Materials and methods for diagnosis of malignant melanoma and prognosis of metastasis of malignant melanoma

Abstract

Methods, probes and kits for diagnosing malignant melanoma and prognosing metastasis thereof in a patient.

What is claimed is: 
     
         1 . A method of prognosing metastasis of malignant melanoma in a patient, which method comprises determining in a sample of malignant melanoma obtained from the patient (i) (a) and/or (b), (ii) (c) and/or (d), (iii) (a) and/or (d), or (iv) (b) and/or (c), wherein:
 (a) is a copy number ratio of CCND1/control centromere or a copy number of CCND1, wherein a copy number ratio of CCND1/control centromere greater than about 1.55 per cell or a copy number of CCND1 greater than about 2.81 per cell indicates that metastasis will likely occur,   (b) is a copy number of MYC, wherein a copy number of MYC greater than about 2.48 per cell indicates that metastasis will likely occur,   (c) is a percentage of cells having a gain of CCND1/control centromere or a percentage of cells having a gain of CCND1, wherein a percentage of cells of greater than or equal to about 30% having a gain of CCND1 or a percentage of cells of greater than or equal to about 54% having a gain of CCND1/control centromere indicates that metastasis will likely occur, and   (d) is a percentage of cells having a gain of MYC, wherein a percentage of cells of greater than about 20% having a gain of MYC indicates that metastasis will likely occur,   whereupon metastasis of malignant melanoma in the patient is prognosticated.   
     
     
         2 . The method of  claim 1 , wherein (a), (b), (c), and (d) are determined by in situ hybridization. 
     
     
         3 . The method of  claim 2 , wherein the in situ hybridization is fluorescent in situ hybridization (FISH). 
     
     
         4 . A method of prognosing metastasis of malignant melanoma in a patient having a melanoma with a Breslow's depth less than about 1 mm, which method comprises determining in a sample of malignant melanoma obtained from the patient a copy number ratio of CCND1/control centromere and a copy number of MYC, wherein a copy number ratio of CCND1/control centromere greater than about 1.55 or a copy number of MYC greater than about 2.48 indicates that metastasis will likely occur, whereupon metastasis of malignant melanoma in a patient having a melanoma with a Breslow's depth less than about 1 mm is prognosticated. 
     
     
         5 . The method of  claim 4 , wherein the copy number ratio is determined by in situ hybridization. 
     
     
         6 . The method of  claim 5 , wherein the in situ hybridization is FISH. 
     
     
         7 . A method of prognosing metastasis of malignant melanoma in a patient having a melanoma with a Breslow's depth less than or equal to 2 mm, which method comprises determining in a sample of malignant melanoma obtained from the patient a copy number ratio of CCND1/control centromere and a copy number of MYC, wherein a copy number ratio of CCND1/control centromere greater than about 1.38 and a copy number of MYC greater than about 2.36 indicates that metastasis will likely occur, whereupon metastasis of malignant melanoma in a patient having a melanoma with a Breslow's depth less than or equal to 2 mm is prognosticated. 
     
     
         8 . The method of  claim 7 , wherein the copy number ratio is determined by in situ hybridization. 
     
     
         9 . The method of  claim 8 , wherein the in situ hybridization is FISH. 
     
     
         10 . A method of prognosing metastasis of malignant melanoma in a patient having a melanoma with a Breslow's depth greater than or equal to 1 mm but less than about 4 mm, which method comprises determining in a sample of malignant melanoma obtained from the patient a copy number ratio of CCND1/control centromere, wherein a copy number ratio of CCND1/control centromere greater than about 1.55 indicates that metastasis will likely occur, whereupon metastasis of malignant melanoma in a patient having a melanoma with a Breslow's depth greater than or equal to 1 mm but less than about 4 mm is prognosticated. 
     
     
         11 . The method of  claim 10 , which further comprises determining in a sample of malignant melanoma obtained from the patient a copy number of MYC, wherein a copy number of MYC greater than about 2.60 also indicates that metastasis will likely occur. 
     
     
         12 . The method of  claim 10 , wherein the copy number ratio is determined by in situ hybridization. 
     
     
         13 . The method of  claim 12 , wherein the in situ hybridization is FISH. 
     
     
         14 . A method of prognosing metastasis of malignant melanoma in a patient having melanoma with a Breslow's depth greater than about 2.0 mm, which method comprises determining in a sample of malignant melanoma obtained from the patient a copy number ratio of CCND1/control centromere or a copy number of MYC, wherein a copy number ratio of CCND1/control centromere greater than about 1.55 or a copy number of MYC greater than about 2.22 indicates that metastasis will likely occur, whereupon metastasis of malignant melanoma in a patient having a melanoma with a Breslow's depth greater than about 2.0 mm is prognosticated. 
     
     
         15 . The method of  claim 14 , wherein the copy number ratio of is determined by in situ hybridization. 
     
     
         16 . The method of  claim 15 , wherein the in situ hybridization is FISH. 
     
     
         17 . A kit comprising (a) a set of one or more probes that enables prognosis of metastasis of malignant melanoma in a patient, wherein the set of one or more probes comprises (i′) a probe for CCND1, alone or in further combination with a probe for a control centromere, and/or (ii′) a probe for MYC, and (b) instructions for prognosing metastasis of malignant melanoma in the patient, wherein the instructions comprise determining in a sample of malignant melanoma obtained from the patient (i) (a) and/or (b), (ii) (c) and/or (d), (iii) (a) and/or (d), or (iv) (b) and/or (c), wherein:
 (a) is a copy number ratio of CCND1/control centromere or a copy number of CCND1, wherein a copy number ratio of CCND1/control centromere greater than about 1.55 per cell or a copy number of CCND1 greater than about 2.81 per cell indicates that metastasis will likely occur, 
 (b) is a copy number of MYC, wherein a copy number of MYC greater than about 2.48 per cell indicates that metastasis will likely occur, 
 (c) is a percentage of cells having a gain of CCND1/control centromere or a percentage of cells having a gain of CCND1, wherein a percentage of cells of greater than or equal to about 30% having a gain of CCND1 or a percentage of cells of greater than or equal to about 54% having a gain of CCND1/control centromere indicates that metastasis will likely occur, and 
 (d) is a percentage of cells having a gain of MYC, wherein a percentage of cells of greater than about 20% having a gain of MYC indicates that metastasis will likely occur. 
 
     
     
         18 . A method of diagnosing malignant melanoma in a patient, which method comprises determining in a number of nuclei in a diagnostic sample, which comprises nucleated cells, obtained from the patient a copy number of RREB1, a copy number of MYC, a copy number of CCND1, and a copy number of CDKN2A, wherein an increase in the copy number of RREB1, an increase in the copy number of MYC, an increase in the copy number of CCND1, and a decrease in the copy number of CDKN2A indicates that the sample comprises a malignant melanoma, whereupon malignant melanoma in a patient is diagnosed. 
     
     
         19 . The method of  claim 18 , wherein the number of nuclei is about 30 and wherein, when increases in copy numbers of RREB1, MYC, and CCND1 and a homozygous deletion of CDKN2A are detected in greater than or equal to 27% of the nuclei, the sample comprises a malignant melanoma. 
     
     
         20 . The method of  claim 18 , wherein the number of nuclei is about 30 and wherein, when increases in copy numbers of RREB1, MYC, and CCND1 and a homozygous deletion of CDKN2A are detected in greater than or equal to 8 nuclei, the sample comprises a malignant melanoma. 
     
     
         21 . A set of probes that enables diagnosis and prognosis of malignant melanoma, wherein the set comprises a probe for RREB1, a probe for MYC, a probe for CCND1, and a probe for CDKN2A. 
     
     
         22 . A kit comprising (a) a set of probes that enables diagnosis and prognosis of malignant melanoma in a patient, wherein the set of probes comprises a probe for RREB1, a probe for MYC, a probe for CCND1, and a probe for CDKN2A, and (b) instructions for diagnosing malignant melanoma in the patient, wherein the instructions comprise determining in a diagnostic sample obtained from the patient a copy number of RREB1, a copy number of MYC, a copy number of CCND1, and a copy number of CDKN2A, wherein an increase in the copy number of RREB1, an increase in the copy number of MYC, an increase in the copy number of CCND1, and a decrease in the copy number of CDKN2A indicates that the patient has malignant melanoma, and/or instructions for prognosing metastasis of malignant melanoma in the patient, wherein the instructions comprise determining in a sample of malignant melanoma obtained from the patient a copy number of RREB1, a copy number of MYC, a copy number of CCND1, and a copy number of CDKN2A, wherein an increase in the copy number of RREB1, an increase in the copy number of MYC, an increase in the copy number of CCND1, and a decrease in the copy number of CDKN2A indicates that metastasis will likely occur. 
     
     
         23 . A method of prognosing metastasis of malignant melanoma in a patient, which method comprises determining in a number of nuclei in a sample, which comprises nucleated cells, obtained from the patient a copy number of RREB1, a copy number of MYC or ZNF217, a copy number of CCND1, and a copy number of CDKN2A, wherein an increase in the copy number of RREB1, an increase in the copy number of MYC or ZNF217, an increase in the copy number of CCND1, and a decrease in the copy number of CDKN2A indicates that metastasis will likely occur, whereupon metastasis of malignant melanoma in a patient is prognosticated. 
     
     
         24 . The method of  claim 23 , wherein the number of nuclei is about 30 and wherein, when increases in copy numbers of RREB1, MYC or ZNF217, and CCND1 and a homozygous deletion of CDKN2A are detected in greater than or equal to 27% of the nuclei, metastasis will likely occur. 
     
     
         25 . The method of  claim 23 , wherein the number of nuclei is about 30 and wherein, when increases in copy numbers of RREB1, MYC or ZNF217, and CCND1 and a homozygous deletion of CDKN2A are detected in greater than or equal to 8 nuclei, metastasis will likely occur. 
     
     
         26 . A set of probes that enables prognosis of metastasis of malignant melanoma, wherein the set comprises a probe for RREB1, a probe for MYC or ZNF217, a probe for CCND1, and a probe for CDKN2A. 
     
     
         27 . A kit comprising (a) a set of probes that enables prognosis of metastasis of malignant melanoma in a patient, wherein the set of probes comprises a probe for RREB1, a probe for MYC or ZNF217, a probe for CCND1, and a probe for CDKN2A, and (b) instructions for prognosing malignant melanoma in the patient, wherein the instructions comprise determining in a sample obtained from the patient a copy number of RREB1, a copy number of MYC or ZNF217, a copy number of CCND1, and a copy number of CDKN2A, wherein an increase in the copy number of RREB1, an increase in the copy number of MYC or ZNF217, an increase in the copy number of CCND1, and a decrease in the copy number of CDKN2A indicates that metastasis will likely occur. 
     
     
         28 . A method of prognosing metastasis of atypical Spitz tumor in a patient, which method comprises determining in a sample of tumor from the patient a copy number of RREB1, CCND1, and/or CDKN2A, wherein an increase in copy number of RREB1 or an increase in copy number of CCND1 or a homozygous deletion of CDKN2A indicates that aggressive metastasis will likely occur and homozygous deletion of CDKN2A indicates that even more aggressive metastasis will likely occur. 
     
     
         29 . A set of probes that enables prognosis of metastasis of atypical Spitz tumor, wherein the probe set comprises a probe for RREB1, a probe for CCND1, and a probe for CDKN2A. 
     
     
         30 . A kit comprising (a) a set of probes that enables prognosis of metastasis of atypical Spitz tumor in a patient, wherein the set of probes comprises a probe for RREB1, a probe for CCND1, and a probe for CDKN2A, and (b) instructions for prognosing metastasis of atypical Spitz tumor in the patient, wherein the instructions comprise determining in a sample of tumor from the patient a copy number of RREB1, CCND1, and/or CDKN2A, wherein an increase in copy number of RREB1 or an increase in copy number of CCND1 or a homozygous deletion of CDKN2A indicates that aggressive metastasis will likely occur and homozygous deletion of CDKN2A indicates that even more aggressive metastasis will likely occur.