Compositions and methods for detecting predisposition to a substance use disorder

1. A method for determining that a subject is a user of tobacco comprising:

(a) providing a biological sample from the subject;

(b) contacting DNA from the biological sample with bisulfite under alkaline conditions; and

(c) contacting the bisulfite-treated DNA with at least one first nucleic acid probe at least 8 nucleotides in length and having a sequence that is complementary to an unmethylated and bisulfite-converted nucleotide at position 233284661 of chromosome 2,

wherein binding by the nucleic acid probe to the bisulfite-treated DNA is indicative of the subject's use of tobacco.

2. The method of claim 1 , wherein the biological sample is peripheral blood.

3. The method of claim 1 , wherein the biological sample is predominantly lymphocytes.

4. The method of claim 1 , further comprising contacting the bisulfite-treated DNA with at least one second nucleic acid probe at least 8 nucleotides in length and having a sequence that is complementary to a methylated and not-bisulfite-converted nucleotide at position 233284661 of chromosome 2.

5. The method of claim 4 , further comprising determining the ratio of methylated nucleotides to unmethylated nucleotides at position 233284661 of chromosome 2.

6. The method of claim 1 , further comprising an amplifying step after the contacting step.

7. The method of claim 1 , further comprising a sequencing step after the contacting step.

8. A kit for determining the methylation status of at least one CpG dinucleotide, the kit comprising at least one first nucleic acid probe at least 8 nucleotides in length and having a sequence that is complementary to a sequence comprising an unmethylated and bisulfite-converted nucleotide at position 233284661 of chromosome 2.

9. The kit of claim 8 , further comprising at least one second nucleic acid probe at least 8 nucleotides in length and having a sequence that is complementary to a methylated and not-bisulfite-converted nucleotide at position 233284661 of chromosome 2.

10. The kit of claim 9 , further comprising at least a third nucleic acid probe at least 8 nucleotides in length and having a sequence that is complementary to a nucleic acid sequence upstream of the nucleotide at position 233284661 of chromosome 2.

11. The kit of claim 10 , further comprising at least a fourth nucleic acid probe at least 8 nucleotides in length and having a sequence that is complementary to a nucleic acid sequence downstream of the nucleotide at position 233284661 of chromosome 2.

12. The kit of claim 10 , wherein the at least third nucleic acid probe is complementary to a bisulfate-converted nucleic acid sequence.

13. The kit of claim 11 , wherein the at least fourth nucleic acid probe is complementary to a bisulfate-converted nucleic acid sequence.

14. The kit of claim 8 , wherein the at least one first nucleic acid probe comprises one or more nucleotide analogs.

15. The kit of claim 8 , wherein the at least one first nucleic acid probe comprises one or more synthetic or non-natural nucleotides.

16. The kit of claim 8 , further comprising a solid substrate to which the at least one first nucleic acid probe is bound.

17. The kit of claim 16 , wherein the solid substrate is a polymer, glass, semiconductor, paper, metal, gel or hydrogel.

18. The kit of claim 16 , wherein the solid substrate is a microarray or microfluidics card.

19. The kit of claim 8 , further comprising a detectable label.

20. A kit for determining the methylation status of at least one CpG dinucleotide, the kit comprising at least one first nucleic acid probe at least 8 nucleotides in length and having a sequence that is complementary to a sequence comprising an unmethylated and bisulfite-converted nucleotide at position 233284661 of chromosome 2, wherein the at least one first nucleic acid probe comprises one or more nucleotide analogs or one or more synthetic or non-natural nucleotides.

21. The kit of claim 20 , further comprising at least one second nucleic acid probe at least 8 nucleotides in length and having a sequence that is complementary to a methylated and not-bisulfite-converted nucleotide at position 233284661 of chromosome 2.

22. The kit of claim 21 , further comprising at least a third nucleic acid probe at least 8 nucleotides in length and having a sequence that is complementary to a nucleic acid sequence upstream of the nucleotide at position 233284661 of chromosome 2.

23. The kit of claim 22 , further comprising at least a fourth nucleic acid probe at least 8 nucleotides in length and having a sequence that is complementary to a nucleic acid sequence downstream of the nucleotide at position 233284661 of chromosome 2.

24. The kit of claim 22 , wherein the at least third nucleic acid probe is complementary to a bisulfite-converted nucleic acid sequence.

25. The kit of claim 23 , wherein the at least fourth nucleic acid probe is complementary to a bisulfite-converted nucleic acid sequence.

26. The kit of claim 21 , wherein the at least one second nucleic acid probe comprises one or more nucleotide analogs.

27. The kit of claim 21 , wherein the at least one second nucleic acid probe comprises one or more synthetic or non-natural nucleotides.

28. The kit of claim 20 , further comprising a solid substrate to which the at least one first nucleic acid probe is bound.

29. The kit of claim 28 , wherein the substrate is a polymer, glass, semiconductor, paper, metal, gel or hydrogel.

30. The kit of claim 28 , wherein the solid substrate is a microarray or microfluidics card.

31. The kit of claim 20 , further comprising a detectable label.

32. A kit for determining the methylation status of at least one CpG dinucleotide, the kit comprising at least one first nucleic acid probe at least 8 nucleotides in length and having a sequence that is complementary to a sequence comprising an unmethylated and bisulfite-converted nucleotide at position 233284661 of chromosome 2; and

a detectable label and/or a solid support.

33. The kit of claim 32 , further comprising at least one second nucleic acid probe at least 8 nucleotides in length and having a sequence that is complementary to a methylated and not-bisulfite-converted nucleotide at position 233284661 of chromosome 2.

34. The kit of claim 33 , further comprising at least a third nucleic acid probe at least 8 nucleotides in length and having a sequence that is complementary to a nucleic acid sequence upstream of the nucleotide at position 233284661 of chromosome 2.

35. The kit of claim 34 , further comprising at least a fourth nucleic acid probe at least 8 nucleotides in length and having a sequence that is complementary to a nucleic acid sequence downstream of the nucleotide at position 233284661 of chromosome 2.

36. The kit of claim 34 , wherein the at least third nucleic acid probe is complementary to a bisulfite-converted nucleic acid sequence.

37. The kit of claim 35 , wherein the at least fourth nucleic acid probe is complementary to a bisulfite-converted nucleic acid sequence.

38. The kit of claim 32 , wherein the at least one first nucleic acid probe comprises one or more nucleotide analogs.

39. The kit of claim 32 , wherein the at least one first nucleic acid probe comprises one or more synthetic or non-natural nucleotides.

40. The kit of claim 32 , wherein the solid substrate is a polymer, glass, semiconductor, paper, metal, gel or hydrogel.

41. The kit of claim 40 , wherein the solid substrate is a microarray or microfluidics card.

42. The method of claim 1 , wherein the at least one first nucleic acid probe is at least 10 nucleotides in length.

43. The method of claim 1 , wherein the at least one first nucleic acid probe is at least 15 nucleotides in length.

44. The method of claim 1 , wherein the at least one first nucleic acid probe is at least 20 nucleotides in length.

45. The kit of claim 8 , wherein the at least one first nucleic acid probe is at least 10 nucleotides in length.

46. The kit of claim 8 , wherein the at least one first nucleic acid probe is at least 15 nucleotides in length.

47. The kit of claim 8 , wherein the at least one first nucleic acid probe is at least 20 nucleotides in length.

48. The kit of claim 20 , wherein the at least one first nucleic acid probe is at least 10 nucleotides in length.

49. The kit of claim 20 , wherein the at least one first nucleic acid probe is at least 15 nucleotides in length.

50. The kit of claim 20 , wherein the at least one first nucleic acid probe is at least 20 nucleotides in length.

51. The kit of claim 32 , wherein the at least one first nucleic acid probe is at least 10 nucleotides in length.

52. The kit of claim 32 , wherein the at least one first nucleic acid probe is at least 15 nucleotides in length.

53. The kit of claim 32 , wherein the at least one first nucleic acid probe is at least 20 nucleotides in length.