Data processing and bioinformatics analysis
tumor
TUMOR
For the 360 gene panel analyses, raw sequence data were aligned to the human reference genome (Build-UCSC hg19) using BWA. Somatic single nucleotide variants were detected by application of CaVEMan and insertions/deletions were detected using Pindel [The tumor mutational burden (TMB) analyses were performed by the TSO500 assay (NextSeq platform, Illumina) at the Science for Life Laboratory, Uppsala University, Sweden, (Supplementary S9) according to the producer´s protocol.Bioinformatic processing of the TCR sequencing results was performed by HS Diagnomics (Berlin, Germany). The libraries were based on a 2-step PCR system using gene-specific primers for 