Prognosis prediction for melanoma cancer
The invention relates to prognostic markers and prognostic signatures, and compositions and methods for determining the prognosis of cancer in a patient, particularly for melanoma. Specifically, the invention relates to the use of genetic and protein markers for the prediction of the risk of progression of a cancer, such as melanoma, based on markers and signatures of markers. In various aspects, the invention provides methods, compositions, kits, and devices based on prognostic cancer markers, specifically melanoma prognostic markers, to aid in the prognosis and treatment of 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 in a melanoma tumor sample from the patient, expression 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 wherein 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( IDH 1)+137.10( MFGE 8)+73.61( PILRA )+211.22( HLA - E )+143.94( TXNDC 5)],
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 (TTP) and overall survival and a qPS score of greater than zero indicates good prognosis with respect to time to progression (TTP) and overall survival.