Table 2: Summary of DA tRFs by clinical comparison and tRF type.

We used Significance Analysis of Microarrays (SAM) to identify tRFs that were differentially abundant (DA) between several clinic contexts, including: EIF1AX mutation status, sex, and development of metastasis are all binary classifications. SCNA, PARADIGM, miRNA, and lncRNA clusters derive from the original TCGA UVM analysis (Robertson et al., 2018). Histology refers to the majority cell type comprising the primary tumor: either spindle or epithelioid. AJCC staging represents primary tumor staging according to the AJCC tumor classification guidelines, where T4 classification represents the worst prognosis2. In this table, we list the number of tRFs that were DA in each comparison, broken down by the type of tRF as determined by the genome of origin – nuclear or mitochondrial – combined by the structural type: 5´-half, 5´-tRF, 3´-half, 3´-tRF, or i-tRF.

	MT 5´-tRF	MT i-tRF	MT 3´-tRF	MT 5´-tRH	Nuc 5´-tRF	Nuc i-tRF	Nuc 3´-tRF	Total
AJCC Clinical Stage	0	0	0	0	1	3	0	4
EIF1AX	0	0	0	0	40	4	2	46
Sex (Male vs Female)	0	0	0	0	9	0	0	9
Histology	0	0	0	0	30	3	24	57
lncRNA_Cluster	1	1	0	0	0	0	0	2
Metastatic Disease	1	23	1	1	1	1	0	28
miRNA Cluster	1	33	2	0	3	0	0	39
PARADIGM Cluster	11	133	25	3	6	15	2	195
SCNA Cluster	7	56	7	0	52	74	3	199