Polymorphism detection
First Claim
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1. A method for detecting polymorphism in a nucleic sequence comprising:
- receiving a first plurality of hybridization intensities for a first group of probes that are complementary to the nucleic acid sequence except that the first group of probes includes all possible monosubstitutions of positions in the sequence that are within n bases of a base in the nucleic sequence that is complementary to said polymorphism;
receiving a second plurality of hybridization intensities for a second and third group of probes complementary to marker-specific regions upstream and downstream of the polymorphism in the nucleic acid sequence; and
analyzing the first plurality of hybridization intensities and the second plurality of hybridization intensities.
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Abstract
The present invention generally provides a rapid efficient method for analyzing polymorphic or biallelic markers, and arrays for carrying out these analyses. In general, the methods of the present invention employ arrays of oligonucleotide probes that are complementary to target nucleic acids which correspond to the marker sequences of an individual. The probes are typically arranged in detection blocks, each block being capable of discriminating the three genotypes for a given marker, i.e., the heterozygote or either of the two homozygotes. The method allows for rapid, automatable analysis of genetic linkage to even complex polygenic traits.
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Citations
12 Claims
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1. A method for detecting polymorphism in a nucleic sequence comprising:
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receiving a first plurality of hybridization intensities for a first group of probes that are complementary to the nucleic acid sequence except that the first group of probes includes all possible monosubstitutions of positions in the sequence that are within n bases of a base in the nucleic sequence that is complementary to said polymorphism; receiving a second plurality of hybridization intensities for a second and third group of probes complementary to marker-specific regions upstream and downstream of the polymorphism in the nucleic acid sequence; and analyzing the first plurality of hybridization intensities and the second plurality of hybridization intensities. - View Dependent Claims (2, 3, 4, 5, 6)
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7. A system for detecting polymorphism in a nucleic sequence comprising:
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a memory component; a processor wherein the memory component is configured to store a first plurality of hybridization intensities for a first group of probes that are complementary to the nucleic acid sequence except that the first group of probes includes all possible monosubstitutions of positions in the sequence that are within n bases of a base in the nucleic sequence that is complementary to said polymorphism; the memory component is further configured to store a second plurality of hybridization intensities for a second and third group of probes complementary to marker-specific regions upstream and downstream of the polymorphism in the nucleic acid sequence; the processor is configured to analyze the first plurality of hybridization intensities and the second plurality of hybridization intensities. - View Dependent Claims (8, 9, 10, 11, 12)
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Specification