Routine multiplex mutational profiling of melanomas enables enrollment in genotype-driven therapeutic trials

Christine M. Lovly, Kimberly Brown Dahlman, Laurel E. Fohn, Zengliu Su, Dora Dias-Santagata, Donna J. Hicks, Donald Hucks, Elizabeth Berry, Charles Terry, Mar Keesa Duke, Yingjun Su, Tammy Sobolik-Delmaire, Ann Richmond, Mark C. Kelley, Cindy L. Vnencak-Jones, A. John Iafrate, Jeffrey Sosman, William Pao

Research output: Contribution to journalArticle

133 Citations (Scopus)

Abstract

Purpose: Knowledge of tumor mutation status is becoming increasingly important for the treatment of cancer, as mutation-specific inhibitors are being developed for clinical use that target only sub-populations of patients with particular tumor genotypes. Melanoma provides a recent example of this paradigm. We report here development, validation, and implementation of an assay designed to simultaneously detect 43 common somatic point mutations in 6 genes (BRAF, NRAS, KIT, GNAQ, GNA11, and CTNNB1) potentially relevant to existing and emerging targeted therapies specifically in melanoma. Methods: The test utilizes the SNaPshot method (multiplex PCR, multiplex primer extension, and capillary electrophoresis) and can be performed rapidly with high sensitivity (requiring 5-10% mutant allele frequency) and minimal amounts of DNA (10-20 nanograms). The assay was validated using cell lines, fresh-frozen tissue, and formalin-fixed paraffin embedded tissue. Clinical characteristics and the impact on clinical trial enrollment were then assessed for the first 150 melanoma patients whose tumors were genotyped in the Vanderbilt molecular diagnostics lab. Results: Directing this test to a single disease, 90 of 150 (60%) melanomas from sites throughout the body harbored a mutation tested, including 57, 23, 6, 3, and 2 mutations in BRAF, NRAS, GNAQ, KIT, and CTNNB1, respectively. Among BRAF V600 mutations, 79%, 12%, 5%, and 4% were V600E, V600K, V600R, and V600M, respectively. 23 of 54 (43%) patients with mutation harboring metastatic disease were subsequently enrolled in genotype-driven trials. Conclusion: We present development of a simple mutational profiling screen for clinically relevant mutations in melanoma. Adoption of this genetically-informed approach to the treatment of melanoma has already had an impact on clinical trial enrollment and prioritization of therapy for patients with the disease.

Original languageEnglish (US)
Article numbere35309
JournalPloS one
Volume7
Issue number4
DOIs
StatePublished - Apr 20 2012
Externally publishedYes

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melanoma
Tumors
Melanoma
Genotype
mutation
therapeutics
Mutation
genotype
Assays
Tissue
Capillary electrophoresis
neoplasms
Paraffin
Formaldehyde
Therapeutics
Genes
Cells
clinical trials
Neoplasms
Clinical Trials

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

Lovly, C. M., Dahlman, K. B., Fohn, L. E., Su, Z., Dias-Santagata, D., Hicks, D. J., ... Pao, W. (2012). Routine multiplex mutational profiling of melanomas enables enrollment in genotype-driven therapeutic trials. PloS one, 7(4), [e35309]. https://doi.org/10.1371/journal.pone.0035309

Routine multiplex mutational profiling of melanomas enables enrollment in genotype-driven therapeutic trials. / Lovly, Christine M.; Dahlman, Kimberly Brown; Fohn, Laurel E.; Su, Zengliu; Dias-Santagata, Dora; Hicks, Donna J.; Hucks, Donald; Berry, Elizabeth; Terry, Charles; Duke, Mar Keesa; Su, Yingjun; Sobolik-Delmaire, Tammy; Richmond, Ann; Kelley, Mark C.; Vnencak-Jones, Cindy L.; Iafrate, A. John; Sosman, Jeffrey; Pao, William.

In: PloS one, Vol. 7, No. 4, e35309, 20.04.2012.

Research output: Contribution to journalArticle

Lovly, CM, Dahlman, KB, Fohn, LE, Su, Z, Dias-Santagata, D, Hicks, DJ, Hucks, D, Berry, E, Terry, C, Duke, MK, Su, Y, Sobolik-Delmaire, T, Richmond, A, Kelley, MC, Vnencak-Jones, CL, Iafrate, AJ, Sosman, J & Pao, W 2012, 'Routine multiplex mutational profiling of melanomas enables enrollment in genotype-driven therapeutic trials', PloS one, vol. 7, no. 4, e35309. https://doi.org/10.1371/journal.pone.0035309
Lovly, Christine M. ; Dahlman, Kimberly Brown ; Fohn, Laurel E. ; Su, Zengliu ; Dias-Santagata, Dora ; Hicks, Donna J. ; Hucks, Donald ; Berry, Elizabeth ; Terry, Charles ; Duke, Mar Keesa ; Su, Yingjun ; Sobolik-Delmaire, Tammy ; Richmond, Ann ; Kelley, Mark C. ; Vnencak-Jones, Cindy L. ; Iafrate, A. John ; Sosman, Jeffrey ; Pao, William. / Routine multiplex mutational profiling of melanomas enables enrollment in genotype-driven therapeutic trials. In: PloS one. 2012 ; Vol. 7, No. 4.
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abstract = "Purpose: Knowledge of tumor mutation status is becoming increasingly important for the treatment of cancer, as mutation-specific inhibitors are being developed for clinical use that target only sub-populations of patients with particular tumor genotypes. Melanoma provides a recent example of this paradigm. We report here development, validation, and implementation of an assay designed to simultaneously detect 43 common somatic point mutations in 6 genes (BRAF, NRAS, KIT, GNAQ, GNA11, and CTNNB1) potentially relevant to existing and emerging targeted therapies specifically in melanoma. Methods: The test utilizes the SNaPshot method (multiplex PCR, multiplex primer extension, and capillary electrophoresis) and can be performed rapidly with high sensitivity (requiring 5-10{\%} mutant allele frequency) and minimal amounts of DNA (10-20 nanograms). The assay was validated using cell lines, fresh-frozen tissue, and formalin-fixed paraffin embedded tissue. Clinical characteristics and the impact on clinical trial enrollment were then assessed for the first 150 melanoma patients whose tumors were genotyped in the Vanderbilt molecular diagnostics lab. Results: Directing this test to a single disease, 90 of 150 (60{\%}) melanomas from sites throughout the body harbored a mutation tested, including 57, 23, 6, 3, and 2 mutations in BRAF, NRAS, GNAQ, KIT, and CTNNB1, respectively. Among BRAF V600 mutations, 79{\%}, 12{\%}, 5{\%}, and 4{\%} were V600E, V600K, V600R, and V600M, respectively. 23 of 54 (43{\%}) patients with mutation harboring metastatic disease were subsequently enrolled in genotype-driven trials. Conclusion: We present development of a simple mutational profiling screen for clinically relevant mutations in melanoma. Adoption of this genetically-informed approach to the treatment of melanoma has already had an impact on clinical trial enrollment and prioritization of therapy for patients with the disease.",
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AU - Dias-Santagata, Dora

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AU - Sobolik-Delmaire, Tammy

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