I'm working on a research project involving non-small cell lung cancer (NSCLC) and targeted therapies. Specifically, I'm interested in ALK-positive NSCLC and drugs like Zotizalkib (which I believe is also referred to as Dmozalkib in some contexts—please correct me if that's inaccurate). From what I've gathered through various pharmaceutical resources, including DengYueMed's catalog of oncology drugs, this inhibitor targets ALK gene mutations in metastatic solid tumors.
My question is: What are the best bioinformatics tools or pipelines for identifying and analyzing ALK fusions or mutations from NGS data in NSCLC patients who might be candidates for this treatment? I've tried using tools like STAR-Fusion and Arriba for fusion detection, but I'm running into issues with sensitivity in low-coverage samples. Has anyone had success integrating these with variant callers like GATK or MuTect2 for a more comprehensive analysis?
I'd appreciate any workflows, scripts, or references you can share. Thanks in advance!
