Computational Molecular Biology 2025, Vol.15, No.4, 208-217 http://bioscipublisher.com/index.php/cmb 21 4 All modules are executed in parallel in Nextflow to fully utilise computing resources. The final output results include the SNV/Indel list, CNV and copy number table, fusion gene list, etc. Figure 1 Identification of tumour-specific genes whose expression potentially impedes T-cell infiltration (Adopted from Nasra et al., 2024) 6.3 Implementation results and clinical application Nearly 200 patient samples were included in the clinical application stage. Doctors generally report that the new process has significantly improved work efficiency. In the past, a senior analyst could produce at most 2 to 3 reports a day, but now the same number of people can complete 5 to 6. The report format is also clearer: the homepage centrally displays key information such as driver genes, therapeutic targets, TMB/MSI, etc., while the appendix section details references and database annotations. For instance, the report of a lung cancer patient clearly indicates the EGFR L858R mutation and amplification, along with information on drugs such as osimertinib and the level of evidence, enabling doctors to directly formulate treatment plans. Another colorectal cancer patient reported MSI-H and high TMB, and the doctor immediately decided to treat with immune checkpoint inhibitors. The optimisation of this report structure not only improves readability but also enhances the efficiency of communication between doctors and patients (Ghoreyshi et al., 2025; Nguyen et al., 2025). Patient
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