| description |
Whole genome sequencing (WGS) from snap-frozen oesophageal tumour tissue and germline nucleic acids isolated from peripheral blood mononuclear cells (PBMC) was performed as part of the International Cancer Genome Consortium project and OCCAMS consortium (1,2). Filtered read sequences were mapped to the human reference genome (GRCh37) using Burrows-Wheeler Alignment (BWA). In the matched tumour/germline samples, somatic acquired mutation identification was performed using a Bayesian algorithm implemented in the tool Seurat (3). Functional annotation of identified somatic mutations was performed with the tool SnpEff (4). CNV detection was performed with the tool Control-FREEC (5) 1) Weaver, J. M. et al. Ordering of mutations in preinvasive disease stages of esophageal carcinogenesis. Nat.Genet. 46, 837-843 (2014). 2) Weaver, J. M., Ross-Innes, C. S. & Fitzgerald, R. C. The '-omics' revolution and oesophageal adenocarcinoma. Nature reviews. Gastroenterology & hepatology 11, 19-27 (2014) 3) Christoforides, A. et al. Identification of somatic mutations in cancer through Bayesian-based analysis of sequenced genome pairs. BMC.Genomics 14, 302 (2013). 4) Cingolani, P. et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly.(Austin.) 6, 80-92 (2012). 5) Boeva V, Popova T, Bleakley K, Chiche P, Cappo J, Schleiermacher G, Janoueix-Lerosey I, Delattre O, Barillot E. (2011) Control-FREEC: a tool for assessing copy number and allelic content using next generation sequencing data. Bioinformatics. 2011 Dec 6 |