Devices and methods for prognosis prediction for melanoma cancer

A kit for determining prognosis of melanoma cancer, comprising:

• forward and reverse oligonucleotide primers for each of 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);
• and
• a labeled oligonucleotide probe for each of said genes, said probe being complementary to a portion of said gene encompassed by said forward and reverse primers for each of said genes.

A device for determining prognosis of melanoma in a patient with stage IIIB or stage IIIC cutaneous melanoma after lymphadenectomy, consisting of:

• a substrate having five or more locations thereon, one of which has an oligonucleotide complementary to a mRNA or a cDNA of MFGE8, and each of said other locations has an oligonucleotide thereon complementary to one of the following genes:
• 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).

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 ΔΔCt for isocitrate dehydrogenase 1, MFGE8 means ΔΔCt for milk fat globule EGF factor 8 protein, PILRA means ΔΔCt for paired immunoglobin-like type 2 receptor alpha, HLA-E means ΔΔCt for major histocompatibility complex, class 1E, and TXHDC5 means ΔΔCt 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 MFGE8 is measured using:
• a forward oligonucleotide primer for MFGE8 having the sequence of SEQ ID NO.11;
• a reverse oligonucleotide primer for MFGE8 having the sequence of SEQ ID NO.12;
• and
• a labeled oligonucleotide probe for MFGE8 having a sequence of Genbank No. NM—005928 that is complementary to a portion of the MEGE8 sequence encompassed by said forward primer and said reverse primer.