Genomic Classification of Cutaneous Melanoma

Cell. Volume 161 Issue 7: 1681-1696, 18 June 2015 10.1016/j.cell.2015.05.044

We describe the landscape of genomic alterations in cutaneous melanomas through DNA, RNA, and protein- based analysis of 333 primary and/or metastatic melanomas from 331 patients. We establish a framework for genomic classification into one of four subtypes based on the pattern of the most prevalent significantly mutated genes: mutant BRAF, mutant RAS, mutant NF1, and Triple-WT (wild-type). Integrative analysis reveals enrichment of KIT mutations and focal amplifications and complex structural rearrangements as a feature of the Triple-WT subtype. We found no significant outcome correlation with genomic classification, but samples assigned a transcriptomic subclass enriched for immune gene expression associated with lymphocyte infiltrate on pathology review and high LCK protein expression, a T cell marker, were associated with improved patient survival. This clinicopathological and multidimensional analysis suggests that the prognosis of melanoma patients with regional metastases is influenced by tumor stroma immunobiology, offering insights to further personalize therapeutic decisionmaking.

Data in the GDC

• GDC Manifests
  • Open-Access Data - Download Manifest (22 Files)
  • Controlled-Access Data - Download Manifest (1 File)

Supplemental Data

These data represent a data freeze from Nov 14 2013.

The data are supported by different organizations. All data marked by [Supplementary] were created by the manuscript authors and you should contact the corresponding author for support.

• Full Disease Sample List:
  • SKCM_Final_Data_Freeze [txt] (39M)
  • Participant List [txt]
  • SKCM patient centric table [xlsx] [Supplementary]
• Exome Sequence BAM File References
  • SKCM publication BAM freeze list
• Clinical
  • nationwidechildrens.org_SKCM.bio.Level_1 [tar.gz] - XML files containing biospecimen processing and clinical data
• DNA Mutation
  • Public DNASeq archive (782 M)
• DNA Copy Number
  • Level 3 Data Archives - broad.mit.edu_SKCM.Genome_Wide_SNP_6.Level_3 [tar.gz]
  • mage-tab Data Archives - broad.mit.edu_SKCM.Genome_Wide_SNP_6.mage-tab [tar.gz]
• RNA Expression
  • Level 3 Data Archives - unc.edu_SKCM.IlluminaHiSeq_RNASeqV2.Level_3 [tar.gz] (3.2G)
  • mage-tab Data Archives - unc.edu_SKCM.IlluminaHiSeq_RNASeqV2.mage-tab [tar.gz]
• miRNA Expression
  • Level 3 Data Archives - bcgsc.ca_SKCM.IlluminaHiSeq_miRNASeq.Level_3 [tar.gz]
  • mage-tab Data Archives - bcgsc.ca_SKCM.IlluminaHiSeq_miRNASeq.mage-tab [tar.gz]
• Methylation
  • Level 3 Data Archives - jhu-usc.edu_SKCM.HumanMethylation450.Level_3 [tar.gz] (3.2G)
  • Level 2 Data Archives - jhu-usc.edu_SKCM.HumanMethylation450.Level_2 [tar.gz] (3.1G)
  • Level 1 Data Archives - jhu-usc.edu_SKCM.HumanMethylation450.Level_1 [tar.gz] (2.6G)
  • mage-tab Data Archives - jhu-usc.edu_SKCM.HumanMethylation450.mage-tab.tar.gz [tar.gz]
• Reverse Phase Protein Array (RPPA) Expression
  • Level 3 Data Archives - mdanderson.org_SKCM.MDA_RPPA_Core.Level_3 [tar.gz]
  • Level 2 Data Archives - mdanderson.org_SKCM.MDA_RPPA_Core.Level_2 [tar.gz]
  • Level 1 Data Archives - mdanderson.org_SKCM.MDA_RPPA_Core.Level_1 [tar.gz] (1.1G)
  • Mage-tab Data Archives - mdanderson.org_SKCM.MDA_RPPA_Core.mage-tab [tar.gz]
• Low Pass Whole Genome sequencing
  • Level 3 Data Archives - hms.harvard.edu_SKCM.IlluminaHiSeq_DNASeqC.Level_3 [tar.gz]
  • Level 3 Data Archives - hms.harvard.edu_SKCM.IlluminaHiSeq_DNASeqC.Level_2 [tar.gz] (Controlled-Access)
  • mage-tab Data Archives - hms.harvard.edu_SKCM.IlluminaHiSeq_DNASeqC.mage-tab [tar.gz]

Additional Resources

• GDC Encyclopedia
• Descriptions of TCGA data are provided in the TCGA Barcode Encyclopedia Page
• Genomic Data Commons Portal