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Course Syllabus

Christopher Wilkinson
Updated

    Course Instructor(s)

    Micheal Evenson, Senior Genomics Scientist

    Samuel Pillay, Genomics Scientist, 

    Srushty Chafekar, Variant Analyst

    Shubhi Shah, Variant Analyst

     

    Course syllabus:

    Level 1 - Prerequisite Knowledge & Variant Characterization and Filtering

     

    Module 1 – Introduction to clinical genomics, next generation sequencing, bioinformatics and quality control.

    Objective - In Module 1, you will learn the basics of cell biology, molecular biology, and genetics; the components of a clinical genomics laboratory; the evolution of and applications for Next Generation Sequencing; quality control; and a working knowledge of bioinformatics and quality control.

    Lesson 1 – Science Background 

    • Just enough Cell biology
    • Molecules in molecular biology
    • Molecular biology structures
    • How variant occurs ?
    • Mendelian Inheritance

     

    Lesson 2 – Intro to Clinical Genomics

    (history of genetic testing and what has been accepted in the clinical domain as standard of care)

    • What is Clinical Genomics?
    • Overview of Clinical Testing Environment
    • Human Biology Related to Clinical Genomics
    • History of Clinical Genomics
    • PCR overview
    • Other Considerations for Clinical Testing

     

    Lesson 3 – NGS 101 

    (taking content from lesson 1 and knowing the evolution of diagnostic testing from lesson 2, we explore the world of NGS)

    • What is Next-Generation Sequencing (NGS)?
    • Evolution of DNA Sequencing
    • The Human Genome Project (HGP)
    • NGS workflow Overview
    • Library Preparation & Best Practices
    • Sequencing Coverage & Sensitivity
    • NGS Applications in Research & Clinics
    • Emerging Technologies in NGS

     

    Lesson 4 – Bioinformatics Overview

    (To understand the biofx basics and a little bit of what happens under the hood, how it’s related to clinical testing and the various applications for it)

    • What is Bioinformatics ?
    • NGS bioinformatics workflow
    • Introduction to NGS bioinformatics file formats
    • Variant callers: Somatic and Germline
    • Initial variant Filtering: Somatic and Germline

     

    Lesson 5 – Quality control (a check to make sure the output is true)

    • Why Quality Control in NGS?
    • Stages of NGS and QC Checkpoints
    • Sample & Library QC
    • Sequencing Run QC
    • Coverage Metrics
    • Example of QC metrics

     

    Module 2 - Variant Characterization and Filtering

    Objective - In Module 2, you will learn the basics of genomic variants, NGS variant filtering, and introduction to different type of variants, functional consequences and HGVS nomenclatures to represent a variant into clinical reports.

    Lesson 1 – Genotype (what is a variant and how do you describe it)

    • What is a Genotype?
    • What is Variant ?
    • Human Reference Genome and Genome Build
    • Variant and Gene Description Components
    • Gene & Transcript Context
    • Zygosity and VAF
    • Functional Domain/Region

     

    Lesson 2 – Variant Filtering in NGS

    (to understand how variant filtering works in NGS report that would give important information for variant analyst to view, implement and apply filters in clinical report)

    • Overview of Variant filtering in NGS workflow
    • Variant attributes used for filtering
    • NGS biofix pipeline filtering (hard filter)
    • Report filtering (soft filter)
    • Validation variant filtering
    • Filtering by Knowledgebase content
    • Example on Graphical Filters in CGW

     

    Lesson 3 – Different variant types, functional consequence and nomenclature (An overview of variant types, its functional consequence and how to represent variant in standardized HGVS compliant formats in clinical report)

    • Sequence Variants - SNVs, MNVs, Insertion, Deletion, Delins.
    • Structural Variants - CNVs, Fusion, Splice alteration.
    • Functional consequence of variants
    • HGVS nomenclature and overview

     

    Level 2 - Variant Analysis, Classification, and Interpretation

     

    Module 3 - Variant Analysis, Classification and Interpretation – Somatic Disease

    Objective - This module aims to build a strong foundation in somatic disease characterization, and variant analysis to enable accurate classification and interpretation of somatic variants across solid and hematologic cancers. Learners will develop the skills to evaluate pathogenicity and actionability, apply professional guidelines and evidence sources, and produce clear, clinically meaningful written interpretations for somatic variant reporting

    Lesson 1 – Somatic Disease Characterization (Build a foundational understanding of somatic disease characterization)

    • The biological basis of cancer
    • Key hallmarks, differences between solid tumors and hematologic malignancies
    • Tumor evolution through subclones
    • The clinical importance of MRD
    • The implications of incidental germline findings identified during somatic testing.

     

    Lesson 2 – Specimens for Somatic and Germline Testing (Build a clear understanding of DNA and RNA specimen types used in molecular testing and how their characteristics influence Next-Generation Sequencing outcomes)

    • This is a document-only reading lesson, designed to help learners recognize the critical role of proper specimen collection, handling, and quality in ensuring accurate, reliable, and clinically meaningful variant analysis.

     

    Lesson 3 – Variant Characterization - Pathogenicity/Actionability (Equip learners with a structured framework for variant characterization)

    • Gene and variant summaries
    • Evaluating variant occurrence using curated databases and analytical tools
    • Distinguish pathogenicity from actionability
    • integrate molecular, biochemical, and computational evidence to support confident, clinically meaningful variant interpretation

     

    Lesson 4A – Building Interpretation for Somatic Applications - Part I (Equip learners with the skills to build clear, structured, and clinically meaningful somatic variant interpretations)

    • Curating diagnostic, prognostic, and therapeutic evidence aligned with professional guidelines
    • Key clinical factors and endpoints
    • How evidence from multiple sources—including literature and clinical trials—is integrated to create meaningful, clinically relevant interpretations

     

    Lesson 4B – Building Interpretation for Somatic Applications - Part II (Guide learners in classifying comprehensive somatic variant interpretations)

    • incorporating disease-specific context, professional AMP/ASCO/CAP guidelines, and variant-type–specific considerations
    • Adapting interpretations across small variants, CNVs, fusions, splice variants, and non-variant biomarkers such as TMB, MSI, and HRD, using real-world case examples to ensure accurate and clinically relevant reporting. 

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