Whole Exome Sequencing of Bone Marrow and Blood

Genomic DNA (1 μg) from the bone marrow and matching blood samples was sheared by Covaris S220 (Covaris, MA, USA) and used for library construction with SureSelect XT Human All Exon v5 and SureSelect XT reagent kit, HSQ (Agilent Technologies, Santa Clara, CA, USA) according to manufacturer's protocols. After multiplexing, the libraries were sequenced on the HiSeq 2500 sequencing platform (Illumina, USA), using the 100 bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina).
Sequencing reads were aligned to the UCSC hg19 reference genome (downloaded from http://genome.ucsc.edu) using Burrows-Wheeler Aligner (BWA) [30 (link)], version0.6.2 with default settings. PCR duplications are marked by Picard-tools-1.8 (http://picard.sourceforge.net/), data cleanup was followed by GATK, and variants were identified with GATK-2.2.9 (https://www.broadinstitute.org/gatk/). Then, point mutations were identified by MuTect (https://github.com/broadinstitute/mutect) and VarScan 2 (http://varscan.sourceforge.net) with paired samples. Perl script and ANNOVAR [31 (link)] were used to annotate variants.