IP Library › Patent Application 11356695
Patent Application
App. No. 11/356,695

Microarray device for identifying splice variants of a gene

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Patent No.
US None
App. No.
11/356,695
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 (35)

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.