Single nucleotide polymorphisms in GH-1

• US 20030170679A1
• Filed: 11/07/2002
• Published: 09/11/2003
• Est. Priority Date: 11/09/2001
• Status: Abandoned Application

• Current Assignee: Pharmacia & Upjohn Company (Pfizer Inc.)
• Original Assignee: Pharmacia & Upjohn Company (Pfizer Inc.)
• Inventors: Wood, Linda Susan, Parodi, Luis A., Wagner, Susanne
• Application Number:
  US10/289,845
• Publication Number:
  US 20030170679A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: A61K 38/00 Medicinal preparations containing peptides peptides containing beta-lactam rings A61K31/00; cyclic dipeptides not having in their molecule any other peptide link than those which form their ring, e.g. piperazine-2,5-diones, A61K31/00; ergot alkaloids of the cyclic peptide type A61K31/48; containing macromolecular compounds having statistically distributed amino acid units A61K31/74; medicinal preparations containing antigens or antibodies A61K39/00; medicinal preparations characterised by the non-active ingredients, e.g. peptides as drug carriers, A61K47/00
• CPC Class Codes: A61P 43/00 Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
• CPC Class Codes: C07K 14/61 Growth hormone [GH], i.e. somatotropin
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers

Abstract

The invention provides nucleic acid segments of the GH-1 gene including polymorphic sites. Allele specific primers and probes hybridizing to regions flanking these sites are also provided. The invention also provides methods for diagnosing GH-1 dysfunction.

Claims

1. An isolated GH-1 diagnostic polynucleotide or its complement comprising between 10 and 800 contiguous nucleotides.

2. The isolated GH-1 diagnostic polynucleotide of claim 1 which is derived from genomic DNA.

3. The isolated GH-1 diagnostic polynucleotide of claim 2 which is derived from the sequence delineated in SEQ ID NO:

4

5. The isolated polynucleotide of claim 1 in which the polymorphic site is S1 and the nucleotide at the polymorphic site is selected from the group of nucleotides A or C

6. The isolated polynucleotide of claim 1 in which the polymorphic site is S2 and the nucleotide at the polymorphic site is selected from the group of nucleotides C or T

7. The isolated polynucleotide of claim 1 in which the polymorphic site is S3 and the nucleotide at the polymorphic site is selected from the group of nucleotides C or T.

8. The isolated polynucleotide of claim 1 in which the polymorphic site is S4 and the nucleotide at the polymorphic site is selected from the group of nucleotides T or A.

9. The isolated polynucleotide of claim 1 in which the polymorphic site is S5 and the nucleotide at the polymorphic site is selected from the group of nucleotides T or A.

10. The isolated polynucleotide of claim 1 in which the polymorphic site is S6 and the nucleotide at the polymorphic site is selected from group of nucleotides C or T

11. The isolated polynucleotide of claim 1 in which the polymorphic site is S7 and the nucleotide at the polymorphic site is selected from the group of nucleotides A or C.

12. The isolated polynucleotide of claim 1 in which the polymorphic site is S8 and the nucleotide at the polymorphic site is selected from the group of nucleotides C or G.

13. The isolated polynucleotide of claim 1 in which the polymorphic site is S9 and the nucleotide at the polymorphic site is selected from group of nucleotides C or G.

14. The isolated polynucleotide of claim 1 that is less than 400 nucleotides

15. The isolated polynucleotide of claim 1 that is less than 50 nucleotides.

16. The isolated polynucleotide of claim 1 that is less than 30 nucleotides.

17. The isolated polynucleotide of claim 1 that is less than 25 nucleotides

18. The isolated polynucleotide of claim 1 wherein the polymorphism is within 4 nucleotides of the center of said polynucleotide.

19. The isolated polynucleotide of claim 1 wherein the polymorphism is at the center of said polynucleotide.

20. The isolated polynucleotide of claim 1 wherein the polymorphism is at the end of said polynucleotide.

21. The isolated polynucleotide of claim 1 wherein the polynucleotide is a probe.

22. The isolated polynucleotide of claim 1 wherein the polynucleotide is a primer.

4. The isolated GH-1 diagnostic polynucleotide of claim which is derived from messenger RNA.

23. A polynucleotide for use in amplifying a segment of SEQ ID NO:

4 comprising a polymorphic site.

24. A single-stranded DNA probe that hybridizes to a variant GH-1 gene and not to a wild type GH-1 gene, wherein the variant GH-1 gene is selected from the group consisting of:

SEQ ID NO;

4 having a “

C”

at position 1665,

SEQ ID NO;

4 having a “

T”

at position 1973,

SEQ ID NO;

4 having a “

T”

at position 2034,

SEQ ID NO;

4 having a “

A”

at position 2069,

SEQ ID NO;

4 having a “

A”

at position 2070,

SEQ ID NO;

4 having a “

T”

at position 2081,

SEQ ID NO;

4 having a “

C”

at position 2345

SEQ ID NO;

4 having a “

G”

at position 2533

SEQ ID NO;

4 having a “

G”

at position 3007

25. An array of nucleic acid molecules attached to a solid support, the array comprising a single stranded DNA probe according to claim 24.

26. A method for classifying a nucleic acid molecule encoding GH-1 or a fragment thereof obtained from an individual for diagnostic or prognostic purposes, comprising;

determining the identity of a nucleotide from said nucleic acid which corresponds to the nucleotide occupying at least one GH-1 polymorphic site selected from the group consisting of;

S1, S2, S3, S4, S5, S6, S7, S8 and S9 on either the coding or non-coding strand.

27. The method of claim 26, wherein the determining comprises determining the identity of the nucleotide of at least two GH-1 polymorphic sites.

28. A method of evaluating therapy with an agent acting on GH-1 dysfunction for treatment of a patient, comprising:

(a) determining the identity of a nucleotide from a nucleic acid obtained from said patient which corresponds to the nucleotide occupying at least one GH-1 polymorphic site on either the coding or non-coding strand;

(b) evaluating whether said patient should undergo therapy with said agent.

29. The method of claim 28 wherein the evaluating comprises:

determining that the patient should undergo therapy with said agent if any of the following conditions exist;

(a) the identity of the nucleotide at S1 on the coding strand is C or G on the non-coding strand

(b) the identity of the nucleotide at S2 on the coding strand is T or A on the non-coding strand

(c) the identity of the nucleotide at S3 on the coding strand is T or A on the non-coding strand

(d) the identity of the nucleotide at S4 on the coding strand is A or T on the non-coding strand

(e) the identity of the nucleotide at S5 on the coding strand is A or T on the non-coding strand

(f) the identity of the nucleotide at S6 on the coding strand is T or A on the non-coding strand

(g) the identity of the nucleotide at S7 on the coding strand is C or G on the non-coding strand

(h) the identity of the nucleotide at S8 on the coding strand is G or C on the non-coding strand

(i) the identity of the nucleotide at S9 on the coding strand is C or G on the non-coding strand.

30. The method of claim 28 wherein said agent is human growth hormone.

31. A method of administering human growth hormone comprising administering human growth hormone to a patient previously determined to have a nucleotide at a GH-1 polymorphic site indicating GH-1 dysfunction wherein the previous determination has ascertained that any of the following conditions exist:

(a) the identity of the nucleotide at S1 on the coding strand is C or G on the non-coding strand

(b) the identity of the nucleotide at S2 on the coding strand is T or A on the non-coding strand

(c) the identity of the nucleotide at S3 on the coding strand is T or A on the non-coding strand

(d) the identity of the nucleotide at S4 on the coding strand is A or T on the non-coding strand

(e) the identity of the nucleotide at S5 on the coding strand is A or T on the non-coding strand

(f) the identity of the nucleotide at S6 on the coding strand is T or A on the non-coding strand

(g) the identity of the nucleotide at S7 on the coding strand is C or G on the non-coding strand

(h) the identity of the nucleotide at S8 on the coding strand is G or C on the non-coding strand

(i) the identity of the nucleotide at S9 on the coding strand is C or G on the non-coding strand.

32. A method of selecting a therapy for a patient comprising,

(a) determining the identity of a nucleotide which corresponds to the nucleotide occupying at least one GH-1 polymorphic site selected from the group consisting of:

S1, S2, S3, S4, S5, S6, S7, S8 and S9. on either the coding or non-coding strand;

(b) transmitting a descriptor of therapy selected based on the identity of the nucleotide at said GH-1 polymorphic site.

33. A method of haplotype determination in an individual for diagnostic or prognostic purposes, comprising

determining a nucleotide on a single chromosome. which corresponds to the nucleotide occupying one or more GH-1 polymorphic sites selected from the group consisting of:

S1, S2, S3, S4, S5, S6, S7, S8 and S9.

34. A diagnostic kit comprising the required components for the determination of the of the identity of the nucleotide or nucleotides occupying a GH-1 polymorphic site selected from the group consisting of:

S1, S2, S3, S4, S5, S6, S7, S8 and S9 in small volumes in a self contained kit.

35. The diagnostic kit of claim 34 comprising an isolated GH-1 diagnostic polynucleotide comprising between 10 and 800 contiguous nucleotides.

36. An antibody selected from the group of antibodies consisting of:

(a) an antibody to an epitope comprising amino acid position 3 of SEQ ID NO;

2 capable of distinguishing a threonine from an alanine at that amino acid position;

or

(b) an antibody to an epitope comprising amino acid position 19 of SEQ ID NO;

2 capable of distinguishing a proline from a serine at that amino acid position;

(c) an antibody to an epitope comprising amino acid position 13 of SEQ ID NO;

3 capable of distinguishing an alanine from a valine at that amino acid position;

(d) an antibody to an epitope comprising amino acid position 25 of SEQ ID NO;

3 capable of distinguishing phenylalanine from isoleucine or tyrosine at that amino acid position;

(e) an antibody to an epitope comprising amino acid position 28 of SEQ ID NO;

3 capable of identifying a terminal tyrosine at that amino acid position;

(f) an antibody to an epitope comprising amino acid position 47 of SEQ ID NO;

3 capable of distinguishing an asparagine from threonine at that amino acid position;

(g) an antibody to an epitope comprising amino acid position 79 of SEQ ID NO;

3 capable of distinguishing a serine from a cysteine at that amino acid position.

(h) an antibody to an epitope comprising amino acid position 153 of SEQ ID NO;

3 capable of distinguishing an aspartic acid from histidine at that amino acid position.

37. A diagnostic kit comprising the antibody of claim 36.

38. A isolated GH-1 mutant polypeptide comprising one or more of the following mutations:

(a) the amino acid encoded by the GH-1 polymorphic site S3 is a valine

(b) the amino acid encoded by the GH-1 polymorphic site S4 is a isoleucine

(c) the amino acid encoded by the GH-1 polymorphic site S5 is a tyrosine

(d) the amino acid encoded by the GH-1 polymorphic site S7 is a threonine

(e) the amino acid encoded by the GH-1 polymorphic site S8 is a cysteine

(f) the amino acid encoded by the GH-1 polymorphic site S9 is a histidine

39. The isolated mutant polypeptide of claim 38 which comprises one mutation.

40. An isolated polynucleotide encoding the GH-1 mutant polypeptide of claim 38.

41. A method for treating a disease state comprising the step of administering to a patient in need of such treatment an amount of a GH-1 mutant polypeptide sufficient to alter GH-1 activity in the tissues of said patient.

42. A method for classifying a GH-1 polypeptide obtained from an individual for diagnostic or prognostic purposes, to determine whether said polypeptide is a GH-1 mutant polypeptide comprising;

determining the identity of an amino acid encoded by at least one GH-1 polymorphic site selected from the group consisting of;

S1, S2, S3, S4, S5, S6, S7, S8 and S9.

43. The method of claim 42, wherein the determining comprises determining the identity of an amino acid encoded by at least two GH-1 polymorphic sites.

44. A method of evaluating therapy with an agent acting on GH-1 dysfunction for treatment of a patient, comprising:

(a) determining whether a GH-i polypeptide obtained from said patient is a GH-1 mutant polypeptide;

(b) evaluating whether the patient should undergo therapy with said agent.

45. The method of claim 44 wherein the evaluating comprises:

determining that the patient should undergo therapy with said agent if any of the following conditions exist;

(a) the identity of the amino acid encoded by the GH-1 polymorphic site S1 is an alanine

(b) the identity of the amino acid encoded by the GH-1 polymorphic site S2 is a serine

(c) the identity of the amino acid encoded by the GH-1 polymorphic site S3 is a valine

(d) the identity of the amino acid encoded by the GH-1 polymorphic site S4 is a isoleucine

(e) the identity of the amino acid encoded by the GH-1 polymorphic site S5 is a tyrosine

(f) the identity of the amino acid adjacent to the the GH-1 polymorphic site S6 is a terminal tyrosine

(g) the identity of the amino acid encoded by the GH-1 polymorphic site S7 is a threonine

(h) the identity of the amino acid encoded by the GH-1 polymorphic site S8 is a cysteine

(i) the identity of the amino acid encoded by the GH-1 polymorphic site S9 is a histidine.

46. The method of claim 44 wherein said agent is human growth hormone.

47. A method of administering human growth hormone comprising administering human growth hormone to a patient previously determined to express a mutant GH-1 polypeptide wherein the previous determination has ascertained that any of the following conditions exist:

(a) the identity of the amino acid encoded by the GH-1 polymorphic site S1 is an alanine

(b) the identity of the amino acid encoded by the GH-1 polymorphic site S2 is a serine

(c) the identity of the amino acid encoded by the GH-1 polymorphic site S3 is a valine

(d) the identity of the amino acid encoded by the GH-1 polymorphic site S4 is a isoleucine

(e) the identity of the amino acid encoded by the GH-1 polymorphic site S5 is a tyrosine

(f) the identity of the amino acid adjacent to the the GH-1 polymorphic site S6 is a terminal tyrosine

(g) the identity of the amino acid encoded by the GH-1 polymorphic site S7 is a threonine

(h) the identity of the amino acid encoded by the GH-1 polymorphic site S8 is a cysteine

(i) the identity of the amino acid encoded by the GH-1 polymorphic site S9 is a histidine

48. A method of selecting a therapy for a patient comprising,

(a) determining whether a GH-1 polypeptide obtained from said patient is a GH-1 mutant polypeptide

(b) transmitting a descriptor of therapy selected based on the identity of an amino acid encoded by a GH-1 polymorphic site.