METHODS AND APPARATUS FOR SCREENING AND DETECTING MULTIPLE GENETIC MUTATIONS

• US 20100167960A1
• Filed: 10/07/2009
• Published: 07/01/2010
• Est. Priority Date: 07/26/2002
• Status: Active Grant

• Current Assignee: Gamida for Life B.V.
• Original Assignee: Gamida for Life B.V.
• Inventors: Menge, Karen, Wallace, Robert B., Held, Lance C., Canter, David, Radtkey, Ray R.
• Granted Patent: US 8,772,467 B2
• Time in Patent Office: Days
• US Class Current: 506/39
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 2525/161 incorporating target specific and non-target specific sites
• CPC Class Codes: C12Q 2525/186 incorporating a non-extendable or blocking moiety
• CPC Class Codes: C12Q 2535/131 Allele specific probes
• CPC Class Codes: C12Q 2537/149 Sequential reactions
• CPC Class Codes: C12Q 2565/518 characterised by the immobilisation of the nucleic acid sample or target
• CPC Class Codes: Y10T 436/143333 Saccharide [e.g., DNA, etc.]

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.

Claims

1-40. -40. (canceled)

41. A system for detecting members of a set of polymorphisms that occur at identified loci in samples of patient nucleic acid comprising:

loading nucleic acid from the identified loci at at least one addressable site of a microarray;

providing mutant discriminator probes comprising oligonucleotides selective for a member of the set of known polymorphisms and having a first common nucleotide sequence;

providing a universal reporter comprising a label and a nucleotide sequence complementary to the first common nucleotide sequence of the mutant discriminator probe.

45. The system of claim 41, wherein the addressable site is a site of an actively addressable electronic microarray.

46. The system of claim 41, further comprising the step of providing unlabeled oligonucleotides that are complementary to at least one of the identified loci.

47. The system of claim 41, further comprising the step of detecting the presence of the universal reporter.

48. The system of claim 41, wherein the nucleic acid from the identified loci comprises multiple segments containing different loci.

49. The system of claim 48, wherein the multiple segments containing different loci are affixed to the same addressable site of the microarray.

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:

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 loci contained in the patient sample nucleic acid; and

at least one universal reporter capable of binding with the at least one discriminator.

43. The kit of claim 42, further comprising at least one amplification control being capable of binding with the patient nucleic acid.

44. The kit of claim 43, further comprising an additional universal reporter capable of binding with the at least one amplification control.

50. The kit of claim 42, further comprising an actively addressable electronic microarray capable of being loaded with patient sample nucleic acid at individually addressable sites.

51. The kit of claim 42, wherein the blocker and the discriminator comprise oligonucleotides that are complementary to the at least one loci contained in the patient sample nucleic acid.

52. The kit of claim 51, wherein the universal reporter comprises a nucleotide sequence that is complementary to the oligonucleotide of the discriminator.

53. The kit of claim 42, wherein the blocker and the discriminator are capable of binding to different loci contained in the patient sample nucleic acid.