Abstract:
Novel sequence tagged sites (STSs), probes and primers useful, e.g., for detecting the presence or absence of an STS in a sample, and methods of using these STSs, probes and primers, e.g., in methods of detecting alterations in the Y chromosome are disclosed. These compositions are also useful in methods of diagnosing or aiding in the diagnosis and/or cause of reduced sperm count and in methods of predicting or aiding in the prediction of the likelihood of success of infertility treatments.

Description:
RELATED APPLICATIONS  
       [0001]     This application claims the benefit of U.S. Provisional Application Ser. No. 60/592,719 filed Jul. 30, 2004, the entire disclosure of which is incorporated herein by reference. 
     
    
     GOVERNMENT SUPPORT  
       [0002]     Work described herein was funded, in whole or in part, by grants from the National Institutes of Health (Grant Nos. NICHD-HD32907 and NHGRI-HG00257). The United States Government has certain rights in the invention. 
     
    
     BACKGROUND OF THE INVENTION  
       [0003]     At least one in every ten couples of reproductive age is unable to bear children despite an extended period of unprotected sexual intercourse. In recent years, there has been an intensive search for genetic causes of infertility in both men and women. Spermatogenic failure is the most common form of male infertility, and here the most striking genetic findings have emerged from studies of the Y chromosome&#39;s long arm (Yq). It is now widely accepted that deletions in any one of three Yq regions—AZFa, AZFb, or AZFc—can severely diminish or extinguish sperm production. The number and type of Y chromosomal deletions in a male can have widely varying effects on the success of infertility treatments that a couple may choose to undergo. However, despite the region&#39;s biological and medical importance, efforts to develop physical maps have been stymied by the region&#39;s unusually repetitive sequence composition, and past studies have suggested that it would be difficult or impossible to identify single-copy DNA markers, localize deletion breakpoints, and accurately identify alterations of the Y chromosome.  
       SUMMARY OF THE INVENTION  
       [0004]     The invention pertains in part to novel sequence tagged sites (STSs), to probes and primers useful, e.g., for detecting the presence or absence of an STS in a sample, and to methods of using these STSs, probes and primers, e.g., in methods of detecting alterations in the Y chromosome. These compositions are also useful in methods of diagnosing or aiding in the diagnosis and/or cause of reduced sperm count (oligospermia or azospermia) and in methods of predicting or aiding in the prediction of the likelihood of success of infertility treatments.  
         [0005]     Described herein are results of the assessment and characterization of the human Y chromosome, particularly the AZFc region of the human Y chromosome. As a result of this work, important sequence landmarks of the Y chromosome, particularly AZFc, have been identified. In particular, STSs that can be used in evaluating Y chromosomal DNA for alterations, e.g., deletions such as microdeletions, have been identified; these alterations may be associated with reduced sperm count (e.g., azoospermia and/or oligospermia). The identified STSs and probes and primers therefor can be used in methods of analyzing Y chromosomal DNA for such alterations and for determining or confirming that a deletion or set of deletions is linked to (indicative of) reduced sperm count (azoospermia or severe oligospermia) in humans.  
         [0006]     Accordingly, in some embodiments the invention pertains to a method of detecting an alteration in the human Y chromosome comprising assessing a nucleic acid sample from an individual to be tested for the presence or absence of one or more nucleic acid molecules comprising a nucleic acid sequence selected from the group consisting of SEQ ID NOS: 1-20, 61-108, 205-273 and 412, wherein the absence of one or more of said nucleic acid sequences is indicative of an alteration in the human Y chromosome in the individual. In one embodiment the AZFc region of the Y chromosome is altered. In a particular embodiment the alteration is a deletion in the Y chromosome, e.g., a deletion selected from the group consisting of the deletions shown in FIGS.  2 ,  3 A- 3 B,  4 A- 4 B and  8 .  
         [0007]     In some embodiments the nucleic acid sample is a is a genomic DNA sample. In particular embodiments the sample is derived from blood, skin, sperm, hair root, saliva or buccal cells, or from cells cultured from blood or skin. In other embodiments the individual to be tested is a male with reduced sperm count.  
         [0008]     In a particular method of the invention, the presence or absence of said one or more nucleic acid molecules is determined using one or more probes complementary to the nucleic acid sequence. For example, said one or more probes can be immobilized on a solid support, such as a microarray.  
         [0009]     In another method of the invention, the presence or absence of said one or more nucleic acid molecules is determined by amplification using one or more primers complementary to the nucleic acid sequence. For example, the primers selected from the group consisting of SEQ ID NOS: 21-60 can be used to determine the presence or absence of a nucleic acid molecule comprising a nucleic acid sequence selected from the group consisting of SEQ ID NOS: 1-20, and the primers selected from the group consisting of SEQ ID NOS: 109-204 can be used to determine the presence or absence of a nucleic acid molecule comprising a nucleic acid sequence selected from the group consisting of SEQ ID NOS: 61-108. Similarly, primers selected from the group consisting of SEQ ID NOS: 274-411 can be used to determine the presence or absence of a nucleic acid molecule comprising a nucleic acid sequence selected from the group consisting of SEQ ID NOS: 205-273, and the primers selected from the group consisting of SEQ ID NOS: 413-414 can be used to determine the presence or absence of a nucleic acid molecule comprising a nucleic acid sequence of SEQ ID NO: 412.  
         [0010]      FIGS. 5A-5F ,  6 A- 6 K and  7 A- 7 P show the relationship between the primers of SEQ ID NOS 21-60 and 413-414 and the STSs of SEQ ID NOS: 1-20 and 412, respectively, the primers of SEQ ID NOS: 109-204 and the STSs of SEQ ID NOS: 61-108, and the primers of SEQ ID NOS: 274-411 and the STSs of SEQ ID NOS: 205-273, respectively. As used herein, a primer “corresponds” to an STS if it serves as a specific primer for that STS in an amplification reaction. For example, SEQ ID NOS: 21 and 22 are primers which serve as specific primers for SEQ ID NO: 1, and thus SEQ ID NOS: 21 and 22 are primers which correspond to the STS of SEQ ID NO: 1.  
         [0011]     The invention also pertains to a method of predicting or aiding in the prediction of the likelihood of success of an infertility treatment of a male having reduced sperm count, comprising assessing a nucleic acid sample from said male for the presence or absence of one or more nucleic acid molecules comprising a nucleic acid sequence selected from the group consisting of SEQ ID NOS: 1-20, 61-108, 205-273 and 412, wherein the absence of one or more of said nucleic acid sequences is indicative of an alteration in the human Y chromosome in the individual, and determining the likelihood of success of a fertility treatment in view of the type of alteration present, if any.  
         [0012]     In one embodiment the AZFc region of the Y chromosome is altered. In a particular embodiment the alteration is a deletion in the Y chromosome, e.g., a deletion selected from the group consisting of the deletions shown in FIGS.  2 ,  3 A- 3 B,  4 A- 4 B and  8 .  
         [0013]     In some embodiments the nucleic acid sample is a genomic DNA sample. In particular embodiments the sample is derived from blood, skin, sperm, hair root, saliva or buccal cells, or from cells cultured from blood or skin. In other embodiments the individual to be tested is a male with reduced sperm count. In a particular method of the invention, the presence or absence of said one or more nucleic acid molecules is determined using one or more probes complementary to the nucleic acid sequence. For example, said one or more probes can be immobilized on a solid support, such as a microarray.  
         [0014]     In another method of the invention, the presence or absence of said one or more nucleic acid molecules is determined by amplification using one or more primers complementary to the nucleic acid sequence. For example, the primers selected from the group consisting of SEQ ID NOS: 21-60 can be used to determine the presence or absence of a nucleic acid molecule comprising a nucleic acid sequence selected from the group consisting of SEQ ID NOS: 1-20, and the primers selected from the group consisting of SEQ ID NOS: 109-204 can be used to determine the presence or absence of a nucleic acid molecule comprising a nucleic acid sequence selected from the group consisting of SEQ ID NOS: 61-108. Similarly, primers selected from the group consisting of SEQ ID NOS: 274-411 can be used to determine the presence or absence of a nucleic acid molecule comprising a nucleic acid sequence selected from the group consisting of SEQ ID NOS: 205-273, and primers selected from the group consisting of SEQ ID NOS: 413-414 can be used to determine the presence or absence of a nucleic acid molecule comprising a nucleic acid sequence of SEQ ID NO: 412.  
         [0015]     The invention also pertains to an isolated nucleic acid molecule comprising a nucleic acid sequence selected from the group consisting of SEQ ID NOS: 21-60, 109-204, 274-411 and 413-414, as well as to an isolated nucleic acid molecule consisting of a nucleic acid sequence selected from the group consisting of SEQ ID NOS: 1-20, 61-108, 205-273 and 412. The invention also pertains to nucleic acid probes capable of specifically hybridizing to a nucleic acid molecule selected from the group consisting of SEQ ID NOS: 1-20, 61-108, 205-273 and 412, and to nucleic acid primers capable of serving as specific primers for amplification of a nucleic acid molecule selected from the group consisting of SEQ ID NOS: 1-20, 61-108, 205-273 and 412.  
         [0016]     In another embodiment, the invention relates to a kit comprising one or more isolated nucleic acid molecules capable of serving as a specific primer for amplification of one or more nucleic acid molecules selected from the group consisting of SEQ ID NOS: 1-20, 61-108, 205-273 and 412, amplification reagents, and instructions for using said nucleic acid molecules and reagents to detect the presence or absence of one or more nucleic acid molecules comprising a nucleic acid sequence selected from the group consisting of SEQ ID NOS: 1-20, 61-108, 205-273 and 412. In one embodiment the isolated nucleic acid molecules comprise or consist of a nucleic acid sequence selected from the group consisting of SEQ ID NOS: 21-60, 109-204, 274-411 and 413-414.  
         [0017]     In an additional embodiment, the invention relates to a kit comprising one or more isolated nucleic acid molecules capable of serving as a specific probe for one or more nucleic acid molecules selected from the group consisting of SEQ ID NOS: 1-20, 61-108, 205-273 and 412, hybridization reagents, and instructions for using said nucleic acid molecules and reagents to detect the presence or absence of one or more nucleic acid molecules comprising a nucleic acid sequence selected from the group consisting of SEQ ID NOS: 1-20, 61-108, 205-273 and 412. For example, the nucleic acid molecules capable of serving as a specific probes may be selected from the group consisting of SEQ ID NOS: 21-60, 109-204, 274-411 and 413-414. 
     
    
     BRIEF DESCRIPTION OF THE DRAWINGS  
       [0018]      FIGS. 1A-1B  are a table listing landmark STSs and their Y chromosomal location.  
         [0019]      FIG. 2  is a table showing plus/minus results for STSs distinguishing different types of Y chromosomal deletions. STSs are shown along the top, and deletions are shown down the left side. A minus (“−”) indicates the absence of the indicated STS, while a filled-in square indicates the presence of the indicated STS.  
         [0020]      FIGS. 3A-3B  are a table showing plus/minus results for a larger set of STSs distinguishing different types of Y chromosomal deletions. A minus (“−”) indicates the absence of the indicated STS, while a filled-in square indicates the presence of the indicated STS.  
         [0021]      FIGS. 4A-4B  are a table showing plus/minus results for a larger set of STSs distinguishing different types of Y chromosomal deletions. A minus (“−”) indicates the absence of the indicated STS, while a filled-in square indicates the presence of the indicated STS.  
         [0022]      FIGS. 5A-5F  show the nucleotide sequences of the STSs in  FIG. 2  (SEQ ID NOS: 1-20 and 412), as well as the nucleotide sequences of probes and primers which can be used to identify the presence or absence of the corresponding STS (SEQ ID NOS: 21-60 and 413-414).  
         [0023]      FIGS. 6A-6K  show the nucleotide sequences of the STSs in  FIGS. 3A-3B  (SEQ ID NOS: 61-108), as well as the nucleotide sequences of probes and primers which can be used to identify the presence or absence of the corresponding STS (SEQ ID NOS: 109-204).  
         [0024]      FIGS. 7A-7P  show the nucleotide sequences of the STSs in  FIGS. 4A-4B  (SEQ ID NOS: 205-273), as well as the nucleotide sequences of probes and primers which can be used to identify the presence or absence of the corresponding STS (SEQ ID NOS: 274-411).  
         [0025]      FIG. 8  is an abbreviated table showing plus/minus results distinguishing different types of deletions involving AZFc.  
         [0026]      FIG. 9  shows a genealogical analysis of SFV patterns associated with b2/b3 and gr/gr deletions. In the SFV patterns, “C” indicates the cut variant described by Fernandes et al. ( N. Am J Hum Genet  74:180-187 (2004)), “U” indicates the uncut variant, “B” indicates both variants, and “+” and “−” indicate the presence or absence, respectively, of the Y-DAZ3 variant. The order of SFVs is as shown in table 2 in the work of Fernandes et al. (2004): DAZ-SNV I, DAZ-SNV II, sY586 (DAZ-SNV III), DAZ-SNV IV, sY587 (DAZ-SNV V), DAZ-SNV VI, AZFc SFV 18 (assayed by Y-DAZ3), TTY4-SNV I, BPY2-SNV, GOLY-SNV I, and AZFc SFV 20 (AZFc-P1-SNV I) (Saxena et al.,  Genomics  67:256-267 (2000); Kuroda-Kawaguchi et al.,  Nat Genet  29:279-286 (2001); Fernandes et al.,  Mol Hum Reprod  8:286-298 (2002); Fernandes et al.,  N. Am J Hum Genet  74:180-187 (2004)). The genealogical tree of extant human Y chromosomes and the branch designations are from the studies by Underhill et al. ( Nat Genet  26:358-361 (2000) and the Y-Chromosome Consortium ( Genome Res  12:339-348 (2002)). 
     
    
     DETAILED DESCRIPTION OF THE INVENTION  
       [0027]     A description of preferred embodiments of the invention follows.  
         [0028]     Sequence tagged sites (STSs) are short sequences for which the exact location in the genome and order of bases are known. Because each is unique, STSs are helpful for chromosome placement of mapping and sequencing data and serve as landmarks on the physical map of the human genome. The primary sequence and presence or absence of alterations in the sequence of the Y chromosome, particularly deletions, are particularly difficult to determine due to the extensive blocks of sequence repeats within this region. As described herein, STSs have been identified which are uniquely suited for use in methods of detecting alterations in the Y chromosome. In particular, these STSs, individually or more preferably in combination, allow the detection of deletions in the Y chromosome which are difficult to detect and/or distinguish from other alterations in the Y chromosome using other markers and methods.  
         [0029]     The ability to detect Y chromosomal alterations, e.g., deletions, and to differentiate between different types of alterations has significant implications for infertility treatment regimens. Infertility treatments can be invasive and the procedures, together with the accompanying stress, can impose a significant burden on both partners physiologically, emotionally and financially. In the end, in some instances these procedures do not result in successful pregnancies. The compositions and methods of the invention provide the couple with additional information which can inform their decision on whether to proceed with infertility treatments and which procedures are likely to be effective, based on the alterations, if any, detected in the male&#39;s Y chromosome. Many Y chromosomal deletions have known effects on the ability of the male to produce viable sperm. Using the methods and compositions of the invention it can be determined which, if any, of the described deletions are present in the male&#39;s Y chromosome and what the effect of the deletion(s) is on the ability to obtain viable sperm from the male. For example, if a p5/p1 Y chromosomal deletion is detected in the male, the likelihood of obtaining viable sperm from him is very low. This information can then guide the couple in determining which, if any, infertility treatments to pursue, rather than proceeding blindly with a course of action unlikely to produce results.  
         [0030]     Thus, the invention pertains, in part, to a method of detecting an alteration in the human Y chromosome comprising assessing a nucleic acid sample from an individual to be tested for the presence or absence of one or more nucleic acid molecules comprising a nucleic acid sequence selected from the group consisting of SEQ ID NOS: 1-20, 61-108, 205-273 and 412, wherein the absence of one or more of said nucleic acid sequences is indicative of an alteration in the human Y chromosome in the individual. While the presence or absence of a single nucleic acid molecule from this group can be informative, the greatest informational value is obtained when the presence or absence of multiple nucleic acid molecules is assessed in combination. That is, the greatest specificity of information can be obtained by assessing the pattern of presence and absence of particular markers. Preferred combinations will be apparent with reference to FIGS.  2 ,  3 A- 3 B,  4 A- 4 B and  8 .  
         [0031]     For example, with reference to  FIG. 2 , assessment of the presence or absence of a single marker, e.g., sY1317, is informative in that the absence of this marker is expected only in AZFa, Xp-→Xq(XG), Xp-→(KALP, VCY), and Iso Yp (centromere) alterations. Thus, absence of this marker indicates that one of these alterations is present in the tested Y chromosome.  
         [0032]     However, the pattern of presence or absence of a set of markers provides more specific information regarding the particular alteration present in the sample. For example, again with reference to  FIG. 2 , an AZFa deletion is indicated by the absence of markers sY1317 and sY1234 along with the presence of the other indicated markers.  
         [0033]     Thus, based on the additional markers assessed the type of alteration can be narrowed from a potential list of alterations (AZFa, Xp-&gt;Xq(XG), Xp-&gt;(KALP, VCY), and Iso Yp (centromere) alterations) to specific identification of an AZFa deletion. The same analytical framework can be applied to the other STSs shown in FIGS.  2 ,  3 A- 3 B,  4 A- 4 B and  8 .  
         [0034]     Accordingly, preferred methods of the invention include the assessment of multiple STSs in combination. For example, one preferred combination of markers to be assessed is all or a subset of nucleic acid molecules comprising SEQ ID NOS: 1-20, SEQ ID NOS: 61-108, SEQ ID NOS: 205-273 or SEQ ID NO: 412. Particularly useful subsets of these markers will be apparent from review of FIGS.  2 ,  3 A- 3 B,  4 A- 4 B and  8  and can be selected, for example, on the basis of the alteration to be assessed. For example, the control markers shown in the Figs. may be substituted or omitted in the judgment of the practitioner. In preferred embodiments the presence or absence of all of SEQ ID NOS: 1-20 or SEQ ID NOS: 1-20 and 412 is assessed, in other preferred embodiments the presence or absence of all of SEQ ID NOS: 61-108 is assessed, and in other preferred embodiments the presence or absence of all of SEQ ID NOS: 205-273 is assessed. Markers in addition to those described herein can also be assessed in conjunction with assessment of the markers described herein.  
         [0035]     The Y chromosomal alteration to be detected (determined) can include any disruption of the chromosome, such as deletion of one or more nucleotides, addition of one or more nucleotides, or change in one or more nucleotides, including total loss of the chromosome. In preferred embodiments the alteration detected is a deletion, and more preferably one of the deletions shown in FIGS.  2 ,  3 A- 3 B,  4 A- 4 B and  8 . The deletions shown in the Figs are referred to by their art-recognized names. For example, in  FIG. 2  the AZFa deletion has been described in Sun et al.,  Hum. Mol. Genet.,  9:2291-2296 (2000); the P5/proxP1 and P5/distP 1 deletions have been described in Repping et al.,  J. Hum. Genet.,  71:906-922 (2002); the gr/gr and b1/b3 deletions have been described in Repping et al.,  Nature Genetics,  35:247-251 (2003); and the AFZc deletion has been described in Kuroda-Kawaguchi et al.,  Nature Genetics,  29:279-286 (2001).  
         [0036]     The nucleic acid sample from the individual to be tested will preferably be genomic DNA and can be obtained from any nucleic acid source. The sample will preferably comprise human nucleic acid molecules in a form suitable for hybridization to probes and primers of the invention or will be treated to render the nucleic acid molecules suitable for hybridiation prior to carrying out the methods of the invention. The nucleic acid molecules in the sample may be isolated, cloned or amplified. As used herein, an “isolated” nucleic acid molecule is intended to mean a nucleic acid molecule which is not flanked by DNA sequences which normally (in nature) flank the nucleic acid molecule. Thus, an isolated nucleic acid molecule can include a nucleic acid molecule which is biologically isolated or synthesized chemically or by recombinant means.  
         [0037]     Methods of isolating cell and tissue samples (sources of nucleic acid molecules) are well known to those of skill in the art and include, but are not limited to, scrapings, aspirations, tissue sections, needle biopsies, and the like. Frequently the sample will be a “clinical sample” which is a sample derived from a patient, including sections of tissues such as frozen sections or paraffin sections taken for histological purposes. The sample can also be derived from supernatants (of cells) or the cells themselves from cell cultures, cells from tissue culture and other media in which it may be desirable to detect chromosomal abnormalities. In some cases, the nucleic acids may be amplified using standard techniques such as PCR, prior to carrying out the methods of the invention. The sample may be isolated nucleic acid molecules immobilized on a solid. The sample may also be prepared such that individual nucleic acids remain substantially intact. Suitable sources include, but are not limited to, blood, skin, sperm, hair root, saliva or buccal cells, or cells cultured from blood or skin.  
         [0038]     The nucleic acid sample will be obtained from a human male, typically from a human male who is part of a couple having difficulty conceiving a child. Even more typically the male will have been, at least preliminarily, determined to have a reduced sperm count. Reduced sperm count is understood to encompass both oligospermia and azoospermia, i.e., a sperm count of less than 20 million per ml, including total absence of sperm. Azoospermia is defined as a condition wherein the concentration of sperm in a semen sample is 0 to occasional sperm per ml, and oligospermia is defined as a condition wherein the concentration of sperm in a semen sample ranges from occasional to less than 20 million per ml.  
         [0039]     The nucleic acid sequences of markers of the invention are shown in  FIGS. 5A-5F ,  6 A- 6 K and  7 A- 7 P. In particular methods of the invention the presence or absence of the markers of the invention can be assessed (determined, analyzed) by any methods known in the art. In particular embodiments the presence or absence is determined by hybridization to specific probes and/or by amplification using specific primers. Based on the nucleic acid sequences of the markers shown in  FIGS. 5A-5F ,  6 A- 6 K and  7 A- 7 P, suitable probes and primers can readily be designed by the skilled artisan.  
         [0040]     In one embodiment, the presence or absence of one or more markers is determined by amplification using specific primers. One or more markers of the invention can be amplified using primer pairs that include or flank the marker sequence. Particularly preferred primers identified as specifically priming the markers of the invention are shown in  FIGS. 5A-5F ,  6 A- 6 K and  7 A- 7 P. Other primers can readily be designed by the skilled artisan. For example, the primers selected from the group consisting of SEQ ID NOS: 21-60 can be used to determine the presence or absence of a corresponding nucleic acid molecule comprising a nucleic acid sequence selected from the group consisting of SEQ ID NOS: 1-20, and the primers selected from the group consisting of SEQ ID NOS: 109-204 can be used to determine the presence or absence of a corresponding nucleic acid molecule comprising a nucleic acid sequence selected from the group consisting of SEQ ID NOS: 61-108. Similarly, primers selected from the group consisting of SEQ ID NOS: 274-411 can be used to determine the presence or absence of a corresponding nucleic acid molecule comprising a nucleic acid sequence selected from the group consisting of SEQ ID NOS: 205-273, and primers selected from the group consisting of SEQ ID NOS: 413-414 can be used to determine the presence or absence of a corresponding nucleic acid molecule comprising SEQ ID NO: 412.  
         [0041]      FIGS. 5A-5F ,  6 A- 6 K and  7 A- 7 P show the relationship between the primers of SEQ ID NOS 21-60 and 413-414 and the STSs of SEQ ID NOS: 1-20 and 412, respectively, the primers of SEQ ID NOS: 109-204 and the STSs of SEQ ID NOS: 61-108, and the primers of SEQ ID NOS: 274-411 and the STSs of SEQ ID NOS: 205-273, respectively. As used herein, a primer “corresponds” to an STS if it serves as a specific primer for that STS in an amplification reaction. For example, SEQ ID NOS: 21 and 22 are primers which serve as specific primers for SEQ ID NO: 1, and thus SEQ ID NOS: 21 and 22 are primers which correspond to the STS of SEQ ID NO: 1.  
         [0042]     Suitable amplification methods include, but are not limited to: polymerase chain reaction, PCR (PCR Protocols, A Guide to Methods and Applications, ed. Innis, Academic Press, N.Y. (1990) and PCR Strategies (1995), ed. Innis, Academic Press, Inc., N.Y. (Innis)); ligase chain reaction (LCR) (Wu (1989)  Genomics  4:560; Landegren (1988)  Science  241:1077; Barringer (1990)  Gene  89:117); transcription amplification (Kwoh (1989)  Proc. Natl. Acad. Sci. USA  86:1173); and self-sustained sequence replication (Guatelli (1990)  Proc. Natl. Acad. Sci. USA,  87:1874); Q Beta replicase amplification and other RNA polymerase mediated techniques (e.g., NASBA, Cangene, Mississauga, Ontario); see Berger (1987)  Methods Enzymol.  152:307-316, Sambrook, and Ausubel, as well as Mullis (1987) U.S. Pat. Nos. 4,683,195 and 4,683,202; Arnheim (1990) C&amp;EN 36-47; Lomell (1989)  J. Clin. Chem.  35:1826; Van Brunt (1990)  Biotechnology  8:291-294; Wu (1989)  Gene  4:560; Sooknanan (1995)  Biotechnology  13:563-564. Methods for cloning in vitro amplified nucleic acids are described in Wallace, U.S. Pat. No. 5,426,039. Methods of amplifying large nucleic acids are summarized in, e.g., Cheng (1994)  Nature  369:684-685.  
         [0043]     The presence or absence of amplification products for one or more markers can be analyzed to identify the presence or absence of one or more markers of the invention. That is, if an amplification product for a particular marker is detected, it can be concluded that that marker is present in the sample, and if an amplification product is not detected it can be concluded that the marker is not present in the sample.  
         [0044]     In another method of the invention, the presence or absence of one or more markers of the invention is determined using nucleic acid probes which specifically hybridize to the markers of the invention. The terms “hybridizing specifically to” and “specific hybridization” and “selectively hybridize to,” as used herein refer to the binding, duplexing, or hybridizing of a nucleic acid molecule preferentially to a particular nucleotide sequence under stringent conditions. The term “stringent conditions” refers to conditions under which a probe will hybridize preferentially to its target subsequence, and to a lesser extent to, or not at all to, other sequences. A “stringent hybridization” and “stringent hybridization wash conditions” in the context of nucleic acid hybridization (e.g., as in array, Southern or Northern hybridizations) are sequence dependent, and are different under different environmental parameters. An extensive guide to the hybridization of nucleic acids is found in, e.g., Tijssen (1993) Laboratory Techniques in Biochemistry and Molecular Biology—Hybridization with Nucleic Acid Probes part I, chapt 2, “Overview of principles of hybridization and the strategy of nucleic acid probe assays,” Elsevier, N.Y. (“Tijssen”). Generally, highly stringent hybridization and wash conditions are selected to be about 5° C. lower than the thermal melting point (T m ) for the specific sequence at a defined ionic strength and pH. The T m  is the temperature (under defined ionic strength and pH) at which 50% of the target sequence hybridizes to a perfectly matched probe. Very stringent conditions are selected to be equal to the T m  for a particular probe. An example of stringent hybridization conditions for hybridization of complementary nucleic acids which have more than 100 complementary residues on an array or on a filter in a Southern or northern blot is 42° C. using standard hybridization solutions (see, e.g., Sambrook), with the hybridization being carried out overnight. An example of highly stringent wash conditions is 0.15 M NaCl at 72° C. for about 15 minutes. An example of stringent wash conditions is a 0.2×SSC wash at 65° C. for 15 minutes (see, e.g., Sambrook (1989) Molecular Cloning: A Laboratory Manual (2nd ed.) Vol. 1-3, Cold Spring Harbor Laboratory, Cold Spring Harbor Press, NY (“Sambrook”). Often, a high stringency wash is preceded by a low stringency wash to remove background probe signal. An example medium stringency wash for a duplex of, e.g., more than 100 nucleotides, is 1×SSC at 45° C. for 15 minutes. An example of a low stringency wash for a duplex of, e.g., more than 100 nucleotides, is 4-6×SSC at 40° C. for 15 minutes.  
         [0045]     Nucleic acid hybridization assays can be performed in an array-based format. Arrays are a multiplicity of different “probe” or “target” nucleic acids (or other compounds) which hybridize with a sample nucleic acid. In an array format a large number of different hybridization reactions can be run essentially “in parallel.” This provides rapid, essentially simultaneous, evaluation of a large number of loci. Methods of performing hybridization reactions in array based formats are also described in, e.g., Pastinen (1997)  Genome Res.  7:606-614; Jackson (1996)  Nature Biotechnology  14:1685; Chee (1995)  Science  274:610; and WO 96/17958.  
         [0046]     Many methods for immobilizing nucleic acids on a variety of solid surfaces are known in the art. A wide variety of organic and inorganic polymers, as well as other materials, both natural and synthetic, can be employed as the material for the solid surface. Illustrative solid surfaces include, e.g., nitrocellulose, nylon, glass, quartz, diazotized membranes (paper or nylon), silicones, polyformaldehyde, cellulose, and cellulose acetate. In addition, plastics such as polyethylene, polypropylene, polystyrene, and the like can be used. Other materials which may be employed include paper, ceramics, metals, metalloids, semiconductive materials, cermets or the like. In addition, substances that form gels can be used. Such materials include, e.g., proteins (e.g., gelatins), lipopolysaccharides, silicates, agarose and polyacrylamides. Where the solid surface is porous, various pore sizes may be employed depending upon the nature of the system.  
         [0047]     In preparing the surface, a plurality of different materials may be employed, particularly as laminates, to obtain various properties. For example, proteins (e.g., bovine serum albumin) or mixtures of macromolecules (e.g., Denhardt&#39;s solution) can be employed to avoid non-specific binding, simplify covalent conjugation, enhance signal detection or the like. If covalent bonding between a compound and the surface is desired, the surface will usually be polyfunctional or be capable of being polyfunctionalized. Functional groups which may be present on the surface and used for linking can include carboxylic acids, aldehydes, amino groups, cyano groups, ethylenic groups, hydroxyl groups, mercapto groups and the like. The manner of linking a wide variety of compounds to various surfaces is well known and is amply illustrated in the literature. For example, methods for immobilizing nucleic acids by introduction of various functional groups to the molecules is known (see, e.g., Bischoff (1987)  Anal. Biochem.,  164:336-344; Kremsky (1987)  Nucl. Acids Res.  15:2891-2910). Modified nucleotides can be placed on the target using PCR primers containing the modified nucleotide, or by enzymatic end labeling with modified nucleotides. Use of membrane supports (e.g., nitrocellulose, nylon, polypropylene) for the nucleic acid arrays of the invention is advantageous because of well developed technology employing manual and robotic methods of arraying targets at relatively high element densities. Such membranes are generally available and protocols and equipment for hybridization to membranes is well known.  
         [0048]     Target elements of various sizes, ranging from 1 mm diameter down to 1 um can be used with these materials. Smaller target elements containing low amounts of concentrated, fixed probe DNA are used for high complexity comparative hybridizations since the total amount of sample available for binding to each target element will be limited. Thus it is advantageous to have small array target elements that contain a small amount of concentrated probe DNA so that the signal that is obtained is highly localized and bright. Such small array target elements are typically used in arrays with densities greater than 10.sup.4/cm.sup.2. Relatively simple approaches capable of quantitative fluorescent imaging of 1 cm.sup.2 areas have been described that permit acquisition of data from a large number of target elements in a single image (see, e.g., Wittrup (1994) Cytometry 16:206-213).  
         [0049]     Arrays on solid surface substrates with much lower fluorescence than membranes, such as glass, quartz, or small beads, can achieve much better sensitivity. Substrates such as glass or fused silica are advantageous in that they provide a very low fluorescence substrate, and a highly efficient hybridization environment. Covalent attachment of the target nucleic acids to glass or synthetic fused silica can be accomplished according to a number of known techniques (described above). Nucleic acids can be conveniently coupled to glass using commercially available reagents. For instance, materials for preparation of silanized glass with a number of functional groups are commercially available or can be prepared using standard techniques (see, e.g., Gait (1984) Oligonucleotide Synthesis: A Practical Approach, IRL Press, Wash., D.C.). Quartz cover slips, which have at least 10-fold lower autofluorescence than glass, can also be silanized.  
         [0050]     Alternatively, probes can also be immobilized on commercially available coated beads or other surfaces. For instance, biotin end-labeled nucleic acids can be bound to commercially available avidin-coated beads. Streptavidin or anti-digoxigenin antibody can also be attached to silanized glass slides by protein-mediated coupling using e.g., protein A following standard protocols (see, e.g., Smith (1992)  Science  258:1122-1126). Biotin or digoxigenin end-labeled nucleic acids can be prepared according to standard techniques. Hybridization to nucleic acids attached to beads is accomplished by suspending them in the hybridization mix, and then depositing them on the glass substrate for analysis after washing. Alternatively, paramagnetic particles, such as ferric oxide particles, with or without avidin coating, can be used.  
         [0051]     In this embodiment of the invention, specific hybridization of a probe to one or more markers of the invention in a nucleic acid sample is indicative of the presence of that marker in the sample, and absence of specific hybridization of a probe to one or more markers of the invention in a nucleic acid sample is indicative of the absence of that marker in the sample.  
         [0052]     In some embodiments of the invention, probes and primers of the invention are detectably labelled. The term “detectably labelled” as used herein refers to a nucleic acid attached to a detectable composition, i.e., a label. The detection can be by, e.g., spectroscopic, photochemical, biochemical, immunochemical, physical or chemical means. For example, useful labels include  32 P,  35 S,  3 H,  14 C,  125 I,  131 I; fluorescent dyes (e.g., FITC, rhodamine, lanthanide phosphors, Texas red), electron-dense reagents (e.g. gold), enzymes, e.g., as commonly used in an ELISA (e.g., horseradish peroxidase, beta-galactosidase, luciferase, alkaline phosphatase), calorimetric labels (e.g., colloidal gold), magnetic labels (e.g. Dynabeads™.), biotin, dioxigenin, or haptens and proteins for which antisera or monoclonal antibodies are available. The label can be directly incorporated into the nucleic acid molecule to be detected, or it can be attached to a probe or antibody which hybridizes or binds to the target.  
         [0053]     In various embodiments, the labels may be coupled to the probes and primers in a variety of ways known to those of skill in the art. Methods of labeling nucleic acids are well known to those of skill in the art. In various embodiments, the nucleic acid probes are labeled using nick translation, PCR, or random primer extension (see, e.g., Sambrook). Preferred labels are those that are suitable for use in arrays and in situ hybridization. In one embodiment, the nucleic acid probes or primers of the invention are detectably labeled. Alternatively, a detectable label which binds to a hybridization product may be used. Such detectable labels include any material having a detectable physical or chemical property, such as those in the field of immunoassays. The particular label used is not critical to the present invention, so long as it does not interfere with hybridization of the probe or primer. However, probes directly labeled with fluorescent labels (e.g. fluorescein, Texas red, etc.) are preferred for chromosomal DNA hybridization. In a preferred embodiment, the label is detectible in as low copy number as possible to maximize the sensitivity of the assay and yet be detectible above any background signal. The label preferably has a highly localized signal. Thus, particularly preferred fluorescent labels include fluorescein-12-dUTP and Texas Red-5-dUTP.  
         [0054]     The present invention also includes the nucleotide sequences described herein, and their complements, which are useful as hybridization probes or primers for an amplification method, such as polymerase chain reaction (PCR), to show the presence or absence of one or more markers of the present invention. Probes and primers can have all or a portion of the nucleotide sequence (nucleic acid sequence) of the probes and primers specifically exemplified herein or all or a portion of their complements. For example, sequences shown in  FIGS. 5A-5F ,  6 A- 6 K and  7 A- 7 P can be used.  
         [0055]     In addition, the invention pertains to isolated nucleic acid molecules consisting of a nucleic acid sequence selected from the group consisting of SEQ ID NOS: 1-20, 61-108, 205-273 and 412.  
         [0056]     This invention also provides diagnostic kits for the detection of chromosomal abnormalities or alterations on the Y chromosome. In a preferred embodiment, a kit includes one or more probes for the markers of the invention. The kits can additionally include blocking nucleic acid (i.e., Cot-1 DNA) and instructional materials describing when and how to use the kit contents. The kits can also include one or more of the following: various labels or labeling agents to facilitate the detection of the probes, reagents for the hybridization including buffers, a metaphase spread, bovine serum albumin (BSA) and other blocking agents, tRNA, SDS sampling devices including fine needles, swabs, aspirators and the like, positive and negative hybridization controls and so forth.  
         [0057]     The invention also provides diagnostic kits for the detection of chromosomal abnormalities or alterations on the Y chromosome using amplification methods. In a preferred embodiment, a kit includes one or more primers for the markers of the invention. The kits can additionally include amplification reagents and instructional materials describing when and how to use the kit contents. The kits can also include one or more of the following: various labels or labeling agents to facilitate the detection of the primers or amplification products, and sampling devices including fine needles, swabs, aspirators and the like, positive and negative hybridization controls and so forth.  
         [0058]     The present invention is illustrated by the following exemplification, which is not intended to be limiting in any way. The teachings of all publication referenced herein are incorporated herein by reference in their entirety.  
         [0000]     Exemplification  
         [0059]     There has been a report of a novel deletion of part of the azoospermia factor c (AZFc [MIM 415000]) region of the human Y chromosome (Fernandes et al. 2004). This article reported that the deletion is found only in branchNof the Y-chromosome genealogical tree, occurs through one mutational pathway, is ˜2.2 Mb in size, and has no effect on spermatogenesis. We, too, recently reported this deletion, which Fernandes et al. termed the “g1/g3” deletion and which we termed the “b2/b3” deletion (Repping et al. 2004). Our findings, however, differed from those of Fernandes et al. in several important particulars: (1) our screening of 1,563 men demonstrated that this deletion is not confined to branch N and that it has at least four independent origins; (2) our analysis revealed two mutational pathways, rather than one, that can generate the deletion, and we confirmed the existence of the inverted AZFc organizations that are the intermediate steps in these pathways; (3) on the basis of the reference sequence of the Y chromosome, we concluded that the size of the deletion is 1.8 Mb, rather than ˜2.2 Mb; (4) using interphase FISH, we confirmed the amplicon organization that was postulated in the deletion and also identified three instances of duplication subsequent to the deletion; and (5) because of the possibility of a compensatory factor on Y chromosomes in branch N and because of the limited number of deletions outside this branch, we concluded that a possible effect of this deletion on risk of spematogenic failure cannot be excluded (Repping et al. 2004).  
         [0060]     Beyond these differences, however, the characterizations of this and other partial deletions of AZFc (Repping et al. 2003) highlight a more important question. At issue is the relative utility of sequence family variants (Saxena et al. 2000), compared with that of plus/minus STSs, for identification and differentiation of deletions involving AZFc. AZFc is composed entirely of amplicons—repeat units 115-678 kb in length that only differ by ˜1 nt per 3,000 bp. These rare differences are called “sequence family variants” (SFVs). We previously relied on SFVs to map and sequence the AZFc region of one man&#39;s Y chromosome (Kuroda-Kawaguchi et al. 2001). The report by Fernandes et al. (2004) emphasized the use of SFVs in identification of the novel deletion, whereas our analysis relied on plus/minus STSs for identification of the deletion, followed, in most instances, by confirmation with FISH.  
         [0061]     Two observations led us to ask whether SFVs, as opposed to plus/minus STSs, offer the simpler and more robust means of detecting and distinguishing deletions in AZFc (see GenBank Web site for STSs and SFV assays). First,  FIGS. 1 and 4  in the report by Fernandes et al. (2004) indicated that negative results at the plus/minus STS sY1192 or 50f2/C combined with positive results at flanking STSs are sufficient to detect the deletion (table 1). Moreover, the b2/b3 deletion and other types of deletions involving AZFc can be distinguished by their plus/minus signatures, without the use of SFVs (table 1). Second, table 2 in the report by Fernandes et al. (2004) showed that the SFV patterns of undeleted chromosomes vary considerably among different branches of the Y chromosome genealogy and that the patterns also vary among individuals within branches. These observations suggested that the link between SFV patterns and particular types of deletions would likely not be consistent across the worldwide diversity of Y chromosomes.  
         [0062]     The diversity of SFV patterns in undeleted chromosomes is not surprising, since AZFc is subject to large inversions, deletions, and duplications caused by ectopic homologous recombination between amplicons (Kuroda-Kawaguchi et al. 2001; Repping et al. 2003, 2004). Such events would rearrange the locations of particular variants and would blur the association between SFV patterns and particular types of deletions. The association would likely be further blurred by gene conversion, which frequently erases small sequence differences (i.e., SFVs) between amplicon copies on the Y chromosome (Rozen et al. 2003).  
         [0063]     We experimentally investigated the consistency of SFV patterns in different types of deletions involving AZFc. First, using the SFVs employed by Fernandes et al. (2004), we typed 20 men reported elsewhere to have the b2/b3 deletion (Repping et al. 2004). These men represented branch N and three other branches of the Ychromosome genealogy ( FIG. 9 ). Second, using the same SFVs, we typed 40 men reported elsewhere to have the gr/gr deletion, the other common deletion in that part of AZFc (Repping et al. 2003). These men represented 14 branches of the Y-chromosome genealogy ( FIG. 9 ). The b2/b3 deletions outside branch N showed diverse SFV patterns, and the gr/gr deletions showed even greater diversity. This greater diversity was likely due to the larger number of independent gr/gr deletions studied. Two branches, F*(xHK) and R1*x, contained numerous deletions and a high diversity of SFV patterns. In these branches, multiple independent deletion events probably account for the high diversity. By contrast, two other branches, D2b and N, contained numerous deletions but uniform SFV patterns. This uniformity is explained by the fact that all chromosomes in these branches descended from deleted founders (Repping et al. 2003, 2004; Fernandes et al. 2004). Thus, the chromosomes in each of these branches represent single-deletion events.  
         [0064]     Our data also showed that the SFV patterns of b2/b3 and gr/gr deletions are not distinct from each other. For example, the b2/b3 pattern UUUCUU-CUUU (branch F*[xHK]) is more similar to the gr/gr pattern UU C CUU + C B U B  (branch F*[xHK], four differences [underlined]) than to the b2/b3 pattern U BBBC U-C C U C  (branch N, six differences). In another example, the gr/gr pattern UBBBCU-UBUB (branch R1*x) is more similar to the b2/b3 pattern UBBBCU- CU U C  (branch I, three differences) than to the gr/gr pattern  BCCCUB+C B CC  (branch R1*x, 10 differences).  
         [0065]     In conclusion, the SFV patterns of b2/b3 and gr/gr deletions vary widely and are not clearly distinct. SFVs can offer insight only if one knows the common SFV organizations in the genealogical branches represented by the Y chromosomes being tested. However, SFV organizations across the Y-chromosome genealogical tree are largely unknown, and SFV patterns vary even among individuals in the same branch. Just as important is that a large number of two-step assays are needed for SFV typing and for determining the Y-chromosome branch. By contrast, six simple plus/minus STSs distinguish between the deletions involving AZFc ( FIG. 8 ). Thus, plus/minus STSs provide a straightforward means of identifying and distinguishing the deletions of part of AZFc, whereas, in most situations, SFVs do not.  
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