Parallel genotyping of multiple patient samples

Abstract

The present invention relates to parallel genotyping (or other sample analysis) of multiple patients by direct sample immobilization onto microspheres of an array. The patient beads can then be used in a variety of target analyte analyses.

1 - 26 . (canceled) 
     
     
         27 . A method comprising:
 a) providing an array composition comprising:
 i) a substrate with a surface comprising discrete sites; and 
 ii) a population of microspheres comprising at least a first and a second microsphere, wherein a plurality of different target analytes from a first individual are covalently attached to said first microsphere, wherein a plurality of different target analytes from a second individual are covalently attached to said second microsphere, and wherein said microspheres are distributed at said discrete sites; 
   b) contacting said array composition with a first set of readout probes; and   c) detecting the presence of a first target analyte.   
     
     
         28 . The method of  claim 27 , wherein said microspheres are randomly distributed at said discrete sites. 
     
     
         29 . The method of  claim 27 , wherein said discrete sites are configured to have only a single microsphere of said population of microspheres. 
     
     
         30 . The method of  claim 27 , wherein said plurality of different target analytes comprises a plurality of different target nucleic acid molecules. 
     
     
         31 . The method of  claim 30 , further comprising identifying a nucleotide at a detection position in at least a first target nucleic acid molecule of said plurality of different target nucleic acid molecules. 
     
     
         32 . The method of  claim 31 , wherein step (b) comprises forming a first hybridization complex between said first target nucleic acid molecule and at least a first readout probe of said first set of readout probes. 
     
     
         33 . The method of  claim 32 , further comprising contacting said hybridization complex with at least a first nucleotide and a polymerase, wherein said polymerase extends said first readout probe with said first nucleotide when said first nucleotide is complementary to said detection position. 
     
     
         34 . The method of  claim 32 , wherein said first target nucleic acid molecule comprises a first and a second target domain, wherein said first hybridization complex comprises said first target nucleic acid molecule, a first readout probe hybridized to said first domain and a second readout probe hybridized to said second domain, wherein at least one of said readout probes comprise a label said determining comprises adding a ligase to form a ligation complex. 
     
     
         35 . The method of  claim 30 , wherein said target nucleic acid molecules comprise genomic DNA sequences. 
     
     
         36 . The method of  claim 27 , wherein said microspheres further comprise identifier binding ligands. 
     
     
         37 . The method of claim  10 , further comprising contacting said microspheres with decoder binding ligands in order to identify the location for each plurality of different target analytes in said array. 
     
     
         38 . A method comprising:
 a) providing an array composition comprising:
 i) a substrate with a surface comprising discrete sites; and 
 ii) a population of microspheres comprising at least a first and a second microsphere, wherein a plurality of different target analytes from a first individual are attached to said first microsphere via receptor-ligand interactions, wherein a plurality of different target analytes from a second individual are attached to said second microsphere via receptor-ligand interactions, and wherein said microspheres are distributed at said discrete sites; 
   b) contacting said array composition with a first set of readout probes; and   c) detecting the presence of a first target analyte.   
     
     
         39 . The method according to  claim 38 , wherein said receptor is streptavidin and said ligand is biotin. 
     
     
         40 . The method according to  claim 39 , wherein said microspheres are streptavidin coated. 
     
     
         41 . The method of  claim 38 , wherein said microspheres are randomly distributed at said discrete sites. 
     
     
         42 . The method of  claim 38 , wherein said discrete sites are configured to have only a single microsphere of said population of microspheres. 
     
     
         43 . The method of  claim 38 , wherein said plurality of different target analytes comprises a plurality of different target nucleic acid molecules. 
     
     
         44 . The method of  claim 43 , further comprising identifying a nucleotide at a detection position in at least a first target nucleic acid molecule of said plurality of different target nucleic acid molecules. 
     
     
         45 . The method of  claim 44 , wherein step (b) comprises forming a first hybridization complex between said first target nucleic acid molecule and at least a first readout probe of said first set of readout probes. 
     
     
         46 . The method of  claim 45 , further comprising contacting said hybridization complex with at least a first nucleotide and a polymerase, wherein said polymerase extends said first readout probe with said first nucleotide when said first nucleotide is complementary to said detection position. 
     
     
         47 . The method of  claim 45 , wherein said first target nucleic acid molecule comprises a first and a second target domain, wherein said first hybridization complex comprises said first target nucleic acid molecule, a first readout probe hybridized to said first domain and a second readout probe hybridized to said second domain, wherein at least one of said readout probes comprise a label said determining comprises adding a ligase to form a ligation complex. 
     
     
         48 . The method of  claim 43 , wherein said target nucleic acid molecules comprise genomic DNA sequences. 
     
     
         49 . The method of  claim 38 , wherein said microspheres further comprise identifier binding ligands. 
     
     
         50 . The method of  claim 49 , further comprising contacting said microspheres with decoder binding ligands in order to identify the location for each plurality of different target analytes in said array.