Computer-aided analysis system for sequencing by hybridization
First Claim
1. A method of identifying a base in a target nucleic acid sequence, comprising:
- obtaining a plurality of H values, each H value corresponding to an extent of hybridization of an oligonucleotide probe with at least one nucleic acid sequence including said target sequence and each oligonucleotide probe differing from each other by at least a single base;
comparing said H values to each other; and
identifying said base according to results of said comparisons.
1 Assignment
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Accused Products
Abstract
The conditions under which oligonucleotide probes hybridize preferentially with entirely complementary and homologous nucleic acid targets are described. Using these hybridization conditions, overlapping oligonucleotide probes associate with a target nucleic acid. Following washes, positive hybridization signals are used to assemble the sequence of a given nucleic acid fragment. Representative target nucleic acids are applied as dots. Up to to 100,000 probes of the type (A,T,C,G)(A,T,C,G)N8(A,T,C,G) are used to determine sequence information by simultaneous hybridization with nucleic acid molecules bound to a filter. Additional hybridization conditions are provided that allow stringent hybridization of 6-10 nucleotide long oligomers which extends the utility of the invention. A computer process determines the information sequence of the target nucleic acid which can include targets with the complexity of mammalian genomes. Sequence generation can be obtained for a large complex mammalian genome in a single process.
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Citations
7 Claims
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1. A method of identifying a base in a target nucleic acid sequence, comprising:
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obtaining a plurality of H values, each H value corresponding to an extent of hybridization of an oligonucleotide probe with at least one nucleic acid sequence including said target sequence and each oligonucleotide probe differing from each other by at least a single base; comparing said H values to each other; and identifying said base according to results of said comparisons. - View Dependent Claims (6, 7)
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2. A method of identifying an unknown base in a target nucleic acid sequence, comprising:
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obtaining a plurality of H values, each H value corresponding to an extent of hybridization of an oligonucleotide probe with at least one nucleic acid sequence including said target sequence and each oligonucleotide probe differing from each other by at least a single base; comparing said H values to each other; and identifying said unknown base according to results of said comparisons.
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3. A method of identifying an unknown base in a target nucleic acid sequence, comprising:
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obtaining a plurality of H values, each H value corresponding to an extent of hybridization of an oligonucleotide probe with said target nucleic acid sequence and each oligonucleotide probe differing from each other by at least a single base; calculating a D value from the ratio of a higher H value to a lower H value; and identifying said unknown base according to results of said calculations if said D value is greater than a predetermined ratio value.
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4. A method of identifying an unknown base in a target nucleic acid sequence, comprising:
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obtaining a first set of H values, each H value corresponding to an extent of hybridization of an oligonucleotide probe with a control nucleic acid sequence and each probe differing from each other by at least a single base; obtaining a second set of H values, each H value corresponding to an extent of hybridization of an oligonucleotide probe with said target nucleic acid sequence and each probe differing from each other by at least a single base; comparing at least one of said H values in said first set and at least one of said H values in said second set; and identifying said unknown base according to results of said comparisons.
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5. A method of identifying an unknown base in a target nucleic acid sequence, comprising:
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obtaining a statistical data set corresponding to statistics about a plurality of experiments producing H values, each H value corresponding to an extent of hybridization of an oligonucleotide probe with a control nucleic acid sequence and each oligonucleotide probe differing from each other by at least a single base; obtaining a plurality of H values, each H value corresponding to an extent of hybridization of an oligonucleotide probe with said target sequence and each probe differing from each other by at least a single base; comparing at least one of said plurality of H values with said statistical data set; and identifying said unknown base of said target according to results of said comparisons.
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Specification