Detecting ovarian cancer

1. A method comprising:

treating genomic DNA from a sample from a subject having or suspected of having ovarian cancer with a reagent that modifies DNA in a methylation-specific manner;

amplifying the treated genomic DNA using a set of primers specific for each of CDO1 and SIM2; and

determining a methylation level of at least one differentially methylated region (DMR) in each of CDO1 and SIM2 using polymerase chain reaction (PCR), nucleic acid sequencing, mass spectrometry, restriction enzyme analysis, mass-based separation, and/or target capture.

2. The method of claim 1 , wherein the sample comprises one or more of a plasma sample, a whole blood sample, a leukocyte sample, a serum sample, and/or a tissue sample.

3. The method of claim 1 , wherein:

the at least one DMR in CDO1 is selected from CDO1_A and CDO1_B; and

the at least one DMR in SIM2 is selected from SIM2_A and SIM2_B.

4. The method of claim 1 , further comprising measuring a level of cancer antigen 125 (CA-125) in the sample.

5. The method of claim 1 , wherein the reagent that modifies DNA in a methylation-specific manner is a bisulfite reagent.

6. The method of claim 1 , wherein determining the methylation level of the at least one DMR in each of CDO1 and SIM2 comprises using one or more methods selected from the group consisting of methylation-specific PCR, quantitative methylation-specific PCR, methylation-specific DNA restriction enzyme analysis, quantitative bisulfite pyrosequencing, flap endonuclease assay analysis, PCR-flap assay analysis, and/or bisulfite genomic sequencing PCR.

7. The method of claim 1 , wherein amplifying the treated genomic DNA comprises:

using primers specific for a CpG site in CDO1, wherein the primers specifically bind at least a portion of a genetic region comprising chromosome 5 coordinates 115152022-115152432 or chromosome 5 coordinates 115152466-115152505; and

using primers specific for a CpG site in SIM2, wherein the primers specifically bind at least a portion of a genetic region comprising chromosome 21 coordinates 38076892-38077026 or chromosome 21 coordinates 38076882-38077036.

8. The method of claim 1 , wherein the at least one DMR is present in a coding region or a regulatory region of CDO1 and SIM2.

9. The method of claim 1 , wherein the ovarian cancer is at least one of clear cell ovarian cancer, endometrioid ovarian cancer, mucinous ovarian cancer, and/or serous ovarian cancer.

10. The method of claim 1 , wherein the method further comprises amplifying the treated genomic DNA using a set of primers for one or more genes selected from FAIM2, CAPN2, and/or IFFO1.

11. The method of claim 10 , wherein the one or more genes is FAIM2.

12. The method of claim 10 , wherein the one or more genes is CAPN2.

13. The method of claim 10 , wherein the one or more genes is IFFO1.