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US 2005/0089920 A1Published application
High throughput methods for haplotyping
AssigneePolyGenyx, Inc.
InventorJohn Landers
Life of this patent
Estimating the term…
Abstract
The invention relates to high throughput methods for determining haplotypes. The high throughput methods are based on hybridization, fluorescence detection, primer extension, MALDI TOF, and HPLC.
Claims37
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A method for haplotyping, comprising:
- analyzing a genotype of a first SNP of a polymorphic locus of a nucleic acid within a sample in solution by detecting the presence or absence of a first labeled probe which specifically identifies a first putative allele of the SNP and detecting the presence or absence of a second labeled probe which specifically identifies a second putative allele of the SNP,
- separating the nucleic acid sample based on the genotype of the first SNP,
- analyzing a second SNP of the polymorphic locus of the separated nucleic acid samples to identify the haplotype of the nucleic acid.
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A method for haplotyping, comprising:
- labeling first and second SNPs of a polymorphic locus of a nucleic acid within a sample in solution with a first, second, third, and fourth labeled probe which specifically identifies a first and second putative allele of the first SNP and a first and second putative allele of the second SNP respectively,
- separating the labeled nucleic acid sample into single nucleic acid molecules,
- detecting the presence or absence of the first, second, third, and fourth labeled probes on the single nucleic acid molecules to identify the haplotype of the nucleic acid.
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A method for haplotyping, comprising:
- performing four hybridization reactions on a nucleic acid sample, each of the four hybridization reactions involving one labeled probe specific for one allele of one of two SNPs, each of the labeled probes labeled with a spectrally distinct label and wherein each label on the probe specific for a first of the two SNPs is a spectral pair with the label on each probe specific for the second of the two SNPs,
- bringing each of the labeled probes in each hybridization reaction within energy transfer distance from one another,
- exciting one of the labeled probes in each hybridization reaction, and
- detecting electromagnetic radiation released from the other labeled probe as a signal, wherein the presence or absence of a signal for each hybridization reaction is an indicator of the haplotype of the nucleic acid sample.
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A kit comprising:
- one or more containers housing:
- a first set of ASOs, wherein the first set of ASOs represents two ASOs, each containing one of the two alleles of a first SNP in a polymorphic locus,
- a second set of ASOs, wherein the second set of ASOs represents two ASOs, each containing one of the two alleles of a second SNP in the polymorphic locus, and
- instructions for performing a hybridization reaction to determine a haplotype from a genomic DNA sample using the first and second sets of ASOs.
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Dependencies are inferred from the claim text.