Methods for prognosis prediction for melanoma cancer

1. A method for predicting the prognosis of a melanoma in a patient with stage IIIB or stage IIIC cutaneous melanoma after lymphadenectomy, comprising:

measuring from a tumor sample from said patient, expression of mRNA for the genes:

milk fat globule EGF factor 8 protein (MFGE8);

isocitrate dehydrogenase 1 (NADPH+soluble (IDH1);

paired immunoglobin-like type 2 receptor alpha (PILRA);

major histocompatibility complex class 1E (HLA-E); and

thioredoxin domain containing 5 (TXNDC5); where

said expression of each of said genes from a sample from a patient is determined using qPCR to quantify mRNA expression; and

calculating a score (“qPS”) according to the formula:

qPS=−[1328.15−187.42(IDH1)+137.10(MFGE8)+73.61(PILRA)+211.22(HLA-E)+143.94(TXNDC5)], where in said formula, IDH1 means ΔΔC t for isocitrate dehydrogenase 1, MFGE8 means ΔΔC t for milk fat globule EGF factor 8 protein, PILRA means ΔΔC t for paired immunoglobin-like type 2 receptor alpha, HLA-E means ΔΔC t for major histocompatibility complex, class 1E, and TXHDC5 means ΔΔC t for thioredoxin domain containing 5;

wherein a qPS score of less than zero indicates poor prognosis with respect to time to progression and overall survival and a qPS score of greater than zero indicates good prognosis with respect to time to progression and overall survival; and

where the expression of IDH1 is measured using:

a forward oligonucleotide primer for IDH1 having the sequence of SEQ ID NO. 13, and

a reverse oligonucleotideprimer for IDH1 having the sequence of SEQ ID NO. 14, further comprising measuring from a tumor sample from said patient, expression of mRNA for one or more of the genes:

inosine triphosphatase (nucleoside triphosphatase) (ITPA);

GTP binding protein 2 (GTPBP2);

mitochondrial ribosomal protein S5 (MRPS3);

Kv channel interacting protein 2 (KCNP2);

carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 4 (CHSTA);

human phosphotyrosine independent ligand (OSIL; A170; P62B);

nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, beta (NFKB1B);

mitochondrial carrier homolog 21C, elegans (MTCH2);

ADP-riboslation factor related protein 1 (ARFRP1);

gene similar to tubulin alpha 6; loc143712;

partial n-myc exon 3; and

plexin B2 (PLXNB2).

2. The method of claim 1 , wherein the expression of ITPA is measured using a forward oligonucleotide primer having the sequence of SEQ ID NO. 7 and a reverse oligonucleotide primer having the sequence of SEQ ID NO. 8.

3. The method of claim 1 , wherein the expression of GTPBP2 is measured using a forward oligonucleotide primer having the sequence of SEQ ID NO. 9 and a reverse oligonucleotide primer having the sequence of SEQ ID NO. 10.

4. The method of claim 1 , wherein the expression of MRSP5 is measured using a forward oligonucleotide primer having the sequence of SEQ ID NO. 15, and a reverse oligonucleotide primer having the sequence of SEQ ID NO. 16.

5. The method of claim 1 , wherein expression of KCNP2 is measured using a forward oligonucleotide primer having the sequence of SEQ ID NO. 17, and a reverse oligonucleotide primer having the sequence of SEQ ID NO. 18.

6. The method of claim 1 , wherein expression of CHSTA is measured using a forward oligonucleotide primer having the sequence of SEQ ID NO. 19, and a reverse oligonucleotide primer having the sequence of SEQ ID NO. 20.

7. The method of claim 1 , wherein expression of OSIL is measured using a forward oligonucleotide primer having the sequence of SEQ ID NO. 21, and a reverse oligonucleotide primer having the sequence of SEQ ID NO. 22.

8. The method of claim 1 , wherein expression of NFKB1B is measured using a forward oligonucleotide primer having the sequence of SEQ ID NO. 23, and a reverse oligonucleotide primer having the sequence of SEQ ID NO. 24.

9. The method of claim 1 , wherein expression of MTCH2 is measured using a forward oligonucleotide primer having the sequence of SEQ ID NO. 25, and a reverse oligonucleotide primer having the sequence of SEQ ID NO. 26.

10. The method of claim 1 , wherein expression of ARFRP1 is measured using a forward oligonucleotide primer having the sequence of SEQ ID NO. 27, and a reverse oligonucleotide primer having the sequence of SEQ ID NO. 28.

11. The method of claim 1 , wherein expression of gene similar to tubulin alpha 6; loc143712 is measured using a forward oligonucleotide primer having the sequence of SEQ ID NO. 29, and a reverse oligonucleotide primer having the sequence of SEQ ID NO. 30.

12. The method of claim 1 , wherein expression of partial n-myc exon 3 is measured using a forward oligonucleotide primer having the sequence of SEQ ID NO. 31, and a reverse oligonucleotide primer having the sequence of SEQ ID NO. 32.

13. The method of claim 1 , wherein expression of PLXNB2 is measured using a forward oligonucleotide primer having the sequence of SEQ ID NO. 33, and a reverse oligonucleotide primer having the sequence of SEQ ID NO. 34.

14. The method of claim 1 , wherein the expression of MFGE8 is measured using:

a forward oligonucleotide primer for MFGE8 having the sequence of SEQ ID NO. 11; and

a reverse oligonucleotide primer for MFGE8 having the sequence of SEQ ID NO. 12.

15. The method of claim 1 , wherein the expression of PILRA is measured using:

a forward oligonucleotide primer for PILRA having the sequence of SEQ ID NO. 3, and a reverse oligonucleotide primer for PILRA having the sequence of SEQ ID NO. 4.

16. The method of claim 1 , wherein the expression of HLA-E is measured using:

a forward oligonucleotide primer for HLA-E having the sequence of SEQ ID NO. 5, and

a reverse oligonucleotide primer for HLA-E having the sequence of SEQ ID NO. 6.

17. The method of claim 1 , wherein the expression of TXNDC5 is measured using:

a forward oligonucleotide primer for TXNDC5 having the sequence of SEQ ID NO. 1, and

a reverse oligonucleotide primer for TXNDC5 having the sequence of SEQ ID NO. 2.

18. The method of claim 1 , said tumor sample taken from a OTC fixed, frozen preparation from said patient.