Methods and apparatus for screening and detecting multiple genetic mutations
First Claim
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1. A method for detecting members of a set of polymorphisms that occur at identified loci in samples of patient nucleic acid, comprising the steps of:
- providing patient sample nucleic acid containing multiple loci at a site;
providing one or more blockers, the blockers being selected for particular loci;
hybridizing the blockers with the patient sample nucleic acid, leaving at least one loci unblocked;
providing at least one discriminator, the discriminator being capable of binding with the at least one unblocked loci;
hybridizing the discriminators with the patient sample; and
detecting the formation of a hyubridization event.
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Abstract
An assay system and methods are described where patient samples containing genomic DNA are analyzed for the presence of known genetic polymorphisms using a universal reporter strategy. In a preferred embodiment, the amplified DNA is localized at test sites in an array of sites on a microchip followed by a series of hybridization reactions that screen for the presence of a single mutation from among a number of mutations, and allow the identification of specific mutations. In addition to universal reporters, the assay may use blockers and discriminators for screening and identification of known polymorphisms.
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Citations
44 Claims
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1. A method for detecting members of a set of polymorphisms that occur at identified loci in samples of patient nucleic acid, comprising the steps of:
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providing patient sample nucleic acid containing multiple loci at a site;
providing one or more blockers, the blockers being selected for particular loci;
hybridizing the blockers with the patient sample nucleic acid, leaving at least one loci unblocked;
providing at least one discriminator, the discriminator being capable of binding with the at least one unblocked loci;
hybridizing the discriminators with the patient sample; and
detecting the formation of a hyubridization event. - 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)
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28. A method for detecting members of a set of polymorphisms that occur at identified loci in samples of patient nucleic acid comprising the steps of:
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providing a patient sample containing multiple loci, performing a screening step, comprising providing at least two probes for different loci, and detecting the presence of a hybridization event between the patient sample and the probes, and, if a hybridization event is detected, providing a first set of blockers to the loci, the set of blockers comprising a subset of the sites corresponding to the probes, and providing probes to patient sample, and detecting a hybridization event. - View Dependent Claims (29, 30, 31, 32, 33)
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34. A method for detecting members of a set of polymorphisms that occur at identified loci in samples of patient nucleic acid comprising the steps of:
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loading a patient sample containing multiple loci at multiple sites, including at least a first site and a second site, and providing a first set of blockers selectively for a subset of the loci to the first site and a second set of blockers, which are different from the first set of blockers, selectively to a different subset of the loci at the second site. - View Dependent Claims (35, 36, 37, 38, 39)
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40. A method for detecting members of a set of polymorphisms that occur at identified loci in samples of patient nucleic acid, comprising the steps of:
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attaching the sample of patient nucleic acid to a test site, the patient sample having multiple identified loci;
providing a blocker set to the patient sample so as to block some, but not all, of the loci; and
providing discriminators for detecting unblocked loci.
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41. A system for detecting members of a set of polymorphisms that occur at identified loci in samples of patient nucleic acid comprising:
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loading nucleic acid from the identified loci at an addressable site, providing mutant discriminator probes comprising oligonucleotides selective for a member of the set of known polymorphisms, providing a first common nucleotide sequence, and providing a universal reporter comprising a label and a nucleotide sequence complementary to the first common nucleotide sequence of the mutant discriminator probe.
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42. A kit for use in a process of detecting members of a set of polymorphisms that occur at identified loci in samples of patient nucleic acid, said kit comprising:
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at least one blocker capable of binding with at least one loci contained in the patient sample nucleic acid;
at least one discriminator capable of binding with at least one different loci in the patient sample nucleic acid; and
at least one universal reporter capable of binding with the at least one discriminator. - View Dependent Claims (43, 44)
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Specification
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Current AssigneeGamida for Life B.V.
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Original AssigneeNanogen, Inc.
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InventorsMenge, Karen, Wallace, Robert B., Held, Lance C., Canter, David, Radtkey, Ray R.
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Granted Patent
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Time in Patent OfficeDays
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Field of Search
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US Class Current435/6
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CPC Class CodesC12Q 1/6827 for detection of mutation o...C12Q 1/6837 using probe arrays or probe...C12Q 2525/161 incorporating target specif...C12Q 2525/186 incorporating a non-extenda...C12Q 2535/131 Allele specific probesC12Q 2537/149 Sequential reactionsC12Q 2565/518 characterised by the immobi...Y10T 436/143333 Saccharide [e.g., DNA, etc.]
