Methods, compositions, and kits for detecting allelic variants
First Claim
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1. A composition comprising:
- a) an allele-specific primer that is complementary to a target sequence comprising a first allelic variant;
b) an allele-specific blocker probe that does not comprise a label and is complementary to said target sequence comprising a second allelic variant, wherein said second allelic variant corresponds to a position in said target sequence that is at the same loci as said first allelic variant in said target sequence, and wherein said allele-specific blocker probe comprises a minor groove binder (MGB) at the 3′
end that is non-extendable;
c) a locus-specific primer that is complementary to a region of the target sequence that is 3′
from the first allelic variant and on the opposite strand; and
d) a locus-specific detector probe wherein the detector probe is a 5′
nuclease probe and has two labels.
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Abstract
In some embodiments, the present inventions relates generally to compositions, methods and kits for use in discriminating sequence variation between different alleles. More specifically, in some embodiments, the present invention provides for compositions, methods and kits for quantitating rare (e.g., mutant) allelic variants, such as SNPs, or nucleotide (NT) insertions or deletions, in samples comprising abundant (e.g., wild type) allelic variants with high specificity and selectivity. In particular, in some embodiments, the invention relates to a highly selective method for mutation detection referred to as competitive allele-specific TaqMan PCR (“cast-PCR”).
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Citations
61 Claims
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1. A composition comprising:
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a) an allele-specific primer that is complementary to a target sequence comprising a first allelic variant; b) an allele-specific blocker probe that does not comprise a label and is complementary to said target sequence comprising a second allelic variant, wherein said second allelic variant corresponds to a position in said target sequence that is at the same loci as said first allelic variant in said target sequence, and wherein said allele-specific blocker probe comprises a minor groove binder (MGB) at the 3′
end that is non-extendable;c) a locus-specific primer that is complementary to a region of the target sequence that is 3′
from the first allelic variant and on the opposite strand; andd) a locus-specific detector probe wherein the detector probe is a 5′
nuclease probe and has two labels. - 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, 28, 29, 55, 56, 57, 58, 59, 60, 61)
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30. A kit comprising, two or more containers comprising the following components independently distributed in one of the two or more containers:
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a) an allele-specific primer that is complementary to a target sequence comprising a first allelic variant; and b) an allele-specific blocker probe that does not comprise a label and is complementary to said target sequence comprising a second allelic variant, wherein said second allelic variant corresponds to a position in said target sequence that is the same as said first allelic variant in said target sequence, and wherein said allele-specific blocker probe comprises a minor groove binder (MGB) at the 3′
end that is non-extendable;c) a locus-specific primer that is complementary to a region of said target sequence that is 3′
from said first allelic variant and on the opposite strand; andd) a locus-specific detector probe wherein the detector probe is a 5′
nuclease probe and wherein the detector probe has two labels. - View Dependent Claims (31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54)
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Specification