US2006142952A1PendingUtilityA1

Microarray device for identifying splice variants of a gene

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Assignee: JIVAN BIOLOG INCPriority: Jul 25, 2001Filed: Feb 17, 2006Published: Jun 29, 2006
Est. expiryJul 25, 2021(expired)· nominal 20-yr term from priority
Inventors:Jonathan BinghamSubha Srinivasan
G16B 25/10G16B 25/00C12Q 1/6827C12Q 1/6809C12Q 1/6837Y10S707/99943
47
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Claims

Abstract

A method and system for identifying mRNA present in a sample. A splice variant technique selects a set of possible exon-exon junctions based on exons of expected mRNA transcripts. The splice variant technique then selects indicator polynucleotides for the exon-exon junctions and detects the expression level of the indicator polynucleotides in the sample. The splice variant technique then may use a mathematical algorithm to identify possible splice variants in the sample from the observed expression levels.

Claims

exact text as granted — not AI-modified
1 - 23 . (canceled)  
   
   
       24 . A nucleotide array, comprising: an indicator polynucleotide for a predicted exon-exon junction of a gene.  
   
   
       25 . The array of  claim 24 , wherein the gene comprises at least a first exon, a second exon, and a third exon, and the indicator polynucleotide indicates a junction between the first exon and the third exon.  
   
   
       26 . The array of  claim 25 , further comprising an indicator polynucleotide for the second exon.  
   
   
       27 . The array of  claim 25 , further comprising an indicator polynucleotide for a junction between the first exon and the second exon.  
   
   
       28 . The array of  claim 25 , further comprising an indicator polynucleotide for a junction between the second exon and the third exon.  
   
   
       29 . The array of  claim 24 , wherein the indicator polynucleotide indicates a trim or extension of an exon of the gene.  
   
   
       30 . A nucleotide array, comprising: a first indicator polynucleotide for an exon-exon junction of a first splice variant of a gene and a second indicator polynucleotide for an exon-exon junction of a second splice variant of the gene.  
   
   
       31 . The array of  claim 30 , wherein the first indicator polynucleotide indicates a predicted exon-exon junction.  
   
   
       32 . The array of  claim 30 , wherein the first indicator polynucleotide indicates a trim or extension of an exon identified by the second indicator polynucleotide.  
   
   
       33 . The array of  claim 30 , wherein the gene comprises at least a first exon, a second exon, and a third exon.  
   
   
       34 . The array of  claim 33  wherein the first indicator polynucleotide indicates a junction between the first exon and the third exon, and the second indicator polynucleotide indicates a junction between the first exon and the second exon.  
   
   
       35 . The array of  claim 34 , further comprising an indicator polynucleotide for the second exon.  
   
   
       36 . The array of  claim 33 , wherein the first indicator polynucleotide indicates a junction between the first exon and the third exon, and the second indicator polynucleotide indicates a junction between the second exon and the third exon.  
   
   
       37 . The array of  claim 36 , further comprising an indicator polynucleotide for the second exon.  
   
   
       38 . The array of  claim 34 , further comprising an indicator polynucleotide for a junction between the second exon and the third exon.  
   
   
       39 . The array of  claim 30 , wherein the gene comprises at least a first exon, a second exon, a third exon, and a fourth exon.  
   
   
       40 . The array of  claim 39  wherein the first indicator polynucleotide indicates a junction between the first exon and the fourth exon, and the second indicator polynucleotide indicates a junction between the second exon and the third exon.  
   
   
       41 . The array of  claim 39 , wherein the first indicator polynucleotide indicates a junction between the first exon and the third exon, and the second indicator polynucleotide indicates a junction between the second exon and the fourth exon.  
   
   
       42 . The array of  claim 39 , wherein the first indicator polynucleotide indicates a junction between the first exon and the fourth exon, and the array further comprises an indicator polynucleotide for the second exon and an indicator polynucleotide for the third exon.  
   
   
       43 . A nucleotide array, comprising: a plurality of indicator polynucleotides for exon-exon junctions.  
   
   
       44 . The array of  claim 43 , wherein the plurality comprises indicator polynucleotides for exon-exon junctions of multiple splice variants of a gene.  
   
   
       45 . The array of  claim 44 , further comprising indicator polynucleotides for exons of the gene.  
   
   
       46 . The array of  claim 43 , wherein the plurality comprises indicator polynucleotides for multiple exon-exon junctions of a first splice variant of a gene.  
   
   
       47 . The array of  claim 46 , wherein the plurality comprises an indicator polynucleotide for an exon-exon junction of a second splice variant of the gene.  
   
   
       48 . The array of  claim 46 , further comprising indicator polynucleotides for exons of the gene.  
   
   
       49 . The array of  claim 43 , wherein the plurality comprises indicator polynucleotides for all exon-exon junctions of a first splice variant of a gene.  
   
   
       50 . The array of  claim 49 , further comprising indicator polynucleotides for all exons of the first splice variant.  
   
   
       51 . The array of  claim 49 , wherein the plurality comprises an indicator polynucleotide for an exon-exon junction of a second splice variant of the gene.  
   
   
       52 . The array of  claim 49 , wherein the plurality comprises indicator polynucleotides for all exon-exon junctions of a second splice variant of the gene.  
   
   
       53 . The array of  claim 49 , further comprising indicator polynucleotides for all exons of the first splice variant.  
   
   
       54 . The array of  claim 52 , further comprising indicator polynucleotides for all exons of the second splice variant.  
   
   
       55 . A nucleotide array comprising: an indicator polynucleotide for an exon-exon junction of a gene and a plurality of indicator polynucleotides for exons of the gene.  
   
   
       56 . The array of  claim 55 , wherein the plurality comprises indicator polynucleotides for all exons of a first splice variant of the gene.  
   
   
       57 . The array of  claim 56 , wherein the plurality comprises indicator polynucleotides for all exons of a second splice variant of the gene.

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