HIGH THROUGHPUT DETECTION OF MICRORNAS AND USE FOR DISEASE DIAGNOSIS
First Claim
1. A method for detecting a target nucleic acid in a sample comprisingproviding a sample potentially containing the target nucleic acidproviding at least one oligonucleotide probe set, wherein said probe set comprises:
- (i) a first oligonucleotide probe having a 5′
target specific region and a first 3′
universal sequence region,(ii) a second oligonucleotide probe having a 3′
target specific region and a second 5′
universal sequence region(iii) a third oligonucleotide probe having a 5′
region complementary to said first 3′
universal sequence region in said first oligonucleotide probe, and(v) a fourth oligonucleotide probe having a 3′
region complementary to the 5′
universal sequence region of said second oligonucleotide probewherein the first and said second oligonucleotides probes are suitable for ligation together when hybridized adjacent to one another to said target nucleic acid, and wherein the third and the fourth oligonucleotides probes are suitable for ligation to the target nucleic acid when hybridized adjacent to said nucleic acid target;
annealing the oligonucleotide probe set to the target nucleic acid such that a complex is formed between the target nucleic acid and the oligonucleotide probe set;
contacting the complex with a linking agent under conditions such that the directly adjacent 5′ and
3′
ends of the first and second oligonucleotide probes, the 3′ and
5′
ends of the third oligonucleotide probe and the target nucleic acid, and the 5′ and
3′
ends of the fourth oligonucleotide probe and the target nucleic acid covalently bond to form a ligated probe product,separating the ligated probe product from the non-ligated first and second oligonucleotide probes; and
detecting whether or not said ligated probe product is formed, wherein the presence of the ligated probe product is indicative of presence of said target nucleic acid in said sample.
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Accused Products
Abstract
Methods, compositions and kits are provided for high throughput detection of micro RNAs (miRNA), especially for sensitive and specific detection of miRNA that are in low abundance and closely related to each other. In particular, an assembly of designed oligonucleotide probes with unique tag sequences is used to achieve these purposes via high throughput microarrays, optionally in conjunction with branched-DNA based array detection. The assays can be used for diagnosis, prognosis or monitoring of diseases or disorders such as cancer, for pharmacogenomic studies of patient stratification and drug responses, for discovery of therapeutic targets, or for forensic analysis.
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Citations
52 Claims
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1. A method for detecting a target nucleic acid in a sample comprising
providing a sample potentially containing the target nucleic acid providing at least one oligonucleotide probe set, wherein said probe set comprises: -
(i) a first oligonucleotide probe having a 5′
target specific region and a first 3′
universal sequence region,(ii) a second oligonucleotide probe having a 3′
target specific region and a second 5′
universal sequence region(iii) a third oligonucleotide probe having a 5′
region complementary to said first 3′
universal sequence region in said first oligonucleotide probe, and(v) a fourth oligonucleotide probe having a 3′
region complementary to the 5′
universal sequence region of said second oligonucleotide probewherein the first and said second oligonucleotides probes are suitable for ligation together when hybridized adjacent to one another to said target nucleic acid, and wherein the third and the fourth oligonucleotides probes are suitable for ligation to the target nucleic acid when hybridized adjacent to said nucleic acid target; annealing the oligonucleotide probe set to the target nucleic acid such that a complex is formed between the target nucleic acid and the oligonucleotide probe set; contacting the complex with a linking agent under conditions such that the directly adjacent 5′ and
3′
ends of the first and second oligonucleotide probes, the 3′ and
5′
ends of the third oligonucleotide probe and the target nucleic acid, and the 5′ and
3′
ends of the fourth oligonucleotide probe and the target nucleic acid covalently bond to form a ligated probe product,separating the ligated probe product from the non-ligated first and second oligonucleotide probes; and detecting whether or not said ligated probe product is formed, wherein the presence of the ligated probe product is indicative of presence of said target nucleic acid in said sample. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 52)
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51. The method claim 506 wherein said detecting comprises binding a branched DNA to said ligated probe.
Specification