Precision Oncology with Liquid Biopsy: ctDNA, Cancer Genomics & Biomarker-Guided Tumor Monitoring

This three-day hands-on workshop explores precision oncology, liquid biopsy, ctDNA, cancer genomics, and biomarker-guided tumor monitoring. Participants will learn how genomic alterations are detected and interpreted, how ctDNA supports treatment monitoring and minimal residual disease assessment, and how actionable biomarkers guide clinical decisions. Hands-on activities using cBioPortal, COSMIC, ClinVar, OncoKB, and CIViC will provide practical experience in genomic analysis, variant interpretation, and longitudinal ctDNA-based tumor monitoring.

To provide participants with a comprehensive understanding of cancer genomics, liquid biopsy, ctDNA analysis, genomic variant interpretation, and biomarker-guided tumor monitoring , while developing practical skills for interpreting cancer genomic data and longitudinal ctDNA profiles in precision oncology.

• Understand the fundamentals of precision oncology and personalized cancer treatment.
• Explain tumor heterogeneity, clonal evolution, and key genomic alterations.
• Understand tissue and liquid biopsy approaches, including cfDNA and ctDNA.
• Explore ctDNA detection using qPCR, ddPCR, and next-generation sequencing.
• Interpret VAF, sequencing depth, sensitivity, and detection limits.
• Differentiate somatic, germline, driver, and passenger variants.
• Use cancer genomics databases for variant annotation and interpretation.
• Identify actionable, diagnostic, prognostic, and resistance biomarkers.
• Apply ctDNA for treatment response, MRD, recurrence, and resistance monitoring.
• Understand key clinical, regulatory, and technical challenges of liquid biopsy.

Day 1: Precision Oncology, Cancer Genomics & Liquid Biopsy Foundations

• Principles of precision oncology and personalized cancer treatment Tumor heterogeneity, clonal evolution, and molecular drivers Key genomic alterations: SNVs, indels, CNVs, gene fusions, and structural variants Molecular biomarkers for diagnosis, prognosis, and therapy selection Tissue biopsy versus liquid biopsy Liquid biopsy analytes: ctDNA, CTCs, extracellular vesicles, and cell-free RNA Biology and clinical significance of cfDNA and ctDNA Factors affecting ctDNA shedding and detectability Pre-analytical considerations in liquid biopsy workflows

Day 2: ctDNA Detection, Genomic Analysis & Variant Interpretation

• qPCR, ddPCR, and sequencing-based ctDNA detection Next-generation sequencing for liquid biopsy Targeted panels, whole-exome, and whole-genome approaches Sequencing depth, variant allele frequency (VAF), sensitivity, and limit of detection Somatic versus germline variants Driver versus passenger mutations Actionable alterations and resistance-associated mutations Variant interpretation using COSMIC, ClinVar, OncoKB, and CIViC Clonal hematopoiesis and potential false-positive findings

Day 3: Biomarker-Guided Tumor Monitoring & Clinical Translation

• Baseline and longitudinal ctDNA profiling Molecular response assessment during treatment Minimal residual disease (MRD) detection Tumor-informed versus tumor-naïve ctDNA monitoring Monitoring recurrence and metastatic progression Tracking acquired resistance and tumor evolution Integrating ctDNA with imaging and clinical parameters Biomarker-guided patient stratification and therapy selection Applications in targeted therapy and immunotherapy Clinical validation, regulatory considerations, and current limitations Emerging directions in liquid biopsy and precision oncology

• Explore cancer genomic datasets usingcBioPortal.
• Identify frequently altered cancer genes and major genomic alterations.
• Interpret clinically relevant cancer variants usingCOSMIC, ClinVar, OncoKB, and CIViC.
• Prioritize potentially actionable and resistance-associated mutations.
• Interpret variant allele frequency and ctDNA dynamics across multiple timepoints.
• Recognize potential confounding factors such as clonal hematopoiesis and false-positive variants.
• Evaluate ctDNA changes associated with treatment response and disease progression.
• Understand the application of ctDNA forminimal residual disease and recurrence monitoring.
• Connect genomic biomarkers with targeted therapies and immunotherapy strategies.
• Integrate genomic, liquid biopsy, and clinical information for biomarker-guided tumor monitoring.
• Prepare a simplifiedbiomarker-guided tumor monitoring reportbased on longitudinal ctDNA data.
• Understand emerging applications of liquid biopsy and cancer genomics in precision oncology.

Undergraduate and postgraduate students in Biotechnology, Bioinformatics, Molecular Biology, Genetics, Genomics, Biochemistry, Biomedical Sciences, and Life Sciences MBBS, MD, and medical students interested in oncology and molecular diagnostics PhD scholars and research fellows working in Cancer Biology, Oncology, Genomics, Molecular Medicine, or Precision Medicine Clinical researchers and translational scientists Bioinformaticians and computational biologists Molecular diagnostic and pathology professionals Oncologists and healthcare professionals interested in precision oncology Researchers working with NGS, cancer biomarkers, ctDNA, cfDNA, or liquid biopsy Faculty members and academicians in biomedical and life-science disciplines Professionals from biotechnology, pharmaceutical, diagnostics, and healthcare industries