Whole-Exome Sequencing of Tumor and Normal Tissues

Tumor and normal tissues were dissected and collected separately from frozen sections under microscopic guidance. DNA was extracted using a ChargeSwitch® gDNA Mini Tissue Kit (Life Technologies, Carlsbad, CA). The extracted DNA was constructed into a fragment library using a SOLiD Fragment Library Construction Kit (Life Technologies) or the AB Library Builder System (Life Technologies). Constructed libraries were subjected to whole-exome enrichment using a SureSelect Human All Exon Kit (Agilent Technologies Inc., Santa Clara, CA) or a TargetSeq™ Target Enrichment Kit (Life Technologies). The prepared exome libraries were sequenced using the massively parallel deep sequencer SOLiD 4 or 5500xl SOLiD System (Life Technologies) using the paired-end sequencing method. Data were analyzed using LifeScope software (Life Technologies) with mapping on the Human Genome Reference, GRCh37/hg19 (The Genome Reference Consortium; http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/index.shtml). All procedures were performed according to the manufacturers' instructions. Obtained data were annotated and stringently filtered to exclude false variation calls using our previously described programs developed in-house25 (link).