Multiplexed analysis of polymorphic loci by concurrent interrogation and enzyme-mediated detection
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Abstract
The invention provides methods and processes for the identification of polymorphisms at one or more designated sites, without interference from non-designated sites located within proximity of such designated sites. Probes are provided capable of interrogation of such designated sites in order to determine the composition of each such designated site. By the methods of this invention, one or more mutations within the CFTR gene and the HLA gene complex can be can be identified.
27 Citations
64 Claims
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1-48. -48. (canceled)
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49. A method of determining the nucleotides at two or more predetermined polymorphic sites in one or more targets, the method comprising the following steps:
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a) providing a set of oligonucleotide primer pairs, each pair capable of annealing with complementary polynucleotide strands to delineate a region of the corresponding target which includes a designated polymorphic site;
b) contacting said set of oligonucleotide primers with said targets under conditions allowing formation of pairs of complementary amplicon strands including designated polymorphic sites corresponding to designated polymorphic sites in corresponding targets;
c) selecting a set of encoded probes wherein different types of encoded probes have different nucleotide sequences and different types of probes are differently encoded and are complementary, in whole or in substantial part, to different amplicon strands or different subsequences of amplicon strands, and wherein at least one type of probe is selected so that the nucleotides in said type which align, upon annealing, with non-designated or non-selected polymorphic sites in amplicon strands are all outside the terminal elongation initiation region;
d) contacting the set of encoded probes with said amplicons under conditions permitting annealing of encoded probes to amplicons and the formation of a probe elongation product by the probes having sites in the terminal elongation region complementary to nucleotides in the aligned region in the amplicons, upon annealing of probes and amplicons, but wherein probes having sites outside the terminal elongation region complementary to non-designated or non-selected polymorphic sites in the aligned region in the amplicons, upon annealing of probes and amplicons, are not elongated;
e) detecting probe elongation products and the probes which are not elongated; and
g) decoding the identities of the elongated and non-elongated probes. - View Dependent Claims (50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64)
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Specification