Fig. 3: Insights into early genetic evolution from 15-GEP discriminant score and BSE cancer cell fraction.
From: Early genetic evolution of driver mutations in uveal melanoma
a Typical Class 1 tumors with high discriminant scores: Case #003-025, near-clonal SF3B1 mutation; Case #007-071, sub-clonal EIF1AX mutation. b Discordant Class 1 tumors with high discriminant score: Case #027-106, near-clonal EIF1AX mutation and subclonal BAP1 mutation. c Discordant Class 1 tumors with low discriminant scores: Case #026-504, clonal BAP1 and SF3B1 mutations and partial LOH3p involving a limited region around the BAP1 locus; Case #017-119, clonal SF3B1 mutation and LOH3p; Case #028-183, near-clonal BAP1 mutation, LOH3p and very low discriminant score (0.02). d Class 2 tumors with high discriminant scores and bi-allelic BAP1 loss: Case #021-013, sub-clonal BAP1 mutation; Case 023-059, near-clonal EIF1AX mutation and subclonal BAP1 mutation. e Class 2 tumors with intermediate discriminant scores: Case #026-435, near-clonal SF3B1 mutation and LOH3p but no detectable BAP1 mutation; Case #019-019, sub-clonal BAP1 mutation and no detectable LOH3p. f Class 2 tumors with low discriminant scores: Case #017-035, near-clonal EIF1AX and BAP1 mutations with LOH3p; Case #021-116, near-clonal BAP1 mutation with no detectable LOH3p. The length of the connector between the ancestor melanoma cell (gray circle) and the melanoma (blue or red circle for Class 1 or Class 2, respectively) is proportional to tumor diameter (in millimeters) at the time of tumor sampling. The length of the extension beyond the melanoma is proportional to time to death or last follow-up (in months) with final status indicated. Survival status for living and dead patients is indicated by gray or black bar, respectively. Mutation nomenclature is described in the “Methods” section. Relevant data are available in the Source data file. 15-GEP 15-gene expression profile, ANM alive no metastasis, DOM dead of metastasis, D-score support vector machine discriminant score, LOH3p loss of heterozygosity of chromosome 3p; (−) PRAME negative, (+) PRAME positive.
