Compositions and methods for detecting cancer metastasis

1. A method for determining the risk of melanoma metastasis in a subject, the method comprising:

a. collecting a sample comprising a BAP1 nucleic acid from a subject,

b. sequencing the BAP1 nucleic acid from a cell in the sample,

c. detecting the presence of a truncating mutation in the BAP1 nucleic acid, wherein the mutation is selected from the group consisting of:

i) a nonsense mutation selected from the group consisting of Q36X, W196X and Q253X of BAP1;

ii) an insertion or deletion mutation in exon 2, 4, 5, 6, 7, 8, 9, 11, 12, 13 or 17 of BAP1; and

iii) a splice acceptor mutation in exon 16 of BAP1; and

d. identifying the subject as having an increased risk for metastasis when a mutation is detected.

2. The method of claim 1 , wherein the melanoma is uveal melanoma.

3. The method of claim 1 , wherein the sample is a tumor sample.

4. The method of claim 3 , wherein the sample is collected from a primary tumor or from a circulating tumor cell.

5. The method of claim 4 , wherein the circulating tumor cell is collected from a bodily fluid.

6. A method for detecting the presence of metastatic melanoma in a subject, the method comprising:

a. collecting a sample comprising a BAP1 nucleic acid from a subject,

b. sequencing the BAP1 nucleic acid in the sample or analyzing the level of BAP1 activity in the sample by measuring the level of expression of BAP1 mRNA using quantitative RT-PCR, and

c. detecting the presence of a truncating mutation in the BAP1 nucleic acid, wherein the mutation is selected from the group consisting of:

i) a nonsense mutation selected from the group consisting of Q36X, W196X and Q253X of BAP1;

ii) an insertion or deletion mutation in exon 2, 4, 5, 6, 7, 8, 9, 11, 12, 13 or 17 of BAP1; and

iii) a splice acceptor mutation in exon 16 of BAP1;

wherein detection of a mutation indicates the presence of metastatic melanoma, or detecting the level of expression of BAP1 mRNA, wherein detection of a decreased level of expression of BAP1 mRNA compared to a standard indicates the presence of metastatic melanoma in the subject.

7. The method of claim 6 , wherein the melanoma is uveal melanoma.

8. The method of claim 6 , wherein the sample is collected from a primary tumor or a circulating tumor cell.

9. The method of claim 8 , wherein the circulating tumor cell is collected from a bodily fluid.