Hybrid Capture-Based Genomic Profiling Identifies BRAF V600 and Non-V600 Alterations in Melanoma Samples Negative by Prior Testing

Lise Boussemart, Annie Nelson, Michael Wong, Jeffrey S. Ross, Jeffrey Sosman, Janice Mehnert, Gregory Daniels, Kari Kendra, Siraj Mahamed Ali, Vincent A. Miller, Alexa B. Schrock

Research output: Contribution to journalReview article

Abstract

Background: BRAF and MEK inhibitors are approved for BRAF V600-mutated advanced melanoma, with response rates of up to 70%. Responses to targeted therapies have also been observed for diverse non-V600 BRAF alterations. Thus, sensitive, accurate, and broad detection of BRAF alterations is critical to match patients with available targeted therapies. Materials and Methods: Pathology reports were reviewed for 385 consecutive melanoma cases with BRAF mutations or rearrangements identified using a hybrid capture-based next-generation sequencing comprehensive genomic profiling (CGP) assay during the course of clinical care. Results: Records of prior BRAF molecular testing were available for 79 (21%) cases. Of cases with BRAF V600 mutations, 11/57 (19%) with available data were negative by prior BRAF testing. Prior negative BRAF results were also identified in 16/20 (80%) cases with non-V600 mutations, 2 of which harbored multiple BRAF alterations, and in 2/2 (100%) cases with activating BRAF fusions. Clinical outcomes for a subset of patients are presented. Conclusion: CGP identifies diverse activating BRAF alterations in a significant fraction of cases with prior negative testing. Given the proven clinical benefit of BRAF/MEK inhibitors in BRAF-mutated melanoma, CGP should be considered for patients with metastatic melanoma, particularly if other testing is negative. Implications for Practice: Published guidelines for melanoma treatment recommend BRAF mutational analysis, but little guidance is provided as to selection criteria for testing methodologies, or as to clinical implications for non-V600 alterations. This study found that hybrid capture-based next-generation sequencing can detect BRAF alterations in samples from a significant fraction of patients with advanced melanoma with prior negative BRAF results. This study highlights the need for oncologists and pathologists to be critically aware of coverage and sensitivity limitations of various assays, particularly regarding non-V600E alterations, of which many are potentially targetable.

Original languageEnglish (US)
Pages (from-to)657-663
Number of pages7
JournalOncologist
Volume24
Issue number5
DOIs
StatePublished - May 1 2019

Fingerprint

Melanoma
Mitogen-Activated Protein Kinase Kinases
Mutation
Practice Guidelines
Patient Selection
Therapeutics
Pathology

All Science Journal Classification (ASJC) codes

  • Oncology
  • Cancer Research

Keywords

  • BRAF testing
  • Hybrid capture-based genomic profiling
  • Melanoma
  • V600E

Cite this

Boussemart, Lise ; Nelson, Annie ; Wong, Michael ; Ross, Jeffrey S. ; Sosman, Jeffrey ; Mehnert, Janice ; Daniels, Gregory ; Kendra, Kari ; Ali, Siraj Mahamed ; Miller, Vincent A. ; Schrock, Alexa B. / Hybrid Capture-Based Genomic Profiling Identifies BRAF V600 and Non-V600 Alterations in Melanoma Samples Negative by Prior Testing. In: Oncologist. 2019 ; Vol. 24, No. 5. pp. 657-663.
@article{979a055253b84bb984dcbf4d92c80bee,
title = "Hybrid Capture-Based Genomic Profiling Identifies BRAF V600 and Non-V600 Alterations in Melanoma Samples Negative by Prior Testing",
abstract = "Background: BRAF and MEK inhibitors are approved for BRAF V600-mutated advanced melanoma, with response rates of up to 70{\%}. Responses to targeted therapies have also been observed for diverse non-V600 BRAF alterations. Thus, sensitive, accurate, and broad detection of BRAF alterations is critical to match patients with available targeted therapies. Materials and Methods: Pathology reports were reviewed for 385 consecutive melanoma cases with BRAF mutations or rearrangements identified using a hybrid capture-based next-generation sequencing comprehensive genomic profiling (CGP) assay during the course of clinical care. Results: Records of prior BRAF molecular testing were available for 79 (21{\%}) cases. Of cases with BRAF V600 mutations, 11/57 (19{\%}) with available data were negative by prior BRAF testing. Prior negative BRAF results were also identified in 16/20 (80{\%}) cases with non-V600 mutations, 2 of which harbored multiple BRAF alterations, and in 2/2 (100{\%}) cases with activating BRAF fusions. Clinical outcomes for a subset of patients are presented. Conclusion: CGP identifies diverse activating BRAF alterations in a significant fraction of cases with prior negative testing. Given the proven clinical benefit of BRAF/MEK inhibitors in BRAF-mutated melanoma, CGP should be considered for patients with metastatic melanoma, particularly if other testing is negative. Implications for Practice: Published guidelines for melanoma treatment recommend BRAF mutational analysis, but little guidance is provided as to selection criteria for testing methodologies, or as to clinical implications for non-V600 alterations. This study found that hybrid capture-based next-generation sequencing can detect BRAF alterations in samples from a significant fraction of patients with advanced melanoma with prior negative BRAF results. This study highlights the need for oncologists and pathologists to be critically aware of coverage and sensitivity limitations of various assays, particularly regarding non-V600E alterations, of which many are potentially targetable.",
keywords = "BRAF testing, Hybrid capture-based genomic profiling, Melanoma, V600E",
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Boussemart, L, Nelson, A, Wong, M, Ross, JS, Sosman, J, Mehnert, J, Daniels, G, Kendra, K, Ali, SM, Miller, VA & Schrock, AB 2019, 'Hybrid Capture-Based Genomic Profiling Identifies BRAF V600 and Non-V600 Alterations in Melanoma Samples Negative by Prior Testing', Oncologist, vol. 24, no. 5, pp. 657-663. https://doi.org/10.1634/theoncologist.2018-0271

Hybrid Capture-Based Genomic Profiling Identifies BRAF V600 and Non-V600 Alterations in Melanoma Samples Negative by Prior Testing. / Boussemart, Lise; Nelson, Annie; Wong, Michael; Ross, Jeffrey S.; Sosman, Jeffrey; Mehnert, Janice; Daniels, Gregory; Kendra, Kari; Ali, Siraj Mahamed; Miller, Vincent A.; Schrock, Alexa B.

In: Oncologist, Vol. 24, No. 5, 01.05.2019, p. 657-663.

Research output: Contribution to journalReview article

TY - JOUR

T1 - Hybrid Capture-Based Genomic Profiling Identifies BRAF V600 and Non-V600 Alterations in Melanoma Samples Negative by Prior Testing

AU - Boussemart, Lise

AU - Nelson, Annie

AU - Wong, Michael

AU - Ross, Jeffrey S.

AU - Sosman, Jeffrey

AU - Mehnert, Janice

AU - Daniels, Gregory

AU - Kendra, Kari

AU - Ali, Siraj Mahamed

AU - Miller, Vincent A.

AU - Schrock, Alexa B.

PY - 2019/5/1

Y1 - 2019/5/1

N2 - Background: BRAF and MEK inhibitors are approved for BRAF V600-mutated advanced melanoma, with response rates of up to 70%. Responses to targeted therapies have also been observed for diverse non-V600 BRAF alterations. Thus, sensitive, accurate, and broad detection of BRAF alterations is critical to match patients with available targeted therapies. Materials and Methods: Pathology reports were reviewed for 385 consecutive melanoma cases with BRAF mutations or rearrangements identified using a hybrid capture-based next-generation sequencing comprehensive genomic profiling (CGP) assay during the course of clinical care. Results: Records of prior BRAF molecular testing were available for 79 (21%) cases. Of cases with BRAF V600 mutations, 11/57 (19%) with available data were negative by prior BRAF testing. Prior negative BRAF results were also identified in 16/20 (80%) cases with non-V600 mutations, 2 of which harbored multiple BRAF alterations, and in 2/2 (100%) cases with activating BRAF fusions. Clinical outcomes for a subset of patients are presented. Conclusion: CGP identifies diverse activating BRAF alterations in a significant fraction of cases with prior negative testing. Given the proven clinical benefit of BRAF/MEK inhibitors in BRAF-mutated melanoma, CGP should be considered for patients with metastatic melanoma, particularly if other testing is negative. Implications for Practice: Published guidelines for melanoma treatment recommend BRAF mutational analysis, but little guidance is provided as to selection criteria for testing methodologies, or as to clinical implications for non-V600 alterations. This study found that hybrid capture-based next-generation sequencing can detect BRAF alterations in samples from a significant fraction of patients with advanced melanoma with prior negative BRAF results. This study highlights the need for oncologists and pathologists to be critically aware of coverage and sensitivity limitations of various assays, particularly regarding non-V600E alterations, of which many are potentially targetable.

AB - Background: BRAF and MEK inhibitors are approved for BRAF V600-mutated advanced melanoma, with response rates of up to 70%. Responses to targeted therapies have also been observed for diverse non-V600 BRAF alterations. Thus, sensitive, accurate, and broad detection of BRAF alterations is critical to match patients with available targeted therapies. Materials and Methods: Pathology reports were reviewed for 385 consecutive melanoma cases with BRAF mutations or rearrangements identified using a hybrid capture-based next-generation sequencing comprehensive genomic profiling (CGP) assay during the course of clinical care. Results: Records of prior BRAF molecular testing were available for 79 (21%) cases. Of cases with BRAF V600 mutations, 11/57 (19%) with available data were negative by prior BRAF testing. Prior negative BRAF results were also identified in 16/20 (80%) cases with non-V600 mutations, 2 of which harbored multiple BRAF alterations, and in 2/2 (100%) cases with activating BRAF fusions. Clinical outcomes for a subset of patients are presented. Conclusion: CGP identifies diverse activating BRAF alterations in a significant fraction of cases with prior negative testing. Given the proven clinical benefit of BRAF/MEK inhibitors in BRAF-mutated melanoma, CGP should be considered for patients with metastatic melanoma, particularly if other testing is negative. Implications for Practice: Published guidelines for melanoma treatment recommend BRAF mutational analysis, but little guidance is provided as to selection criteria for testing methodologies, or as to clinical implications for non-V600 alterations. This study found that hybrid capture-based next-generation sequencing can detect BRAF alterations in samples from a significant fraction of patients with advanced melanoma with prior negative BRAF results. This study highlights the need for oncologists and pathologists to be critically aware of coverage and sensitivity limitations of various assays, particularly regarding non-V600E alterations, of which many are potentially targetable.

KW - BRAF testing

KW - Hybrid capture-based genomic profiling

KW - Melanoma

KW - V600E

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U2 - 10.1634/theoncologist.2018-0271

DO - 10.1634/theoncologist.2018-0271

M3 - Review article

VL - 24

SP - 657

EP - 663

JO - Oncologist

JF - Oncologist

SN - 1083-7159

IS - 5

ER -