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US 7,563,576 B2Granted
Combinatorial decoding of random nucleic acid arrays
AssigneeIllumina, Inc.
InventorsMark S. Chee, David R. Walt
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Abstract
The invention provides methods and compositions for combinatorially decoding arrays.
Claims31
A method of determining the location of a decoding sequence on an array, said method comprising the steps of:
- a) providing an array substrate comprising individual sites, wherein a first and second subpopulation of identifier nucleic acids are distributed among said individual sites, said first and second subpopulation of identifier nucleic acids comprising the same primer sequence and a different decoding sequence adjacent to said primer sequence;
- b) providing a set of combinatorial decoding probes comprising a priming sequence complementary to said primer sequence and a variable region adjacent to said priming sequence, wherein said variable region comprises at least one decoding nucleotide that will basepair with a nucleotide of at least one of said different decoding sequences, wherein said set of combinatorial decoding probes comprises subsets, each subset having a different decoding nucleotide at the same position and a label unique to each different decoding nucleotide;
- and
- c) adding to said array substrate a subset of said set of combinatorial decoding probes and detecting the presence of said label, thereby determining the location of said decoding sequence on said array.
1 more element
A method of determining the location of a decoding sequence on an array, said method comprising the steps of:
- a) providing an array surface comprising individual sites and a population of microspheres comprising at least a first and a second subpopulation distributed among said individual sites, wherein each subpopulation comprises identifier nucleic acids comprising:
- 1) the same primer sequence;
- and
- 2) a different decoding sequence adjacent to said primer sequence;
- b) providing a first set of combinatorial decoding probes comprising a priming sequence complementary to said primer sequence, a variable region adjacent to said priming sequence, wherein said variable region comprises at least one decoding nucleotide that will basepair with a nucleotide of at least one of said decoding sequences, wherein said first set of combinatorial decoding probes comprises subsets, each subset having a different decoding nucleotide at the same position and a label unique to each different decoding nucleotide;
- and
- c) adding to said array substrate a subset of said first set of combinatorial decoding probes and detecting the presence of said label, thereby determining the location of said decoding sequence on said array.
4 more elements
A method of determining the location of a decoding sequence on an array, said method comprising the steps of:
- a) providing an array substrate comprising individual sites, wherein a first and second subpopulation of identifier nucleic acids are distributed among said individual sites, said first and second subpopulation of identifier nucleic acids comprising the same primer sequence and a different decoding sequence adjacent to said primer sequence;
- b) adding to the array a first combinatorial decoding probe and a second combinatorial decoding probe, each combinatorial decoding probe comprising a priming sequence complementary to said primer sequence and a variable region adjacent to said priming sequence, each variable region comprising a decoding nucleotide that will basepair with a nucleotide of at least one of said different decoding sequences, wherein said first combinatorial decoding probe and said second combinatorial decoding probe have a different decoding nucleotide at the same position and a label unique to the different decoding nucleotide;
- and
- c) determining the location of said decoding sequence on said array by detecting the presence of said label.
1 more element
Dependencies are inferred from the claim text.