Method for the detection and quantification of genetic alterations

Abstract

Disclosed is a method of simultaneously capturing and identifying distinct targets within a DNA sample, wherein the distinct targets comprise a defined target region and an undefined target region, wherein the undefined target region comprises a structural variation or rearrangement or fusion. Also disclosed is a kit comprising the reagents for use in the methods as described herein.

1 - 30 . (canceled) 
     
     
         31 . A kit comprising:
 a plurality of primer A, primer A comprising a barcode sequence and a target-specific sequence A, wherein the target-specific sequence A is an oligonucleotide complementary to a sequence at or close to a 3′ end of a single strand of a double stranded DNA fragment A;   a plurality of primer B, primer B comprising a separation molecule, a barcode sequence, and a target-specific sequence B, wherein the target-specific sequence B is an oligonucleotide complementary to a sequence within a single strand of a double stranded DNA fragment B;   a plurality of primer C, primer C comprising a target-specific sequence C that is an oligonucleotide complementary to a sequence at or close to a 3′ end of the primer A, wherein the primer A is elongated and complementary to the single strand of the double stranded DNA fragment A;   a bead that binds the separation molecule, and   a double stranded oligonucleotide comprising a nucleotide overhang that is complementary to a 3′ end of the primer B, wherein the primer B is elongated and complementary to the single strand of the double stranded DNA fragment B, and wherein the elongated primer B and the single strand of the double stranded DNA fragment B form a double stranded product B.   
     
     
         32 . The kit according to  claim 31 , wherein the kit further comprises a DNA polymerase, a Taq polymerase, a ligase, and a plurality of deoxyribonucleotide triphosphate (dNTPs). 
     
     
         33 . The kit according to  claim 31 , wherein the 3′ end of the elongated primer B of the double stranded product B further comprises an additional single nucleotide.