Neoantigen prediction and truncality estimation
Tumour, tumour
TUMOUR, TUMOUR
Tumour biopsy samples from patients and the matched normal sample from PBMCs were sequenced to identify expressed NSMs. Although most of the analysis was the same, there were 3 versions of the pipeline used throughout the clinical trial and the differences are described below. Samples from patients 0010, 0026, 0503, 0506, 0603, 0604, 0605, 0612 and 0613 were processed using v.1.0. Samples from patients 0030, 0038, 0404, 0411 and 0611 were processed using v.2.0. Samples from patients 0417 and 1003 were processed using v.30. In brief, WES and RNA-seq from a recent tumour sample in a FFPE section and PBMCs were performed using an Illumina HiSeq 2500 platform or a NovaSeq 6000 platform (Illumina). First, WES sequences were aligned to the human reference genome build 37 (GRCh37/hg19) using BWA-MEM