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Primary tumors themselves can be heterogeneous, reflecting ongoing genomic changes as they progress toward metastasizing. We developed a computational method to explore this heterogeneity and to predict metastatic progression of the primary tumors. We applied our method separately to gene expression and to micro<jats:styled-content style=\"fixed-case\">RNA<\/jats:styled-content> (mi<jats:styled-content style=\"fixed-case\">RNA<\/jats:styled-content>) expression data from ~450 primary and metastatic skin cutaneous melanoma (<jats:styled-content style=\"fixed-case\">SKCM<\/jats:styled-content>) samples from the Cancer Genome Atlas (<jats:styled-content style=\"fixed-case\">TCGA<\/jats:styled-content>). Metastatic progression scores from <jats:styled-content style=\"fixed-case\">RNA<\/jats:styled-content>\u2010seq data were significantly associated with clinical staging of patients\u2019 lymph nodes, whereas scores from mi<jats:styled-content style=\"fixed-case\">RNA<\/jats:styled-content>\u2010seq data were significantly associated with Clark's level. The loss of expression of many characteristic epithelial lineage genes in primary <jats:styled-content style=\"fixed-case\">SKCM<\/jats:styled-content> tumor samples was highly correlated with predicted progression scores. We suggest that those genes\/mi<jats:styled-content style=\"fixed-case\">RNA<\/jats:styled-content>s might serve as putative biomarkers for <jats:styled-content style=\"fixed-case\">SKCM<\/jats:styled-content> metastatic progression.<\/jats:p>","DOI":"10.1111\/pcmr.12374","type":"journal-article","created":{"date-parts":[[2015,4,3]],"date-time":"2015-04-03T14:59:06Z","timestamp":1428073146000},"page":"453-463","source":"Crossref","is-referenced-by-count":26,"title":["Toward predicting metastatic progression of melanoma based on gene expression data"],"prefix":"10.1111","volume":"28","author":[{"given":"Yuanyuan","family":"Li","sequence":"first","affiliation":[{"name":"Biostatistics and Computational Biology Branch National Institute of Environmental Health Sciences NIH Research Triangle Park NC USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Juno M.","family":"Krahn","sequence":"additional","affiliation":[{"name":"Genome Integrity &amp; Structural Biology 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