Figure 1.

Gene expression profiling of Class 1 primary uveal melanomas based on metastatic status. (A) Heatmap showing the 50 most highly up-regulated and down-regulated genes in 5 Class 1 primary uveal melanomas that metastasized (Class1^met+ tumors, indicated by diamonds) versus 8 that did not (Class1^met− tumors). Gene expression profiles were obtained using Illumina Human HT12v4 BeadChip arrays and analyzed with Significance Analysis of Microarrays (SAM). Blue = decreased gene expression, red = increased gene expression in Class1^met+ versus Class1^met− tumors. (B) Unsupervised principal component analysis of the same dataset, showing differential clustering of Class1^met+ (red) and Class1^met− (blue) tumors. Red and blue ellipsoids represent 95% confidence intervals for each respective group. (C) Circos plot of the same dataset demonstrating genes that are significantly up-regulated (red) or down-regulated (blue) in Class1^met+ compared to Class1^met− tumors with respect to chromosomal location. (D) Box-and-whisker plots of PRAME mRNA expression in Class1^met+ versus Class1^met− tumors ≥1 year of follow-up using the Illumina Human HT12v4 BeadChip array dataset. (E) Box-and-whisker plots of PRAME mRNA expression in Class1^met+ versus Class1^met− tumors with ≥3 years of follow-up using qPCR. (F) Representative examples of immunohistochemical staining for PRAME in Class1^PRAME+ and Class1^PRAME− tumors, 100x magnification. Blue, PRAME nuclear staining (arrow); brown, intrinsic melanin pigment; red, nuclear counterstain. (G) Analysis of PRAME mRNA expression with respect to Class 1A versus Class 1B designation. In box-and-whiskers plots, the central box represents the 25^th to 75^th percentiles, the middle line represents the median, the horizontal bars represent the minimum and maximum values, except for “far out” values, indicated by red boxes and defined as values larger than the upper 75% plus 3 times the interquartile range.