Parallel Polymer Sequencing Methods
First Claim
1. A method of sequencing a target polynucleotide comprising:
- (a) carrying out template derived nucleotide synthesis utilizing a labeled nucleotide;
(b) detecting the presence or absence of said labeled nucleotide;
(c) replacing said labeled nucleotide with an unlabeled nucleotide; and
(d) repeating a) to c) with the proviso that if said labeled nucleotide is labeled with a label directly attached to the nucleotide, then the replacement of said labeled nucleotide comprises removal of the whole of said labeled nucleotide and replacement with an unlabled nucleotide, and only said labeled nucleotide can be removed.
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Abstract
The present invention relates to a method of sequencing a target polynucleotide by enzymatic and/or chemical means. The sequencing method includes a method for characterizing multiple alleles in a sample, a method of calculating confidence levels in ascertained sequences, a method for comparing polynucleotide sequences, and a method of resolving ambiguities in a polynucleotide sequence. It also provides methods for appropriately preparing samples, for immobilizing template molecules, for organizing the template molecules, and to conduct the sequencing of many molecules in parallel. The method involves analyzing molecules as members of an array. Many target polynucleotides or many segments of a single target polynucleotide can be sequenced simultaneously. In a preferred embodiment, the method involves analyzing individual molecules within an array and base calls are based on the signals from two or more molecules. A method to prevent non-specific signal in sequencing is also provided. The invention is readily automated, both for small-scale and large-scale operation and relevant algorithms and the composition of kits and systems are provided.
113 Citations
57 Claims
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1. A method of sequencing a target polynucleotide comprising:
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(a) carrying out template derived nucleotide synthesis utilizing a labeled nucleotide;
(b) detecting the presence or absence of said labeled nucleotide;
(c) replacing said labeled nucleotide with an unlabeled nucleotide; and
(d) repeating a) to c) with the proviso that if said labeled nucleotide is labeled with a label directly attached to the nucleotide, then the replacement of said labeled nucleotide comprises removal of the whole of said labeled nucleotide and replacement with an unlabled nucleotide, and only said labeled nucleotide can be removed. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47)
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35. A method of sequencing a target polynucleotide comprising:
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(a) carrying out template derived nucleotide synthesis by ligating a labeled oligonucleotide to a primer annealed to said target polynucleotide, wherein said ligating forms a degradation resistant bond, and wherein said oligonucleotide comprises the structure;
Terminal nucleotide-N-nucleotide attached to a fluorescent label-M-nucleotide attached to a quencher, wherein N and M are each independently a bond or at least one nucleotide; and
M comprises a first degradation labile intranucleoside bond;
(b) contacting said oligonucleotide with a first degradation agent;
(c) detecting the presence or absence of said labeled oligonucleotide;
(d) contacting said oligonucleotide with a second degradation agent; and
(e) repeating (a)-(d).
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37. (canceled)
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48. A method of comparing two or more polynucleotide sequences comprising:
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a) differentially labeling the nucleotide sequences being compared;
b) immobilizing said nucleotide sequences on a surface;
c) detecting the locus of each nucleotide sequence; and
d) sequencing said polynucleotide sequences using a method comprising;
(1) carrying out template derived nucleotide synthesis utilizing a labeled nucleotide;
(2) detecting the presence or absence of said labeled nucleotide;
(3) replacing said labeled nucleotide with an unlabeled nucleotide; and
(4) repeating
1) to
3) with the proviso that if said labeled nucleotide is labeled with a label directly attached to the nucleotide then the replacement of said labeled nucleotide comprises removal of the whole of said labeled nucleotide and replacement with an unlabled nucleotide, and only said labeled nucleotide can be removed. - View Dependent Claims (49)
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50. A method of resolving ambiguities in a polynucleotide sequence comprising:
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a) identifying an area of ambiguity in a polynucleotide sequence;
b) designing probes for each of the suspected sequence possibilities; and
c) utilizing the primers formed to sequence said polynucleotide sequence by a method comprising;
(1) carrying out template derived nucleotide synthesis utilizing a labeled nucleotide;
(2) detecting the presence or absence of said labeled nucleotide;
(3) replacing said labeled nucleotide with an unlabeled nucleotide; and
(4) repeating
1) to
3) with the proviso that if said labeled nucleotide is labeled with a label directly attached to the nucleotide, then the replacement of said labeled nucleotide comprises removal of the whole of said labeled nucleotide and replacement with an unlabled nucleotide, and only said labeled nucleotide can be removed.
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51. A method of sequencing mRNA comprising:
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a) contacting an array of probes designed to hybridize to mRNA molecules with a sample of mRNA under conditions whereby the mRNA will hybridize to said probes; and
b) sequencing said mRNA utilizing a method (1) carrying out template derived nucleotide synthesis utilizing a labeled nucleotide;
(2) detecting the presence or absence of said labeled nucleotide;
(3) replacing said labeled nucleotide with an unlabeled nucleotide; and
(4) repeating
1) to
3) with the proviso that if said labeled nucleotide is labeled with a label directly attached to the nucleotide, then the replacement of said labeled nucleotide comprises removal of the whole of said labeled nucleotide and replacement with an unlabled nucleotide, and only said labeled nucleotide can be removed. - View Dependent Claims (52)
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53. A method of sequencing a target polynucleotide comprising:
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(a) treating said target polynucleotide with an intercalating dye;
(b) extending a primer annealed to said target polynucleotide utilizing a nucleotide labeled with a label which acts as a fluorescence resonance energy transfer (FRET) partner to said DNA intercalating dye;
(c) detecting the presence or absence of said nucleotide by means of an imaging technique that FRET; and
(d) repeating (a)-(c);
wherein (a) and (b) can occur in any order.
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54. A method of sequencing a target polynucleotide comprising:
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(a) extending a primer annealed to said target polynucleotide utilizing a labeled nucleotide wherein the label is directly attached to the nucleotide;
(b) detecting the presence or absence of said labeled nucleotide within said extended primer;
(c) removing said labeled nucleotide, and replacing said labeled nucleotide with an unlabeled degradation resistant nucleotide; and
(d) repeating (a)-(c);
wherein the 3′
end of said primer comprises at least one degradation resistant nucleotide.
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55. A method of sequencing a target polynucleotide comprising:
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(a) extending a primer annealed to said target polynucleotide utilizing a labeled nucleotide wherein the label is attached to the nucleotide via a cleavable linkage;
(b) detecting the presence or absence of said labeled nucleotide within said extended primer;
(c) cleaving said label from said nucleotide; and
(d) repeating (a)-(c).
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56. A method of sequencing a target polynucleotide comprising:
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(a) extending a primer annealed to said target polynucleotide using a nucleotide attached by a cleavable linkage to one member of a binding pair;
(b) contacting said nucleotide with a label attached to the other member of a binding pair under conditions such that the two members of the binding pair bind to one another;
(c) detecting the presence or absence of said label;
(d) removing said label and said binding pair by cleaving said cleavable linkage; and
(e) repeating (a)-(d).
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57. A method of sequencing a target polynucleotide, comprising:
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(a) carrying out template derived polynucleotide synthesis utilizing a nucleotide labeled with a fluorescence resonance energy transfer (FRET) partner and at least one other polymerization reaction component labeled with a FRET partner;
(b) determining the nucleotide incorporated by detecting FRET interactions; and
(c) repeating (a) and (b).
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Specification