Microarray-based single nucleotide polymorphism, sequencing, and gene expression assay method
First Claim
1. A microarray-based single nucleotide polymorphism, sequencing, and gene expression assay method comprising:
- (a) providing a microarray having a plurality of probes;
(b) forming a plurality of hybridized structures on the microarray, wherein each hybridized structure is formed by contacting the microarray under a hybridizing condition to a hybridizing solution comprising a plurality of tagged targets and a plurality of detection sequences, wherein each hybridized structure comprises one tagged target hybridized to one probe and to one detection sequence;
(c) extending each hybridized structure using an extension-ligation solution;
(d) ligating each hybridized structure having a terminal nucleotide that is complementary to a target nucleotide using the extension-ligation solution;
(e) removing non-bound material by washing the microarray using a wash solution; and
(f) identifying the target nucleotide and a hybridized sequence from the hybridized structures having ligation.
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Abstract
There is disclosed a microarray-based single nucleotide polymorphism, sequencing, and gene expression assay method. Specifically, there is disclosed a method using a microarray device wherein a plurality of hybridized structures is formed by contacting the microarray under a hybridizing condition to a hybridizing solution comprising a plurality of tagged targets and a plurality of detection sequences. The detection sequences of each hybridized structure is extended using an extension-ligation solution and an extension-ligation condition. After extension, ligation of the extended sequence occurs to a probe if the terminal nucleotide of a probe is complementary to the hybridized tagged targets. Non-bound material is removed by using a washing solution and a washing method. The target nucleotide and the target sequence of the tagged targets is determined by which probe is ligated to the detection sequences.
21 Citations
44 Claims
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1. A microarray-based single nucleotide polymorphism, sequencing, and gene expression assay method comprising:
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(a) providing a microarray having a plurality of probes;
(b) forming a plurality of hybridized structures on the microarray, wherein each hybridized structure is formed by contacting the microarray under a hybridizing condition to a hybridizing solution comprising a plurality of tagged targets and a plurality of detection sequences, wherein each hybridized structure comprises one tagged target hybridized to one probe and to one detection sequence;
(c) extending each hybridized structure using an extension-ligation solution;
(d) ligating each hybridized structure having a terminal nucleotide that is complementary to a target nucleotide using the extension-ligation solution;
(e) removing non-bound material by washing the microarray using a wash solution; and
(f) identifying the target nucleotide and a hybridized sequence from the hybridized structures having ligation. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17)
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18. A microarray-based single nucleotide polymorphism, sequencing, and gene expression assay method comprising:
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(a) providing a microarray having a plurality of probe DNA;
(b) forming a plurality of hybridized structure DNA on the microarray, wherein each hybridized structure DNA is formed by contacting the microarray under a hybridizing condition to a hybridizing solution comprising a plurality of tagged target DNA and a plurality of detection sequence DNA, wherein each hybridized structure DNA comprises one tagged target DNA hybridized to one probe DNA and to one detection sequence DNA;
(c) extending each hybridized structure DNA using an extension-ligation solution;
(d) ligating each hybridized structure DNA having a terminal nucleotide DNA that is complementary to a target nucleotide DNA using the extension-ligation solution;
(e) removing non-bound material by washing the microarray using a wash solution; and
(f) identifying the target nucleotide DNA and a hybridized sequence DNA from the hybridized structures having ligation. - View Dependent Claims (19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34)
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35. A microarray-based single nucleotide polymorphism, sequencing, and gene expression assay method comprising:
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(a) providing a microarray having a plurality of probe DNA;
(b) forming a plurality of hybridized structure DNA/RNA on the microarray, wherein each hybridized structure DNA/RNA is formed by contacting the microarray under a hybridizing condition to a hybridizing solution comprising a plurality of tagged target RNA and a plurality of detection sequence DNA, wherein each hybridized structure DNA/RNA comprises one tagged target RNA hybridized to one probe DNA and to one detection sequence DNA;
(c) extending each hybridized structure DNA/RNA using an extension-ligation solution and an extension-ligation condition;
(d) ligating each hybridized structure DNA/RNA having a terminal nucleotide DNA that is complementary to a target nucleotide RNA using the extension-ligation solution and the extension-ligation condition;
(e) removing non-bound material by washing the microarray using a wash solution and a wash method; and
(f) identifying the target nucleotide RNA and a hybridized sequence RNA from the hybridized structures having ligation. - View Dependent Claims (36, 37, 38, 39, 40, 41, 42, 43, 44)
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Specification