University of California

Leland Stanford Junior University

The University of British Columbia

Abbott Molecular Inc.

Boris C Bastian

Daniel Pinkel

Catherine D Van Raamsdonk

Gregory S Barsh

Larry E Morrison

Susan S Jewell

John A Curtin

The present invention is based on the discovery of methods and combinations of probes to chromosomal regions that are gained or lost or imbalanced in melanoma that provide highly specific and sensitive assays for the detection of melanoma cells.

Methods and probe combinations for detecting melanoma

The present invention provides methods of detecting c-KIT-dependent-melanoma for diagnostic and prognostic purposes. The invention further provides methods of treating such melanoma by inhibiting c-KIT.

C-kit oncogene mutations in melanoma

This invention provides methods of detecting melanoma. The methods comprises detecting a gain or loss of certain chromosomal regions that undergo copy number changes in melanoma.

Detection of chromosomal region copy number changes to diagnose melanoma

The present invention provides methods of detecting mutations in a GNA11 gene in a melanocytic neoplasm for diagnostic and prognostic purposes. The invention further provides methods of treating such melanocytic neoplasm by modulating the activity of the mutated GNA11 gene.

GNA11 mutations in melanoma

The present invention provides methods of detecting mutations in a Gnaq gene in a melanocytic neoplasm for diagnostic and prognostic purposes. The invention further provides methods of treating such melanocytic neoplasm by modulating the activity of the mutated Gnaq gene.

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The present invention provides methods of screening for the presence of premalignant melanocytes in a sample from a patient. The methods comprise contacting a nucleic acid sample from a biological sample from the patient with a probe which binds selectively to a target polynucleotide sequence on a chromosomal region which is amplified in melanoma cells.

Method of screening for melanoma by detecting an increase in cyclin D1

The invention provides methods of distinguishing benign growths arising from congenital melanocytic nevi from malignant melanoma. The methods comprise detecting a change in chromosome number that is specifically associated with benign growths. These changes include a gain of chromosome 10, a gain of chromosome 11, and a loss of chromosome 7.

Genetic changes in atypical nodular proliferations in congenital melanocytic nevi

The present invention provides for methods of typing a melanocytic neoplasm, in particular for classifying a Spitz nevus. The methods comprise detecting in a tumor sample the presence of an increase in copy number of the whole chromosome 11p arm, particularly the presence of an 11p isochromosome, which is associated with the presence of a Spitz nevus. The invention further provides methods of typing a melanocytic neoplasm by detecting the presence of a mutated H-RAS gene, which is also associated with the presence of a Spitz nevus.

Detection of gene mutations or amplifications in melanocytic neoplasms

Detection of premalignant melanocytes

The present invention provides for methods of distinguishing melanocytic nevi, such as Spitz nevi, from malignant melanoma. The methods comprise contacting a nucleic acid sample from a patient with a probe which binds selectively to a target polynucleotide sequence on a chromosomal region such as 11p, which is usually amplified in Spitz nevi. The nucleic acid sample is typically from skin tumor cells located within a tumor lesion on the skin of the patient. Using another probe which binds selectively to a chromosomal region such as 1q, 6p, 7p, 9p, or 10q, which usually show altered copy number in melanoma, the method can determine that those tumor cells with no changes in copy number of 1q, 6p, 7p, 9p, or 10q, are not melanoma cells but rather Spitz nevus cells. The finding of amplifications of chromosome 11p would be an additional indication of Spitz nevus.

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Mill Valley, CA, United States of America

Boris C Bastian