Bioinformatics of Shallow Whole Genome Sequencing Data of Circulating Tumor Cells to Inform Cancer Diagnosis and...

Shallow whole-genome sequencing (sWGS) is a cost-effective method for rapidly detecting large-scale genome alterations like copy number alterations. The sWGS workflow involves DNA extraction, library preparation, and sequencing, followed by specialized bioinformatics analyses, which we carefully review at each step. This workflow includes data preprocessing and alignment to a reference genome, with each bioinformatics stage carefully detailed as it plays a pivotal role in ensuring the accuracy and biological relevance of the results. The application of this process enables reliable data collection and analysis for monitoring cancer evolution and treatment responses by identifying critical genome changes, providing significant insights for prognosis and therapeutic decision-making across various cancer types.