Karyotyping assay

Abstract

This disclosure relates to methods and kits for karyotyping in which chromosomes are interrogated by amplifying loci that are not within copy number variable regions thereof.

1 - 21 . (canceled) 
     
     
         22 . A composition comprising:
 a plurality of oligonucleotide probes,   wherein each probe has a portion that is specific for at least one target locus in at least one chromosome,   wherein the target locus is located on a region of the chromosome that is not within a copy number variable region (CNVR), and   wherein each probe includes a detectable label.   
     
     
         23 . The composition of  claim 22 , wherein the plurality of oligonucleotide probes are immobilized on a solid support. 
     
     
         24 . The composition of  claim 22 , wherein the plurality of oligonucleotide probes comprise subsets of probes that are specific for at least two target loci outside of a CNVR from at least one chromosome. 
     
     
         25 . The composition of  claim 22 , wherein the at least one chromosome is selected from human chromosomes 1-22, X and Y. 
     
     
         26 . The composition of  claim 22 , wherein the oligonucleotide probes are selected from the group consisting of SEQ ID NO: 193-288. 
     
     
         27 . The composition of  claim 22 , further comprising a first pair of primers configured to target a first target locus outside of a CNVR and enable formation of a first amplification product, wherein at least a first probe of the plurality of oligonucleotide probes is configured to hybridize to the first amplification product. 
     
     
         28 . (canceled) 
     
     
         29 . The composition of  claim 27 , further comprising at least one additional set of primers corresponding to a reference test locus. 
     
     
         30 - 35 . (cancelled) 
     
     
         36 . The composition of  claim 27 , wherein each primer of the first pair of primers are selected from the group consisting of SEQ ID NO: 1-192. 
     
     
         37 . The composition of  claim 22 , wherein the at least one chromosome is selected from human chromosomes 1, 5, 13, 18, 21, X and Y. 
     
     
         38 . The composition of  claim 22 , wherein at least one of the plurality of oligonucleotide probes includes a minor groove binder (MGB). 
     
     
         39 . The composition of  claim 22 , wherein the detectable label comprises a fluorescent label and a quencher molecule capable of quenching the fluorescence of said fluorescent label. 
     
     
         40 . The composition of  claim 27 , further comprising a second pair of primers configured to target a second target locus outside of a CNVR and enable formation of a second amplification product, wherein at least at least a second probe of the plurality of oligonucleotide probes is configured to hybridize to the second amplification product. 
     
     
         41 . The composition of  claim 40 , wherein the first target locus and the second target locus are located on separate arms of the same chromosome. 
     
     
         42 . A composition comprising:
 a first pair of primers configured to target a first target locus outside of a copy number variable region (CNVR) and enable formation of a first amplification product;   a second pair of primers configured to target a second target locus outside of a CNVR and enable formation of a second amplification product;   a first probe configured to hybridize to the first amplification product, the first probe comprising a detectable label; and   a second probe configured to hybridize to the second amplification product, the second probe comprising a detectable label.   
     
     
         43 . The composition of  claim 42 , wherein the detectable labels of the first and second probes are different. 
     
     
         44 . The composition of  claim 42 , wherein each of the detectable labels comprise a fluorescent label and a quencher molecule capable of quenching the fluorescence of said fluorescent label. 
     
     
         45 . The composition of  claim 42 , wherein each primer of the first and second pairs of primers are selected from the group consisting of SEQ ID NO: 1-192. 
     
     
         46 . The composition of  claim 42 , wherein the first and second probes are selected from the group consisting of SEQ ID NO: 193-288.