Genotyping by polymerase binding

Abstract

A method for identifying target alleles, that includes steps of (a) forming a plurality of stabilized ternary complexes at a plurality of features on an array, wherein the stabilized ternary complexes each has a polymerase, a template nucleic acid having a target allele of a locus, a primer hybridized to the locus, and a next correct nucleotide having a cognate in the locus, wherein either (i) the primer is an allele-specific primer having a 3′ nucleotide that is a cognate nucleotide for the target allele, or (ii) the primer is a locus-specific primer and the next correct nucleotide hybridizes to the target allele; and (b) detecting stabilized ternary complexes at the features, thereby identifying the target alleles.

1 .- 20 . (canceled) 
     
     
         21 . A method for identifying target alleles in a mixture of nucleic acids, comprising
 (a) providing an array of features, wherein different template nucleic acids are attached at different features of the array;   (b) contacting the array with a plurality of primers, polymerases and nucleotides to form a plurality of stabilized ternary complexes at a plurality of the features, wherein the stabilized ternary complexes at the features each comprises a polymerase, a template nucleic acid attached to a feature of the array and comprising a target allele of a locus, a primer hybridized to the locus, and a next correct nucleotide having a cognate in the locus, wherein either
 (i) the primer is an allele-specific primer comprising a 3′ nucleotide that is a cognate nucleotide for the target allele, or 
 (ii) the primer is a locus-specific primer and the next correct nucleotide hybridizes to the target allele; and 
   (c) detecting stabilized ternary complexes at the features, thereby identifying the target alleles.   
     
     
         22 . The method of  claim 21 , wherein the primers of the array comprise blocking groups that preclude enzymatic incorporation of the next correct nucleotide into the primer. 
     
     
         23 . The method of  claim 22 , wherein the blocking groups comprise reversible terminators. 
     
     
         24 . The method of  claim 22 , wherein the blocking groups comprise irreversible terminators. 
     
     
         25 . The method of  claim 21 , wherein the next correct nucleotide comprises an exogenous label that is detected in step (c). 
     
     
         26 . The method of  claim 21 , wherein the array of features is in a flow cell. 
     
     
         27 . The method of  claim 21 , wherein the stabilized ternary complexes are stabilized by a non-catalytic metal ion or a blocking group on the primers. 
     
     
         28 . The method of  claim 21 , wherein the primer is an allele-specific primer comprising a 3′ nucleotide that is a cognate nucleotide for the target allele. 
     
     
         29 . The method of  claim 21 , wherein the primer is a locus-specific primer and the next correct nucleotide hybridizes to the target allele. 
     
     
         30 . The method of  claim 21 , wherein the next correct nucleotides are non-covalently bound to the stabilized ternary complexes during step (c). 
     
     
         31 . The method of  claim 21 , wherein the target allele occurs at a locus and the different template nucleic acids further comprises another allele at the locus. 
     
     
         32 . The method of  claim 31 , wherein the locus comprises a single nucleotide polymorphism, INDEL polymorphism, or alternative mRNA splice site polymorphism. 
     
     
         33 . The method of  claim 25 , wherein (c) comprises detecting stabilized ternary complexes at the features by detecting the exogenous labels, thereby identifying the target alleles. 
     
     
         34 . The method of  claim 21 , wherein at least two types of nucleotides are contacted with the array in step (b), and wherein different exogenous labels distinguish at least two alleles at each locus in step (c). 
     
     
         35 . The method of  claim 21 , wherein a single type of nucleotide is contacted with the array in step (b). 
     
     
         36 . The method of  claim 21 , further comprising
 (d) dissociating the next correct nucleotide from each feature of the array after the detecting of the stabilized ternary complexes.   
     
     
         37 . The method of  claim 21 , further comprising washing the array after the dissociating. 
     
     
         38 . The method of  claim 21 , wherein the polymerases comprise exogenous labels. 
     
     
         39 . The method of  claim 38 , wherein (c) comprises detecting stabilized ternary complexes at the features by detecting the exogenous labels, thereby identifying the target alleles. 
     
     
         40 . The method of  claim 21 , wherein the ternary complex that is detected in step (c) lacks exogenous labels.