Exome Sequencing of SUM Cell Lines

Exome sequencing of SUM cell line DNA was performed essentially as described previously^{53 (link)}. Briefly, Agilent Sure Select XT reagents were used to prepare sequencing libraries. Hybrid capture was performed using Agilent Sure SelectXT Human All Exon V4 + UTRs, and 100 bp paired-end sequencing was performed on a HighSeq2000 achieving a median coverage of greater than 50-fold. Reads were aligned to the human reference genome GRCh37 using the Burrow-Wheeler Aligner. The data were processed further using the Genome Analysis Toolkit (GATK). For inclusion in the SLKBase, we cross-referenced all called SNVs with data in COSMIC and only report mutations that have occurred in COSMIC > 5 times. For the data from DepMap portal, we only report on the SLKBase mutations considered to be hot-spot mutations in COSMIC.