High throughput polymorphism screening
First Claim
1. A method of determining the identity of a polymorphic nucleotide, said method comprising:
- contacting under hybridizing conditions, a target nucleic acid comprising a polymorphic site, and a solid substrate comprising one or more bound locus-specific primer pairs;
amplifying said target nucleic acid with said locus-specific primer pair, wherein said amplifying results in an amplification product bound to the solid support at each end;
contacting said amplification product with a labeled probe comprising at least one detecting nucleotide that will specifically base pair with said polymorphic nucleotide, in the presence of an enzyme that catalyzes the formation of a covalent bond between said detecting nucleotide and said amplification product; and
detecting said label;
wherein the identity of the label on said detecting nucleotide indicates the complement of the polymorphic nucleotide.
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Abstract
Methods are provided for determining the identity of a polymorphic nucleotide in a complex mixture of nucleic acids where one or more distinct polymorphisms can be present in the mixture, and multiple polymorphisms can be screened in parallel. Target nucleic acids are amplified using bridge amplification techniques. The detection and identification of the specific polymorphic residue(s) is based on readout methods that utilize the specificity of specific enzymes for complementary DNA sequences. These approaches result in a labeled nucleotide covalently attached to the amplicon, where the identity of the nucleotide is informative of the polymorphic sequence. In one aspect, the readout process uses primer extension protocols, where the specific base incorporated by DNA polymerase is determined by the sequence at the polymorphic site. In another aspect, the identity of a specific base hybridized and ligated to the amplicon is determined by the sequence at the polymorphic site. The polynucleotide to which the label has been attached can be detected in situ, i.e. bound to the solid substrate used for amplification; or can be released and detected.
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Citations
14 Claims
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1. A method of determining the identity of a polymorphic nucleotide, said method comprising:
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contacting under hybridizing conditions, a target nucleic acid comprising a polymorphic site, and a solid substrate comprising one or more bound locus-specific primer pairs;
amplifying said target nucleic acid with said locus-specific primer pair, wherein said amplifying results in an amplification product bound to the solid support at each end;
contacting said amplification product with a labeled probe comprising at least one detecting nucleotide that will specifically base pair with said polymorphic nucleotide, in the presence of an enzyme that catalyzes the formation of a covalent bond between said detecting nucleotide and said amplification product; and
detecting said label;
wherein the identity of the label on said detecting nucleotide indicates the complement of the polymorphic nucleotide. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14)
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10. The method of claim 10, wherein at least two different labels are used.
Specification