Methods for controlling cross-hybridization in analysis of nucleic acid sequences
First Claim
1. A method for selecting a set of target-specific oligonucleotide probes for use in analyzing a target nucleic acid sequence, said method comprising:
- (a) identifying a cross-hybridization oligonucleotide probe based on a candidate target-specific oligonucleotide probe for said target nucleic acid sequence wherein said cross-hybridization oligonucleotide probe measures the extent of occurrence of a cross-hybridization event, having a predetermined probability, to an interfering nucleic acid sequence, (b) determining cross-hybridization results employing said cross-hybridization oligonucleotide probe and said target-specific oligonucleotide probe wherein said cross-hybridization results are determined by a hybridization study of a sample suspected of containing a target nucleic acid sequence using said target-specific oligonucleotide probe and said cross-hybridization probe and (c) selecting or rejecting said target-specific oligonucleotide probe for said set of target specific oligonucleotide probes based on said cross-hybridization results.
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Accused Products
Abstract
Methods, reagents and kits are disclosed for selecting target-specific oligonucleotide probes, which may be used in analyzing a target nucleic acid sequence. In one aspect the present invention is directed to selecting a set of target-specific oligonucleotide probes. A cross-hybridization oligonucleotide probe is identified based on a candidate target-specific oligonucleotide probe for the target nucleic acid sequence. The cross-hybridization oligonucleotide probe measures the extent of occurrence of a cross-hybridization event having a predetermined probability. Cross-hybridization results are determined employing the cross-hybridization oligonucleotide probe and the target-specific oligonucleotide probe. The target-specific oligonucleotide probe is selected or rejected for the set based on the cross-hybridization results.
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Citations
28 Claims
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1. A method for selecting a set of target-specific oligonucleotide probes for use in analyzing a target nucleic acid sequence, said method comprising:
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(a) identifying a cross-hybridization oligonucleotide probe based on a candidate target-specific oligonucleotide probe for said target nucleic acid sequence wherein said cross-hybridization oligonucleotide probe measures the extent of occurrence of a cross-hybridization event, having a predetermined probability, to an interfering nucleic acid sequence, (b) determining cross-hybridization results employing said cross-hybridization oligonucleotide probe and said target-specific oligonucleotide probe wherein said cross-hybridization results are determined by a hybridization study of a sample suspected of containing a target nucleic acid sequence using said target-specific oligonucleotide probe and said cross-hybridization probe and (c) selecting or rejecting said target-specific oligonucleotide probe for said set of target specific oligonucleotide probes based on said cross-hybridization results. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23)
(a) an oligonucleotide probe specific for said target nucleic acid sequence, (b) a set of cross-hybridization oligonucleotide probes based on said target nucleic acid sequence wherein cross-hybridization results obtained with said set measures the extent of the occurrence of cross-hybridization events, having a predetermined probability, between an interfering nucleic acid sequence and said oligonucleotide probe specific for said target nucleic sequence and wherein said predetermined probability is a threshold level based on information about said target nucleic acid sequence and said oligonucleotide specific for a target nucleic acid sequence, (c) a written description of a method according to claim 1.
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20. A kit according to claim 19 wherein said set of cross-hybridization oligonucleotide probes is obtained from a homology algorithm.
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21. A kit according to claim 19 wherein said target-specific oligonucleotide probe comprises a label.
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22. A kit according to claim 19 wherein said target-specific oligonucleotide probe is bound to a support.
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23. A kit according to claim 22 wherein said support comprises an array of different target-specific oligonucleotide probes.
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12. A method for selecting a set of target-specific oligonucleotide probes for use in analyzing a target nucleic acid sequence, said method comprising:
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(a) identifying a cross-hybridization oligonucleotide probe based on said target nucleic acid sequence by a process comprising determining homologous sequences in target genes that meet predetermined criteria with respect to said oligonucleotide probe specific for said target nucleic acid sequence, (b) determining cross-hybridization results employing said cross-hybridization oligonucleotide probe and target-specific oligonucleotide probe wherein said cross-hybridization results are determined by a hybridization study of a sample suspected of containing a target nucleic acid sequence using said target-specific oligonucleotide probe and said cross-hybridization probe and (c) selecting or rejecting said target-specific oligonucleotide probe for said set based on said cross-hybridization results. - View Dependent Claims (13, 14, 15)
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16. A method for selecting a set of target-specific oligonucleotide probes for use in analyzing a target nucleic acid sequence, said method comprising:
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(a) identifying a cross-hybridization oligonucleotide probe based on said target nucleic acid sequence by a process comprising incorporating a selected combination of possible nucleotide substitutions at one or more positions in a single cross-hybridization oligonucleotide probe, (b) determining cross-hybridization results employing said cross-hybridization oligonucleotide probe and target-specific oligonucleotide probe and (c) selecting or rejecting said target-specific oligonucleotide probe for said set based on said cross-hybridization results.
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17. A method for selecting a set of target-specific oligonucleotide probes for use in analyzing a target nucleic acid sequence, said method comprising:
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(a) identifying a cross-hybridization oligonucleotide probe based on said target nucleic acid sequence by a process comprising deleting nucleotides at one or more positions in a single cross-hybridization oligonucleotide probe, (b) determining cross-hybridization results employing said cross-hybridization oligonucleotide probe and target-specific oligonucleotide probe and (c) selecting or rejecting said target-specific oligonucleotide probe for said set based on said cross-hybridization results.
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18. A method for selecting a set of target-specific oligonucleotide probes for use in analyzing a target nucleic acid sequence, said method comprising:
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(a) identifying a cross-hybridization oligonucleotide probe based on said target nucleic acid sequence by a process comprising inserting nucleotides at one or more positions in a single cross-hybridization oligonucleotide probe, (b) determining cross-hybridization results employing said cross-hybridization oligonucleotide probe and target-specific oligonucleotide probe and (c) selecting or rejecting said target-specific oligonucleotide probe for said set based on said cross-hybridization results.
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24. A computer based method for selecting a set of target-specific oligonucleotide probes for use in analyzing a target nucleic acid sequence, said method comprising:
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(a) identifying under computer control a cross-hybridization oligonucleotide probe based on said target nucleic acid sequence wherein said cross-hybridization oligonucleotide probe measures the extent of the occurrence of a cross-hybridization event, having a predetermined probability, to an interfering nucleic acid sequence, (b) determining under computer control cross-hybridization results employing said cross-hybridization oligonucleotide probe and target-specific oligonucleotide probe wherein said cross-hybridization results are determined by a hybridization study of a sample suspected of containing a target nucleic acid sequence using said target-specific oligonucleotide probe and said cross-hybridization probe and (c) selecting or rejecting under computer control said target-specific oligonucleotide probe for said set of target specific oligonucleotide probes based on said cross-hybridization results.
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25. A computer system for selecting a set of target-specific oligonucleotide probes for use in analyzing a target nucleic acid sequence, said system comprising:
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(a) input means for introducing a target nucleotide sequence into said computer system, (b) means for determining a cross-hybridization oligonucleotide probe based on said target nucleic acid sequence wherein said cross-hybridization oligonucleotide probe measures the extent of the occurrence of a cross-hybridization event, having a predetermined probability, to an interfering nucleic acid sequence wherein said cross-hybridization results are determined by a hybridization study of a sample suspected of containing a target nucleic acid sequence using said target-specific oligonucleotide probe and said cross-hybridization probe, (c) memory means for determining cross-hybridization results employing said cross-hybridization oligonucleotide probe and target-specific oligonucleotide probe, (d) means for storing said cross-hybridization results, (e) means for controlling said computer system to select or reject said target-specific oligonucleotide probe for said set of target specific oligonucleotide probes based on said cross-hybridization results, (f) means for storing selection results from step (e), and (g) means for outputting data relating to said selection results.
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26. A computer program product comprising a computer readable storage medium having a computer program stored thereon which, when loaded into a computer, selects a set of target-specific oligonucleotide probes for use in analyzing a target nucleic acid sequence by performing steps comprising:
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(a) identifying under computer control a cross-hybridization oligonucleotide probe based on said target nucleic acid sequence wherein said cross-hybridization oligonucleotide probe measures the extent of the occurrence of a cross-hybridization event, having a predetermined probability, to an interfering nucleic acid sequence, (b) determining under computer control cross-hybridization results employing said cross-hybridization oligonucleotide probe and target-specific oligonucleotide probe wherein said cross-hybridization results are determined by a hybridization study of a sample suspected of containing a target nucleic acid sequence using said target-specific oligonucleotide probe and said cross-hybridization probe and (c) selecting or rejecting under computer control said target-specific oligonucleotide probe for said set of target specific oligonucleotide probes based on said cross-hybridization results. - View Dependent Claims (27, 28)
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Specification