Molecular detection of chromosome aberrations

Abstract

The invention relates to the field of cytogenetics and the application of genetic diagnostic techniques in pathology and hematology. Specifically, the invention relates to nucleic acid probes that can be used in hybridization techniques for the detection of chromosomal aberrations and other gene rearrangements such as immunoglobulin and T-cell receptor gene rearrangements. The probes provided by the invention are a distinct and balanced set of probes of comparable size, each preferably being from 1 to 100 kb, or smaller, and flanking a potential breakpoint in a chromosome.

1 - 16 . (canceled) 
     
     
         17 . A pair of nucleic acid probes for the detection of at least one chromosomal aberration involving a chromosomal breakpoint in interphase nuclei by in situ hybridization,
 wherein each of the nucleic acid probes is made up of multiple oligonucleotides,   wherein each of the nucleic acid probes is labeled directly with at least one different reporter molecule,   wherein each of the nucleic acid probes hybridizes to a sequence such that the pair of nucleic acid probes flank the chromosomal breakpoint cluster region upon hybridization to the chromosome,   wherein the nucleic acid probes hybridize at a genomic distance resulting in colocalization of the reporter molecule signals if no chromosome aberration is present,   and wherein the probes detect one or more of the following aberrations: t(1;19), t(2;5), t(2;8), t(2;18), t(4;11), t(8;14), t(8;22), t(9;22), t(11;14), t(12;21), t(14;18), t(18;22), t(1;11)(q21;q23), t(1;11)(p32;q23), t(2;11)(p21;q23), t(2;18)(p12;q21), t(4;11)(q21;q23), t(6;11)(q27;q23), t(7;22)(p22;q12), t(9;11)(p22;q23), t(11;19)(q23;p13), t(11;22)(q24;q21), t(14;18)(q23;q21), t(14;18)(q32;q21), t(18;22)(q21;q11), or t(21;22)(q22;q12).   
     
     
         18 . A pair of nucleic acid probes according to  claim 17 , wherein the at least one different reporter molecule comprises at least one chromophore. 
     
     
         19 . A pair of nucleic acid probes according to  claim 18 , wherein each of the nucleic acid probes is larger than 25 kb. 
     
     
         20 . A pair of nucleic acid probes according to  claim 17 , wherein the pair of nucleic acid probes are labeled with the at least one reporter molecule resulting in signals of comparable intensity between the pair of nucleic acid probes. 
     
     
         21 . A pair of nucleic acid probes according to  claim 17 , wherein the combination of relative size of each of the nucleic acid probes, intensity of the at least one reporter molecule labeling each of the nucleic acid probes, and genomic distance between each of the nucleic acid probes following hybridization to the chromosome, results in signals from the nucleic acid probes of comparable intensity. 
     
     
         22 . A pair of nucleic acid probes according to  claim 17 , wherein there is no overlap of the pair of nucleic acid probes with the breakpoint cluster region of the chromosome. 
     
     
         23 . A pair of nucleic acid probes according to  claim 17 , wherein each of the nucleic acid probes does not contain major repetitive sequences. 
     
     
         24 . A pair of nucleic acid probes according to  claim 17 , wherein the pair of nucleic acid probes hybridizes to a single corresponding nucleic acid molecule. 
     
     
         25 . A pair of nucleic acid probes according to  claim 24 , wherein the corresponding nucleic acid molecule is at least a fragment of a chromosome. 
     
     
         26 . A pair of nucleic acid probes for the detection of at least one chromosomal aberration involving a chromosomal breakpoint in interphase nuclei by in situ hybridization,
 wherein each of the nucleic acid probes is made up of multiple oligonucleotides,   wherein each of the nucleic acid probes is larger than 25 kb,   wherein each of the nucleic acid probes is labeled directly with at least one different reporter molecule,   wherein the at least one different reporter molecule comprises at least one chromophore,   wherein each of the nucleic acid probes hybridizes to a sequence such that the pair of nucleic acid probes flank the chromosomal breakpoint cluster region upon hybridization to the chromosome,   wherein the nucleic acid probes hybridize at a genomic distance resulting in colocalization of the reporter molecule signals if no chromosome aberration is present   and wherein the probes detect one or more of the following aberrations: t(1;19), t(2;5), t(2;8), t(2;18), t(4;11), t(8;14), t(8;22), t(9;22), t(11;14), t(12;21), t(14;18), t(18;22), t(1;11)(q21;q23), t(1;11)(p32;q23), t(2;11)(p21;q23), t(2;18)(p12;q21), t(4;11)(q21;q23), t(6;11)(q27;q23), t(7;22)(p22;q12), t(9;11)(p22;q23), t(11;19)(q23;p13), t(11;22)(q24;q21), t(14;18)(q23;q21), t(14;18)(q32;q21), t(18;22)(q21;q11), or t(21;22)(q22;q12).   
     
     
         27 . A pair of nucleic acid probes according to  claim 26 , wherein the pair of nucleic acid probes are labeled with the at least one reporter molecule resulting in signals of comparable intensity between the pair of nucleic acid probes. 
     
     
         28 . A pair of nucleic acid probes according to  claim 26 , wherein the combination of relative size of each of the nucleic acid probes, intensity of the at least one reporter molecule labeling each of the nucleic acid probes, and genomic distance between each of the nucleic acid probes following hybridization to the chromosome, results in signals from the nucleic acid probes of comparable intensity. 
     
     
         29 . A pair of nucleic acid probes according to  claim 26 , wherein there is no overlap of the pair of nucleic acid probes with the breakpoint cluster region of the chromosome. 
     
     
         30 . A pair of nucleic acid probes according to  claim 26 , wherein each of the nucleic acid probes does not contain major repetitive sequences. 
     
     
         31 . A pair of nucleic acid probes according to  claim 26 , wherein the pair of nucleic acid probes hybridizes to a single corresponding nucleic acid molecule. 
     
     
         32 . A pair of nucleic acid probes according to  claim 31 , wherein the corresponding nucleic acid molecule is at least a fragment of a chromosome. 
     
     
         33 . A diagnostic kit comprising at least a pair of nucleic acid probes for the detection of at least one chromosomal aberration involving a chromosomal breakpoint in interphase nuclei by in situ hybridization,
 wherein each of the nucleic acid probes is made up of multiple oligonucleotides,   wherein each of the nucleic acid probes is labeled directly with at least one different reporter molecule,   wherein each of the nucleic acid probes hybridizes to a sequence such that the pair of nucleic acid probes flank the chromosomal breakpoint cluster region upon hybridization to the chromosome,   wherein the nucleic acid probes hybridize at a genomic distance resulting in colocalization of the reporter molecule signals if no chromosome aberration is present   and wherein the probes detect one or more of the following aberrations: t(1;19), t(2;5), t(2;8), t(2;18), t(4;11), t(8;14), t(8;22), t(9;22), t(11;14), t(12;21), t(14;18), t(18;22), t(1;11)(q21;q23), t(1;11)(p32;q23), t(2;11)(p21;q23), t(2;18)(p12;q21), t(4;11)(q21;q23), t(6;11)(q27;q23), t(7;22)(p22;q12), t(9;11)(p22;q23), t(11;19)(q23;p13), t(11;22)(q24;q21), t(14;18)(q23;q21), t(14;18)(q32;q21), t(18;22)(q21;q11), or t(21;22)(q22;q12).   
     
     
         34 . A method for the detection of at least one chromosomal aberration involving a chromosomal breakpoint in interphase nuclei by in situ hybridization, said method comprising:
 providing a pair of nucleic acid probes,
 wherein each of the nucleic acid probes is made up of multiple oligonucleotides, 
 each of the nucleic acid probes is labeled directly with at least one different reporter molecule, 
 each of the nucleic acid probes hybridizes to a sequence such that the pair of nucleic acid probes flank the chromosomal breakpoint upon hybridization to the chromosome, and 
 the nucleic acid probes hybridize at a genomic distance resulting in colocalization of the reporter molecule signals if no chromosome aberration is present; 
   
       and either
 detecting colocalization of the reporter molecule signals indicating that no chromosomal aberration is present, 
 or 
 detecting two separate reporter molecule signals indicating that a chromosomal aberration is present. 
 
     
     
         35 . A method for the detection of at least one chromosomal aberration involving a chromosomal breakpoint in interphase nuclei by in situ hybridization, said method comprising:
 providing a pair of nucleic acid probes,   wherein each of the nucleic acid probes is made up of multiple oligonucleotides,   each of the nucleic acid probes is larger than 25 kb,   each of the nucleic acid probes is labeled directly with at least one different reporter molecule,   the at least one different reporter molecule comprises at least one chromophore,   each of the nucleic acid probes hybridizes to a sequence such that the pair of nucleic acid probes flank the chromosomal breakpoint upon hybridization to the chromosome, and   wherein the nucleic acid probes hybridize at a genomic distance resulting in colocalization of the reporter molecule signals if no chromosome aberration is present;   
       and either
 detecting colocalization of the reporter molecule signals indicating that no chromosomal aberration is present, 
 or 
 detecting two separate reporter molecule signals indicating that a chromosomal aberration is present.