Efficient arrays of amplified polynucleotides

Abstract

The present invention is related generally to analysis of polynucleotides, particularly polynucleotides derived from genomic DNA. The invention provides methods, compositions and systems for such analysis. Encompassed by the invention are arrays of polynucleotides in which the polynucleotides have undergone multiple rounds of amplification in order to increase the strength of signals associated with single polynucleotide molecules.

1 . A method of determining sequence information for a plurality of different target polynucleotides, said method comprising:
 providing a plurality of macromolecular structures, each containing one of the plurality of target polynucleotides and an adaptor oligonucleotide;   providing a surface that comprises a plurality of discrete spaced apart regions to which the macromolecular structures will bind, wherein the discrete spaced apart regions are surrounded by inert inter-regional areas;   arraying the macromolecular structures amongst the discrete regions on the surface such that a majority of the discrete regions is each occupied by a single macromolecular structure;   amplifying the target polynucleotides in the macromolecular structures arrayed on the surface by bridge PCR (polymerase chain reaction); and   obtaining sequence reads of the target polynucleotides from products of the bridge PCR.   
     
     
         2 . The method of  claim 1 , wherein the macromolecular structures comprise branched polynucleotides. 
     
     
         3 . The method of  claim 1 , wherein the macromolecular structures each includes replicates of one of the different target polynucleotides. 
     
     
         4 . The method of  claim 1 , wherein the macromolecular structures comprise concatemers. 
     
     
         5 . The method of  claim 1 , wherein the macromolecular structures have been prepared by a process that includes emulsion PCR. 
     
     
         6 . The method of  claim 1 , wherein the macromolecular structures each include a bead to which replicates of the target polynucleotide are attached. 
     
     
         7 . The method of  claim 6 , further comprising disposing the beads onto a surface such that substantially every bead occupies a separate region of the surface. 
     
     
         8 . The method of  claim 1 , wherein the discrete regions contain a number of reactive functionalities or capture oligonucleotides that are complementary to the adaptor oligonucleotide. 
     
     
         9 . The method of  claim 1 , whereby the macromolecular structures are adsorbed to the discrete regions through non-specific interactions between the macromolecular structures and the surface. 
     
     
         10 . The method of  claim 1 , wherein substantially all of the discrete regions are each occupied by one of the macromolecular structures containing one of the target polynucleotides. 
     
     
         11 . The method of  claim 1 , wherein the discrete regions are distributed across the surface in a regular pattern. 
     
     
         12 . The method of  claim 1 , wherein the discrete regions are distributed across the surface in a rectilinear pattern. 
     
     
         13 . The method of  claim 1 , wherein the sequence reads are obtained by a sequencing process that includes probe anchor ligation. 
     
     
         14 . The method of  claim 1 , wherein the sequence reads are obtained by a sequencing process that includes sequencing by synthesis.