Course

Unit 1

Unit 1:

Introduction to Liquid Biopsy and Circulating Biomarkers, Definition and scope of liquid biopsy, Advantages over traditional tissue biopsies, Key circulating biomarkers: cfDNA, ctDNA, CTCs, EVs, Clinical relevance and current applications, Regulatory and ethical considerations.

Unit 2

Unit 2:

Sample Collection and Pre-analytical Variables, Types of biological fluids used (blood, urine, CSF, saliva), Protocols for blood collection and plasma separation, Pre-analytical challenges: degradation, contamination, and storage, Importance of standardization and quality control.

Unit 3

Unit 3:

Circulating Free DNA (cfDNA), Characteristics of cfDNA, Isolation techniques: column-based, magnetic bead-based, size selection, Quantification and quality assessment, Mutation detection methods: PCR, qPCR, ddPCR, NGS.

Unit 4

Unit 4:

Circulating Tumor Cells (CTCs), Biology and clinical significance of CTCs, Enrichment and isolation methods: immunoaffinity, size-based filtration, Enumeration and molecular profiling, Clinical applications and limitations.

Unit 5

Unit 5:

Extracellular Vesicles and Exosomes, Overview of EVs: exosomes, microvesicles, apoptotic bodies, Biogenesis and biomolecular cargo (RNA, DNA, proteins), Isolation and characterization techniques (ultracentrifugation, precipitation, microfluidics), Diagnostic and prognostic applications.

Unit 6

Unit 6:

Analytical Approaches and Clinical Integration, Data analysis and interpretation in liquid biopsy, Bioinformatics pipelines for ctDNA and exosomal RNA, Integration into clinical workflows and decision-making, Future directions and innovations in non-invasive diagnostics.

(45 classes)

Preamble

This course explores non-invasive diagnostic techniques focused on circulating biomarkers such as cfDNA, ctDNA, CTCs, and extracellular vesicles. Liquid Biopsy and Circulating Biomarkers emphasizes the potential of blood-based diagnostics in oncology, prenatal testing, and disease monitoring. Students will learn sample collection, isolation of biomarker molecules, and analytical approaches for circulating biomarkers.

Course outcomes

CO1: Principles, scope, and clinical relevance of liquid biopsy and key circulating biomarkers.

CO2: Demonstrate knowledge of sample collection techniques and address pre-analytical challenges in biomarker analysis.

CO3: Apply appropriate methods for isolation, quantification, and mutation analysis of circulating free DNA (cfDNA).

CO4: Describe the biology, isolation, and diagnostic use of circulating tumor cells (CTCs).

CO5: Analyze the role of extracellular vesicles in diagnostics and evaluate methods for their isolation and characterization.

CO6: Interpret analytical outputs and explore clinical integration and future innovations in liquid biopsy diagnostics.

Program outcome

PO1: Bioscience Knowledge

PO2: Problem Analysis

PO3: Design/Development of Solutions

PO4: Conduct Investigations of complex problems

PO5: Modern tools usage

PO6: Bioscientist and Society

PO7: Environment and Sustainability

PO8: Ethics

PO9: Individual & Team work

PO10: Communication

PO11: Project management & Finance

PO12: Lifelong learning

0 – No affinity; 1 – low affinity; 2 – Medium affinity; 3 – High affinity

Program-specific outcome

PSO 1 – Emerging technologies in clinical diagnostics

PSO 2 – Biomolecules in Medicine

PSO 3 – Molecular dysregulation in diseases

PSO 4 – Molecular technology in diagnosis and therapy

PSO 5 – Applying lab discoveries to clinical practice

PSO 6 – Microorganisms in Medicine

PSO 7 – Statistical methods to interpret and validate diagnostic results

PSO 8 – Integrate molecular diagnostics into personalized medicine

PSO 9 – Compounds as biomarkers and its specificity

PSO 10 – Bioinformatics and biological data use

0 – No affinity; 1 – low affinity; 2 – Medium affinity; 3 – High affinity

Textbook:

Alix-Panabières C, Pantel K. Liquid Biopsy: Advances in Research and Clinical Applications. Springer; 2019.

Reference Book:

Wan JCM, Massie C, Garcia-Corbacho J, Mouliere F, Brenton JD, Caldas C, et al. Liquid biopsies come of age: towards implementation of circulating tumour DNA. Nat Rev Cancer. 2017;17(4):223–238.