High throughput mass spectrometry-based mutation profiling of primary uveal melanoma

Anthony B. Daniels, Joo Eun Lee, Laura E. MacConaill, Emanuele Palescandolo, Paul Van Hummelen, Scott M. Adams, Margaret M. DeAngelis, William C. Hahn, Evangelos S. Gragoudas, J. William Harbour, Levi A. Garraway, Ivana K. Kim

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Abstract

Purpose. We assessed for mutations in a large number of oncogenes and tumor suppressor genes in primary uveal melanomas using a high-throughput profiling system. Methods. DNA was extracted and purified from 134 tissue samples from fresh-frozen tissues (n = 87) or formalin-fixed, paraffin-embedded tissues (n = 47) from 124 large uveal melanomas that underwent primary treatment by enucleation. DNA was subjected to whole genome amplification and MALDI-TOF mass spectrometry-based mutation profiling (>1000 mutations tested across 120 oncogenes and tumor suppressor genes) using the OncoMap3 platform. All candidate mutations, as well as commonly occurring mutations in GNAQ and GNA11, were validated using homogeneous mass extension (hME) technology. Results. Of 123 samples, 97 (79%, representing 89 unique tumors) were amplified successfully, passed all quality control steps, and were assayed with the OncoMap platform. A total of 58 mutation calls was made for 49 different mutations across 26 different genes in 34/98 (35%) samples. Of 91 tumors that underwent hME validation, 83 (91%) harbored mutations in the GNAQ (47%) or GNA11 (44%) genes, while hME validation revealed two tumors with mutations in EGFR. These additional mutations occurred in tumors that also had mutations in GNAQ or GNA11. Conclusions. The vast majority of primary large uveal melanomas harbor mutually-exclusive mutations in GNAQ or GNA11, but very rarely have the oncogenic mutations that are reported commonly in other cancers. When present, these other mutations were found in conjunction with GNAQ/GNA11 mutations, suggesting that these other mutations likely are not the primary drivers of oncogenesis in uveal melanoma.

Original languageEnglish (US)
Pages (from-to)6991-6996
Number of pages6
JournalInvestigative Ophthalmology and Visual Science
Volume53
Issue number11
DOIs
StatePublished - Oct 1 2012

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ASJC Scopus subject areas

  • Ophthalmology
  • Sensory Systems
  • Cellular and Molecular Neuroscience

Cite this

Daniels, A. B., Lee, J. E., MacConaill, L. E., Palescandolo, E., Van Hummelen, P., Adams, S. M., DeAngelis, M. M., Hahn, W. C., Gragoudas, E. S., William Harbour, J., Garraway, L. A., & Kim, I. K. (2012). High throughput mass spectrometry-based mutation profiling of primary uveal melanoma. Investigative Ophthalmology and Visual Science, 53(11), 6991-6996. https://doi.org/10.1167/iovs.12-10427