Clinical mutational profiling and categorization of BRAF mutations in melanomas using next generation sequencing

Parvez M Lokhandwala,Christopher D Gocke,James R Eshleman,Ming-Tseh Lin,Erika Rodriguez,Li-Hui Tseng,Aparna Pallavajjalla,Gang Zheng

doi:10.1186/s12885-019-5864-1

Parvez M Lokhandwala, Christopher D Gocke + Show 6 more

Open Access

https://doi.org/10.1186/s12885-019-5864-1

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Abstract

BackgroundAnalysis of melanomas for actionable mutations has become the standard of care. Recently, a classification scheme has been proposed that categorizes BRAF mutations based on their mechanisms for activation of the MAPK pathway.MethodsIn this analysis BRAF, KIT, NRAS, and PIK3CA mutations were examined by next generation sequencing (NGS) in 446 melanomas in a clinical diagnostic setting. KRAS and HRAS were also analyzed to elucidate coexisting BRAF and RAS mutations. BRAF mutations were categorized into class-1 (kinase-activated, codon 600), class-2 (kinase-activated, non-codon 600) and class-3 (kinase-impaired), based on the newly proposed classification scheme.ResultsNGS demonstrated high analytic sensitivity. Among 355 mutations detected, variant allele frequencies were 2–5% in 21 (5.9%) mutations and 2–10% in 47 (13%) mutations. Mutations were detected in BRAF (42%), NRAS (25%), KIT (4.9%) and PIK3CA (2.7%). The incidence of class-1, class-2 and class-3 mutations were 33% (26% p.V600E and 6.1% p.V600K), 3.1 and 4.9% respectively. With a broader reportable range of NGS, class-1, class-2 and class-3 mutations accounted for 77, 7.4 and 12% of all BRAF mutations. Class-3 mutations, commonly affecting codons 594, 466 and 467, showed a higher incidence of coexisting RAS mutations, consistent with their RAS-dependent signaling. Significant association with old age and primary tumors of head/neck/upper back suggest chronic solar damage as a contributing factor for melanomas harboring BRAF p.V600K or class-3 mutations.ConclusionThis study categorizes the range, frequency, coexisting driver mutations and clinical characteristics of the three classes of BRAF mutations in a large cohort of melanomas in a clinical diagnostic setting. Further prospective studies are warranted to elucidate the clinical outcomes and benefits of newly developed targeted therapy in melanoma patients carrying each class of BRAF mutation.

Highlights

Analysis of melanomas for actionable mutations has become the standard of care
We demonstrated coexisting mutations of these driver genes in melanomas, and categorize BRAF mutations based on the new classification system to elucidate their association with clinical characteristics
Eighteen (9%) mutations were located within exon 11 and 172 (91%) within exon 15. p.V600E (62%) and p.V600K (14%) were the two most common BRAF mutations (Fig. 1)

Summary

Introduction

Analysis of melanomas for actionable mutations has become the standard of care. Recently, a classification scheme has been proposed that categorizes BRAF mutations based on their mechanisms for activation of the MAPK pathway. Most melanomas had potentially actionable mutations in the mitogen-activated protein kinase (MAPK) pathway and phosphatidylinositol 3-kinase (PI3K/AKT/mTOR) pathway. These included BRAF mutations affecting codon 600, NRAS mutations affecting codon 61 (and less frequently codons 12 and 13), and KIT mutations within exons 9 and 11. Tyrosine kinase inhibitors (imatinib, nilotinib and dasatinib) have shown benefits for melanoma patients with activating KIT mutations [12,13,14]. Mutation detection among these genes is recommended for standard of care targeted therapy in patients with metastatic melanoma

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Conclusion