SEQUENCING METHODS
First Claim
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1. A method for obtaining nucleic acid sequence information, said method comprising the steps of:
- (a) providing a first sequencing reagent to a target nucleic acid in the presence of a polymerase, said first sequencing reagent comprising one or more nucleotide monomers, wherein said one or more nucleotide monomers pair with no more than three nucleotide types in said target, thereby forming a polynucleotide complementary to at least a portion of said target; and
(b) providing a second sequencing reagent to said target nucleic acid, said second sequencing reagent comprising at least one nucleotide monomer, said at least one nucleotide monomer of said second sequencing reagent comprising a reversibly terminating moiety, wherein said second sequencing reagent is provided subsequent to providing said first sequencing reagent, whereby sequence information for at least a portion of said target nucleic acid is obtained.
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Abstract
The present technology relates to molecular sciences, such as genomics. More particularly, the present technology relates to nucleic acid sequencing.
73 Citations
50 Claims
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1. A method for obtaining nucleic acid sequence information, said method comprising the steps of:
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(a) providing a first sequencing reagent to a target nucleic acid in the presence of a polymerase, said first sequencing reagent comprising one or more nucleotide monomers, wherein said one or more nucleotide monomers pair with no more than three nucleotide types in said target, thereby forming a polynucleotide complementary to at least a portion of said target; and (b) providing a second sequencing reagent to said target nucleic acid, said second sequencing reagent comprising at least one nucleotide monomer, said at least one nucleotide monomer of said second sequencing reagent comprising a reversibly terminating moiety, wherein said second sequencing reagent is provided subsequent to providing said first sequencing reagent, whereby sequence information for at least a portion of said target nucleic acid is obtained. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19)
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20. A method for obtaining nucleic acid sequence information, said method comprising the steps of:
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(a) providing a first sequencing reagent to a target nucleic acid in the presence of a polymerase, said first sequencing reagent comprising a plurality of different nucleotide monomers, wherein at least one nucleotide monomer of said plurality of nucleotide monomers comprises a reversibly terminating moiety, thereby forming a polynucleotide complementary to at least a portion of said target; and (b) removing the reversibly terminating moiety of said at least one nucleotide monomer of said first sequencing reagent; and (c) providing a second sequencing reagent to said target nucleic acid, said second sequencing reagent comprising at least one nucleotide monomer, said at least one nucleotide monomer of said second sequencing reagent comprising a reversibly terminating moiety, wherein said second sequencing reagent is provided subsequent to providing said first sequencing reagent, whereby sequence information for at least a portion of said target nucleic acid is obtained.
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21. A method for obtaining nucleic acid sequence information, said method comprising the steps of:
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(a) providing a first sequencing reagent to a target nucleic acid in the presence of a ligase, wherein the first sequencing reagent comprises at least one oligonucleotide, wherein said oligonucleotide comprises a reversibly terminating moiety; (b) removing the reversibly terminating moiety of said at least one oligonucleotide of said first sequencing reagent; and (c) providing a second sequencing reagent to said target nucleic acid in the presence of a polymerase wherein said second sequencing reagent comprises at least one nucleotide monomer, wherein said nucleotide monomer comprises a reversibly terminating moiety, and wherein said second sequencing reagent is provided subsequent to providing said first sequencing reagent, whereby sequence information for at least a portion of said target nucleic acid is obtained.
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22. A method for obtaining nucleic acid sequence information, said method comprising the steps of:
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(a) providing a first sequencing reagent to a target nucleic acid in the presence of a polymerase, said first sequencing reagent comprising one or more nucleotide monomers, wherein said one or more nucleotide monomers pair with no more than three nucleotide types in said target, thereby forming a polynucleotide complementary to at least a portion of said target; and (b) providing a second sequencing reagent to said target nucleic acid, said second sequencing reagent comprising at least one nucleotide monomer, wherein said at least one nucleotide monomer pairs with no more than three nucleotide types in said target, wherein said second sequencing reagent is provided subsequent to providing said first sequencing reagent, and wherein a signal that indicates the incorporation of said at least one nucleotide monomer into the polynucleotide is generated, whereby sequence information for at least a portion of said target nucleic acid is obtained.
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23. A method for obtaining nucleic acid sequence information, said method comprising the steps of:
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(a) providing a first low resolution sequence representation for a target nucleic acid, wherein said first low resolution sequence representation comprises an ordered series of determined regions and dark regions, wherein said determined regions comprise a sequence of at least two discrete nucleotides, wherein said dark regions are indicative of degenerate sequence composition, and wherein said dark regions intervene between said determined regions; (b) providing a second low resolution sequence representation for said target nucleic acid, wherein said second low resolution sequence representation comprises an ordered series of determined regions and dark regions, wherein said determined regions comprise a sequence of at least two discrete nucleotides, wherein said dark regions are indicative of degenerate sequence composition, and wherein said dark regions intervene between said determined regions and wherein said sequence of at least two discrete nucleotides in said first low resolution sequence representation is different from said sequence of at least two discrete nucleotides in said second low resolution sequence representation; and (c) comparing said first low resolution sequence representation and said second low resolution sequence representation to determine a sequence representation having a resolution higher than either the first low resolution sequences representation or second low resolution sequence representation alone. - View Dependent Claims (24, 25, 26, 27, 28, 29, 30, 31)
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32. A method for determining the presence of a target nucleic acid, said method comprising the steps of:
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(a) providing a first low resolution sequence representation for a target nucleic acid, wherein said target nucleic acid is obtained from a first sample, wherein said first low resolution sequence representation comprises an ordered series of determined regions and dark regions, wherein said determined regions comprise a sequence of at least two discrete nucleotides, wherein said dark regions are indicative of degenerate sequence composition, and wherein said dark regions intervene between said determined regions; (b) providing a second low resolution sequence representation for a second target nucleic acid, wherein said second target nucleic acid is obtained from a reference sample and has the sequence expected for the target nucleic acid, wherein said second low resolution sequence representation comprises an ordered series of determined regions and dark regions, wherein said determined regions comprise a sequence of at least two discrete nucleotides, wherein said dark regions are indicative of degenerate sequence composition, and wherein said dark regions intervene between said determined regions and wherein said sequence of at least two discrete nucleotides in said first low resolution sequence representation is different from said sequence of at least two discrete nucleotides in said second low resolution sequence representation; and (c) comparing said first low resolution sequence representation and said second low resolution sequence representation to determine the presence of said target nucleic acid in said target sample. - View Dependent Claims (33, 34, 35, 36, 37, 38, 39, 40)
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41. A method for determining the presence of a target nucleic acid in a sample, said method comprising the steps of:
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(a) providing a barcode sequence from a target nucleic acid, wherein said target nucleic acid is obtained from said sample; and (b) comparing said barcode sequence with a reference sequence, wherein the target nucleic acid is present in said sample if said reference sequence comprises a region corresponding to each determined region of the bar code sequence. - View Dependent Claims (42, 43, 44, 45, 46, 47, 48, 49, 50)
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Specification