title: Next-Generation Sequencing Reveals Pathway Activations and New Routes to Targeted Therapies in Cutaneous Metastatic Melanoma.
abstract: BACKGROUND
  Comprehensive genomic profiling of clinical samples by next-generation sequencing (NGS) can identify one or more therapy targets for the treatment of metastatic melanoma (MM) with a single diagnostic test.
  
  
  METHODS
  NGS was performed on hybridization-captured, adaptor ligation-based libraries using DNA extracted from 4 formalin-fixed paraffin-embedded sections cut at 10 microns from 30 MM cases. The exons of 182 cancer-related genes were fully sequenced using the Illumina HiSeq 2000 at an average sequencing depth of 1098X and evaluated for genomic alterations (GAs) including point mutations, insertions, deletions, copy number alterations, and select gene fusions/rearrangements. Clinically relevant GAs (CRGAs) were defined as those identifying commercially available targeted therapeutics or therapies in registered clinical trials.
  
  
  RESULTS
  The 30 American Joint Committee on Cancer Stage IV MM included 17 (57%) male and 13 (43%) female patients with a mean age of 59.5 years (range 41-83 years). All MM samples had at least 1 GA, and an average of 2.7 GA/sample (range 1-7) was identified. The mean number of GA did not differ based on age or sex; however, on average, significantly more GAs were identified in amelanotic and poorly differentiated MM. GAs were most commonly identified in BRAF (12 cases, 40%), CDKN2A (6 cases, 20%), NF1 (8 cases, 26.7%), and NRAS (6 cases, 20%). CRGAs were identified in all patients, and represented 77% of the GA (64/83) detected. The median and mean CRGAs per tumor were 2 and 2.1, respectively (range 1-7).
  
  
  CONCLUSIONS
  Comprehensive genomic profiling of MM, using a single diagnostic test, uncovers an unexpectedly high number of CRGA that would not be identified by standard of care testing. Moreover, NGS has the potential to influence therapy selection and can direct patients to enter relevant clinical trials evaluating promising targeted therapies.
authors.affiliation: *Professor of Pathology and Dermatology, Albany Medical College, Albany, NY; †Pathology Resident, Unversidade Estadual Paulista, Botucatu, Brazil; ‡Pathology Resident, Albany Medical College, Albany, NY; §Director of Research, Associate Professor, Department of Pathology, Albany, Medical College, Albany, NY; ¶Research and Development, Foundation Medicine, Inc, Cambridge, MA; ‖Chief Medical Officer, Foundation Medicine, Inc, Cambridge, MA; #Chief Scientific Officer, Foundation Medicine, Inc, Cambridge, MA; **Associate Medical Officer, Foundation Medicine, Inc, Cambridge, MA; ††Associate Medical Director, Foundation Medicine, Inc, Cambridge, MA; ‡‡Research Scientist, Foundation Medicine, Inc, Cambridge, MA; §§Chief, Professor of Pathology, Albany, Medical College, Albany, NY; and ¶¶Medical Director, Foundation Medicine, Inc, Cambridge, MA.
authors.forename: J Andrew
authors.initials: JA
authors.lastname: Carlson
authors.forename: Jose Candido
authors.initials: JC
authors.lastname: Caldeira Xavier
authors.forename: Ashley
authors.initials: A
authors.lastname: Tarasen
authors.forename: Christine E
authors.initials: CE
authors.lastname: Sheehan
authors.forename: Geoff
authors.initials: G
authors.lastname: Otto
authors.forename: Vincent A
authors.initials: VA
authors.lastname: Miller
authors.forename: Philip J
authors.initials: PJ
authors.lastname: Stephens
authors.forename: Julia A
authors.initials: JA
authors.lastname: Elvin
authors.forename: Jo-Anne
authors.initials: JA
authors.lastname: Vergilio
authors.forename: James
authors.initials: J
authors.lastname: Suh
authors.forename: Laurie M
authors.initials: LM
authors.lastname: Gay
authors.forename: Jeffrey S
authors.initials: JS
authors.lastname: Ross
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D000970:Antineoplastic Agents / Q000627:therapeutic use; D014408:Biomarkers, Tumor / Q000235:genetics*; D019295:Computational Biology; D030541:Databases, Genetic; D015195:Drug Design; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods*; D020022:Genetic Predisposition to Disease; D014644:Genetic Variation; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008297:Male; D008545:Melanoma / Q000188:drug therapy / Q000235:genetics* / Q000556:secondary; D008875:Middle Aged; D058990:Molecular Targeted Therapy; D009367:Neoplasm Staging; D010641:Phenotype; D057285:Precision Medicine; D011237:Predictive Value of Tests; D012878:Skin Neoplasms / Q000188:drug therapy / Q000235:genetics* / Q000473:pathology
chemical_list: D000970:Antineoplastic Agents; D014408:Biomarkers, Tumor