Illumina whole genome DNA sequencing of normal control for 7316_84
PLGGs and normal controls from CHOP and DFCI were sequenced at BGI@CHOP. DNA was randomly fragmented, and libraries prepared for paired-end sequencing on an Illumina HiSeq 2000. Exome hybrid capture was performed with NimbleGen SeqCap EZ Exome Library SR v2.2, Agilent. Sequencing files from recently published PLGG datasets were accessed [Zhang J et al.,Nat Gen,2013; Jones DTW et al.,Nat Gen,2013]. Read pairs were aligned to reference genome hg19 (Build 37) using the Burrows-Wheeler Aligner (bra) with options −q 5 −l 32 −k 2 −o 12. Reads were sorted by coordinates, normalized, cleaned and duplicates were marked using SAMtools and Picard (URLs : samtools.sourceforge.net, picard.sourceforge.net). Base quality score assignments were recalibrated to control for biases due to flow cell, lane, dinucleotide context and machine cycle using the Genome Analysis Toolkit (GATK) [McKenna A et al.,Genome Res,2010]. Copy-number alterations were evaluated using SegSeq [Chiang D et al.,Nat Meth,2009]. GISTIC2 was used to identify recurrent copy-number alterations [Mermel CH et al.,Genome Res.,2011]. Somatic point mutations and short indels were called using Mutect IndelLocator [Cibulskis K et.al.,Nat Biotech,2013], and visual inspection in IGV. Mutsig version 2.0  was applied to detect significantly recurrent mutations [Lawrence MS et al.,Nature,2014]. Rearrangements and breakpoints were identified using dRanger, BreakPointer [Drier Y et al.,Genome Res,2013] and visual inspection with IGV [Robinson JT et al.,Nat Biotech,2011].