Method and System for Multiplex Genetic Analysis

Abstract

A method for identifying nucleotides in a nucleic acid sequence is disclosed. A plurality of polymerization complexes are provided within a plurality of confined reaction environments. Each complex comprises a polymerase enzyme and a template nucleic acid. The plurality of complexes are contacted with a plurality of types of nucleotide analogs labeled with distinguishable fluorescent labels under conditions suitable for polymerization. Fluorescent signals associated with incorporation of a nucleotide analog are transmitted to a detector, wherein the location of the fluorescent signal on the detector is indicative of the individual confined reaction environment and the type of nucleotide incorporated. The nucleotide in a nucleic acid sequence is identified based upon the type of nucleotide incorporated and the confined reaction environment.

1 . A method of identifying nucleotides in a nucleic acid sequence, comprising:
 providing a plurality of polymerization complexes within a plurality of confined reaction environment, wherein each complex comprises a polymerase enzyme, and a template nucleic acid;   contacting the plurality of complexes with a plurality of types of nucleotide analogs labeled with distinguishable fluorescent labels under conditions suitable for polymerization;   transmitting fluorescent signals associated with incorporation of a nucleotide analog to a detector, wherein location of the fluorescent signals on the detector is indicative of an individual confined reaction environment and a type of nucleotide incorporated; and   identifying a nucleotide in a nucleic acid sequence based upon the type of nucleotide incorporated and the confined reaction environment.   
     
     
         2 . The method of  claim 1 , wherein the transmitting step comprises collecting fluorescent signals from the plurality of confined reaction environments and passing the fluorescent signals through an optical train that directs different spectral components of the fluorescent signals to different locations on the detector. 
     
     
         3 . The method of  claim 2 , wherein the optical train comprises a dispersive optical element selected from a prism and an optical grating. 
     
     
         4 . The method of  claim 1 , wherein the confined reaction environments comprise zero mode waveguides. 
     
     
         5 . The method of  claim 1 , wherein fluorescent signals associated with incorporation of a plurality of nucleotide analogs in a complex are transmitted to the detector, and a plurality of nucleotides in the nucleic acid sequence are identified. 
     
     
         6 . The method of  claim 1 , wherein the optical train comprises at least a first prism to direct spectrally different fluorescent signals to different locations on the detector. 
     
     
         7 . A method of identifying nucleotides incorporated in polymerase mediated, template dependent nucleic acid synthesis reactions, comprising:
 providing a plurality template nucleic acid/polymerase complexes on a substrate;   contacting the plurality of complexes with a plurality of nucleotide analogs having spectrally distinct fluorescent labels, wherein incorporation of nucleotides produces characteristic incorporation signals;   directing incorporation signals to a single detector, wherein a location of a signal on the detector is indicative of a complex incorporating the nucleotide and a type of nucleotide incorporated; and   identifying the nucleotide incorporated into a template mediated nucleic acid synthesis reaction from the location of the signal on the detector.   
     
     
         8 . The method of  claim 7 , wherein the directing step comprises passing optical signals through dispersive optical element to separate signals from the spectrally distinct labels and image the signals onto different regions of the signal detector. 
     
     
         9 . The method for  claim 7 , wherein the complexes are individually optically resolvable. 
     
     
         10 . The method of  claim 7 , wherein the plurality of complexes are optically confined. 
     
     
         11 . The method of  claim 10 , wherein the plurality of complexes are disposed within an array of zero mode waveguides. 
     
     
         12 . A method of analyzing a reaction, comprising:
 providing a first reactant immobilized on a substrate;   contacting the first reactant with a second reactant and a third reactant, each bearing a spectrally distinct label;   directing signals from the spectrally distinct labels that are characteristic of interaction of the first reactant with one of the second and third reactants to a location on a first detector, wherein the location on the detector is indicative of the first reactant location on the substrate and the second or third reactant with which the first reactant interacted; and   identifying the first reactant and the second or third reactant with which the first reactant interacted.   
     
     
         13 . The method of  claim 12 , wherein the first reactant comprises at least a first nucleic acid. 
     
     
         14 . The method of  claim 13 , wherein the first reactant further comprises a polymerase enzyme. 
     
     
         15 . The method of  claim 13 , wherein the second and third reactants comprise second and third nucleic acids, respectively. 
     
     
         16 . The method of  claim 14 , wherein the second and third reactants comprise first and second nucleotide analogs, respectively. 
     
     
         17 . The method of  claim 15 , wherein the second and third nucleic acids each comprise a spectrally distinct fluorescent label. 
     
     
         18 . The method of  claim 16 , wherein the first and second nucleotide analogs each comprises a spectrally distinct fluorescent label.