Molecular profiling of metastatic uveal melanoma

Study ID Alternative Stable ID Type
EGAS00001004296 Other

Study Description

Metastatic uveal melanoma is less well understood than its primary counterpart, has a distinct biology compared to skin melanoma and lacks effective treatments. Here we genomically profile metastatic tumors and infiltrating lymphocytes. BAP1 alterations were overrepresented and occurred in 29/32 of cases. An outlier tumor had high mutational burden associated with UV-damage. CDKN2A deletions also occurred, which are rarely present in primaries. We profiled recurrent copy number alterations associated with metastasis and performed a focused knockdown screen on overexpressed targets. We investigated the role of BAP1 by reintroducing a functional allele into a deficient patient-derived cell line, revealing a broad shift towards a transcriptomic subtype associated with better prognosis. Tumor-infiltrating lymphocytes were in several cases tumor-reactive, but expression of the immune checkpoint receptors TIM-3, TIGIT and LAG3 was abundant. This study represents the largest whole-genome analysis of uveal melanoma to date and presents an updated view of the metastatic disease.

Study Datasets 1 dataset.

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Dataset ID Description Technology Samples
Whole genome, exome and RNA sequencing of uveal melanoma metastases, primary tumors and matched normal DNA.
HiSeq X Ten,Illumina HiSeq 2500,Illumina NovaSeq 6000,NextSeq 500 240

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