Methods of preparing dual-indexed DNA libraries for bisulfite conversion sequencing

1. A method of determining a methylation profile of an individual comprising:

a) obtaining a biological sample from the individual;

b) converting an unmethylated cytosine to a uracil in a nucleic acid molecule of the biological sample, thereby producing a converted nucleic acid molecule, wherein the converted nucleic acid molecule is single stranded and has a converted nucleic acid sequence;

c) ligating, with a ligase, a single stranded nucleic acid adapter comprising a unique molecular identifier to the converted nucleic acid molecule, thereby producing a single stranded adapter ligated product comprising the converted nucleic acid molecule;

d) annealing a primer to the single stranded nucleic acid adapter in the single stranded adapter ligated product and extending the primer to form a double stranded complex comprising the single stranded adapter ligated product and an extension product;

e) ligating an at least partially double-stranded nucleic acid adapter to a 3′ end of the extension product, wherein the ligating the at least partially double-stranded nucleic acid adapter to the 3′ end of the extension product creates a gap between a 5′ end of the converted nucleic acid molecule and a 3′ end of one strand of the at least partially double-stranded adapter that is not ligated to the extension product;

f) amplifying the double stranded complex comprising the single stranded adapter ligated product, the extension product, and the at least partially double stranded nucleic acid adapter that is ligated to the 3′ end of the extension product, wherein the strand of the double stranded complex comprising the gap is not amplified during the amplifying step;

g) determining the converted nucleic acid sequence of the converted nucleic acid molecule of the single stranded adapter ligated product or amplification products thereof; and

h) comparing the converted nucleic acid sequence to a reference nucleic acid sequence to determine the methylation profile of the individual.

2. The method of claim 1 , wherein the biological sample comprises blood, serum, plasma, urine, cerebral spinal fluid, or lymph.

3. The method of claim 1 , further comprising enriching the converted nucleic acid molecule.

4. The method of claim 1 , wherein the converting an unmethylated cytosine to a uracil comprises incubation of the nucleic acid molecule with bisulfite ion.

5. The method of claim 1 , wherein the converting an unmethylated cytosine to a uracil comprises incubation of the nucleic acid molecule with a cytidine deaminase.

6. The method of claim 1 , wherein the nucleic acid molecule is DNA.

7. The method of claim 6 , wherein the DNA is cell-free DNA (cfDNA).

8. The method of claim 1 , wherein the single stranded nucleic acid adapter comprises a universal priming site.

9. The method of claim 1 , wherein the single stranded nucleic acid adapter is attached to a solid support.

10. The method of claim 1 , wherein the amplifying results in addition of sequencing adapters to the converted nucleic acid molecule or amplification products thereof.

11. The method of claim 1 , further comprising determining the methylation profile, wherein the methylation profile is used to screen for or diagnose cancer.

12. The method of claim 1 , further comprising determining the methylation profile, wherein the methylation profile is used to determine a tissue or origin of a cell-free DNA.

13. The method of claim 1 , wherein the ligase is an RNA ligase.

14. The method of claim 8 , wherein the single stranded nucleic acid adapter is ligated to a 3′ end of the converted nucleic acid molecule, and the single stranded adapter ligated product comprises the universal priming site.

15. The method of claim 14 , wherein the primer of step (d) binds to the universal priming site.