Illumina whole exome DNA sequencing of tumor PL3510
WES was performed from FFPE samples (without matched control). These samples were used to confirm driver alterations identified by the WGS. DNA was extracted using the QIAGEN DNA Blood and Tissue kit.  Libraries with a 250 bp average insert size were prepared by Covaris sonication, followed by double-size selection (Agencourt AMPure XP beads) and ligation to specific barcoded adaptors (Illumina TruSeq) for multiplexed analysis. Exome hybrid capture was performed with the Agilent Human All Exon v2 (44 Mb) bait set. Sequence data were aligned to the hg19 (b37) reference genome with the Burrows-Wheeler Aligner [Li H & Durbin R,Bioinformatics,2009] with parameters ‘-q 5 -l 32 -k 2 -t 4 -o 1’. Aligned data were sorted, duplicate-marked, and indexed with Picard tools. Base-quality score recalibration and local realignment around insertions and deletions was achieved with the Genome Analysis Toolkit.