*. >— OJ © t σ σs 4s ^- o n »— so © oo -o to so σs oo o to -t 04. J- 0\ W O O ι- *O ^{W O ∞ α}

ΩΩΩΩHΩOHOOOΩ OHHOOOHJ ΩH Ω HΩ^;ΩOOOΩOOH O > O H O on ΩOΩ HΩOHθdδ OOHH$^ΩH ΩH Ω ^ r5δHdΩddH O O H O ^

HθOOΩΩθHHθθΩH- ΩH Ω HΩ

Ω Ω Ω Ω H Cl O HOO~dΩΩδ~H^"H^"θOΩH^"> ~H>H>HΩ H O T

ΩOΩ^H C)^OOΩOQ|HιHθθΩ^ΩH_l Ω^HΩ^ΩO^ . Q^ O > O H O OJ ΩΩΩΩHHOHOOOΩΩdHHO~OΩH HH^">r5>HΩ>Ω Ω O H O jj.

ΩΩΩ_ HΩQ;H QOΩOΩHHθθΩH ΩH>Ω HΩ^ ΩθHθΩθθHθ θHθto fiθ >HΩOHOOθnθO^H^ΩH>f5H^ H f5θH^ ^H^>OH g

4-- -!-. 4i. OJ J OJ OJ OJ OJ OJ OJ OJ OJ t tO tO tO I t tO tO tO tO >— ►— ►— ►— »— ►— ►— ►— t— - so oo ~o σs on J OJ to i— © vo oo -o σs n 4-. θJ to >— © so oo ~-j os on -t> J to >— © so oo -~J Os on 4s OJ to >— © to >— 2 T) _O CO

,f°.

ΩO - H OH O OHHO ΩHΪ Ω_!H- ΩΪ ^Ω ΩQHOΩ OH ^; |H to

OJ ΩΩΩ>HΩdHOOOΩOOHHOO^H ΩH Ω>HΩ>ΩOHOΩθdHO>OHO

TJ to &

ΩOΩ H_ΩQHQQOΩΩQH^Q ΩH;>Ω OJ CT

ΩΩΩΩ^ΩOHOOOΩΩOHHOOΩH Ω H Ω>HΩ>>O OHOOHO>OHO on CT

TJ Q ^Ω0H0 0ΩΩ0^H5QΩH^Ω^Ω ^Ω^ΩQQ0Ω00^0^^ <—• £ —.." Ω~ΩΩΩ~HΩOHOOOΩΩOΩHOOOH^' ΩH H^HΩ>ΩΩO O

TJ s

ΩΩΩΩHΩθHθQOOΩθHHθOΩHΪ _!H^_^>Ω^ HΩ^;ΩθOO^ΩO^ 0|Hθto a» ΩOΩ>HΩOHOOOΩΩOHHOOΩH>ΩH>r5>HΩ r5θHOΩθδHO 0 to

Ω0O^;HΩ0H0 0Ω00H H00ΩH^ ΩHΪ Ω^;^ΩΪ Ω0!H0Ω00^0 0_!H0w ΩΩΩ>HΩδHδθδθδδHHδδθH>ΩH δ HΩ>δδθδ?5δ

ΩΩΩΩHΩθHQOQΩΩO^!HQQΩH^|H|H^Ω^|HΩ ΩΩQO|HQθHθ>;0 H O to ΩΩΩδHΩOHδδδΩδδH δδΩH ΩH H ^Ωδδ

Q Q ^Q0HQQ0 0^50Ω^ ^^π^Ω ΩQ00H 0H0>0 H O to ΩΩΩΩHΩ^^OΩΩOHHOOΩ^>Ω^ Ω HO^ ^ H Ω to

OS

n on to — '

—» oo to ©

OOΩJ>H_ΩθH_ QQOOQiHHθOOH;>Ω H Ω>HQΪ Ω !HθΩΩθHθ QHQw ΩΩ ΩHΩδHOOOΩΩOHHθδδH Ω ^?5^HO OOOHOOHO OHO^

ΩΩΩ !HΩθ!H ΩΩθ^^ ΩH^H^^Ω^^Ω Ω OQ!H θHθϊ QHQ^ ΩΩΩΩHΩOHOOOΩΩOHHOOΩH>ΩH>Ω>HΩ ^:ΩδδδΩδδHδ>δ Oto

Ω Ω Ω Ω JH Ω O IH Q O Ω Ω ^ IH O Ω H ^ Ω H- Ω>HΩj ΩOO ΩθθHθ^ θHθon ΩOΩ>HΩOHO>^:OΩΩOHHδδΩH>Ω H 0 HO> 0^;:SOHOOHO OHO^r 4^'J

4-. 4i. 4^ 0J OJ OJ OJ OJ J OJ OJ OJ OJ tO tO tO tO t tO tO tO tO tO ι— . — • ►— i— — . ►— — ^■ — • >— so oo -o σs on -t oj to >— 2' d to — O C oo o α J- u t H Ό VO O -J OS UI J- U I I- » © so oo -~j σs on -t-- θJ to — • o co

(J_l lΛ 4s 4i to — < -i w to

>— oo w oo

W O Wι* 4s

OΩΩΩHΩOHOOΩOΩΩHHOOOH;>ΩH >Ω; HΩ;>ΩOOΩOOOHΩ;>OHQ

ΩΩΩΩHΩδ^δδ^ΩΩδHHδθ H ΩH Ω HΩ ΩθδθΩδδHδ OHO

ΩOΩ HΩOHOOOΩOOHHOOΩ^- ΩH^;ΩJ HΩ^;ΩO|HOΩOOHO^;QHQ ΩδδΩHΩδ^δδδθδδHHδδΩH ΩH Ω HΩ δθδΩ δ-Hδ OHO

Q O J> H_ Ω Q H Q Ω O O H^ O Q Ω H_ ;> Ω H_ ; Ω ;> H Ω > C^ ΩΩδΩHΩδ^δδδΩΩθHHδδΩH ΩH Ω HO δθδHδδHδ OHO

OΩ ΩiH QH OΩΩOHHO Q^^Ω^ ^Ω^Ω QOΩOO^ ^QH ΩΩΩΩHδ HδδδΩΩOHHδδΩH ΩH Ω Hδ δδδΩ δHδ δ^O o

00 to

Ω O Ω > H Ω O H O O Q Ω O O H H O O Ω H_ ;> Ω H ;> Ω > H Ω ;> Ω O H_ Ω Ω Ω O H O _ Ω H Ω_ J

Ω O Ω ,> H_ Ω Ω H Q Ω O O Ω O H H O Q Ω H ,> Ω H^ Ω H Ω ; Ω H Ω O O H_ 0 Q H to

OJ ΩΩΩ HΩOHδδδΩΩδ^HδδΩ^ ΩH Ω ^HΩ Ωδ^δΩ Ω δ'^:?0 on

OJ

Ω Ω Ω H_^ Ω Q H Q Q Ω Ω O H_ H^ O Ω H^ H_ H Ω > H Ω ;^ to ΩO HΩ~δHδδδΩδδHHδδΩH^ΩH^Ω HΩ δδδδΩδθHδ δHO Ω Ω|HΩθHQOθΩΩΩHHθ Ω|H^Ω_!H^Ω -HΩ^ΩQ θΩ Q^O^;QHθ on ΩΩΩΩHΩδHδ^δΩΩδHHδδΩH ΩH Ω HO δδδHΩOHδ OHO to

OS

^/3/85/7 ^1514223/28 ¹ ^{pyp() ()}o^{te FI} H^{a lairca}rt ⁴ ^" ^* 4-. 4i- 4s. OJ OJ J OJ OJ OJ OJ OJ OJ OJ tO tO tO tO t tO tO tO tO tO >— ►— ►— >— >— !-- ►— ►— so oo ~-j σs θn 4*. J to to »— o so oo o σs on 4^ θJ tθ ι— ' so oo _^J θs on J>- θJ to — ' © so oo ^ι σs on -1-. θJ to o O

ΩOΩ H θ^OQΩOQHHQOΩH^ H^Ω^HΩ ΩQHQΩQO^ ^Q QK ΩΩΩΩHΩδH^"δδδθθδHHδδΩH ΩH>Ω>HΩ>ΩδθδΩΩ;>Hδ>0 H O C5N

Ω O O > H Ω O H O O Ω O H H O O Ω H ; Ω H ;> Ω ^ H Ω > Ω Q H Ω Q H O Ω H_ O OJ' ΩΩΩΩ H ΩδH θδδθΩO H H δδδH ^H>Ω H Ω Ω OOO H OOH δ>OH δ^

—. —. so oo ~-a σs on -t- OJ t TJ >— co

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OΩΩ>HΩ0H000Ω00HHΩ0ΩΩ ΩH>Ω>HΩ>Ω000Ω00H0>0H0- ι-.

O era Ω0Ω>HΩ0H000Ω00HH00Ω0>OH>Ω HΩ>Ω0O0ΩOOHO OH0f g

ΩΩΩ>HΩOHOOOΩOOHHOOΩH>ΩH>Ω>HΩ>ΩOOOΩOOHO>OHOc> ΩOΩ HΩOHOOOΩOOHHOOΩH>ΩH>Ω HΩ>ΩOOΩΩOOHO OHθr.-;

ΩΩΩΩHΩOΩOOOΩΩOHHOOΩH>ΩH>H>HΩ>ΩOOOΩOOHO>OHO_∞

ΩΩΩΩHΩOHOOOΩΩOHHOOΩH ΩH>H HΩ>ΩOOOΩOOHO>OHO o ΩOΩ HΩOHOOOΩOOHHO>ΩH ΩH>Ω>HΩ>ΩOHOΩOOHO OHθg

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O era

ΩΩΩ>HΩ0H000Ω00HH00OH ΩH>Ω>HΩ Ω0H0Ω00H0 0H0K|

ΩΩΩΩHΩOHO>OΩΩOHHθOΩH>ΩH>Ω>HO>>OOOHOOHO OHθ_σ^

ΩΩ>ΩHΩOHOΩΩΩΩOHHOOΩH>ΩH>Ω HO>>OOOHOOHO>OHO!_O

ΩΩΩΩHΩΩHΩOOΩΩOHHOOΩH>ΩH>Ω>HO>>OOOHOOHO OHO

ΩΩ>ΩHΩOHOOOΩΩOHHOOΩH>ΩH>Ω>HOO OOOHOOHO>OHO^

Region PS PS Isogene Number(d) (Part 4)

Examined(a) No.(b) Position(c) 31 32 33 34

378-1363 1 636 G G G G

378-1363 2 678 T T T T

378-1363 3 769 G G G G

378-1363 4 776 A A A A

378-1363 5 825 G G G G

378-1363 6 915 T T T T

378-1363 7 1019 G G G G

378-1363 8 1031 G G G G

378-1363 9 1100 T T T T

1701-2203 10 1827 G G G G

1701-2203 11 1843 G G G T

1701-2203 12 1966 G G G G

1701-2203 13 1974 C C C A

1701-2203 14 1984 A A A A

1701-2203 15 1997 C C C G

1701-2203 16 2014 T T T T

1701-2203 17 2022 A A A A

1701-2203 18 2023 C C C C

1701-2203 19 2028 A A A A

1701-2203 20 2036 T T T T

1701-2203 21 2039 T T T C

1701-2203 22 2062 A A A A

1701-2203 23 2067 T T T T

1701-2203 24 2118 C C C C

1701-2203 25 2170 G G G G

1701-2203 26 2179 G G G G

2342-4555 27 2611 T T T T

2342-4555 28 2635 T T T T

2342-4555 29 2659 G G G G

2342-4555 30 2661 C C C C

2342-4555 31 2704 C C C C

2342-4555 32 2716 G G G G

2342-4555 33 2846 A G G A

2342-4555 34 3292 G G G G

2342-4555 35 3470 T T T T

2342-4555 36 4183 G G G G

2342-4555 37 4201 C C T C

2342-4555 38 4254 T T T T

2342-4555 39 4384 C C C A

2342-4555 40 4435 C C C C

4651-5435 41 5180 C C C G

4651-5435 42 5212 C C C C

(b) PS = polymoφhic site;

(c) Position of PS within SEQ ID NOJ;

(d) Alleles for CYP2D6 isogenes are presented 5' to 3' in each column.