Detection of nucleic acid sequence differences using the ligase detection reaction with addressable arrays
DC CAFCFirst Claim
1. A collection of capture oligonucleotides, wherein each type of capture oligonucleotide of the collection has greater than sixteen nucleotides and comprises a nucleotide sequence that differs from the nucleotide sequence of other types of capture oligonucleotides in the collection by at least 25% when aligned, and wherein each capture oligonucleotide of the collection hybridizes to a nucleic acid molecule comprising a complementary nucleotide sequence under uniform hybridization conditions.
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Abstract
The present invention describes a method for identifying one or more of a plurality of sequences differing by one or more single base changes, insertions, deletions, or translocations in a plurality of target nucleotide sequences. The method includes a ligation phase, a capture phase, and a detection phase. The ligation phase utilizes a ligation detection reaction between one oligonucleotide probe, which has a target sequence-specific portion and an addressable array-specific portion, and a second oligonucleotide probe, having a target sequence-specific portion and a detectable label. After the ligation phase, the capture phase is carried out by hybridizing the ligated oligonucleotide probes to a solid support with an array of immobilized capture oligonucleotides at least some of which are complementary to the addressable array-specific portion. Following completion of the capture phase, a detection phase is carried out to detect the labels of ligated oligonucleotide probes hybridized to the solid support.
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Citations
27 Claims
- 1. A collection of capture oligonucleotides, wherein each type of capture oligonucleotide of the collection has greater than sixteen nucleotides and comprises a nucleotide sequence that differs from the nucleotide sequence of other types of capture oligonucleotides in the collection by at least 25% when aligned, and wherein each capture oligonucleotide of the collection hybridizes to a nucleic acid molecule comprising a complementary nucleotide sequence under uniform hybridization conditions.
- 4. A group of beads, wherein each bead of the group comprises one or more types of capture oligonucleotides from a collection of capture oligonucleotides, said capture oligonucleotides comprising greater than sixteen nucleotides with each type of capture oligonucleotide of the collection comprising a nucleotide sequence that differs from the nucleotide sequence of other types of capture oligonucleotides of the collection by at least 25% when aligned, and wherein each capture oligonucleotide in the collection hybridizes to a nucleic acid molecule comprising a complementary nucleotide sequence under uniform hybridization conditions.
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7. A device comprising:
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a solid support having an array of positions each suitable for attachment of a capture oligonucleotide; an array of capture oligonucleotides on the solid support at the array of positions, wherein each type of capture oligonucleotide on the solid support comprises a nucleotide sequence that is greater than sixteen nucleotides with a nucleotide sequence that differs from the nucleotide sequence of other types of capture oligonucleotides on the solid support by at least 25% when aligned; and one or more target nucleic acid molecules hybridized to complementary portions of the capture oligonucleotides on the solid support, wherein the capture oligonucleotides hybridize to the complementary portions of the target nucleic acid molecules under uniform hybridization conditions. - View Dependent Claims (8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27)
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Specification