Fusion event calling from raw read files of tumor-adjacent tissues and tumor lesions was performed using FusionMap 29 which was designed to detect and align fusion junction-spanning reads to the genome directly 29. Fusions were filtered out if 1) seed reads were ≤3 or were listed in the in-family analysis or found in a paralog gene list; 2) fusions were associated with uncharacterized genes, immunoglobin genes, mitochondrial genes or repeat regions; and 3) fusions were reported in normal samples. High confidence fusions were input into FusionHub to search for reported fusions and predict the fusion effects.

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