Compositions and methods for detecting predisposition to a substance use disorder
View Patent ↗The present invention provides screening kits, compositions, and diagnostic methods for determining whether a subject has a predisposition to, or likelihood of having, a substance use disorder by determining a nucleic acid methylation profile from a biological sample from the subject, wherein a given profile indicates that the subject has a predisposition to a substance use disorder.
1. A kit for determining the methylation status of at least one CpG dinucleotide, the kit comprising:
at least one first nucleic acid primer at least 8 nucleotides in length that is complementary to a bisulfite-converted nucleic acid sequence comprising a CpG dinucleotide at position 373378 of chromosome 5 within the aryl hydrocarbon receptor repressor (AHRR) gene, wherein the at least one first nucleic acid primer detects the unmethylated CpG dinucleotide.
2. The kit of claim 1 , further comprising at least one second nucleic acid primer at least 8 nucleotides in length that is complementary to a bisulfite-converted nucleic acid sequence comprising a CpG dinucleotide at position 373378 of chromosome 5 within the AHRR gene, wherein the at least one second nucleic acid primer detects the methylated CpG dinucleotide.
3. The kit of claim 2 , further comprising at least a third nucleic acid primer at least 8 nucleotides in length that is complementary to a nucleic acid sequence upstream of the CpG dinucleotide at position 373378 of chromosome 5 within the AHRR gene.
4. The kit of claim 3 , further comprising at least a fourth nucleic acid primer at least 8 nucleotides in length that is complementary to a nucleic acid sequence downstream of the CpG dinucleotide at position 373378 of chromosome 5 within the AHRR gene.
5. The kit of claim 3 , wherein the at least third nucleic acid primer is complementary to a bisulfite-converted nucleic acid sequence.
6. The kit of claim 4 , wherein the at least fourth nucleic acid primer is complementary to a bisulfite-converted nucleic acid sequence.
7. The kit of claim 1 , wherein the at least one first nucleic acid primer comprises one or more nucleotide analogs.
8. The kit of claim 1 , wherein the at least one first nucleic acid primer comprises one or more synthetic or non-natural nucleotides.
9. The kit of claim 1 , further comprising a solid substrate to which the at least one first nucleic acid primer is bound.
10. The kit of claim 9 , wherein the substrate is a polymer, glass, semiconductor, paper, metal, gel or hydrogel.
11. The kit of claim 9 , wherein the solid substrate is a microarray or microfluidics card.
12. The kit of claim 1 , further comprising a detectable label.
13. A kit for determining the methylation status of at least one CpG dinucleotide, the kit comprising:
at least one first nucleic acid primer at least 8 nucleotides in length that is complementary to a bisulfite-converted nucleic acid sequence comprising a CpG dinucleotide at position 373378 of chromosome 5 within the aryl hydrocarbon receptor repressor (AH RR) gene, wherein the at least one first nucleic acid primer comprises one or more nucleotide analogs or one or more synthetic or non-natural nucleotides, and wherein the at least one nucleic acid primer detects either the unmethylated CpG dinucleotide or the methylated CpG dinucleotide.
14. The kit of claim 13 , further comprising at least one second nucleic acid primer at least 8 nucleotides in length that is complementary to a bisulfite-converted nucleic acid sequence comprising a CpG dinucleotide at position 373378 of chromosome 5 within the AHRR gene, wherein the at least one second nucleic acid primer detects the unmethylated CpG dinucleotide or the methylated CpG dinucleotide, the opposite that is detected by the at least one first nucleic acid primer.
15. The kit of claim 13 , wherein the at least one first nucleic acid primer detects the unmethylated CpG dinucleotide.
16. The kit of claim 13 , wherein the at least one first nucleic acid primer detects the methylated CpG dinucleotide.
17. The kit of claim 14 , wherein the at least one first nucleic acid primer detects the unmethylated CpG dinucleotide and wherein the at least one second nucleic acid primer detects the methylated CpG dinucleotide.
18. The kit of claim 14 , wherein the at least one first nucleic acid primer detects the methylated CpG dinucleotide and wherein the at least one second nucleic acid primer detects the unmethylated CpG dinucleotide.
19. The kit of claim 14 , further comprising at least a third nucleic acid primer at least 8 nucleotides in length that is complementary to a nucleic acid sequence upstream of the CpG dinucleotide at position 373378 of chromosome 5 within the AHRR gene.
20. The kit of claim 19 , further comprising at least a fourth nucleic acid primer at least 8 nucleotides in length that is complementary to a nucleic acid sequence downstream of the CpG dinucleotide at position 373378 of chromosome 5 within the AHRR gene.
21. The kit of claim 19 , wherein the at least third nucleic acid primer is complementary to a bisulfite-converted nucleic acid sequence.
22. The kit of claim 20 , wherein the at least fourth nucleic acid primer is complementary to a bisulfite-converted nucleic acid sequence.
23. The kit of claim 14 , wherein the at least one second nucleic acid primer comprises one or more nucleotide analogs.
24. The kit of claim 14 , wherein the at least one second nucleic acid primer comprises one or more synthetic or non-natural nucleotides.
25. The kit of claim 13 , further comprising a solid substrate to which the at least one first nucleic acid primer is bound.
26. The kit of claim 25 , wherein the substrate is a polymer, glass, semiconductor, paper, metal, gel or hydrogel.
27. The kit of claim 25 , wherein the solid substrate is a microarray or microfluidics card.
28. The kit of claim 13 , further comprising a detectable label.
29. A kit for determining the methylation status of at least one CpG dinucleotide, the kit comprising:
at least one first nucleic acid primer at least 8 nucleotides in length that is complementary to a bisulfite-converted nucleic acid sequence comprising a CpG dinucleotide at position 373378 of chromosome 5 within the aryl hydrocarbon receptor repressor (AH RR) gene, and wherein the at least one nucleic acid primer detects either the unmethylated CpG dinucleotide or the methylated CpG dinucleotide; and
a detectable label selected from the group consisting of an enzyme label, a fluorescent label, and a colorimetric label.
30. The kit of claim 29 , further comprising at least one second nucleic acid primer at least 8 nucleotides in length that is complementary to a bisulfite-converted nucleic acid sequence comprising a CpG dinucleotide at position 373378 of chromosome 5 within the AHRR gene, wherein the at least one second nucleic acid primer detects the unmethylated CpG dinucleotide or the methylated CpG dinucleotide, the opposite that is detected by the at least one first nucleic acid primer.
31. The kit of claim 29 , wherein the at least one first nucleic acid primer detects the unmethylated CpG dinucleotide.
32. The kit of claim 29 , wherein the at least one first nucleic acid primer detects the methylated CpG dinucleotide.
33. The kit of claim 30 , wherein the at least one first nucleic acid primer detects the unmethylated CpG dinucleotide and wherein the at least one second nucleic acid primer detects the methylated CpG dinucleotide.
34. The kit of claim 30 , wherein the at least one first nucleic acid primer detects the methylated CpG dinucleotide and wherein the at least one second nucleic acid primer detects the unmethylated CpG dinucleotide.
35. The kit of claim 30 , further comprising at least a third nucleic acid primer at least 8 nucleotides in length that is complementary to a nucleic acid sequence upstream of the CpG dinucleotide at position 373378 of chromosome 5 within the AHRR gene.
36. The kit of claim 30 , further comprising at least a fourth nucleic acid primer at least 8 nucleotides in length that is complementary to a nucleic acid sequence downstream of the CpG dinucleotide at position 373378 of chromosome 5 within the AHRR gene.
37. The kit of claim 35 , wherein the at least third nucleic acid primer is complementary to a bisulfite-converted nucleic acid sequence.
38. The kit of claim 37 , wherein the at least fourth nucleic acid primer is complementary to a bisulfite-converted nucleic acid sequence.
39. The kit of claim 29 , wherein the at least one first nucleic acid primer comprises one or more nucleotide analogs.
40. The kit of claim 29 , wherein the at least one first nucleic acid primer comprises one or more synthetic or non-natural nucleotides.
41. The kit of claim 29 , further comprising a solid substrate to which the at least one first nucleic acid primer is bound.
42. The kit of claim 41 , wherein the substrate is a polymer, glass, semiconductor, paper, metal, gel or hydrogel.
43. The kit of claim 41 , wherein the solid substrate is a microarray or microfluidics card.
44. A kit for determining the methylation status of at least one CpG dinucleotide, the kit comprising:
at least one first nucleic acid primer at least 8 nucleotides in length that is complementary to a bisulfite-converted nucleic acid sequence comprising a CpG dinucleotide at position 373378 of chromosome 5 within the aryl hydrocarbon receptor repressor (AH RR) gene, and wherein the at least one nucleic acid primer detects either the unmethylated CpG dinucleotide or the methylated CpG dinucleotide; and
a solid substrate to which the at least one first nucleic acid primer is bound.
45. The kit of claim 44 , further comprising at least one second nucleic acid primer at least 8 nucleotides in length that is complementary to a bisulfite-converted nucleic acid sequence comprising a CpG dinucleotide at position 373378 of chromosome 5 within the AHRR gene, wherein the at least one second nucleic acid primer detects the unmethylated CpG dinucleotide or the methylated CpG dinucleotide, the opposite that is detected by the at least one first nucleic acid primer.
46. The kit of claim 44 , wherein the at least one first nucleic acid primer detects the unmethylated CpG dinucleotide.
47. The kit of claim 44 , wherein the at least one first nucleic acid primer detects the methylated CpG dinucleotide.
48. The kit of claim 45 , wherein the at least one first nucleic acid primer detects the unmethylated CpG dinucleotide and wherein the at least one second nucleic acid primer detects the methylated CpG dinucleotide.
49. The kit of claim 45 , wherein the at least one first nucleic acid primer detects the methylated CpG dinucleotide and wherein the at least one second nucleic acid primer detects the unmethylated CpG dinucleotide.
50. The kit of claim 45 , further comprising at least a third nucleic acid primer at least 8 nucleotides in length that is complementary to a nucleic acid sequence upstream of the CpG dinucleotide at position 373378 of chromosome 5 within the AHRR gene.
51. The kit of claim 50 , further comprising at least a fourth nucleic acid primer at least 8 nucleotides in length that is complementary to a nucleic acid sequence downstream of the CpG dinucleotide at position 373378 of chromosome 5 within the AHRR gene.
52. The kit of claim 50 , wherein the at least third nucleic acid primer is complementary to a bisulfite-converted nucleic acid sequence.
53. The kit of claim 51 , wherein the at least fourth nucleic acid primer is complementary to a bisulfite-converted nucleic acid sequence.
54. The kit of claim 44 , wherein the at least one first nucleic acid primer comprises one or more nucleotide analogs.
55. The kit of claim 44 , wherein the at least one first nucleic acid primer comprises one or more synthetic or non-natural nucleotides.
56. The kit of claim 44 , wherein the substrate is a polymer, glass, semiconductor, paper, metal, gel or hydrogel.
57. The kit of claim 44 , wherein the solid substrate is a microarray or microfluidics card.
58. The kit of claim 44 , further comprising a detectable label.