WXS fastq files from patient st034, Healthy tissue (blood)
Genomic DNA from fresh tumour samples was extracted using the DNeasy Blood and Tissue Kit (QIAGEN), following the manufacturers protocol; or the genomic DNA from the tumours was extracted from 2 m-thick FFPE sections (8-10 sections per sample) using Maxwell RSC DNA FFPE Kit (Promega Corporation) on Maxwell RSC 48 Instrument (Promega Corporation) following the manufacturers protocol. DNA from peripheral blood samples was used as a matching reference and extracted with the automatic QIAcube extractor (Qiagen), following the instructions of the DNeasy Blood & Tissue Kit (Qiagen). Whole exome was captured from genomic DNA for tumour and matched normal tissue using the SureSelectXT Human All Exon V6 + COSMIC (Agilent), following the manufacturers protocol. Somatic and germline variants were identified according to GATK Best Practices, implemented via the HaTSPiL framework. Sequencing reads were aligned to the GRCh37/hg19 reference genome using Novoalign (http://www.novocraft.com/) with default settings, allowing up to three mismatches per read. PCR duplicates were marked with Picards MarkDuplicates, and local realignment around indels was performed with GATKs RealignerTargetCreator and IndelRealigner.
SUB15758673
Lib_127