Germline Genetic Variants in Cancer-Susceptibility Genes in Patients With Osteosarcoma: Sample SB618891
"WES was performed on a discovery set of 1,004 confirmed osteosarcoma cases and 1,062 DCEG controls on germline DNA extracted from either leukocytes or buccal samples. WES detailed methods have been previously described.11-13 In brief, NimbleGen's SeqCap EZ Human Exome Library, Exome+UTR (Roche NimbleGen, Inc., Madison, WI, USA), capture kit was used for all cases and controls, and sequencing was performed on an Illumina HiSeq2500 (with 125bp paired end reads) with the Bioo Nextflex (Perkin Elmer, Inc., Austin, TX) library prep (all DCEG controls and 721 cases) or on an Illumina HiSeq4000 (with 150bp paired end reads) with Kapa HyperPlus (Roche Sequencing and Life Science, Kapa Biosystems, Wilmington, MA) library prep (285 cases). For all samples, library fragmentation was performed with parameters optimized to obtain insert sizes of 250bp-350bp. The human reference genome and the ""known gene"" transcript annotation were downloaded from the UCSC database, version hg19. Reads were trimmed and aligned to the hg19 reference genome using the Novoalign software (v3.00.05). High-quality alignments for each individual were created, local realignments refined, and BAM file level recalibrations were done with modules from the Genome Analysis Toolkit (GATK v3.1)"