Set of Oligonucleotide Probes as Well as Methods and Uses Thereto

Abstract

The present disclosure relates to a set of at least 100 single-stranded oligonucleotide probes directed against (or complementary to) portions of a genomic target sequence of interest. The present disclosure also relates to a method of detecting a genomic target sequence of interest using the set of oligonucleotide probes and a method of generating the set of oligonucleotide probes. Further, the present disclosure relates to a kit comprising the set of oligonucleotide probes and at least one further component.

1 . A kit for the detection of a first genomic target sequence of interest comprising: a first probe set comprising at least 100 different first oligonucleotide probes, wherein each of the first oligonucleotide probes of the first probe set comprises a different nucleotide sequence complementary to a different subsequence of the first genomic target sequence of interest; wherein each of the first oligonucleotide probes of the first probe set comprises at least one first label; and wherein the at least one first label is the same for each of the first oligonucleotide probes of the first probe set. 
     
     
         2 . The kit of  claim 1 , further comprising a first detection agent. 
     
     
         3 . The kit of  claim 2 , wherein the first detection agent is specific for the detection of hybridization of at least one of the first oligonucleotide probes to at least one of the subsequences of the first genomic target of interest in a chromogenic reaction or a metallographic reaction. 
     
     
         4 . The kit of  claim 1 , wherein the at least one first label is selected from the group consisting of a hapten, a radioisotope, or a fluorophore. 
     
     
         5 . The kit of  claim 1 , wherein the at least one first label is selected from biotin, digoxigenin, or a 2,4-dinitrophenyl moiety. 
     
     
         6 . The kit of  claim 1 , wherein the first probe set comprises at least 200 different oligonucleotide probes. 
     
     
         7 . The kit of  claim 1 , wherein the first probe set comprises at least 500 different oligonucleotide probes. 
     
     
         8 . The kit of  claim 1 , wherein the at least one first label is attached to a moiety selected from the group consisting of a base, a sugar, and a phosphate. 
     
     
         9 . The kit of  claim 8 , wherein the at least one first label is attached indirectly to the moiety via a linker. 
     
     
         10 . The kit of  claim 1 , wherein each of the first oligonucleotide probes of the first probe set comprises at least five labels, and wherein a length of each of the first oligonucleotide probes ranges from between about 20 nucleotides to about 200 nucleotides. 
     
     
         11 . The kit of  claim 10 , wherein the length ranges from between about 60 to about 150 nucleotides. 
     
     
         12 . The kit of  claim 10 , wherein the length ranges from between about 80 to about 120 nucleotides. 
     
     
         13 . The kit of  claim 1 , further comprising a second probe set comprising at least 100 different second oligonucleotide probes, wherein each of the second oligonucleotide probes of the second probe set comprises a different nucleotide sequence complementary to a different subsequence of the second genomic target sequence of interest; wherein each of the second oligonucleotide probes of the second probe set comprise at least one second label; and wherein the at least one second label is the same for each of the second oligonucleotide probes of the second probe set, and wherein the at least one second label is different than the at least one first label. 
     
     
         14 . The kit of  claim 13 , further comprising a second detection reagent. 
     
     
         15 . The kit of  claim 1 , wherein the first genomic target sequence comprises a locus within an epidermal growth factor receptor gene. 
     
     
         16 . The kit of  claim 1 , wherein the first genomic target sequence of interest comprises a HER2 gene locus. 
     
     
         17 . The kit of  claim 16 , wherein the second genomic target sequence of interest is other than a HER2 gene locus. 
     
     
         18 . The kit of  claim 1 , wherein the first genomic target sequence of interest is a region which is spread over different regions of one chromosome or spread over different chromosomes. 
     
     
         19 . A method of detecting a genomic target sequence of interest in a sample, said method comprising the steps of: incubating a first set of oligonucleotide probes with a sample comprising a genomic target sequence of interest under conditions for the binding of the first set of oligonucleotide probes to the genomic target sequence of interest; and detecting hybridizations of a plurality of the oligonucleotide probes of the first set of oligonucleotide probes with the target sequence of interest, thereby detecting the genomic target sequence of interest in the sample by one of a chromogenic reaction or a metallographic reaction, wherein the first set of oligonucleotide probes comprises at least 100 different oligonucleotide probes, each of the oligonucleotide probes of the first set of oligonucleotide probes comprising a different nucleotide sequence complementary to a different subsequence of the genomic target sequence of interest, each of the oligonucleotide probes of the first set of oligonucleotide probes comprising at least three first labels, each of the at least three first labels attached to one of a base, a sugar, or a phosphate moiety of a nucleotide in each of the oligonucleotide probes of the first set of oligonucleotide probes at about equally spaced positions. 
     
     
         20 . A method of detecting a genomic target sequence of interest in a sample, wherein the genomic target sequence of interest is a region spread over different chromosomes, said method comprising the steps of: incubating a first set of oligonucleotide probes with a sample comprising the genomic target sequence of interest under conditions for the binding of the first set of oligonucleotide probes to the genomic target sequence of interest; and detecting hybridizations of a plurality of the oligonucleotide probes of the first set of oligonucleotide probes with the target sequence of interest, thereby detecting the genomic target sequence of interest in the sample, wherein the first set of oligonucleotide probes comprises at least 100 different oligonucleotide probes, each of the oligonucleotide probes of the first set of oligonucleotide probes comprising a different nucleotide sequence complementary to a different subsequence of the genomic target sequence of interest, each of the oligonucleotide probes of the first set of oligonucleotide probes comprising at least three first labels, each of the at least three first labels attached to one of a base, a sugar, or a phosphate moiety of a nucleotide in each of the oligonucleotide probes of the first set of oligonucleotide probes at about equally spaced positions, and wherein the at least three first labels are the same for each of the oligonucleotide probes of the first set of oligonucleotide probes.