high throughput sequence alignment protocol
Reads were aligned to HG19 using TMAP. Variants were identified using the Ion Variant Caller plug-in; all settings default with the exception of a SNP QV minimum of 14.
nucleic acid sequencing protocol
Eight barcoded libraries were pooled for each run, and sequenced on Ion 318 chips
Three mm cores were removed from formalin fixed paraffin embedded tissue blocks, and the top 2mm removed with a sterile scalpel blade.
nucleic acid extraction protocol
DNA was extracted from tissue core fragments using a 24 hour proteinase K digestion (Arcturus Picopure DNA Extraction kit), follwed by clean up using DNEasy columns (Qiagen).
nucleic acid library construction protocol
Libraries were prepared using the Ion Ampliseq Cancer Panel kit (Life Technologies) and the Ion AmpliSeq Library Kit, after which individual libraries were barcoded using the Ion Xpress Barcode Adaptor Kit (Life Technologies)