Nucleic acid analysis by joining barcoded polynucleotide probes
AssigneeAffymetrix, Inc.
InventorsHeather Koshinsky, John D. Curry, Robert O'Callahan, Adam Mccoy, Daniel Fitzpatrick, Philip H. Dickinson, Anthony C. Schweitzer
Life of this patent
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Abstract
Disclosed are compositions, methods and kits for determining the presence, absence, amount, copy number, or other characteristics of one or more polynucleotide sequences in two or more samples and use thereof in genotyping, evaluation of copy number variation, expression analysis, determination of splice variants and fusion genes, and other genetic analyses.
Claims20
A composition for analyzing a target polynucleotide in a sample, the composition comprising:
- a first probe configured to hybridize to a first target sequence of the target polynucleotide, the first probe including
- (i) an interrogation site bar code that is non-complementary to the first target sequence,
- (ii) a first complementary sequence portion 5′ of the interrogation site barcode, the first complementary sequence portion being complementary to the first target sequence,
- (iii) a second complementary sequence portion 3′ of the interrogation site barcode, the second complementary sequence portion being complementary to the first target sequence, and
- (iv) a universal sequence that is non-complementary to the first target sequence, the universal sequence being 5′ of the first complementary sequence portion;
- and
- a second probe configured to hybridize to a second target sequence of the target polynucleotide, the second probe including
- (i) a complementary sequence portion that is complementary to the second target sequence, and
- (ii) a non-complementary sequence that is non-complementary to the second target sequence.
A composition for analyzing a target polynucleotide in a sample, the composition comprising:
- a first probe configured to hybridize to a first target sequence of the target polynucleotide, the first probe including
- (v) an interrogation site bar code that is non-complementary to the first target sequence,
- (vi) a first complementary sequence portion 5′ of the interrogation site barcode, the first complementary sequence portion being complementary to the first target sequence,
- (vii) a second complementary sequence portion 3′ of the interrogation site barcode, the second complementary sequence portion being complementary to the first target sequence, and
- (viii) a universal sequence that is non-complementary to the first target sequence;
- and
- a second probe configured to hybridize to a second target sequence of the target polynucleotide, the second probe including
- (iii) a complementary sequence portion that is complementary to the second target sequence, and
- (iv) a non-complementary sequence that is non-complementary to the second target sequence,
- wherein the first probe is configured to hybridize to the target polynucleotide 5′ of the second probe.
Dependencies are inferred from the claim text.