RMC57_EOT_WES
Genomic DNA for whole exome sequencing (WES) was isolated from 8 RMC tumor specimens and their matched blood samples by the MD Anderson Biospecimen Extraction Resource, with blood-derived DNA serving as the germline control. For each sample, 500 ng of DNA was prepared into sequencing libraries using the Agilent SureSelect XT HS and XT Low Input Reagent kits. Whole-exome capture employed Agilent SureSelect Human All Exon V4 biotinylated probes per the manufacturers instructions, and libraries were sequenced on an Illumina HiSeq 2500. Paired-end FASTQ reads were generated from BCL files with Illumina bcl2fastq/2.20.0, aligned to the hg19 reference genome using BWA 0.7.15, de-duplicated with Picard 1.112, and locally realigned with GATK 3.3-0. The resulting BAM files were used for downstream analyses.