Methods and Means for Nucleic Acid Sequencing
First Claim
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1. A nucleic acid sequencing method comprising:
- providing a DNA sample containing a plurality of circular single-stranded DNA template molecules each comprising a primer annealing sequence and a target sequence;
forming a random array of immobilized and amplified template molecules, by contacting said template molecules with an amplification primer to anneal to the primer annealing sequence thereby forming annealed primer/template complexes, amplifying said template molecules by rolling-circle amplification, ensuring said amplified template molecules are immobilized on a solid support by immobilizing the amplification primer before annealing the template, the primer/template complexes before amplification, or the amplified templates after amplification;
probing the tandem-repeated amplification product with a panel of probes under test conditions, determining for each probe whether it hybridizes to the target sequences or not under the test conditions, thereby obtaining a hybridization spectrum of the target;
comparing the hybridization spectrum to a hybridization spectrum for reference sequences in a reference database comprising a plurality of reference sequences, wherein the reference database is expected to contain within it one or more reference sequences for the sequence of the DNA template, thereby determining the likely location or locations of the target sequence within one or more reference sequences;
optionally computing the likely sequence of the target sequence and/or a difference in sequence of the target sequence compared with one or more reference sequences by comparing the actual hybridization spectrum with the expected hybridization spectrum at the location or locations.
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Abstract
Nucleic acid sequencing, especially high-density fingerprinting, in which a panel of nucleic acid probes is annealed to nucleic acid containing a template for which sequence information is desired, with determination of the presence or absence of sequence complementary to each probe within the template, thus providing sequence information. A reference sequence at least partly related to the template is used.
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Citations
45 Claims
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1. A nucleic acid sequencing method comprising:
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providing a DNA sample containing a plurality of circular single-stranded DNA template molecules each comprising a primer annealing sequence and a target sequence;
forming a random array of immobilized and amplified template molecules, by contacting said template molecules with an amplification primer to anneal to the primer annealing sequence thereby forming annealed primer/template complexes, amplifying said template molecules by rolling-circle amplification, ensuring said amplified template molecules are immobilized on a solid support by immobilizing the amplification primer before annealing the template, the primer/template complexes before amplification, or the amplified templates after amplification;
probing the tandem-repeated amplification product with a panel of probes under test conditions, determining for each probe whether it hybridizes to the target sequences or not under the test conditions, thereby obtaining a hybridization spectrum of the target;
comparing the hybridization spectrum to a hybridization spectrum for reference sequences in a reference database comprising a plurality of reference sequences, wherein the reference database is expected to contain within it one or more reference sequences for the sequence of the DNA template, thereby determining the likely location or locations of the target sequence within one or more reference sequences;
optionally computing the likely sequence of the target sequence and/or a difference in sequence of the target sequence compared with one or more reference sequences by comparing the actual hybridization spectrum with the expected hybridization spectrum at the location or locations. - 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)
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32. A random array of single-stranded DNA molecules, wherein
each said molecule consists of at least two tandem-repeated copies of an initial sequence, each said molecule is immobilized on a surface at random locations with a density of between 103 and 107 per cm2, each said initial sequence represents a random fragment from an initial target DNA or RNA library comprising a mixture of single- or double-stranded RNA or DNA molecules, said initial sequences of all said DNA molecules have approximately the same length.
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39. A set of probes wherein
each probe consists of one or more oligonucleotides, each said oligonucleotide is stabilized, each said oligonucleotide carries a reporter moiety, the effective specificity of each probe is between 3 and 10 bp, the set of probes is such that at least 10% of all positions in a random or arbitrary target sequence statistically hybridize with at least one probe in the set of probes.
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45. A spectral search instrument comprising a field-programmable gate array (FPGA) attached to a host computer and a computer-readable memory device, wherein
said FPGA is configured to perform spectral search, said computer-readable memory device stores a reference nucleotide sequence and a set of hybridization spectra, said host computer is configured to provide said FPGA with the reference nucleotide sequence and with each said hybridization spectrum, said FPGA, when provided with a reference nucleotide sequence and a hybridization spectrum, writes to said computer-readable memory to store the location or locations of best matches between said hybridization spectrum and said reference nucleotide sequence.
Specification