title: Targeted next generation sequencing identifies clinically actionable mutations in patients with melanoma.
abstract: Somatic sequencing of cancers has produced new insight into tumorigenesis, tumor heterogeneity, and disease progression, but the vast majority of genetic events identified are of indeterminate clinical significance. Here, we describe a NextGen sequencing approach to fully analyzing 248 genes, including all those of known clinical significance in melanoma. This strategy features solution capture of DNA followed by multiplexed, high-throughput sequencing and was evaluated in 31 melanoma cell lines and 18 tumor tissues from patients with metastatic melanoma. Mutations in melanoma cell lines correlated with their sensitivity to corresponding small molecule inhibitors, confirming, for example, lapatinib sensitivity in ERBB4 mutant lines and identifying a novel activating mutation of BRAF. The latter event would not have been identified by clinical sequencing and was associated with responsiveness to a BRAF kinase inhibitor. This approach identified focal copy number changes of PTEN not found by standard methods, such as comparative genomic hybridization (CGH). Actionable mutations were found in 89% of the tumor tissues analyzed, 56% of which would not be identified by standard-of-care approaches. This work shows that targeted sequencing is an attractive approach for clinical use in melanoma.
authors.affiliation: Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, NC, USA.
authors.forename: William R
authors.initials: WR
authors.lastname: Jeck
authors.forename: Joel
authors.initials: J
authors.lastname: Parker
authors.forename: Craig C
authors.initials: CC
authors.lastname: Carson
authors.forename: Janiel M
authors.initials: JM
authors.lastname: Shields
authors.forename: Maria J
authors.initials: MJ
authors.lastname: Sambade
authors.forename: Eldon C
authors.initials: EC
authors.lastname: Peters
authors.forename: Christin E
authors.initials: CE
authors.lastname: Burd
authors.forename: Nancy E
authors.initials: NE
authors.lastname: Thomas
authors.forename: Derek Y
authors.initials: DY
authors.lastname: Chiang
authors.forename: Wenjin
authors.initials: W
authors.lastname: Liu
authors.forename: David A
authors.initials: DA
authors.lastname: Eberhard
authors.forename: David
authors.initials: D
authors.lastname: Ollila
authors.forename: Juneko
authors.initials: J
authors.lastname: Grilley-Olson
authors.forename: Stergios
authors.initials: S
authors.lastname: Moschos
authors.forename: D
authors.initials: D
authors.lastname: Neil Hayes
authors.forename: Norman E
authors.initials: NE
authors.lastname: Sharpless
mesh_terms: D045744:Cell Line, Tumor; D005260:Female; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008297:Male; D008545:Melanoma / Q000235:genetics*; D009154:Mutation; D009363:Neoplasm Proteins / Q000235:genetics*
chemical_list: D009363:Neoplasm Proteins
keywords: clinical trials; diagnostics; genomics; resequencing; therapeutics