Figure 1.

From tissue to data—steps of whole exome sequencing. Tissue preprocessing starts with the identification of tumor regions by an experienced pathologist, followed by DNA extraction, library construction, and amplification. Data procession commences with the quality check of reads. If the quality of trimmed reads is sufficient, the alignment of the reads to a reference genome is launched. When Binary Alignment Map (BAM) files are processed, the calling of single nucleotide variants, insertions and deletions, and copy number variants comes next, using one or more of the numerous existing algorithms. The data can be further utilized to detect microsatellite instability status, intratumor heterogeneity, tumor mutational burden, and homologous recombination deficiency.