Methods and Compositions for Detecting Targets

Abstract

The present invention relates to methods and kits for detecting the presence or absence of (or quantitating) target nucleic acid sequences using ligation and amplification. The invention also relates to methods, reagents, and kits that employ addressable portions and labeled probes.

1 - 28 . (canceled)  
     
     
         29 . A method of making a library of probes comprising: 
 synthesizing a first library of 4 X  probes each comprising a primer-specific portion, a target-specific portion X nucleotides in length, and a first addressable portion located between the primer-specific portion and the target-specific portion, wherein each of the 4 X  probes of the first library of 4 X  probes comprises a different target-specific portion, wherein X is 4 to 8.    
     
     
         30 . The method of  claim 29 , further comprising: 
 synthesizing a second library of 4 X  probes each comprising a primer-specific portion, a target-specific portion X nucleotides in length, and a second addressable portion located between the primer-specific portion and the target-specific portion, wherein each of the 4 X  probes of the second library of 4 X  probes comprises a different target-specific portion, and wherein the second addressable portion has a different sequence than the first addressable portion, wherein X is 4 to 8.    
     
     
         31 . (canceled)  
     
     
         32 . A first library of 4 X  probes each comprising a primer-specific portion, a target-specific portion X nucleotides in length, and a first addressable portion located between the primer-specific portion and the target-specific portion, wherein each of the 4 X  probes of the first library of 4 X  probes comprises a different target-specific portion, wherein X is 4 to 8.  
     
     
         33 . A method of making a library of (4 (X−1)  multiplied by 6) pairs of probes, comprising synthesizing a library of (4 (X−1)  multiplied by 6) pairs of probes; 
 wherein one probe of each pair comprises a primer-specific portion, a target-specific portion comprising a sequence of X nucleotides, and a first addressable portion located between the primer-specific portion and the target-specific portion,    wherein the other probe of each pair comprises a primer-specific portion, a target-specific portion comprising a sequence of X nucleotides, and a second addressable portion located between the primer-specific portion and the target-specific portion,    wherein the sequence of X nucleotides of the target-specific portion of each probe in a pair of probes is identical except for one nucleotide difference;    wherein each of the (4 (X−1)  multiplied by 6) pairs of probes can be used to determine whether a target nucleic acid sequence comprising X nucleotides has one of two possible nucleic acid sequences, wherein the two possible nucleic acid sequences differ by one nucleotide at a single position, and wherein at least one separate pair of probes of the library is provided for each separate possible one nucleotide difference at one position in a target nucleic acid comprising X nucleotides; and    wherein X is 4 to 8.    
     
     
         34 . A library of (4 (X−1)  multiplied by 6) pairs of probes; 
 wherein one probe of each pair comprises a primer-specific portion, a target-specific portion comprising a sequence of X nucleotides, and a first addressable portion located between the primer-specific portion and the target-specific portion,    wherein the other probe of each pair comprises a primer-specific portion, a target-specific portion comprising a sequence of X nucleotides, and a second addressable portion located between the primer-specific portion and the target-specific portion,    wherein the sequence of X nucleotides of the target-specific portion of each probe in a pair of probes is identical except for one nucleotide difference;    wherein each of the (4 (X−1)  multiplied by 6) pairs of probes can be used to determine whether a target nucleic acid sequence comprising X nucleotides has one of two possible nucleic acid sequences, wherein the two possible nucleic acid sequences differ by one nucleotide at a single position, and wherein at least one separate pair of probes of the library is provided for each separate possible one nucleotide difference at one position in a target nucleic acid comprising X nucleotides; and    wherein X is 4 to 8.    
     
     
         35 - 44 . (canceled)