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Pipeline publication

[…] removal of the unbound fragments, the enriched library was eluted from the capture beads and prepared for a second round of hybridization for 14.5 h to a maximum of 24 h. After the second wash, enriched fragments were eluted and amplified with 12 PCR cycles with Illumina-specific primers from the Rapid Capture kit (Illumina). For PCR cleanup, 45 μl of Sample Purification Beads was used and the final elution volume was decreased to 22 μl. The enriched library pools were checked for quality on a Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA), quantified using quantitative PCR and sequenced on an Illumina MiSeq (Illumina)., Illumina reads were mapped to the human (hg19) genome using bwa mem. Duplicates were marked and reads were realigned using picard and the Genome Analysis Toolkit respectively. SNPs were called using the Unified Genotyper method of the Genome Analysis Toolkit and annotated using annovar., TCGA data were downloaded using firehose_get provided by the Broad Institute. SCNA data generated by the Broad Institute on the Affymetrix Genome-Wide Human SNP Array 6.0 from the 2015_02_04 run were used. We used copy-number changes of the following genes for mapping segment sizes and copy numbers of focal amplifications: MYC, CCND1, ERBB2, CDK4, NKX2-1, MDM2, EGFR, MCL1, FGFR1, KRAS, CCNE1, CRKL, HMGA2, TERT, PRKCI, IGF1R, MYCL, MYCN, CDK6, BCL2L1, MYB, MET, JUN, BIRC2, YAP1, PDGFRA, KIT, PIK3CA, MDM4 and AR. For focal deletions, we used the following genes: CDKN2A, CDKN2B, FHIT, WWOX, PTPRD, MACROD2, PARK2, RB1, LRP1B, PDE4D, RBFOX1, PTEN, CSMD1, DMD, OPCML, NTM, ETV6, NF1, ATM, PRKG1, PAX5, TP53, PTPRN2, APC, NEGR1, GP […]

Pipeline specifications

Software tools BWA, Picard, GATK, ANNOVAR, firehose_get
Organisms Homo sapiens
Diseases Neoplasms, Urogenital Neoplasms, Genital Neoplasms, Male, Prostatic Diseases