Multiplex nucleic acid amplification

Abstract

In some embodiments, the disclosure relates generally to compositions, comprising a single reaction mixture containing a plurality of different populations of discrete supports, and a plurality of different populations of target nucleic acids. The single reaction mixture can contain a first population of beads; a second population of beads; a first population of target nucleic acids, where at least two different target nucleic acids in the first population of target nucleic acids can bind to a bead in the first population of beads; and a second population of target nucleic acids, where at least two different target nucleic acids in the second population of target nucleic acids can bind to a bead in the second population of beads. The single reaction mixture can be employed to monoclonally amplify the first target nucleic acids on the first beads, and monoclonally amplify the second target nucleic acids on the second beads.

What is claimed: 
     
         1 . A method of nucleic acid synthesis, comprising:
 a) providing a single reaction mixture containing a plurality of beads of a first type, the beads of the first type including first capture primers; a plurality of beads of a second type, the beads of the second type including second capture primers, wherein the first and second capture primers are different; a first population of target nucleic acids, wherein the first population includes at least one target nucleic acid of a first type that binds to the first capture primers; a second population of target nucleic acids, wherein the second population includes at least one target nucleic acid of a second type that binds to the second capture primers;   b) forming a first amplified population of nucleic acids by amplifying one or more target nucleic acids of the first population, wherein the first amplified population is attached to one or more beads of the first type; and   c) forming a second amplified population of nucleic acids by amplifying one or more target sequences from the second population of target nucleic acids, wherein the second amplified population is attached to one or more beads of the second type.   
     
     
         2 . The method of  claim 1 , wherein the forming the first amplified population includes amplifying the first target sequence by PCR, isothermal, rolling circle, or emulsion based amplification. 
     
     
         3 . The method of  claim 1 , wherein the forming the second amplified population includes amplifying the second target sequence by PCR, isothermal, rolling circle, or emulsion based amplification. 
     
     
         4 . The method of  claim 1 , wherein the first amplified population is covalently attached to one or more beads of the first type. 
     
     
         5 . The method of  claim 1 , wherein the second amplified population is covalently attached to one or more beads of the second type. 
     
     
         6 . The method of  claim 1 , wherein the single reaction mixture includes at least two, three, four, five, six, seven, eight, nine, ten, or more types of beads, each type of bead including a different type of capture primer. 
     
     
         7 . The method of  claim 1 , further comprising sequencing one or more nucleic acids of the first amplified population and one or more nucleic acids from the second amplified population in parallel. 
     
     
         8 . The method of  claim 7 , wherein the sequencing includes detection of one or more nucleotide incorporation byproducts. 
     
     
         9 . The method of  claim 7 , wherein the sequencing includes detecting hydrogen ions or pyrophosphate. 
     
     
         10 . The method of  claim 1 , wherein the first and second capture primers are present in about the same concentration. 
     
     
         11 . The method of  claim 1 , wherein the forming the first amplified population includes hybridizing at least one target sequence from the first population to a first capture primer on the first type of beads; and the forming the second amplified population includes hybridizing at least one target sequence from the second population to a second capture primer on the second type of beads. 
     
     
         12 . The method of  claim 1 , further including extending one or more first and second capture primers in a template-dependent fashion. 
     
     
         13 . The method of  claim 1 , wherein the first amplified population is substantially monoclonal. 
     
     
         14 . The method of  claim 1 , wherein the second amplified population is substantially monoclonal. 
     
     
         15 . The method of  claim 1 , wherein the first amplified population, the second amplified population, or both, are substantially monoclonal. 
     
     
         16 . A method of monoclonally amplifying a first target sequence from a first population of target nucleic acids and a first target sequence from a second population of target nucleic acids comprising:
 (a) providing a single reaction mixture having a plurality of a first type of beads including first capture primers; a plurality of a second type of beads including second capture primers, wherein the first and second capture primers are different; a first population of target nucleic acids, wherein the first population includes at least one target nucleic acid that binds to a first fusion primer; a first fusion primer that includes a portion complementary to the first capture primers; a second population of target nucleic acids, wherein the second population includes at least one target nucleic acid that binds to a second fusion primer; a second fusion primer that includes a portion complementary to the second capture primers;   (b) forming a substantially monoclonal population of the first target sequence from the first population of target nucleic acids on the first type of beads using the first fusion primer; and   (c) forming a substantially monoclonal population of the first target sequence from the second population of target nucleic acids on the second type of beads using the second fusion primer.   
     
     
         17 . A method for amplifying a plurality of different nucleic acid populations in a single reaction mixture, comprising:
 a) providing a single reaction mixture including a first and a second population of nucleic acids, wherein the first population of nucleic acids contain a first primer binding sequence and the second population of nucleic acids contain a second primer binding sequence, and wherein the first and second primer binding sequences are different; a first plurality of beads including a first capture sequence that can bind to the first primer binding sequence; a second plurality of beads including a second capture sequence that can bind to the second primer binding sequence, wherein the first and second capture sequences are different;   b) amplifying, within the single reaction mixture, one or more nucleic acids from the first population to form a first amplified population, and one or more nucleic acids from the second population to form a second amplified population, wherein the first amplified population is bound to one or more beads of the first type and the second amplified population is bound to one or more beads of the second type.   
     
     
         18 . The method of  claim 17 , wherein the first amplified population, the second amplified population, or both, are substantially monoclonal. 
     
     
         19 . The method of  claim 17 , wherein the amplifying in step (b) include PCR, isothermal, rolling circle, or emulsion based amplification. 
     
     
         20 . The method of  claim 19 , wherein the emulsion based amplification includes water-in-oil emulsions. 
     
     
         21 . The method of  claim 17 , wherein the first amplified population is covalently bound to one or more beads of the first type. 
     
     
         22 . The method of  claim 17 , wherein the second amplified population is bound to one or more beads of the second type. 
     
     
         23 . The method of  claim 17 , wherein the single reaction mixture further includes at least two, three, four, five, six, seven, eight, nine, ten, or more types of beads, each type of bead including a different type of primer binding sequence. 
     
     
         24 . The method of  claim 17 , further comprising sequencing one or more nucleic acids of the first amplified population and one or more nucleic acids from the second amplified population in parallel. 
     
     
         25 . The method of  claim 24 , wherein the sequencing includes detection of one or more nucleotide incorporation byproducts. 
     
     
         26 . The method of  claim 24 , wherein the sequencing includes detecting hydrogen ions or pyrophosphate. 
     
     
         27 . The method of  claim 17 , wherein the first and second primer binding sequences are present in about the same concentration. 
     
     
         28 . The method of  claim 17 , wherein the amplifying in step (b) includes hybridizing at least one target sequence from the first population to a first primer binding sequence on the first type of beads; and the forming the second amplified population includes hybridizing at least one target sequence from the second population to a second primer binding sequence on the second type of beads. 
     
     
         29 . The method of  claim 17 , further including extending one or more first and second primer binding sequence in a template-dependent fashion. 
     
     
         30 . The method of  claim 17 , wherein the first amplified population is substantially monoclonal. 
     
     
         31 . The method of  claim 17 , wherein the second amplified population is substantially monoclonal. 
     
     
         32 . The method of  claim 17 , wherein the first amplified population, the second amplified population, or both, are substantially monoclonal.