AU2004318681A1 - Nucleic acid based assays for identification of FC receptor polymorphisms - Google Patents

Description

WO 2005/102379 PCT/US2004/043726 NUCLEIC ACID BASED ASSAYS FOR IDENTIFICATION OF FC RECEPTOR POLYMORPHISMS TECHNICAL FIELD 5 The present invention pertains generally to genotyping. In particular, the invention relates to nucleic acid-based assays for accurately and efficiently determining FcyRIII genotype of an individual. BACKGROUND 10 IgG receptors (FcyR) are membrane bound glycoproteins that are expressed on the surface of neutrophils, macrophages, natural killer (NK) cells and other cell types. Fc'yRIIIA (CD1 6), for example, has been shown to be involved in a variety of processes such as phagocytosis, endocytosis, antibody-dependent cellular cytotoxicity (ADCC), release of inflammatory mediators, and enhancement of antigen 15 presentation. Van de Winkel et al. (1993) Immunol Today 14(5):215-21. IgG binding to the low affinity FcyRIIIA receptor expressed on the surface of NK cells is considered to be a fundamental mechanism contributing to ADCC. See, e.g., Clynes et al. (2000) Nature Med. 6:443-446; Cooper et al. (2001) Trends Immunol. 22:633 640; Leibson (1997) Immunity 6:655-661; Roitt et al. (2001) Immunology (6th ed.; 20 Mosby, Edinburgh, UK). Two FcyRIII genes, FcyRIIIa (gene A) or FcyRIlb (gene B), have been identified. Ravetch and Perussia (1989) J. Exp Med 170:481. FcyRlI receptors have been mapped to the long arm of chromosome 1. Van de Winkel et al. (1993) Immunol Today 14(5):215-21. Furthermore, various functional polymorphisms have 25 been identified in FcyRIIIA including a bi-allelic functional polymorphism of FcyRIla (G-+T at nucleotide 559), which predicts a valine (V) to phenylalanine (F) substitution at amino acid position 158. Koene et al. (1997) Blood 90:1109-1114. The FcyRIIIA 158V allele has been shown to bind human IgG1 better than the 158F allele, and the increased binding of the 158V allele results in enhanced activation of 30 effector cells and better ADCC. Shields et al. (2001) J. Biol. Chem. 176:6591-6604; Vance et al. (1993) J Immunol. 151:6429-6439. Treatment outcomes have also been WO 2005/102379 PCT/US2004/043726 shown to be affected by the 158V/F polymorphism -- FcyRIIa 158 F/F homozygotes exhibit a decreased response to therapeutic antibodies such as ritubimab. Cartron et al. (2002) Blood 99:754-758; Weng and Levy (2003) J. Clin. Oncol. 21:1-8. Given the functional and clinical implications of the FcyRlIA 158V/F 5 polymorphism, several groups have proposed PCR-based methods for genotyping a particular individual. See, e.g., Koene et al. (1997) Blood 90(3):1109-1114; Lepperts et al. (2000) J. Immuno Methods 242:127-132; Jiang et al. (1996) J. Immunol. Methods 199:55-59; Morgan et al. (2003) Rheumatology 42:528-533; Dall'Ozzo et al. (2003) J. Immunol. Methods 277:185-192; and U.S. Patent Nos. 5,830,652 and 10 5,985,561. However, currently available assays have error rates of at least 10% with respect to determining polymorphisms and, in addition, do not efficiently or accurately distinguish between FcyRIIIA (gene A) and FcyRIIIB (gene B). Therefore, there remains a need for the development of compositions and methods that can be used to accurately and efficiently determine a subject's FcyRII 15 genotype. SUMMARY The present invention is based on the development of sensitive, reliable nucleic acid-based tests for determining the FcyRLII genotype from any sample. 20 In one aspect, the invention includes an isolated oligonucleotide comprising a nucleotide sequence of between 10 and 60 nucleotides in length, the nucleotide sequence comprising: (a) a sequence selected from the group consisting of SEQ ID NOs: 1 to 19; (b) a nucleotide sequence having 80% sequence identity to a nucleotide sequence of (a); or (c) complements of (a) and (b). Any of the isolated nucleotides 25 described herein may further comprise a detectable label, for example a fluorescent label (e.g., 6-carboxyfluorescein (6-FAM), tetramethyl rhodamine (TAMRA), and/or 2', 4', 5', 7',- tetrachloro -4-7- dichlorofluorescein (TET)). In another aspect, described herein is a method of determining the FcyRIII genotype of a subject, the method comprising the steps of: (a) isolating nucleic acids 30 from a biological sample obtained from the subject; (b) amplifying the isolated nucleic acids using at least first and second combinations comprising at least one of 2 WO 2005/102379 PCT/US2004/043726 the oligonucleotides described herein (e.g., SEQ ID NOs: 1-19) as sense and antisense primers; and (c) detecting the presence or absence of amplified nucleic acids with each combination of oligonucleotides, wherein the presence or absence of amplified nucleic acids is indicative of the FcyRIII genotype of the subject. In certain 5 embodiments, the at least one of the oligonucleotides is specific for an FcyRIII polymorphism. Alternatively, in other embodiments, at least one of the oligonucleotides is generic for at least one FcyRII polymorphism. In any of the methods described herein additional combinations of oligonucleotides can be used to amplify nucleic acids from the sample, for example by repeating steps (b) and (c) with 10 one more additional combinations of oligonucleotide primers. In some embodiments, the first and second combinations of oligonucleotides each comprise one primer in common. In any of the methods described herein, the genotype at the 158V/F site of FcyRIa may be determined. Thus, in certain embodiments, the first combination of 15 oligonucleotide primers comprises SEQ ID NO:5 and SEQ ID NO:2 and the second combination of oligonucleotide primers comprises SEQ ID NO:5 and SEQ ID NO:1. In methods employing these combinations of primers, the presence of an amplification product using the first combination of oligonucleotide primers and the absence of an amplification product using the second combination of oligonucleotide primers is 20 indicative of a 158VV genotype; the absence of an amplification product using the first combination of oligonucleotide primers and the presence of an amplification product using the second combination of oligonucleotide primers is indicative of a 158FF genotype; and the presence of an amplification product using the first combination of oligonucleotide primers and the presence of an amplification product 25 using the second combination of oligonucleotide primers is indicative of a 158FV genotype. Furthermore, in any of the methods described herein, the FcRIII genotype of the subject at additional nucleotide positions may also be determined, for example additional nucleotide positions are selected from the group consisting of positions 30 121, 153, 179, 207, 313 and combinations thereof. Any of the methods described herein may further comprise the step of 3 WO 2005/102379 PCT/US2004/043726 sequencing the amplified nucleic acid product. In certain embodiments, the sequencing primers used include one or more of the oligonucleotides described herein. In another aspect, a method of determining the Fc'yRIH genotype of a subject is provided, the method comprising the steps of: (a) isolating nucleic acids from a 5 biological sample obtained from the subject; (b) amplifying the isolated nucleic acids; (c) sequencing the amplified nucleic acid products using at least one suitable combination of oligonucleotides comprising at least one oligonucleotide as described herein (e.g., SEQ ID NOs: 1-19) as sequencing primers; and (d) determining the nucleotide residue at one or more FcyRII polymorphisms, thereby determining the 10 FcyRII genotype of the subject. In certain embodiments, amplification (step (b)) is performed using at least first and second combinations of oligonucleotides comprising at least one oligonucleotide as described herein as sense and antisense primers. In any of the sequencing methods described herein, the genotype at the 158V/F site of FcyRIIla may be determined, for example by determining the nucleotide at position 15 207 (e.g., only G nucleotides at position 207 is indicative of a 158VV genotype; only T nucleotides only at position 207 is indicative of a 158FF genotype; and G and T nucleotides at position 207 is indicative of a 158FV genotype. In another aspect of the invention, a method of distinguishing FcyRIIa from FcyRIIIb is provided, the method comprising the steps of: (a) isolating nucleic acids 20 from a biological sample obtained from the subject; (b) amplifying the isolated nucleic acids using at least first and second combinations of oligonucleotides comprising at least one oligonucleotide as described herein (e.g., SEQ ID NOs: 1-19) as sense and antisense primers, wherein at least one of the oligonucleotide primers in each combination is specific for FeyRIIIa or FeyRIb; and (c) detecting the presence 25 or absence of amplified nucleic acids with each combination of oligonucleotides, wherein the presence or absence of amplified nucleic acids is distinguishes FcyRIIIa from FcyRIIlb. In yet another aspect, the invention provides a method of distinguishing FeyRIHa from FcyRIIlb, the method comprising the steps of: (a) isolating nucleic 30 acids from a biological sample obtained from the subject; (b) amplifying the isolated nucleic acids; (c) sequencing the amplified nucleic acids using at least one suitable 4 WO 2005/102379 PCT/US2004/043726 combination of oligonucleotides according to any of claims 1 to 4 as sequencing primers; and (d) determining the nucleotides at positions 121, 153, 179 and 313, thereby distinguishing between FcyRIHa from FcyRIflb. In certain embodiments, wherein step (b) comprises amplifying the isolated nucleic acids using at least first 5 and second combinations of oligonucleotides comprising at least one of the oligonucleotides described herein as sense and antisense primers. In yet another aspect, the invention includes a kit for FcyRIIIa genotyping, the kit comprising: one or more pairs of primer oligonucleotides comprising at least one oligonucleotide as described herein; and written instructions for genotyping a 10 biological sample for FcyRIa. In certain embodiments, the kit further comprises sequencing primers, e.g., one or more oligonucleotides as described herein. In certain embodiments, the methods involve using multiple pairs of oligonucleotide primers as described herein to determine haplotype. In any of the methods described herein, the amplification may comprise PCR, 15 RT-PCR, transcription-mediated amplification (TMA) or TaqMan T M , or a combination thereof. In further embodiments, the invention is directed to a kit for FcyRIIla genotyping, the kit comprising: one or more pairs of primer oligonucleotides as described herein; and 20 written instructions for genotyping a biological sample for FcyRIIa. Sequencing primers and instructions regarding sequencing may also be included in a kit as described herein or, alternatively, sequencing reagents and instructions may be contained in a separate kit. In additional embodiments, the kit(s) may further comprise a polymerase and buffers. In certain embodiments, the kit further comprises 25 one or more pairs of sequencing oligonucleotides as described herein. These and other aspects of the present invention will become evident upon reference to the following detailed description and attached drawings. In addition, various references are set forth herein which describe in more detail certain procedures or compositions, and are therefore incorporated by reference in their 30 entirety. 5 WO 2005/102379 PCT/US2004/043726 BRIEF DESCRIPTION OF THE DRAWINGS Figure 1, panels A and B, depict alignments of nucleotide sequences from FcyRIIa and FcyRIlb genes. FIG. IA aligns partial cDNA sequence from FCyRIIa (top line, labeled HSFCGR31 and also referred to as gene B) and FcyRIfb (bottom 5 line, labeled HSFCGR32 and also referred to as gene A). Also shown in FIG. lA in boxes are: positions indicating gene A or gene B (position 473, 531 and 641) as well as the single nucleotide polymorphism (occurring only in gene A) at position 559 that predicts a V-F substitution. FIG lB aligns exon 4 of gene A and gene B and shows various nucleotide differences between the two genes, including the highly specific 10 nucleotide variation at position 313, numbered relative to the first base of exon 4. FIG. 2 depicts the location of exemplary oligonucleotide sequences designated SEQ ID NOs: 1 to 5 and their alignment in relation to HSFCGR31 (gene B) and HSFCGR32 (gene A). FIG. 3 depicts the location of amplification and sequencing primers as 15 described herein. Exemplary amplification (PCR) primers are indicated by the thick, dark arrows. Polymorphisms occurring in the native sequences are depicted in the dark bar (positions numbered relative to the first base of exon 4. Exemplary sequencing primers are indicated by the thin arrows. The polymorphism designated 313 (A/C) is numbered relative to the first base of exon 4. 20 FIG. 4 depicts the location of various primers as described herein (SEQ ID NOs:6-19), numbered relative to the first base of exon 4. FIG. 5, panels A to D, are reproductions of gels showing PCR amplification products from the various combinations of primers (SEQ ID NOs: 1-5). Each lane indicates a different combination of primers. From left to right in each panel, lane 1 25 shows the result of PCR using primers designated SEQ ID NOs:4 and 1; lane 2 shows the result of PCR using primers designated SEQ ID NOs:4 and 2; lane 3 shows the result of PCR using primers designated SEQ ID NOs:3 and 1; lane 4 shows the result of PCR using primers designated SEQ ID NOs:3 and 2; lane 5 shows the result of PCR using primers designated SEQ ID NOs:5 and 1; and lane 6 shows the result of 30 PCR using primers designated SEQ ID NOs:5 and 2. The presence of an amplification product in lane 5 and the absence of an amplification product in lane 6 6 WO 2005/102379 PCT/US2004/043726 (Donor 1360, panel A and Donor U03-313, panel D) indicates that the subject's genotype is 158FF. The absence of an amplification product in lane 5 and the presence of an amplification product in lane 6 (Donor 1714, panel B) indicates that the subject's genotype is 158VV. The presence of amplification products in both lanes 5 5 and 6 (Donor 1210, panel C) indicates the subject's genotype is 158 FV. FIG. 6 depicts results of genotyping of 80 samples as described herein (e.g., PCR followed by sequencing). The middle column of each table shows genotypic results obtained using PCR-sequencing assays described herein. The right column of each table (labeled "Koene") indicates genotyping results obtained with methods 10 described in the art. FIG. 7 depicts the sequences of exemplary oligonucleotide as described herein. FIG. 8 depicts the sequences of other exemplary oligonucleotide as described herein. FIG. 9 is a schematic depiction of a 96-well plate for PCR that contains 2 15 columns of 8 wells each of 6 different primer combinations. FIG. 10 is a schematic depiction of addition of a 96-well plate genotyping assay using the plate depicted in FIG. 9. Three controls and thirteen patient samples are screened against the six different primer combinations. FIG. 11 depicts the reference sequence used for PCR-sequencing assays. 20 DETAILED DESCRIPTION The practice of the present invention will employ, unless otherwise indicated, conventional methods of chemistry, biochemistry, recombinant DNA techniques and virology, within the skill of the art. Such techniques are explained fully in the 25 literature. See, e.g., A.L. Lehninger, Biochemistry (Worth Publishers, Inc., current addition); Sambrook, et al., Molecular Cloning: A Laboratory Manual (2nd Edition, 1989); Methods In Enzymology (S. Colowick and N. Kaplan eds., Academic Press, Inc.); Oligonucleotide Synthesis (N. Gait, ed., 1984); A Practical Guide to Molecular Cloning (1984). 30 All publications, patents and patent applications cited herein, whether supra or infra, are hereby incorporated by reference in their entirety. 7 WO 2005/102379 PCT/US20041043726 It must be noted that, as used in this specification and the appended claims, the singular forms "a", "an" and "the" include plural referents unless the content clearly dictates otherwise. Thus, for example, reference to "an oligonucleotide" includes a mixture of two or more oligonucleotides, and the like. 5 The following amino acid abbreviations are used throughout the text: Alanine: Ala (A) Arginine: Arg (R) Asparagine: Asn (N) Aspartic acid: Asp (D) Cysteine: Cys (C) Glutamine: Gln (Q) Glutamic acid: Glu (E) Glycine: Gly (G) 10 Histidine: His (H) Isoleucine: Ile (I) Leucine: Leu (L) Lysine: Lys (K) Methionine: Met (M) Phenylalanine: Phe (F) Proline: Pro (P) Serine: Ser (S) Threonine: Thr (T) Tryptophan: Trp (W) 15 Tyrosine: Tyr (Y) Valine: Val (V) I. Definitions In describing the present invention, the following terms will be employed, and are intended to be defined as indicated below. 20 The terms "genotyping," "haplotyping," and "DNA typing" are used interchangeably to refer to the determination of the alleles of a selected chromosome or portion of a chromosome of an individual. By "isolated" is meant, when referring to a polypeptide, that the indicated molecule is separate and discrete from the whole organism with which the molecule is 25 found in nature or is present in the substantial absence of other biological macro molecules of the same type. The term "isolated" with respect to a polynucleotide is a nucleic acid molecule devoid, in whole or part, of sequences normally associated with it in nature; or a sequence, as it exists in nature, but having heterologous sequences in association therewith; or a molecule disassociated from the chromosome. 30 The terms "polynucleotide," "oligonucleotide," "nucleic acid" and "nucleic acid molecule" are used herein to include a polymeric form of nucleotides of any 8 WO 2005/102379 PCT/US2004/043726 length, either ribonucleotides or deoxyribonucleotides. This term refers only to the primary structure of the molecule. Thus, the term includes triple-, double- and single stranded DNA, as well as triple-, double- and single-stranded RNA. It also includes modifications, such as by methylation and/or by capping, and unmodified forms of the 5 polynucleotide. More particularly, the terms "polynucleotide," "oligonucleotide," "nucleic acid" and "nucleic acid molecule" include polydeoxyribonucleotides (containing 2-deoxy-D-ribose), polyribonucleotides (containing D-ribose), any other type of polynucleotide which is an N- or C-glycoside of a purine or pyrimidine base, and other polymers containing nonnucleotidic backbones, for example, polyamide 10 (e.g., peptide nucleic acids (PNAs)) and polymorpholino (commercially available from the Anti-Virals, Inc., Corvallis, Oregon, as Neugene) polymers, and other synthetic sequence-specific nucleic acid polymers providing that the polymers contain nucleobases in a configuration which allows for base pairing and base stacking, such as is found in DNA and RNA. There is no intended distinction in length between the 15 terms "polynucleotide," "oligonucleotide," "nucleic acid" and "nucleic acid molecule," and these terms will be used interchangeably. These terms refer only to the primary structure of the molecule. Thus, these terms include, for example, 3' deoxy-2', 5'-DNA, oligodeoxyribonucleotide N3' P5' phosphoramidates, 2'-O-alkyl substituted RNA, double- and single-stranded DNA, as well as double- and single 20 stranded RNA, DNA:RNA hybrids, and hybrids between PNAs and DNA or RNA, and also include known types of modifications, for example, labels which are known in the art, methylation, "caps," substitution of one or more of the naturally occurring nucleotides with an analog, internucleotide modifications such as, for example, those with uncharged linkages (e.g., methyl phosphonates, phosphotriesters, 25 phosphoramidates, carbamates, etc.), with negatively charged linkages (e.g., phosphorothioates, phosphorodithioates, etc.), and with positively charged linkages (e.g., aminoalklyphosphoramidates, aminoalkylphosphotriesters), those containing pendant moieties, such as, for example, proteins (including nucleases, toxins, antibodies, signal peptides, poly-L-lysine, etc.), those with intercalators (e.g., acridine, 30 psoralen, etc.), those containing chelators (e.g., metals, radioactive metals, boron, oxidative metals, etc.), those containing alkylators, those with modified linkages (e.g., 9 WO 2005/102379 PCT/US2004/043726 alpha anomeric nucleic acids, etc.), as well as unmodified forms of the polynucleotide or oligonucleotide. In particular, DNA is deoxyribonucleic acid. A polynucleotide "derived from" or "specific for" a designated sequence refers to a polynucleotide sequence which comprises a contiguous sequence of 5 approximately at least about 6 nucleotides, preferably at least about 8 nucleotides, more preferably at least about 10-12 nucleotides, and even more preferably at least about 15-20 nucleotides corresponding, i.e., identical or complementary to, a region of the designated nucleotide sequence. The derived polynucleotide will not necessarily be derived physically from the nucleotide sequence of interest, but may be generated 10 in any manner, including, but not limited to, chemical synthesis, replication, reverse transcription or transcription, which is based on the information provided by the sequence of bases in the region(s) from which the polynucleotide is derived. As such, it may represent either a sense or an antisense orientation of the original polynucleotide. 15 "Homology" refers to the percent similarity between two polynucleotide or two polypeptide moieties. Two polynucleotide, or two polypeptide sequences are "substantially homologous" to each other when the sequences exhibit at least about 50% , preferably at least about 75%, more preferably at least about 80%-85%, preferably at least about 90%, and most preferably at least about 95%-98% sequence 20 similarity over a defined length of the molecules. As used herein, substantially homologous also refers to sequences showing complete identity to the specified polynucleotide or polypeptide sequence. In general, "identity" refers to an exact nucleotide-to-nucleotide or amino acid to-amino acid correspondence of two polynucleotides or polypeptide sequences, 25 respectively. Percent identity can be determined by a direct comparison of the sequence information between two molecules by aligning the sequences, counting the exact number of matches between the two aligned sequences, dividing by the length of the shorter sequence, and multiplying the result by 100. Readily available computer programs can be used to aid in the analysis of 30 homology and identity, such as ALIGN, Dayhoff, M.O. in Atlas ofProtein Sequence and Structure M.O. Dayhoff ed., 5 Suppl. 3:353-358, National biomedical Research 10 WO 2005/102379 PCT/US2004/043726 Foundation, Washington, DC, which adapts the local homology algorithm of Smith and Waterman Advances in AppL. Math. 2:482-489, 1981 for peptide analysis. Programs for determining nucleotide sequence homology are available in the Wisconsin Sequence Analysis Package, Version 8 (available from Genetics Computer 5 Group, Madison, WI) for example, the BESTFIT, FASTA and GAP programs, which also rely on the Smith and Waterman algorithm. These programs are readily utilized with the default parameters recommended by the manufacturer and described in the Wisconsin Sequence Analysis Package referred to above. For example, percent homology of a particular nucleotide sequence to a reference sequence can be 10 determined using the homology algorithm of Smith and Waterman with a default scoring table and a gap penalty of six nucleotide positions. Another method of establishing percent homology in the context of the present invention is to use the MPSRCH package of programs copyrighted by the University of Edinburgh, developed by John F. Collins and Shane S. Sturrok, and distributed by 15 IntelliGenetics, Inc. (Mountain View, CA). From this suite of packages the Smith Waterman algorithm can be employed where default parameters are used for the scoring table (for example, gap open penalty of 12, gap extension penalty of one, and a gap of six). From the data generated the "Match" value reflects "sequence homology." Other suitable programs for calculating the percent identity or similarity 20 between sequences are generally known in the art, for example, another alignment program is BLAST, used with default parameters. For example, BLASTN and BLASTP can be used using the following default parameters: genetic code = standard; filter = none; strand = both; cutoff= 60; expect = 10; Matrix = BLOSUM62; Descriptions = 50 sequences; sort by = HIGH SCORE; Databases = non-redundant, 25 GenBank + EMBL + DDBJ + PDB + GenBank CDS translations + Swiss protein + Spupdate + PIR. Details of these programs can be found at the following internet address: http://www.ncbi.nlm.gov/cgi-bin/BLAST. Alternatively, homology can be determined by hybridization of polynucleotides under conditions that form stable duplexes between homologous 30 regions, followed by digestion with single-stranded-specific nuclease(s), and size determination of the digested fragments. DNA sequences that are substantially I 1 WO 2005/102379 PCT/US2004/043726 homologous can be identified in a Southern hybridization experiment under, for example, stringent conditions, as defined for that particular system. Defining appropriate hybridization conditions is within the skill of the art. See, e.g., Sambrook et al., supra; DNA Cloning, supra; Nucleic Acid Hybridization, supra. 5 "Recombinant" as used herein to describe a nucleic acid molecule means a polynucleotide of genomic, cDNA, viral, semisynthetic, or synthetic origin, which, by virtue of its origin or manipulation, is not associated with all or a portion of the polynucleotide with which it is associated in nature. The term "recombinant" as used with respect to a protein or polypeptide means a polypeptide produced by expression 10 of a recombinant polynucleotide. In general, the gene of interest is cloned and then expressed in transformed organisms, as described further below. The host organism expresses the foreign gene to produce the protein under expression conditions. A "DNA-dependent DNA polymerase" is an enzyme that synthesizes a complementary DNA copy from a DNA template. Examples are DNA polymerase I 15 from E. coli and bacteriophage T7 DNA polymerase. All known DNA-dependent DNA polymerases require a complementary primer to initiate synthesis. Under suitable conditions, a DNA-dependent DNA polymerase may synthesize a complementary DNA copy from an RNA template. 20 A "DNA-dependent RNA polymerase" or a "transcriptase" is an enzyme that synthesizes multiple RNA copies from a double-stranded or partially-double stranded DNA molecule having a (usually double-stranded) promoter sequence. The RNA molecules ("transcripts") are synthesized in the 5' to 3' direction beginning at a specific position just downstream of the promoter. Examples of transcriptases are the 25 DNA-dependent RNA polymerase from E. coli and bacteriophages T7, T3, and SP6. An "RNA-dependent DNA polymerase" or "reverse transcriptase" is an enzyme that synthesizes a complementary DNA copy from an RNA template. All known reverse transcriptases also have the ability to make a complementary DNA copy from a DNA 30 template; thus, they are both RNA- and DNA-dependent DNA polymerases. A primer is required to initiate synthesis with both RNA and DNA templates. 12 WO 2005/102379 PCT/US2004/043726 "RNAse H" is an enzyme that degrades the RNA portion of an RNA:DNA duplex. These enzymes may be endonucleases or exonucleases. Most reverse transcriptase enzymes normally contain an RNAse H activity in addition to their polymerase activity. However, other sources of the RNAse H are available without an 5 associated polymerase activity. The degradation may result in separation of RNA from a RNA:DNA complex. Alternatively, the RNAse H may simply cut the RNA at various locations such that portions of the RNA melt off or permit enzymes to unwind portions of the RNA. As used herein, the term "target nucleic acid region" or "target nucleic acid" 10 denotes a nucleic acid molecule with a "target sequence" to be amplified. The target nucleic acid may be either single-stranded or double-stranded and may include other sequences besides the target sequence, which may not be amplified. The term "target sequence" refers to the particular nucleotide sequence of the target nucleic acid that is to be amplified. The target sequence may include a probe-hybridizing region 15 contained within the target molecule with which a probe will form a stable hybrid under desired conditions. The "target sequence" may also include the complexing sequences to which the oligonucleotide primers complex and extended using the target sequence as a template. Where the target nucleic acid is originally single-stranded, the term "target sequence" also refers to the sequence complementary 20 to the "target sequence" as present in the target nucleic acid. If the "target nucleic acid" is originally double-stranded, the term "target sequence" refers to both the plus (+) and minus (-) strands. The term "primer" or "oligonucleotide primer" as used herein, refers to an oligonucleotide which acts to initiate synthesis of a complementary nucleic acid strand 25 when placed under conditions in which synthesis of a primer extension product is induced, i.e., in the presence of nucleotides and a polymerization-inducing agent such as a DNA or RNA polymerase and at suitable temperature, pH, metal concentration, and salt concentration. The primer is preferably single-stranded for maximum ef ficiency in amplification, but may alternatively be double-stranded. If 30 double-stranded, the primer can first be treated to separate its strands before being used to prepare extension products. This denaturation step is typically affected by 13 WO 2005/102379 PCT/US2004/043726 heat, but may alternatively be carried out using alkali, followed by neutralization. Thus, a "primer" is complementary to a template, and complexes by hydrogen bonding or hybridization with the template to give a primer/template complex for initiation of synthesis by a polymerase, which is extended by the addition of 5 covalently bonded bases linked at its 3' end complementary to the template in the process of DNA or RNA synthesis. As used herein, the term "probe" or "oligonucleotide probe" refers to a structure comprised of a polynucleotide, as defined above, that contains a nucleic acid sequence complementary to a nucleic acid sequence present in the target nucleic acid 10 analyte. The polynucleotide regions of probes may be composed of DNA, and/or RNA, and/or synthetic nucleotide analogs. When an "oligonucleotide probe" is to be used in a 5' nuclease assay, such as the TaqMan T M technique, the probe will contain at least one fluorescer and at least one quencher that is digested by the 5' endonuclease activity of a polymerase used in the reaction in order to detect any amplified target 15 oligonucleotide sequences. In this context, the oligonucleotide probe will have a sufficient number of phosphodiester linkages adjacent to its 5' end so that the 5' to 3' nuclease activity employed can efficiently degrade the bound probe to separate the fluorescers and quenchers. When an oligonucleotide probe is used in the TMA technique, it will be suitably labeled, as described below. 20 It will be appreciated that the hybridizing sequences need not have perfect complementarity to provide stable hybrids. In many situations, stable hybrids will form where fewer than about 10% of the bases are mismatches, ignoring loops of four or more nucleotides. Accordingly, as used herein the term "complementary" refers to an oligonucleotide that forms a stable duplex with its "complement" under assay 25 conditions, generally where there is about 90% or greater homology. The terms "hybridize" and "hybridization" refer to the formation of complexes between nucleotide sequences which are sufficiently complementary to form complexes via Watson-Crick base pairing. Where a primer "hybridizes" with target (template), such complexes (or hybrids) are sufficiently stable to serve the priming 30 function required by, e.g., the DNA polymerase to initiate DNA synthesis. As used herein, the term "binding pair" refers to first and second molecules 14 WO 2005/102379 PCT/US2004/043726 that specifically bind to each other, such as complementary polynucleotide pairs capable of forming nucleic acid duplexes. "Specific binding" of the first member of the binding pair to the second member of the binding pair in a sample is evidenced by the binding of the first member to the second member, or vice versa, with greater 5 affinity and specificity than to other components in the sample. The binding between the members of the binding pair is typically noncovalent. Unless the context clearly indicates otherwise, the terms "affinity molecule" and "target analyte" are used herein to refer to first and second members of a binding pair, respectively. The terms "specific-binding molecule" and "affinity molecule" are used 10 interchangeably herein and refer to a molecule that will selectively bind, through chemical or physical means to a detectable substance present in a sample. By "selectively bind" is meant that the molecule binds preferentially to the target of interest or binds with greater affinity to the target than to other molecules. For example, a DNA molecule will bind to a substantially complementary sequence and 15 not to unrelated sequences. The "melting temperature" or "Tm" of double-stranded DNA is defined as the temperature at which half of the helical structure of DNA is lost due to heating or other dissociation of the hydrogen bonding between base pairs, for example, by acid or alkali treatment, or the like. The Tm of a DNA molecule depends on its length and 20 on its base composition. DNA molecules rich in GC base pairs have a higher Tm than those having an abundance of AT base pairs. Separated complementary strands of DNA spontaneously reassociate or anneal to form duplex DNA when the temperature is lowered below the Tm. The highest rate of nucleic acid hybridization occurs approximately 25 0 C below the Tm. The Tm may be estimated using the following 25 relationship: Tm = 69.3 + 0.41(GC)% (Marmur et al. (1962) J Mol. Biol. 5:109-118). As used herein, the terms "label" and "detectable label" refer to a molecule capable of detection, including, but not limited to, radioactive isotopes, fluorescers, chemiluminescers, chromophores, enzymes, enzyme substrates, enzyme cofactors, enzyme inhibitors, chromophores, dyes, metal ions, metal sols, semiconductor 30 nanocrystals, ligands (e.g., biotin, avidin, strepavidin or haptens) and the like. The term "fluorescer" refers to a substance or a portion thereof that is capable of 15 WO 2005/102379 PCT/US2004/043726 exhibiting fluorescence in the detectable range. As used herein, a "solid support" refers to a solid surface such as a magnetic bead, latex bead, microtiter plate well, glass plate, nylon, agarose, acrylamide, and the like. 5 As used herein, a "biological sample" refers to a sample of tissue or fluid isolated from a subject such as, but not limited to, blood, plasma, serum, fecal matter, urine, bone marrow, bile, spinal fluid, lymph fluid, samples of the skin, secretions of the skin, respiratory, intestinal, and genitourinary tracts, tears, saliva, milk, blood cells, organs, biopsies and also samples of in vitro cell culture constituents including 10 but not limited to conditioned media resulting from the growth of cells and tissues in culture medium, e.g., recombinant cells, and cell components. The samples detailed above need not necessarily be in the form obtained directly from the source. For example, the sample can be treated prior to use, such as, for example, by heating, centrifuging, etc. prior to analysis. 15 By "vertebrate subject" is meant any member of the subphylum cordata, including, without limitation, mammals such as horses, and humans, and avian species. The term does not denote a particular age. Thus, adult and newborn animals, as well as fetuses, are intended to be covered. 20 II. General Overview A variety of compositions and methods are provided herein for determining the FcyRII genotype of a subject. In particular, novel oligonucleotides (e.g., primers) are described that can be used to determine a subject's genotype at the 158V/F site of Fc'yRIHa (gene A). The accuracy of the assays described herein derived, in part, from 25 the fact that the compositions and methods described herein are able to clearly distinguish between gene A and gene B. Although both gene A and gene B map to chromosome 1, the present disclosure conclusively demonstrates that gene B does not include the 158V/F polymorphism, but, rather is, always VV homozygous. Also described are methods for FcyRII genotyping involving use of one or 30 more of the oligonucleotides described herein. FcyRIla genotype at the 158F/V site may be determined by a single PCR reaction (e.g., one set of primers); by evaluating 16 WO 2005/102379 PCT/US2004/043726 multiple PCR reactions (e.g., different combinations of primers); and/or by single or multiple PCR reactions followed by sequencing or other nucleic acid based assay technique. Using the compositions and methods described herein, a particular individual 5 can readily be genotyped, for example to better determine a treatment protocol. Thus, pharmacogenetic analyses of any subject can be readily performed. Before describing the present invention in detail, it is to be understood that this invention is not limited to particular formulations or process parameters as such may, of course, vary. It is also to be understood that the terminology used herein is for the 10 purpose of describing particular embodiments of the invention only, and is not intended to be limiting. Although a number of compositions and methods similar or equivalent to those described herein can be used in the practice of the present invention, the preferred materials and methods are described herein. 15 III. Oligonucleotides Described herein are novel nucleotide sequences that are useful in determining the FcyRIl haplotype of an individual. Furthermore, the primer sequences described herein have been used to accurately distinguish between FcyRIIIA (gene A) and 20 FcyRIIIB (gene B). For convenience, the numbering and alignment of primers recognizing coding sequences (cDNA) of both genes A and B is done relative to Ravetch and Perussia (1989) J. Exp Med 170:481 and NCBI Accession No. NM_000569. Likewise, the numbering and alignment of primers recognizing genomic DNA is done relative to the 25 first base of exon 4. The sequences described herein are generally useful as primers, for example PCR primers and/or sequencing primers. As noted in Table 1, the primers may be non-specific or specific for gene A or gene B and, additionally, may also be specific for one or more polymorphisms, preferably, the 158F/V single nucleotide 30 polymorphism. (FIG. 1). In certain embodiments, the oligonucleotides will also amplify sequences that include one or more additional polymorphisms, for example as 17 WO 2005/102379 PCT/US2004/043726 depicted in FIG. 2. Non-limiting examples of such sequences are shown in Table 1. Table 1 Name Sequence Seq Id Specificity 158-3'A CTGAAGACACATTTTTACTCCCAAA I 158F 158-3'C CTGAAGACACATTTTTACTCCCAAC 2 158V 158-5T TCCAAAAGCCACACTCAAAGAT 3 gene B 158-5'A TTCCAAAAGCCACACTCAAAGA 4 no 158-5'C TCCAAAAGCCACACTCAAAGAC 5 gene A forward GGGTGTCTGTGTCTTTCAG 6 no cp13297 forward CTTTCAGGCTGGCTGTTGCT 7 no ep13462 forward AGGCTGGCTGTTGCTCCA 8 no cp13463 reverse CCGGCATTCCAGGGTGGCACAT 9 no cp13928 reverse TCAGGAATCTCCTCCCAACTCA 10 no cp13466 reverse AATCTCCTCCCAACTCAACTTCC 11 no cp13465 forward TTTCATCATAATTCTGACATCT 12 gene A cp13560 forward TTTTCATCATAATTCTGACATCT 13 gene A cp13561 reverse CAACTCAACTTCCCAGTGTAAT 14 gene A cp13516 reverse CAACTCAACTTCCCAGTGTGTT 15 gene A cp13515 reverse CTTCTCAACTTCCCAGTATGAT 16 gene A cp13517 18 WO 2005/102379 PCT/US2004/043726 forward ATATTACAGAATGGCACAGA 17 gene B cp13452 reverse CAACTCAACTTCCCAGTGAGAG 18 gene B cp13497 reverse CAACTCAACTTCCCAGTGTGAG 19 gene B cp13496 Therefore, the oligonucleotides described herein preferably include one or more nucleotides defining polymorphisms (e.g., 158F/V polymorphism) and/or nucleotides that distinguish gene A from gene B. Preferably, the primers used amplify 5 a sequence including at least the 158F/V polymorphism. In certain embodiments, the primers used amplify a sequence including multiple polymorphisms. For example, as shown in FIG. 3, primers that amplify sequences that include, but not necessarily limited to, polymorphisms at position 121 (G/A), 153 (T/C), 179 (C/T), 207 (G/T), and 313 (C/A), as numbered relative to the first base in exon 4. The first four 10 positions correspond to positions 473 (G/A), 505 (T/C), 531 (C/T) and 559 (G/T), as numbered relative to NM_000569). Furthermore, as described in detail in the Examples below, the present disclosure also marks the discovery that a single nucleotide (A/C) difference at position 313, numbered relative to the first base of exon 4 is highly specific for gene 15 A or gene B. In particular, in gene A, an A residue is always found at this position, while in gene B, a C residue is always found at this position. Thus, in certain embodiments, the primer will include this residue and, accordingly, be specific for gene A or gene B. In certain embodiments, the distinguishing base (e.g., polymorphism and/or 20 gene A- or B-specific base) is the terminal base of the oligonucleotide (primer) sequence. For example, as depicted in FIG. 2, the 3' nucleotide in 3' primer 158-3'A (SEQ ID NO:1) is specific for the 158F haplotype (e.g., T as position 559) while the 3' nucleotide in 3'-primer 158-3'C (SEQ ID NO:2) is specific for the 158V haplotype (e.g., G at position 559). Similarly, the 5' nucleotide in 3' primer 5'T (SEQ ID NO:3) 25 is specific for gene B (T at position 531) while the 3' nucleotide in 5' primer 5'C (SEQ 19 WO 2005/102379 PCT/US2004/043726 ID NO:5) is specific for gene A (C at position 531). 5' primer 5'A (SEQ ID NO:4) is generic to both gene A and gene B, as it ends at position 530. The primers as disclosed herein may also include one or more mismatches with native gene A or gene B sequences. In certain instances, introduction of a 5 mismatched base pair provides enhanced specificity for gene. Mismatches are preferably internal to the primer. Particularly useful oligonucleotides comprise the nucleotide sequences of the various oligonucleotides depicted in, respectively), or sequences displaying at least about 80-90% or more sequence identity thereto, including any percent identity within these ranges, such as 81, 82, 83, 84, 85, 86, 87, 10 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99% sequence identity thereto. As explained above, the regions from which the oligonucleotides are derived generally include one or more polymorphisms. In addition, the oligonucleotides can be derivatized using methods well known in the art in order to improve the affinity of binding to the target nucleic acid. 15 The particular length of the oligonucleotide primer is not critical and can be readily designed by those of skill in the art. The oligonucleotides can include from about 5 to about 500 nucleotides of the particular conserved region, preferably about 10 to about 100 nucleotides, or more preferably about 10 to about 60 nucleotides, or any integer within these ranges, such as a sequence including 18, 19, 20, 21, 22, 23, 20 24, 25, 26...35...40, etc. nucleotides from the conserved region of interest. Preferably, the primer sequences are at least 10 nucleotides in length, more preferably between about 15 and 30 nucleotides in length (including nucleotides of 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 or 30 nucleotides in length), and even more preferably between about 15 and 25 nucleotides in length. 25 Oligonucleotides as described herein (e.g., primers and probes) are readily synthesized by standard techniques, e.g., solid phase synthesis via phosphoramidite chemistry, as disclosed in U.S. Patent Nos. 4,458,066 and 4,415,732, incorporated herein by reference in their entireties; Beaucage et al. (1992) Tetrahedron 48:2223 2311; and Applied Biosystems User Bulletin No. 13 (1 April 1987). Other chemical 30 synthesis methods include, for example, the phosphotriester method described by Narang et al., Meth. Enzymol. (1979) 6:90 and the phosphodiester method disclosed 20 WO 2005/102379 PCT/US2004/043726 by Brown et al., Meth. Enzymol. (1979) 68:109. Poly A or poly C, or other non complementary nucleotide extensions may be incorporated into probes using these same methods. Hexaethylene oxide extensions may be coupled to probes by methods known in the art. Cload et al. (1991) J. Am. Chem. Soc. 113:6324-6326; U.S. Patent 5 No. 4,914,210 to Levenson et al.; Durand et al. (1990) Nucleic Acids Res. 18:6353 6359; and Horn et al. (1986) Tet. Lett. 27:4705-4708. Moreover, the oligonucleotides may be coupled to labels for detection. There are several means known for derivatizing oligonucleotides with reactive functionalities that permit the addition of a label. For example, several approaches are 10 available for biotinylating probes so that radioactive, fluorescent, chemiluminescent, enzymatic, or electron dense labels can be attached via avidin. See, e.g., Broken et al., Nucl. Acids Res. (1978) 5:363-384 that discloses the use of ferritin-avidin-biotin labels; and Chollet et al. Nucl. Acids Res. (1985) 13:1529-1541 which discloses biotinylation of the 5' termini of oligonucleotides via an aminoalkylphosphoramide 15 linker arm. Several methods are also available for synthesizing amino-derivatized oligonucleotides which are readily labeled by fluorescent or other types of compounds derivatized by amino-reactive groups, such as isothiocyanate, N-hydroxysuccinimide, or the like, see, e.g., Connolly (1987) Nucl. Acids Res. 15:3131-3139, Gibson et al. (1987) Nucl. Acids Res. 15:6455-6467 and U.S. Patent No. 4,605,735 to Miyoshi et al. 20 Methods are also available for synthesizing sulfhydryl-derivatized oligonucleotides that can be reacted with thiol-specific labels, see, e.g., U.S. Patent No. 4,757,141 to Fung et al., Connolly et al. (1985) Nucl. Acids Res. 13:4485-4502 and Spoat et al. (1987) NucL. Acids Res. 15:4837-4848. A comprehensive review of methodologies for labeling DNA fragments is provided in Matthews et al., Anal. Biochem. (1988) 25 169:1-25. For example, oligonucleotides may be fluorescently labeled by linking a fluorescent molecule to the non-ligating terminus of the probe. Guidance for selecting appropriate fluorescent labels can be found in Smith et al., Meth. Enzymol. (1987) 155:260-301; Karger et al., Nucl. Acids Res. (1991) 19:4955-4962; Haugland (1989) 30 Handbook of Fluorescent Probes and Research Chemicals (Molecular Probes, Inc., Eugene, OR). Preferred fluorescent labels include fluorescein and derivatives thereof, 21 WO 2005/102379 PCT/US2004/043726 such as disclosed in U.S. Patent No. 4,318,846 and Lee et al., Cytometry (1989) 10:151-164, and 6-FAM, JOE, TAMRA, ROX, HEX-1, HEX-2, ZOE, TET-1 or NAN-2, and the like. Additionally, oligonucleotides can be labeled with an acridinium ester (AE) 5 using the techniques described below. Current technologies allow the AE label to be placed at any location within the probe. See, e.g., Nelson et al. (1995) "Detection of Acridinium Esters by Chemiluminescence" in Nonisotopic Probing, Blotting and Sequencing, Kricka L.J.(ed) Academic Press, San Diego, CA; Nelson et al. (1994) "Application of the Hybridization Protection Assay (HPA) to PCR" in The 10 Polymerase Chain Reaction, Mullis et al. (eds.) Birkhauser, Boston, MA; Weeks et al., Clin. Chem. (1983) 29:1474-1479; Berry et al., Clin. Chem. (1988) 34:2087-2090. An AE molecule can be directly attached to the probe using non-nucleotide-based linker arm chemistry that allows placement of the label at any location within the probe. See, e.g., U.S. Patent Nos. 5,585,481 and 5,185,439. 15 IV. Nucleic Acid Based Assays One or more of the oligonoucleotides described herein are then used in one or more nucleic acid based assays in order to determine FcyRIII haplotype, for example FcyRIIla haplotype at the 158V/F polymorphism. 20 Genotyping can be performed on any suitable sample. For instance, nucleic acids can be readily isolated from cells expressing FcyRIII using by standard techniques such as guanidium thiocyanate-phenol-chloroform extraction (Chomocyznski et al. (1987) Anal. Biochem. 162:156). RNA and/or genomic DNA can be isolated. The isolated nucleic acids (RNA or DNA) are then preferably 25 subjected to amplification. Amplifying a target nucleic acid typically uses a nucleic acid polymerase to produce multiple copies of the target nucleic acid or fragments thereof. Suitable amplification techniques are well known in the art, such as, for example transcription mediated amplification, polymerase chain reaction (PCR), replicase mediated 30 amplification, and ligase chain reaction (LCR). 22 WO 2005/102379 PCT/US2004/043726 A. Polymerase Chain Reaction (PCR) In certain embodiments, the amplification process comprises a polymerase chain reaction (PCR)-based technique, such as RT-PCR, to determine the FcRIII haplotype in any biological sample. PCR is a technique for amplifying a desired 5 target nucleic acid sequence contained in a nucleic acid molecule or mixture of molecules. In PCR, a pair of primers is employed in excess to hybridize to the complementary strands of the target nucleic acid. The primers are each extended by a polymerase using the target nucleic acid as a template. The extension products become target sequences themselves after dissociation from the original target strand. 10 New primers are then hybridized and extended by a polymerase, and the cycle is repeated to geometrically increase the number of target sequence molecules. The PCR method for amplifying target nucleic acid sequences in a sample is well known in the art and has been described in, e.g., Innis et al. (eds.) PCR Protocols (Academic Press, NY 1990); Taylor (1991) Polymerase chain reaction: basic principles and 15 automation, in PCR: A Practical Approach, McPherson et al. (eds.) IRL Press, Oxford; Saiki et al. (1986) Nature 324:163; as well as in U.S. Patent Nos. 4,683,195, 4,683,202 and 4,889,818, all incorporated herein by reference in their entireties. In particular, PCR uses relatively short oligonucleotide primers which flank the target nucleotide sequence to be amplified, oriented such that their 3' ends face 20 each other, each primer extending toward the other. The polynucleotide sample is extracted and denatured, preferably by heat, and hybridized with first and second primers that are present in molar excess. Polymerization is catalyzed in the presence of the four deoxyribonucleotide triphosphates (dNTPs -- dATP, dGTP, dCTP and dTTP) using a primer- and template-dependent polynucleotide polymerizing agent, 25 such as any enzyme capable of producing primer extension products, for example, E. coli DNA polymerase I, Klenow fragment of DNA polymerase I, T4 DNA polymerase, thermostable DNA polymerases isolated from Thermus aquaticus (Taq), available from a variety of sources (for example, Perkin Elmer), Thermus thermophilus (United States Biochemicals), Bacillus stereothermophilus (Bio-Rad), or 30 Thermococcus litoralis ("Vent" polymerase, New England Biolabs). This results in two "long products" which contain the respective primers at their 5' ends covalently 23 WO 2005/102379 PCT/US2004/043726 linked to the newly synthesized complements of the original strands. The reaction mixture is then returned to polymerizing conditions, e.g., by lowering the temperature, inactivating a denaturing agent, or adding more polymerase, and a second cycle is initiated. The second cycle provides the two original strands, the two long products 5 from the first cycle, two new long products replicated from the original strands, and two "short products" replicated from the long products. The short products have the sequence of the target sequence with a primer at each end. On each additional cycle, an additional two long products are produced, and a number of short products equal to the number of long and short products remaining at the end of the previous cycle. 10 Thus, the number of short products containing the target sequence grows exponentially with each cycle. Preferably, PCR is carried out with a commercially available thermal cycler, e.g., Perkin Elmer. RNAs may be amplified by reverse transcribing the mRNA into cDNA, and then performing PCR (RT-PCR), as described above. Alternatively, a single enzyme 15 may be used for both steps as described in U.S. Patent No. 5,322,770. mRNA may also be reverse transcribed into cDNA, followed by asymmetric gap ligase chain reaction (RT-AGLCR) as described by Marshall et al. (1994) PCR Meth. App. 4:80 84. Particular PCR conditions (e.g., temperature, cycling time, etc.) are not critical to the practice of the invention can be readily determined by one skilled in the art. 20 In certain embodiments, genotyping accuracy is achieved by a single PCR reaction, through the judicious design and selection of primers. For instance, the sequences resulting from PCR amplification using primers that amplify sequences including the polymorphism at position 559 and the gene specific polymorphism at position 313 (numbered relative to the first base of exon 4) typically provides 25 sufficient information for determining 158V/F haplotype and for distinguishing gene A from gene B. For PCR-based techniques, it may be preferable in certain instances to use primers that include multiple polymorphisms. The inclusion of multiple polymorphisms provides built-in internal controls. The primers selected may amplify 30 gene A or gene B only, or alternatively, may amplify sequences from both genes. Representative examples of a single pair of primer combinations that can be used are 24 WO 2005/102379 PCT/US20041043726 shown in FIG. 7 (SEQ ID NOs:1-I 1) and include, for example, combinations of one of SEQ ID NOs:6, 7 or 8 with one of SEQ ID NOs:9, 10 or 11 or combinations of one of SEQ ID NOs:l or 2, with one of SEQ ID NOs:3, 4 or 5. Furthermore, although amplification of DNA samples obtained from the 5 subject using one suitable pair of primers disclosed in Table 1 may itself be sufficient to determine genotype, the present disclosure also provides for additional assays that enhance genotyping accuracy, including additional PCR and/or sequencing. For instance, in certain embodiments, PCR amplification is performed using multiple combinations of primers and the resulting pattern of amplified bands 10 obtained from each combination is evaluated to accurate determine genotype of the subject. In particularly preferred embodiments, multiple different PCR assays are performed on each sample, for example multiple reactions using various 3' (reverse) primers in various combinations with a 5' (forward) primer. By way of example, six PCR amplifications may be performed using the 3' 15 primers of SEQ ID NOs: 1 and 2 in combination with the 5' primers of SEQ ID NOs:3, 4 and 5 (e.g., SEQ ID NOs:1 and 3; SEQ ID NOs: 2 and 3; SEQ ID NOs:1 and 4; SEQ ID NOs:2 and 4; SEQ ID NOs:1 and 5; SEQ ID NOs:2 and 5). The results of each amplification reaction can be compared (e.g., by gel electrophoresis) and the particularly pattern used to readily haplotype the subject. Using primer pairs where 20 one primer is gene A-specific, gene B- specific or generic to gene A and B and the other primer is 15 8V- or 158F-specific allows for efficient and accurate genotyping at this important site. FIG. 5 shows results obtained from analysis of multiple PCR amplification reactions, each of which contain a different combination of primers. Following 25 amplification, the resulting product is run on a standard 4% agarose gel (see, also Examples) and the resulting product (if any) visualized. The lanes in FIG. 5 are labeled to correspond to the particular combination of primer used in the PCR reaction. The pattern of panels A and D indicates a subject that is 158FF (homozygous) in gene A. Panel B shows a subject that is 158VV homozygous in gene 30 A, while panel C shows a subject that is 158FV (heterozygous) in gene A. All panels include a internal control in that the combination of 5 primer T (gene B specific, SEQ 25 WO 2005/102379 PCT/US2004/043726 ID NO:3) and 3' primer A (158F-specific, SEQ ID NO:1) should not produce a PCR product because gene B does not contain the polymorphism at position 559. B. Seguencing 5 In still other embodiments, genotyping as described herein further comprises sequencing the products of PCR amplification. Any of the primers disclosed herein can be used as sequencing primers. Particularly preferred as sequencing primers are those that bind at a polymorphism and when bound, allow sequencing of portion of the gene corresponding to polymorphism 158V/F. Representative sequencing primers 10 are depicted in FIG. 8 (SEQ ID NOs:12-19). Direct sequencing may be accomplished by chemical sequencing, for example, using the Maxam-Gilbert method, or by enzymatic sequencing, for example, using the Sanger method. In the latter case, specific oligonucleotides are synthesized using standard methods and used as primers for the dideoxynucleotide sequencing reaction. 15 See, e.g., Sambrook, supra and Examples below. FIG. 6 shows genotyping results at the gene A 158V/F site after PCR using primers described herein followed by sequencing ("PCR-SEQ") as compared to PCR alone using previously described primers ("Koene"). Of the 80 samples compared, 10 were incorrectly genotyped using the primers and PCR methods previously described 20 in Koene et al., supra. Specifically, samples designated A609201, A609372, A610260, A612201, A701320, NCM460, A609203, A701017, Kyse410, and kidney were inaccurately genotyped using previously described methods. In addition, unlike the assays described herein, previously described methods do not distinguish between gene A and gene B. 25 C. TagMan TM The fluorogenic 5' nuclease assay, known as the TaqMan T M assay (see, e.g., Holland et al., Proc. Natl. Acad.Sci. USA (1991) 88:7276-7280), is a powerful and versatile PCR-based detection system for nucleic acid targets. Hence, primers and 30 probes described herein can also be used in TaqManTM analyses to determine a subject's FeyRII genotype. Analysis is performed in conjunction with thermal cycling 26 WO 2005/102379 PCT/US2004/043726 by monitoring the generation of fluorescence signals. The assay system dispenses with the need for gel electrophoretic analysis, and has the capability to generate quantitative data allowing the determination of target copy numbers. For example, standard curves can be produced using serial dilutions of previously analyzed samples. 5 A standard graph can be produced with copy numbers of each of the panel members against which sample unknowns can be compared. The fluorogenic 5' nuclease assay is conveniently performed using, for example, AmpliTaq GoldTM DNA polymerase, which has endogenous 5' nuclease activity, to digest an internal oligonucleotide probe labeled with both a fluorescent 10 reporter dye and a quencher (see, Holland et al., Proc. NatL. Acad.Sci. USA (1991) 88:7276-7280; and Lee et al., Nucl. Acids Res. (1993) 21:3761-3766). Assay results are detected by measuring changes in fluorescence that occur during the amplification cycle as the fluorescent probe is digested, uncoupling the dye and quencher labels and causing an increase in the fluorescent signal that is proportional to the amplification of 15 target nucleic acid. The amplification products can be detected in solution or using solid supports. In this method, the TaqMan T M probe is designed to hybridize to a target sequence within the desired PCR product. The 5' end of the TaqManTm probe contains a fluorescent reporter dye. The 3' end of the probe is blocked to prevent probe 20 extension and contains a dye that will quench the fluorescence of the 5' fluorophore. During subsequent amplification, the 5' fluorescent label is cleaved off if a polymerase with 5' exonuclease activity is present in the reaction. Excision of the 5' fluorophore results in an increase in fluorescence that can be detected. For a detailed description of the TaqManM assay, reagents and conditions for 25 use therein, see, e.g., Holland et al., Proc. Natl. Acad. Sci, US.A. (1991) 88:7276 7280; U.S. Patent Nos. 5,538,848, 5,723,591, and 5,876,930, all incorporated herein by reference in their entireties. D. Transcription-Mediated Amplification Assays (TMA) 30 The sequences described herein may also be used as a basis for transcription mediated amplification (TMA) assays. TMA provides a method of identifying target 27 WO 2005/102379 PCT/US2004/043726 nucleic acid sequences present in very small amounts in a biological sample. Such sequences may be difficult or impossible to detect using direct assay methods. In particular, TMA is an isothermal, autocatalytic nucleic acid target amplification system that can provide more than a billion RNA copies of a target sequence. The 5 assay can be done qualitatively, to accurately detect the presence or absence of the target sequence in a biological sample. The assay can also provide a quantitative measure of the amount of target sequence over a concentration range of several orders of magnitude. TMA provides a method for autocatalytically synthesizing multiple copies of a target nucleic acid sequence without repetitive manipulation of reaction 10 conditions such as temperature, ionic strength and pH. Generally, TMA includes the following steps: (a) isolating nucleic acid, including RNA, from the biological sample of interest to be haplotyped; and (b) combining into a reaction mixture (i) the isolated nucleic acid, (ii) first and second oligonucleotide primers, the first primer having a complexing sequence sufficiently 15 complementary to the 3' terminal portion of an RNA target sequence, if present (for example the (+) strand), to complex therewith, and the second primer having a complexing sequence sufficiently complementary to the 3' terminal portion of the target sequence of its complement (for example, the (-) strand) to complex therewith, wherein the first oligonucleotide further comprises a sequence 5' to the complexing 20 sequence which includes a promoter, (iii) a reverse transcriptase or RNA and DNA dependent DNA polymerases, (iv) an enzyme activity which selectively degrades the RNA strand of an RNA-DNA complex (such as an RNAse H) and (v) an RNA polymerase which recognizes the promoter. The components of the reaction mixture may be combined stepwise or at once. 25 The reaction mixture is incubated under conditions whereby an oligonucleotide/target sequence is formed, including DNA priming and nucleic acid synthesizing conditions (including ribonucleotide triphosphates and deoxyribonucleotide triphosphates) for a period of time sufficient to provide multiple copies of the target sequence. The reaction advantageously takes place under conditions suitable for maintaining the 30 stability of reaction components such as the component enzymes and without requiring modification or manipulation of reaction conditions during the course of the 28 WO 2005/102379 PCT/US2004/043726 amplification reaction. Accordingly, the reaction may take place under conditions that are substantially isothermal and include substantially constant ionic strength and pH. The reaction conveniently does not require a denaturation step to separate the RNA-DNA complex produced by the first DNA extension reaction. 5 Suitable DNA polymerases include reverse transcriptases, such as avian myeloblastosis virus (AMV) reverse transcriptase (available from, e.g., Seikagaku America, Inc.) and Moloney urine leukemia virus (MMLV) reverse transcriptase (available from, e.g., Bethesda Research Laboratories). Promoters or promoter sequences suitable for incorporation in the primers are 10 nucleic acid sequences (either naturally occurring, produced synthetically or a product of a restriction digest) that are specifically recognized by an RNA polymerase that recognizes and binds to that sequence and initiates the process of transcription whereby RNA transcripts are produced. The sequence may optionally include nucleotide bases extending beyond the actual recognition site for the RNA polymerase 15 that may impart added stability or susceptibility to degradation processes or increased transcription efficiency. Examples of useful promoters include those that are recognized by certain bacteriophage polymerases such as those from bacteriophage T3, T7 or SP6, or a promoter from E. coli. These RNA polymerases are readily available from commercial sources, such as New England Biolabs and Epicentre. 20 Some of the reverse transcriptases suitable for use in the methods herein have an RNAse H activity, such as AMV reverse transcriptase. It may, however, be preferable to add exogenous RNAse H, such as E. coli RNAse H, even when AMV reverse transcriptase is used. RNAse H is readily available from, e.g., Bethesda Research Laboratories. 25 The RNA transcripts produced by these methods may serve as templates to produce additional copies of the target sequence through the above-described mechanisms. The system is autocatalytic and amplification occurs autocatalytically without the need for repeatedly modifying or changing reaction conditions such as temperature, pH, ionic strength or the like. 30 Detection may be done using a wide variety of methods, including direct sequencing, hybridization with sequence-specific oligomers, gel electrophoresis and 29 WO 2005/102379 PCT/US20041043726 mass spectrometry. These methods can use heterogeneous or homogeneous formats, isotopic or nonisotopic labels, as well as no labels at all. TMA is described in detail in, e.g., U.S. Patent No. 5,399,491, the disclosure of which is incorporated herein by reference in its entirety. In one example of a 5 typical assay, an isolated nucleic acid sample from a subject to be genotyped, is mixed with a buffer concentrate containing the buffer, salts, magnesium, nucleotide triphosphates, primers, dithiothreitol, and spermidine. The reaction is optionally incubated at about 100 *C for approximately two minutes to denature any secondary structure. After cooling to room temperature, reverse transcriptase, RNA polymerase, 10 and RNAse H are added and the mixture is incubated for two to four hours at 37 'C. The reaction can then be assayed by denaturing the product, adding a probe solution, incubating 20 minutes at 60 'C, adding a solution to selectively hydrolyze the unhybridized probe, incubating the reaction six minutes at 60 *C, and measuring the remaining chemiluminescence in a luminometer. 15 As noted above, two or more of the tests described above may be performed to confirm the genotype. For example, if the first test used the transcription mediated amplification (TMA) to amplify the nucleic acids for detection, then an alternative nucleic acid testing (NAT) assay is performed, for example, by using PCR amplification, RT PCR, and the like, as described herein. Thus, any sample from any 20 patient can be specifically and selectively haplotyped. As is readily apparent, design of the assays described herein are subject to a great deal of variation, and many formats are known in the art. The above descriptions are merely provided as guidance and one of skill in the art can readily modify the described protocols, using techniques well known in the art. 25 E. Kits The above-described assay reagents, including the primers, PCR buffers, sequencing reagents, etc., can be provided in kits, with suitable instructions and other necessary reagents, in order to conduct the assays as described above. The kit will 30 normally contain in separate containers the combination of primers and probes (either already bound to a solid matrix or separate with reagents for binding them to the 30 WO 2005/102379 PCT/US2004/043726 matrix), control formulations (positive and/or negative), labeled reagents when the assay format requires same and signal generating reagents (e.g., enzyme substrate) if the label does not generate a signal directly. Instructions (e.g., written, tape, VCR, CD-ROM, etc.) for carrying out the assay usually will be included in the kit. The kit 5 can also contain, depending on the particular assay used, other packaged reagents and materials (i.e. wash buffers and the like). Standard assays, such as those described above, can be conducted using these kits. F. Applications 10 As noted above, the present invention is based on the discovery of novel compositions and assays for accurately determining the FcyRII haplotype of a vertebrate subject, particularly the haplotype at the 158F/V site in both FcyRIIIa. The ability to accurately determine FcyRIII genotype has many applications, including but not limited to, pharmacogenetics. Pharmacogenetics refers to the 15 determination of a particular individual's genotype in order to determine a suitable treatment protocol. As noted above, subjects with the 158F/F genotype response less well to antibody treatments (e.g., ritubimab) than subjects with a 158V/F and 158V/V genotype. Furthermore, it has been demonstrated that response to antibody-mediated therapies such as ritubimab can be enhanced by pre-treatment with cytokines (e.g., IL 20 2). See, also, co-owned Provisional Patent Application titled "USE OF FC RECEPTOR POLYMORPHISMS AS DIAGNOSTICS FOR TREATMENT STRATEGIES FOR IMMUNE-RESPONSE DISORDERS," filed March 10, 2004, incorporated by reference in its entirety herein. Thus, using the compositions and methods described herein individuals in 25 need of treatment for an immune disorder and can be efficiently and accurately genotyped and, accordingly, designated as suitable candidates for intervention with one or more immunotherapeutics that mediate the FcyRIII-triggered ADCC pathway (e.g., 11L-2). IL-2 proteins and muteins are known in the art. See, e.g., U.S. Patent No. 4,752,585; U.S. Patent No. 4,766,106; U.S. Patent No. 4,931,543; U.S. Patent No. 30 5,700,913; U.S. Serial No. 60/585,980, filed July 7, 2004 and titled "Combinatorial Interleukin-2 Muteins," and U.S. Serial No. 60/550,868, filed March 5, 2004, and 31 WO 2005/102379 PCT/US2004/043726 titled "Improved Interleukin-2 Muteins;" incorporated by reference in their entireties herein. IL-2 muteins are commerically available and are also described in the following documents: International Publications Nos. WO 91/04282; WO 99/60128; WO 00/58456; WO 00/04048; European Patent (EP) Publication No. EP 136,489; 5 European Patent Application No. 83306221.9, filed October 13, 1983 (published May 30, 1984 under Publication No. EP 109,748), which is the equivalent to Belgian Patent No. 893,016, and commonly owned U.S. Patent No. 4,518,584); European Patent Publication No. EP 200,280 (published December 10, 1986), European Patent Publication No. EP 118,617, which patents and applications are all incorporated by 10 reference herein in their entireties. In certain applications, genotyping is performed on a individual suffering from an immune disorder, particularly a cancer, in order to determine the suitability of adjunct therapies (e.g., IL-2 immunotherapy alone) to be used in combination with an anti-cancer monoclonal antibody. Examples of cancers in which genotyping as 15 described herein may aid in designing treatment protocols include, but are not limited to, B-cell lymphomas listed below, breast cancer, ovarian cancer, cervical cancer, prostate cancer, colon cancers, melanoma, renal cell carcinoma, acute mycloid leukemia (AML); and chronic lymphocytic leukemia (CLL). 20 EXPERIMENTAL Below are examples of specific embodiments for carrying out the present invention. The examples are offered for illustrative purposes only, and are not intended to limit the scope of the present invention in any way. Efforts have been made to ensure accuracy with respect to numbers used (e.g., 25 amounts, temperatures, etc.), but some experimental error and deviation should, of course, be allowed for. In the following examples, enzymes were purchased from commercial sources, and used according to the manufacturers' directions. In the isolation of DNA fragments, except where noted, all DNA 30 manipulations were done according to standard procedures. See, Sambrook et al., supra. Restriction enzymes, T 4 DNA ligase, E. coli, DNA polymerase I, Klenow 32 WO 2005/102379 PCT/US2004/043726 fragment, and other biological reagents can be purchased from commercial suppliers and used according to the manufacturers' directions. Double stranded DNA fragments were separated on agarose gels. 5 Example 1: Extraction of DNA from Samples Whole blood samples were obtained from a subject. The samples were collected in PreAnalytiX's PAXgeneTM Blood DNA Tubes (Qiagen Inc., catalog #769989) following the manufacturer's instructions. Genomic DNA was isolated from whole blood using a PreAnalytiX's PAXgeneTM Blood DNA Kit (Qiagen Inc) 10 also following the manufacturer's instructions. Example 2: PCR-Based Genotyping A. PCR amplification PCR assays were performed as follows. In brief, PCR was performed in 96 15 well plate format on a GeneAmp PCR System 9600 Perkin Elmer machine (Perkin Elmer, Boston, MA). A master mix was prepared as follows. In a 1.5 ml Eppendorf test tube, the following reagents were prepared as a master mix, 300 Pl of lOX Stoffel Buffer (Applied Biosystems); 600 pl of 25 mM MgC 2 solution; 300 1d of a dNTP mix 20 (Applied Biosystems, catalog #0032 003.109); and 270 pl of H 2 0 and stored in aliquots at -20"C. All buffers were stored according to the manufacturer's instructions. 30 pl of AmpliTaq DNA Polymerase Stoffel Fragment (Applied Biosystems, catalog #N808-0038) was added to a thawed aliquot of master mix. Tubes were 25 prepared with different combinations of primers (e.g., 6 tubes), each containing 9 I of the forward primer, 9 1J of the reverse primer, 225 pl of the Master Mix Solution and 117 1 H 2 0. As depicted in FIG. 9, 20 pl of each tube was added to a 2 columns of a 96 well plate (e.g., for six primer combinations there were 2 columns of 8 wells each for 30 each primer combination). Genomic DNA isolated as described in Example I was diluted to 1 Ong/pi and 5 sl added to columns containing the different primer 33 WO 2005/102379 PCT/US20041043726 combinations (e.g., columns 1-6 when six different primer combinations are used, FIG. 10). Controls were also included. The plates were sealed and placed into the GeneAmp PCR system 9600 machine for PCR. PCR conditions were: a single cycle of incubation at 95"C for 5 5 minutes; 35 cycles of: incubation at 94"C for 30 seconds; incubation at 64 0 C for 30 seconds and incubation at 72 0 C for 30 seconds; and a single cycle of incubation at 72"C for 8 minutes. The 96-well plate was cooled at 4"C before subject the samples to agarose gel. 10 B. Electrophoresis TAE Gel electrophoresis was performed on the PCR products of Section A using standard techniques. A stock of 50X concentrated gel buffer (for final concentration of 40 mM Tris-Acetate, 1 mM Na 2 EDTA, pH 8.0) contained 242 g Tris Base; 57.1 ml glacial acetic acid; 100 ml 0.5 M Na 2 EDTA. Gel Loading buffer 15 contained 0.25 % bromophenol blue; 0.25 % xylene cyanol FF; and 15 % Ficoll (Type 400; Pharmacia) in H 2 0. Molecular weight markers (0.07-12.2 kbp) from Boehringer Mannheim (catalog #1498 037) were also used. A standard 4 % Agarose horizontal gel in TEA buffer containing 10 pg/ml of ethidium bromide was prepared. 5 pl of each PCR reaction was mixed with I l of 20 standard 6X loading buffer and loaded into in adjacent lanes of the gel in order from reaction 1 through 6. See, FIG. 5. The gel was fun at constant 100 Volts for 15-20 minutes, visualized and photographed under Ultra Violet (UV) light in a standard UV trans-illuminator. Exemplary results are shown in FIG. 5. These results confirm that At position 25 158, FCGR3A is polymorphic a Valine (V158) or a phenylalanine (F158). FCGR3B is not polymorphic at this position encoding only Valine. The use of primers as described herein allow genotyping of the FCGR3A 158V/F site by using primers that identify this site (e.g., SEQ ID NOs:1-2) as well as a non-specific primer (SEQ ID NO:4) and primers that identify a single nucleotide difference as between gene A and 30 B at position 531 (SEQ ID NOs:3 and 5). Position 531 does not result in an amino acid difference. 34 WO 2005/102379 PCT/US2004/043726 As described above, a PCR product obtained using 5'primer C (SEQ ID NO:5) and 3'primer C (SEQ ID NO:2), indicates the V genotype. If this product is observed for an individual sample and a PCR product obtained using 5' primer C (SEQ ID NO:5) and 3' primer A (SEQ ID NO:1) is not visible, the result indicates that the 5 subject is homozygous for V. See, FIG. 5, panel B. Similarly, if a PCR product obtained using 5' primer C (SEQ ID NO:5) and 3' primer A (SEQ ID NO: 1) is visible and a product obtained using 5' primer C (SEQ ID NO:5) and 3' primer C (SEQ ID NO:2) is not visible, the subject is homozygous for F in gene A. See, FIG. 5, panels A and D. A product in both of these reactions indicates a subject that is heterozygous 10 for F and V. See, FIG. 5, panel C. Internal controls are also present inasmuch as gene B is not polymorphic and the combination of 5' primer T and 3' primer A should never result in a visible product. Thus, using the methods described herein FcyRIIIa genotype at the 158F/V polymorphism can be accurately determined. 15 Example 5: PCR-Sequencing For genotyping, experiments in which sample DNA was amplified (PCR) and the products sequenced using oligonucleotide primers as disclosed herein were also conducted. 20 A. PCR PCR of genomic DNA was performed using a BD AdvantageT 2 PCR kit (product #639206 or #639207) according to the manufacturer's instructions. Each reaction contained 5 1 I OX BD Advantage 2 PCR Buffer; 1 [1 of SuM/each primer 25 mixture (total primer concentration 10uM); 1 .1 50X dNTP Mix (10 mM each); 1 A1 50X BD Advantage 2 Polymerase Mix; sample DNA to a final concentration of 10 100 ng; and a volume of water to make the final reaction volume 50 pl. Cycling conditions were 95 "C for 5 minutes; 30 cycles of 95 "C for 30 seconds, 62 "C for 30 seconds; 72"C for 40 seconds; and incubated at 4 "C. Following cycling, the PCR 30 reaction products were purified using the Qiagen's MinElute PCR purification kit (catalog no. 28004 or 28006) and following the manufacturer's recommended 35 WO 2005/102379 PCT/US2004/043726 protocol, except that the final elution volume was 50 p1. Controls were also included in the assays. Positive controls were genomic DNA of known FcyRIII genotype (e.g., G, T, and G/T at the 158VF polymorphism of gene A) while negative controls typically included all reagents except genomic DNA 5 (which yielded negative PCR and sequencing results). B. Sequencing Sequencing reactions on the PCR products obtained in as described above were performed using BigDye terminator v3.0 on either 3100 or 3730xl platforms 10 (Applied Biosystems). Each sequencing reaction contained 2 p1 of BigDye Terminator v3.0 Ready reaction mix (part no. 4390246), 1 111 5x Buffer (part no. 4336699), 1 l PCR product (about 0.02 gl/Rg); 2 gl of 2 gM primer (various combinations of the SEQ ID NOs:12-19) and 4 g1 of water. A total of 30 cycles were performed on each reaction: 95 *C for 10 seconds; 15 50"C for 5 seconds; and 60 "C for 3 minutes. After cycling, reactions were incubated at 4 *C. The reactions were purified by adding 45 pl of dry Sephadex G-75 Resin from Amersham (catalog #17-0051-01 or 17-0052-03) to a dry filter plate (Millipore Cat.#MAHV N45 10) with a multiscreen Column Loader (Millipore catalog 20 #MCL09645). Subsequently, 300 g1 of water was added into each well and the plate covered and incubated at room temperature for at least 30 minutes. The filter plate was stacked with a 96-well microtiter plate (Nunc catalog #12565263) and spun for 3 minutes at 1650 RPM in Eppendorf Model 5810R with an A-4-62 swing bucket rotor. The filter plate was placed on top of a clean 96-well PCR 25 plate (Sorenson Bioscience Inc., catalog #12565263 or equivalent) and on top of a 96 well base (Applied Biosystems, catalog #N801-053 1). All of the samples were transferred into the center of designated filter columns and spun for 5 minutes at 1800 RPM in Eppendorf Model 581 OR with an A-4-62 swing bucket rotor. The final sample volumes were adjusted to be about 15 g1 with autoclaved sterile purified 30 water. The plates were then assembled according to the manufacturer's instructions 36 WO 2005/102379 PCT/US2004/043726 (3100 User's Manual or 3730x1 User's Manual). The parameter programmed were: POP6 as separation medium and default module "StdSeq50_POP6" for the 3100 platform and POP7 as separation medium and default module "LongSeq50_POP7_1" for the 3739 platform. Run times in the default module were 6500 seconds (3100 5 platform) and 5640 seconds (3730 platform). For targets less than about 300 bases, run time in the default module was shortened to 4000 seconds (3100 platform) or 3600 seconds (3730 platform) if no other samples with longer read length were included in the same run. 10 C. Analysis The sequencing data was transferred to a desktop computer and imported into the Sequencer T project. Sequences for FCGR3A specific primers (Table 1 and FIG. 8) from each individual sample were aligned with a reference sequence (FIG. 11). Sequences from FCGR3B specific primers from each individual samples and 15 sequences from primers used in PCR reactions were aligned with reference sequence. Sequences beyond reference sequence are edited out. Subsequently, genotyping was conducted as follows. If A, C, T and/or C were found in positions 121, 153, 179, and 313 respectively (numbered relative to first base of exon 4), the reactions were deemed to be non-gene A-specific and were repeated. 20 If signals at these positions matched gene A reference sequence signals only, the sample was considered FCGR3A and the signal from position 207 (numbered relative to first base of exon 4, position 559 in cDNA) analyzed. If only a G signal was obtained at position 207, the genotype of the individual from which the sample was obtained was 158VV homozygous. If only a T signal was obtained at position 207, the 25 genotype of the individual from which the sample was obtained was 158FF homozygous. If G and T signals were obtained at position 207, the sample was obtained from a 158VF heterozygous subject. Similarly, FcyRIIIb genotype was confirmed as follows. If G, T, C, A signals were found in positions 121, 153, 179, 313 respectively (numbered relative to first 30 base of exon 4), the reactions were deemed to be non gene B-specific and were repeated. If signals at these positions matched gene B reference sequence signals, the 37 WO 2005/102379 PCT/US2004/043726 sample was deemed FCGR3B. Samples determined to be gene B did not contain the 158VF polymorphism and a G signal was seen at the corresponding nucleotide. 136 samples were tested as described and 135 were accurately FcyRII genotyped. In one case, the sample did not contain gene B. In cases in which either 5 gene A or gene B are absent from a subject's genome, it may be desirable to sequence using PCR primers. Sequencing with PCR primers allows estimation of the ratio of FCGR3A and FCGR3B genes based on signals from both A and B genes in position 121, 153, 179, and 313. Results of genotypic analyses are summarized in FIG. 6 and are also compared 10 to methods described in Koene et al, supra. The PCR-sequencing methods described herein determined the subject's genotype in all 80 samples, whereas previously described methods had greater than 10% error rate (10 samples). Thus, PCR-sequencing assays are highly sensitive and are capable of accurately determining FcgRIII genotype. 15 Accordingly, novel sequences and genotyping assays using these sequences have been disclosed. From the foregoing, it will be appreciated that, although specific embodiments of the invention have been described herein for purposes of illustration, various modifications may be made without deviating from the spirit and scope 20 thereof. 38

Claims (29)

1. An isolated oligonucleotide comprising a nucleotide sequence of between 5 10 and 60 nucleotides in length, the nucleotide sequence comprising: (a) a sequence selected from the group consisting of SEQ ID NOs: Ito 19; (b) a nucleotide sequence having 80% sequence identity to a nucleotide sequence of (a); or (c) complements of (a) and (b). 10

2. The isolated oligonucleotide of claim 1, further comprising a detectable label.

3. The isolated oligonucleotide of claim 2, wherein the detectable label is a 15 fluorescent label.

4. The isolated oligonucleotide of claim 3, wherein the fluorescent label is selected from the group consisting of 6-carboxyfluorescein (6-FAM), tetramethyl rhodamine (TAMRA), and 2', 4', 5', 7',- tetrachloro -4-7- dichlorofluorescein (TET). 20

5. A method of determining the FcyRII genotype of a subject, the method comprising the steps of: (a) isolating nucleic acids from a biological sample obtained from the subject; (b) amplifying the isolated nucleic acids using at least first and second 25 combinations of oligonucleotides according to any of claims I to 4 as sense and antisense primers; and (c) detecting the presence or absence of amplified nucleic acids with each combination of oligonucleotides, wherein the presence or absence of amplified nucleic acids is indicative of the FcyRII genotype of the subject. 30

6. The method of claim 5, wherein at least one of the oligonucleotides is 39 WO 2005/102379 PCT/US2004/043726 specific for an FcyRIII polymorphism.

7. The method of claim 5, wherein at least one of the oligonucleotides is generic for at least one FcyRIII polymorphism. 5

8. The method of claim 5 further comprising repeating steps (b) and (c) with one more additional combinations of oligonucleotide primers.

9. The method of any of claims 5 to 8, wherein the first and second 10 combinations of oligonucleotides each comprise one primer in common.

10. The method of claim 9, wherein the genotype at the 158V/F site of FeyRiIa is determined. 15

11. The method of claim 10, wherein the first combination of oligonucleotide primers comprises SEQ ID NO:5 and SEQ ID NO:2.

12. The method of claim 11, wherein the second combination of oligonucleotide primers comprises SEQ ID NO:5 and SEQ ID NO:1. 20

13. The method of claim 12, wherein the presence of an amplification product using the first combination of oligonucleotide primers and the absence of an amplification product using the second combination of oligonucleotide primers is indicative of a 158VV genotype. 25

14. The method of claim 12, wherein the absence of an amplification product using the first combination of oligonucleotide primers and the presence of an amplification product using the second combination of oligonucleotide primers is indicative of a 158FF genotype. 30

15. The method of claim 12, wherein the presence of an amplification product 40 WO 2005/102379 PCT/US2004/043726 using the first combination of oligonucleotide primers and the presence of an amplification product using the second combination of oligonucleotide primers is indicative of a 158FV genotype. 5

16. The method of any of claims 5 to 10, wherein the FcRIHI genotype of the subject at additional nucleotide positions is determined.

17. The method of claim 16, wherein the additional nucleotide positions are selected from the group consisting of positions 121, 153, 179, 207, 313 and 10 combinations thereof.

18. The method of any of claims 5 to 17, wherein the nucleic acids are amplified by PCR amplification, RT-PCR, transcription-mediated amplification (TMA), TaqManTM and a combination thereof. 15

19. A method of determining the FcyRIII genotype of a subject, the method comprising the steps of: (a) isolating nucleic acids from a biological sample obtained from the subject; (b) amplifying the isolated nucleic acids; 20 (c) sequencing the amplified nucleic acid products using at least one suitable combination of oligonucleotides according to any of claims 1 to 4 as sequencing primers; and (d) determining the nucleotide residue at one or more FecyRIII polymorphisms, thereby determining the Fc-yRIII genotype of the subject. 25

20. The method of claim 19, wherein step (b) comprises amplifying the isolated nucleic acids using at least first and second combinations of oligonucleotides according to claim 1 as sense and antisense primers. 30

21. The method of claim 19 or claim 20, wherein the genotype at the 158V/F site of FcyRIIla is determined by determining the nucleotide at position 207. 41 WO 2005/102379 PCT/US2004/043726

22. The method of claim 21, wherein only G nucleotides at position 207 is indicative of a 158VV genotype. 5

23. The method of claim 21, wherein only T nucleotides only at position 207 is indicative of a 158FF genotype.

24. The method of claim 21, wherein G and T nucleotides at position 207 is indicative of a 158FV genotype. 10

25. A method of distinguishing FcyRIHa from FcyRIIb, the method comprising the steps of: (a) isolating nucleic acids from a biological sample obtained from the subject; (b) amplifying the isolated nucleic acids using at least first and second 15 combinations of oligonucleotides according to any of claims I to 4 as sense and antisense primers, wherein at least one of the oligonucleotide primers in each combination is specific for FcyRIla or FcyRI]Ib; and (c) detecting the presence or absence of amplified nucleic acids with each combination of oligonucleotides, wherein the presence or absence of amplified nucleic 20 acids is distinguishes FcyRIIa from FEcyRIIb.

26. A method of distinguishing FcyRIla from FecyRIlIb, the method comprising the steps of: (a) isolating nucleic acids from a biological sample obtained from the subject; 25 (b) amplifying the isolated nucleic acids; (c) sequencing the amplified nucleic acids using at least one suitable combination of oligonucleotides according to any of claims 1 to 4 as sequencing primers; and (d) determining the nucleotides at positions 121, 153, 179 and 313, thereby 30 distinguishing between FcyRIHa from FcyRIHb. 42 WO 2005/102379 PCT/US2004/043726

27. The method of claim 26, wherein step (b) comprises amplifying the isolated nucleic acids using at least first and second combinations of oligonucleotides according to any of claims 1 to 4 as sense and antisense primers. 5

28. A kit for FcyRIIla genotyping, the kit comprising: one or more pairs of primer oligonucleotides according to claims 1 to 4; and written instructions for genotyping a biological sample for FcyRlIa.

29. The kit of claim 28, further comprising sequencing primers. 10 43