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1. (WO2005067643) DETERMINATION D'UN GENOTYPE DU VIRUS DE L'HEPATITE C
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CLAIMS

We claim:

1. A composition comprising an invasive cleavage detection assay, wherein said invasive cleavage detection assay is configured for detecting a single nucleotide polymorphism in a position of a 5' UTR sequence of HCV selected from the group consisting of: -245, -167, -163, -155, -144, -118, and -80.

2. The composition of Claim 1, wherein said invasive cleavage assay comprises a first oligonucleotide, wherein said first oligonucleotide comprises a 5' portion and a 3' portion, wherein said 3' portion is configured to hybridize to said 5' UTR sequence of HCV, and wherein said 5' portion is configured to not hybridize to said 5' UTR sequence of HCV.

3. The composition of Claim 2, wherein said first oligonucleotide is a sequence selected from the group consisting of SEQ TD NOs:2-4, 7, 8, 10, 14, 16, 17, 19, 22, 24, 26, 30, 33, 34, 36, 42, 43, 45-47, 49, 50, 55, 57, 59, and 63.

4. The composition of Claim 1, wherein said invasive cleavage assay comprises a second oligonucleotide, wherein said second oligonucleotide comprises a 5' portion and a 3' portion, wherein said 5' portion is configured to hybridize to said 5' UTR sequence of HCV, and wherein said 3' portion is configured to not hybridize to said 5' UTR sequence of HCV.

5. The composition of Claim 4, wherein said second oligonucleotide is a sequence selected from the group consisting of SEQ LD NOs:l, 5, 6, 9, 11-13, 15, 18, 20, 21, 23, 25, 29, 31, 32, 35, 37-41, 44, 48, 51-54, 56, and 58.

6. The composition of Claim 1, wherein said 5' UTR sequence of HCV comprises RNA.

7. The composition of Claim 1, wherein said 5' UTR sequence of HCV comprises DNA.

8. A method comprising;
a) providing;
i) a sample from a subject, wherein said sample is suspected of containing HCV, and
ii) a composition comprising an invasive cleavage detection
assay, wherein said invasive cleavage detection assay is configured for
detecting a single nucleotide polymorphism in a position of a 5' UTR
sequence of HCV selected from the group consisting of: -245, -167, -163, - 155, -144, -118, and -80; and
b) contacting said composition with said sample under conditions such that at least one of said single nucleotide polymorphisms is detected.

9. The method of Claim 8, wherein said contacting determines the identity of the base at said position.

10. The method of Claim 8, wherein said sample is from a subject.

11. The method of Claim 8, wherein said invasive cleavage assay comprises a first oligonucleotide, wherein said first oligonucleotide comprises a 5' portion and a 3' portion, wherein said 3' portion is configured to hybridize to said 5' UTR sequence of HCV, and wherein said 5' portion is configured to not hybridize to said 5' UTR sequence of HCV.

12. The method of Claim 11 , wherein said first oligonucleotide is a sequence selected from the group consisting of SEQ TD NOs:2-4, 7, 8, 10, 14, 16, 17, 19, 22, 24, 26,

30, 33, 34, 36, 42, 43, 45-47, 49, 50, 55, 57, 59, and 63.

13. The method of Claim 8, wherein said invasive cleavage assay comprises a second oligonucleotide, wherein said second oligonucleotide comprises a 5' portion and a 3' portion, wherein said 5' portion is configured to hybridize to said 5' UTR sequence of HCV, and wherein said 3' portion is configured to not hybridize to said 5' UTR sequence of HCV.

14. The method of Claim 13, wherein said second oligonucleotide is a sequence selected from the group consisting of SEQ LD NOs:l, 5, 6, 9, 11-13, 15, 18, 20, 21, 23, 25, 29, 31, 32, 35, 37-41, 44, 48, 51-54, 56, and 58.

15. A method comprising;
a) providing;
i) a sample from a subject, wherein said sample is suspected of containing hepatitis C virus, and
ii) a plurality of oligonucleotide detection assays, wherein each of said oligonucleotide detections assays is configured for detecting a single nucleotide polymorphisms in a 5' UTR sequence of HCV, and
b) contacting said sample with said plurality of oligonucleotide
detection assays under conditions such that at least partial genotype information for each of said single nucleotide polymorphisms is determined thereby generating a 5' UTR genotype profile, wherein said 5' UTR genotype profile is sufficient to
genotype said hepatitis C virus.

16. The method of Claim 15, further comprising c) genotyping said hepatitis C virus based on said 5' UTR genotype profile as Genotype I, II, III, IV, V, or VI.

17. The method of Claim 16, wherein said genotyping classifies said hepatitis C virus as being Genotype I, IV or V.

18. The method of Claim 15, wherein said plurality of oligonucleotide detection assays comprise invasive cleavage structure type assays.

19. The method of Claim 15 , wherein said plurality of oligonucleotide detection assays comprise non-amplifying oligonucleotide type detection assays.

20. The method of Claim 15, wherein at least one of said plurality of said oligonucleotide detection assays comprises a first oligonucleotide, wherein said first oligonucleotide comprises a 5' portion and a 3' portion, wherein said 3' portion is configured to hybridize to said 5' UTR sequence of HCV, and wherein said 5' portion is configured to not hybridize to said 5' UTR sequence of HCV.

21. The method of Claim 15, wherein at least one of said plurality of said oligonucleotide detection assays comprises a second oligonucleotide, wherein said second oligonucleotide comprises a 5' portion and a 3' portion, wherein said 5' portion is configured to hybridize to said 5' UTR sequence of HCV, and wherein said 3' portion is configured to not hybridize to said 5' UTR sequence of HCV.