For the 438 tumors included in our previous work8, library preparation was performed using ScriptSeq (EpiCentre) followed by sequencing on an Illumina HiSeq 2000. For the 97 tumors added in this study, library preparation was performed with KAPA RNA HyperPrep Kit (RiboErase HMR; Roche) using 500 ng input. Libraries were paired-end sequenced using an Illumina NovaSeq6000.

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