Diagnostic test for predicting metastasis and recurrence in cutaneous melanoma

Abstract

The invention as disclosed herein in encompasses a method for predicting the risk of metastasis of a primary cutaneous melanoma tumor, the method encompassing measuring the gene-expression levels of at least eight genes selected from a specific gene set in a sample taken from the primary cutaneous melanoma tumor; determining a gene-expression profile signature from the gene expression levels of the at least eight genes; comparing the gene-expression profile to the gene-expression profile of a predictive training set; and providing an indication as to whether the primary cutaneous melanoma tumor is a certain class of metastasis or treatment risk when the gene expression profile indicates that expression levels of at least eight genes are altered in a predictive manner as compared to the gene expression profile of the predictive training set.

1 . A method for predicting the risk of metastasis of a primary cutaneous melanoma tumor in a patient, the method comprising:
 (a) obtaining a primary cutaneous melanoma tumor sample from the patient;   (b) determining expression levels of genes in a gene set, wherein the expression levels of the genes in the gene set are determined by measuring a level of fluorescence by a sequence detection system following RT-PCR, and wherein the gene set comprises the genes:
 (1) BAP1_var1, BAP1_var2, MGP, SPP1, CXCL14, CLCA2, S100A8, BTG1, SAP130, ARG1, KRT6B, GJA, ID2, EIF1B, S100A9, CRABP2, KRT14, ROBO1, RBM23, TACSTD2, DSC1, SPRR1B, TRIM29, AQP3, TYRP1, PPL, LTA4H, and CST6; 
 (2) KRT6B, GJA1, AQP3, TRIM29, TYRP1, RBM23, MGP and EIF1B; 
 (3) SAP130, ARG1, KRT6B, EIF1B, S100A9, KRT14, ROBOT, RBM23, TRIM29, AQP3, TYRP1 and CST6; 
 (4) GJA1, PPL, ROBOT, MGP, TRIM29, AQP3, RBM23, TACSTD2, TYRP1, KRT6B, EIF1B and DSC1; 
 (5) CRABP2, TYRP1, PPL, EIF1B, SPRR1B, DSC1, GJA1, AQP3, MGP, RBM23, CLCA2 and TRIM29; 
 (6) RBM23, TACSTD2, CRABP2, PPL, GJA1, SPP1, CXCL14, EIF1B, AQP3, MGP, LTA4H and KRT6B; 
 (7) S100A8, TACSTD2, BAP1_var1, KRT6B, EIF1B, TRIM29, TYRP1, CST6, PPL, RBM23, AQP3, GJA1, SPRR1B and ARG1; or 
 (8) CST6, KRT6B, LTA4H, CLCA2, CRABP2, TRIM29, CXCL14, PPL, ARG1, RBM23, GJA1, AQP3, TYRP1, SPP1, DSC1, TACSTD2, EIF1B, and BAP1_var1; 
   (c) determining a gene-expression profile comprising the expression levels of the genes in the gene set;   (d) comparing the gene-expression profile for the gene set to the gene-expression profile of a predictive training set; and   (e) providing an indication as to whether the primary cutaneous melanoma tumor is class 1 or class 2 of metastasis when the gene-expression profile for the gene set indicates that expression levels of the genes in the gene set are altered in a predictive manner as compared to the gene-expression profile of the predictive training set.   
     
     
         2 . The method of  claim 1 , wherein the cutaneous melanoma tumor sample is obtained from a formalin-fixed, paraffin embedded wide local excision sample. 
     
     
         3 . The method of  claim 1 , wherein the cutaneous melanoma tumor sample is obtained from formalin-fixed, paraffin embedded punch biopsy sample. 
     
     
         4 . A method for predicting the risk of metastasis of a primary cutaneous melanoma tumor in a patient, the method comprising:
 (a) obtaining a primary cutaneous melanoma tumor sample from the patient;   (b) determining expression levels of genes in a gene set, wherein the expression levels of the genes in the gene set are determined by measuring a level of fluorescence by a sequence detection system following RT-PCR, and wherein the gene set comprises the genes:
 (1) BAP1_var1, BAP1_var2, MGP, SPP1, CXCL14, CLCA2, S100A8, BTG1, SAP130, ARG1, KRT6B, GJA, ID2, EIF1B, S100A9, CRABP2, KRT14, ROBO1, RBM23, TACSTD2, DSC1, SPRR1B, TRIM29, AQP3, TYRP1, PPL, LTA4H, and CST6; 
 (2) KRT6B, GJA1, AQP3, TRIM29, TYRP1, RBM23, MGP and EIF1B; 
 (3) SAP130, ARG1, KRT6B, EIF1B, S100A9, KRT14, ROBOT, RBM23, TRIM29, AQP3, TYRP1 and CST6; 
 (4) GJA1, PPL, ROBOT, MGP, TRIM29, AQP3, RBM23, TACSTD2, TYRP1, KRT6B, EIF1B and DSC1; 
 (5) CRABP2, TYRP1, PPL, EIF1B, SPRR1B, DSC1, GJA1, AQP3, MGP, RBM23, CLCA2 and TRIM29; 
 (6) RBM23, TACSTD2, CRABP2, PPL, GJA1, SPP1, CXCL14, EIF1B, AQP3, MGP, LTA4H and KRT6B; 
 (7) S100A8, TACSTD2, BAP1_var1, KRT6B, EIF1B, TRIM29, TYRP1, CST6, PPL, RBM23, AQP3, GJA1, SPRR1B and ARG1; or 
 (8) CST6, KRT6B, LTA4H, CLCA2, CRABP2, TRIM29, CXCL14, PPL, ARG1, RBM23, GJA1, AQP3, TYRP1, SPP1, DSC1, TACSTD2, EIF1B, and BAP1_var1; 
   (c) determining a gene-expression profile comprising the expression levels of the genes in the gene set;   (d) comparing the gene-expression profile for the gene set to the gene-expression profile of a predictive training set; and   (e) providing an indication as to whether the primary cutaneous melanoma tumor is class A, class B, or class C of metastasis when the gene expression profile for the gene set indicates that expression levels of the genes in the gene set are altered in a predictive manner as compared to the gene-expression profile of the predictive training set.   
     
     
         5 . The method of  claim 4 , wherein the cutaneous melanoma tumor sample is obtained from a formalin-fixed, paraffin embedded wide local excision sample. 
     
     
         6 . The method of  claim 4 , wherein the cutaneous melanoma tumor sample is obtained from formalin-fixed, paraffin embedded punch biopsy sample. 
     
     
         7 . A method for predicting the risk of metastasis of a primary cutaneous melanoma tumor in a patient, the method comprising:
 (a) obtaining a primary cutaneous melanoma tumor sample from the patient;   (b) determining the expression levels of genes in a gene set, wherein the expression levels of the genes in the gene set are determined by measuring a level of fluorescence by a sequence detection system following RT-PCR, and wherein the gene set comprises the genes:
 (1) BAP1_var1, BAP1_var2, MGP, SPP1, CXCL14, CLCA2, S100A8, BTG1, SAP130, ARG1, KRT6B, GJA, ID2, EIF1B, S100A9, CRABP2, KRT14, ROBO1, RBM23, TACSTD2, DSC1, SPRR1B, TRIM29, AQP3, TYRP1, PPL, LTA4H, and CST6; 
 (2) KRT6B, GJA1, AQP3, TRIM29, TYRP1, RBM23, MGP and EIF1B; 
 (3) SAP130, ARG1, KRT6B, EIF1B, S100A9, KRT14, ROBO1, RBM23, TRIM29, AQP3, TYRP1 and CST6; 
 (4) GJA1, PPL, ROBO1, MGP, TRIM29, AQP3, RBM23, TACSTD2, TYRP1, KRT6B, EIF1B and DSC1; 
 (5) CRABP2, TYRP1, PPL, EIF1B, SPRR1B, DSC1, GJA1, AQP3, MGP, RBM23, CLCA2 and TRIM29; 
 (6) RBM23, TACSTD2, CRABP2, PPL, GJA1, SPP1, CXCL14, EIF1B, AQP3, MGP, LTA4H and KRT6B; 
 (7) S100A8, TACSTD2, BAP1_var1, KRT6B, EIF1B, TRIM29, TYRP1, CST6, PPL, RBM23, AQP3, GJA1, SPRR1B and ARG1; or 
 (8) CST6, KRT6B, LTA4H, CLCA2, CRABP2, TRIM29, CXCL14, PPL, ARG1, RBM23, GJA1, AQP3, TYRP1, SPP1, DSC1, TACSTD2, EIF1B, and BAP1_var1; 
   (c) determining a gene-expression profile comprising the expression levels of the genes in the gene set;   (d) comparing the gene-expression profile for the gene set to the gene-expression profile of a predictive training set; and   (e) providing an indication as to whether the primary cutaneous melanoma tumor has a low risk to high of metastasis when the gene-expression profile for the gene set indicates that expression levels of the genes in the gene set are altered in a predictive manner as compared to the gene expression profile of the predictive training set.   
     
     
         8 . The method of  claim 7 , wherein the cutaneous melanoma tumor sample is obtained from a formalin-fixed, paraffin embedded wide local excision sample. 
     
     
         9 . The method of  claim 7 , wherein the cutaneous melanoma tumor sample is obtained from formalin-fixed, paraffin embedded punch biopsy sample.