The complete genomes of seven prostate tumors and patient-matched normal samples were sequenced to approximately 30-fold haploid coverage on an Illumina GA II sequencer. DNA was extracted from patient blood and from tumors following radical prostatectomy, and was subjected to extensive quality control procedures to monitor DNA structural integrity, genotype concordance, and tumor purity and ploidy. Standard paired-end libraries (~400bp inserts) were sequenced as 101bp paired-end reads. Raw sequencing data were processed by Illumina software and passed to the Picard pipeline, which produced a single BAM file for each sample storing all reads with well-calibrated quality scores together with their alignments to the reference genome. BAM files for each tumor/normal sample pair were analyzed by the Firehose pipeline to characterize the full spectrum of somatic mutations in each tumor, including base pair substitutions, short insertions and deletions, and large-scale structural rearrangements. A subset of base pair mutations and rearrangements were validated using independent technologies in order to assess the specificity of the detection algorithms. Fluorescence in situ hybridization (FISH) was also performed for selected recurrent rearrangements. The locations of all rearrangement breakpoints were compared to previously published chromatin immunoprecipitation (ChIP) binding peaks from related cell types to test for global associations between rearrangements and a range of epigenetic marks.
A complete description of the materials and methods is provided in the Supplementary Information. All Illumina sequence data have been deposited in dbGaP (http://www.ncbi.nlm.nih.gov/gap) and are available at accession phs000330.v1.p1.
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