Molecular malignancy in melanocytic lesions

Abstract

Disclosed are methods for determining whether a melanocyte-containing sample (such as a nevus or other pigmented lesion) is benign or a primary melanoma. These methods can include detecting (at the molecular level, e.g., mRNA, miRNA, or protein) the expression of at least two disclosed genes in a biological sample obtained from a subject. Also provided are arrays and kits that can be used with the methods.

Description

[0001] Cross References to Related Applications

[0002] This application claims priority to US Provisional Application 61 / 663,428, filed June 22, 2012, which is incorporated herein by reference in its entirety. technical field

[0003] The present disclosure relates to biomarkers for characterizing melanocytic lesions as benign or malignant. In particular, the present disclosure relates to the identification of biomarkers (including mRNA and / or miRNA) that are significantly differentially expressed in nevus and primary melanoma samples, clinical prediction algorithms based on the expression of such biomarkers, and Methods and compositions using them.

[0004] Parties to a joint research agreement

[0005] HTG Molecular Diagnosis and the John Wayne Cancer Institute are parties to a joint research agreement governing the invention disclosed herein. Background technique

[0006] Skin cancer is the most common of all cancers in the United States. Melanoma -- cancer that ori...

Examples

preparation example Construction

[0247] Detection can also be accomplished by visual comparison of the extent of enzymatic reaction of the substrate compared to a similarly prepared standard. Exemplary fluorescently labeled compounds include fluorescein isothiocyanate, rhodamine, phycoerythrin, phycocyanin, allophycocyanin, o-phthalaldehyde, Cy3, Cy5, Cy7, tetramethylrhodamine isothiocyanate , Phycoerythrin, Allophycocyanin, Texas Red and Fluorescamine. Fluorescent emitting metals such as 152 Eu, or another metal of the lanthanide series detectably labels the antibody. Other metal compounds that can be conjugated to the antibody include, but are not limited to, ferritin, colloidal gold such as colloidal superparamagnetic beads. These metals can be attached to the antibody using such metal chelating groups as diethylenetriaminepentaacetic acid (DTPA) or ethylenediaminetetraacetic acid (EDTA). The antibodies may also be detectably labeled by coupling them to chemiluminescent compounds. Examples of chemilumi...

Embodiment approach

[0337] The methods described herein can be implemented in a variety of ways, such as those involving classifiers. Several representative, non-limiting embodiments are described below.

[0338] In some method embodiments, gene expression data is input (e.g., manually or automatically) into a computer or other device, machine or device for application of the various algorithms described herein, when collecting and processing large numbers of gene expression data points This is particularly advantageous when . Other embodiments include the use of communication infrastructure, such as the Internet. Various forms of hardware, software, firmware, processors, or combinations thereof can be used to implement particular classifier and method embodiments. The software may be implemented as an application program tangibly embodied on a program storage device or as distinct portions of the software (e.g., as applets) implemented in the user's computing environment and in the inspector's...

Embodiment 1

[0403] Gene selection using discovery sets of clinically characterized skin samples

[0404] Nevus and melanoma cells, like all cells, also expressed a large number of genes, but most of these genes were not associated with these differences between the groups. Therefore, in order to extract useful gene information and reduce the scope, this example describes the initial screening of the expression of more than 2600 mRNA targets to identify the expression in formalin fixed and paraffin embedded (“FFPE”) from Significantly differentially expressed mRNAs in biopsied skin samples from human subjects. Details of the methods used throughout the examples are also described.

[0405] A discovery set of 39 FFPE tissue sections was provided by the John Wayne Cancer Institute Tissue Bank, each section approximately 5um thick, and mounted on glass slides. This set included 14 normal skin samples, 10 nevus samples, 5 primary melanoma samples, and 10 melanoma metastases samples.

[0406...

[0001] Cross References to Related Applications

[0002] This application claims priority to US Provisional Application 61 / 663,428, filed June 22, 2012, which is incorporated herein by reference in its entirety. technical field

[0003] The present disclosure relates to biomarkers for characterizing melanocytic lesions as benign or malignant. In particular, the present disclosure relates to the identification of biomarkers (including mRNA and / or miRNA) that are significantly differentially expressed in nevus and primary melanoma samples, clinical prediction algorithms based on the expression of such biomarkers, and Methods and compositions using them.

[0004] Parties to a joint research agreement

[0005] HTG Molecular Diagnosis and the John Wayne Cancer Institute are parties to a joint research agreement governing the invention disclosed herein. Background technique

[0006] Skin cancer is the most common of all cancers in the United States. Melanoma -- cancer that ori...

Examples

preparation example Construction

[0247] Detection can also be accomplished by visual comparison of the extent of enzymatic reaction of the substrate compared to a similarly prepared standard. Exemplary fluorescently labeled compounds include fluorescein isothiocyanate, rhodamine, phycoerythrin, phycocyanin, allophycocyanin, o-phthalaldehyde, Cy3, Cy5, Cy7, tetramethylrhodamine isothiocyanate , Phycoerythrin, Allophycocyanin, Texas Red and Fluorescamine. Fluorescent emitting metals such as 152 Eu, or another metal of the lanthanide series detectably labels the antibody. Other metal compounds that can be conjugated to the antibody include, but are not limited to, ferritin, colloidal gold such as colloidal superparamagnetic beads. These metals can be attached to the antibody using such metal chelating groups as diethylenetriaminepentaacetic acid (DTPA) or ethylenediaminetetraacetic acid (EDTA). The antibodies may also be detectably labeled by coupling them to chemiluminescent compounds. Examples of chemilumi...

Embodiment approach

[0337] The methods described herein can be implemented in a variety of ways, such as those involving classifiers. Several representative, non-limiting embodiments are described below.

[0338] In some method embodiments, gene expression data is input (e.g., manually or automatically) into a computer or other device, machine or device for application of the various algorithms described herein, when collecting and processing large numbers of gene expression data points This is particularly advantageous when . Other embodiments include the use of communication infrastructure, such as the Internet. Various forms of hardware, software, firmware, processors, or combinations thereof can be used to implement particular classifier and method embodiments. The software may be implemented as an application program tangibly embodied on a program storage device or as distinct portions of the software (e.g., as applets) implemented in the user's computing environment and in the inspector's...

Embodiment 1

[0403] Gene selection using discovery sets of clinically characterized skin samples

[0404] Nevus and melanoma cells, like all cells, also expressed a large number of genes, but most of these genes were not associated with these differences between the groups. Therefore, in order to extract useful gene information and reduce the scope, this example describes the initial screening of the expression of more than 2600 mRNA targets to identify the expression in formalin fixed and paraffin embedded (“FFPE”) from Significantly differentially expressed mRNAs in biopsied skin samples from human subjects. Details of the methods used throughout the examples are also described.

[0405] A discovery set of 39 FFPE tissue sections was provided by the John Wayne Cancer Institute Tissue Bank, each section approximately 5um thick, and mounted on glass slides. This set included 14 normal skin samples, 10 nevus samples, 5 primary melanoma samples, and 10 melanoma metastases samples.

[0406...

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