Abstract: Methods and systems disclosed herein can improve analysis capabilities of genomic materials. The methods provided herein may examine transcription factor binding site accessibility to diagnose a disease or monitor progression of a disease in a subject.

Abstract: Methods and compositions for diagnosing and prognosing neoplasms, particularly malignant melanomas, and for identifying patients at high risk for melanocytic nevi and/or melanomas or other cancers are provided. Methods for distinguishing between nevi at high and low risk for malignant transformation and for characterizing or classifying lesions or nevi are also disclosed. Assays and kits for prognosis of melanoma in a human subject comprising assessment of BAP1 protein and/or BAP1 nucleic acid are provided.