Regulatory single nucleotide polymorphisms and methods therefor
OwnerVolker Nowotnyinventor
Life of this patent
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Abstract
Polynucleotides containing single nucleotide polymorphisms which are present in transcription factor binding site clusters are disclosed. The polynucleotides can be used in diagnostic assays, in testing systems for finding new drugs, and in methods for treating diseases. Also disclosed are methods for identifying single nucleotide polymorphisms which are present in transcription factor binding site clusters.
Claims56
A set of regulatory SNP polynucleotides or a set of polynucleotides complementary thereto, the set of regulatory SNP polynucleotides comprising a plurality of polynucleotides of at least 6 contiguous nucleotides, each polynucleotide of the set containing a regulatory SNP with 5′, 3′ or both 5′ and 3′ genomic flanking sequence, wherein the set of regulatory SNP polynucleotides contains a plurality of regulatory SNPs which collectively map to a plurality of TFC sequences such that each SNP lies within a TFC sequence and a genomic nucleic acid sequence from 30 nucleotides 5′ to 30 nucleotides 3′ to said each SNP is identical or complementary except for the SNP, to a portion of a genomic nucleic acid sequence from 30 nucleotides 5′ to 30 nucleotides 3′ to the TFC sequence.
A method of identifying regulatory SNPs, the method comprising determining that a SNP is a regulatory SNP if the SNP maps to a TFC wherein the SNP lies within a TFC sequence and a genomic nucleic acid sequence from at least 20 nucleotides 5′ to at least 20 nucleotides 3′ to said candidate SNP is identical or complementary except for the SNP, to a portion of a genomic nucleic acid sequence from at least 20 nucleotides 5′ to at least 20 nucleotides 3′ to the TFC sequence.
A computer readable medium having a data structure for use in reporting regulatory SNPs, the data structure comprising a first field containing either or both of sequence and genomic mapping location sequence information on SNPs;
- a second field containing either or both of sequence and genomic mapping location of TFCs;
- and a third field containing information on regulatory SNPs, the SNPs being identified by identities of either or both of sequences and genomic mapping locations of SNPs and TFCs.
Dependencies are inferred from the claim text.