IDENTIFICATION OF MOLECULAR SEQUENCE SIGNATURES AND METHODS INVOLVING THE SAME
First Claim
8. A method of determining whether a nucleic acid in a sample is a member of a gene family, comprising:
- selecting a hierarchy of assay techniques comprising at least a first and second assay, said first assay being selected to provide a determination of a presence, absence, or variant of a first sequence signature and said second assay being selected to provide a determination of a presence, absence or variant of a second sequence signature;
wherein at least one of said assays employs a high-density nucleic acid array;
analyzing said nucleic acid sample using said first assay; and
determining whether said nucleic acid is a member of said gene family based on the results of said first and second assays.
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Abstract
Novel means and methods for analyzing hybridization data derived from hybridization assays between a target nucleic acid and differently sequenced polynucleotide probes involve selecting probe sets that define reference sequences for sequence signatures and deriving useful data about the nature of the target nucleic acid molecule based on its hybridization to the probes. The methods are useful for determining whether the target contains a nucleic acid or polypeptide sequence signature, whether the target encodes a member of a gene family, or whether the target is derived from one of any number of genes.
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Citations
17 Claims
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8. A method of determining whether a nucleic acid in a sample is a member of a gene family, comprising:
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selecting a hierarchy of assay techniques comprising at least a first and second assay, said first assay being selected to provide a determination of a presence, absence, or variant of a first sequence signature and said second assay being selected to provide a determination of a presence, absence or variant of a second sequence signature;
wherein at least one of said assays employs a high-density nucleic acid array;analyzing said nucleic acid sample using said first assay; and determining whether said nucleic acid is a member of said gene family based on the results of said first and second assays. - View Dependent Claims (9, 10, 11, 12)
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13-1. The method of claim 13, wherein said first or second sequence signature is between 18 and 30 nucleotides in length.
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14. A method of selecting clones for analysis comprising:
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providing a support having a variety of clones associated therewith; exposing said support to one or more polynucleotides under low, medium, or high stringency conditions to permit at least some hybridization between said clones and said polynucleotides; identifying said clones that hybridize with said polynucleotides; and selecting at least one of said clones not identified in said identifying step for analysis. - View Dependent Claims (15)
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16. A method of narrowing a sample for analysis, comprising,
providing a sample containing nucleic acids; -
analyzing whether said sample contains a sequence signature using a high-density nucleic acid array; and further analyzing said nucleic acid sample only if said sequence signature is not present.
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17. A high density nucleic acid array comprising sequence signatures from the TGF-beta gene family.
Specification