🏥 Three Longitudinal Patient Case Studies Across the Specialization
Real-World Pathology • Actionable Targeted TherapyStage IV Lung Adenocarcinoma
Primary EGFR exon 21 p.L858R sensitizing mutation with subsequent acquired exon 20 p.T790M gatekeeper resistance tracked via serial plasma liquid biopsy ctDNA; guidance on 3rd-generation TKI (Osimertinib).
Metastatic Colorectal Carcinoma
Concurrent KRAS exon 2 p.G13D and PIK3CA exon 9 p.E545K mutations; contraindication to anti-EGFR monoclonal antibodies (Cetuximab/Panitumumab) and downstream clinical trial evaluation.
High-Grade Metastatic Breast Cancer
Clonal TP53 missense, deleterious germline/somatic BRCA1 frameshift with high HRD genomic instability score (PARP inhibitor eligibility), and focal ERBB2 (HER2) amplification.
12 Modular Curriculum Chapters
Comprehensive practical manuals with Galaxy somatic recipes, Mutect2 command lines, IGV hotspot inspection guides, and AMP/ASCO/CAP clinical tiers.
Module 1: Clinical Cancer NGS & Assay Strategy: Targeted Panels, CGP, WES & Liquid Biopsy
Evolution of diagnostic cancer testing from single-gene assays to Comprehensive Genomic Profiling (CGP) and cell-free DNA (cfDNA) liquid biopsies, somatic vs germline concepts, and driver vs actionable alterations.
Module 2: Wet-Lab Quality Control, Library Metrics & Oncology Panel Design
Amplicon vs hybrid-capture chemistry, FFPE deamination artifacts, library preparation QC metrics (Q-scores, insert size, uniformity), and designing an oncology 10-gene panel.
Module 3: Pan-Cancer Biomarkers: TMB, MSI, VAF, CNV & Loss of Heterozygosity
Mathematical and clinical definitions of Tumor Mutational Burden (TMB), Microsatellite Instability (MSI), Variant Allele Fraction (VAF), Copy Number Alterations (CNV), and Loss of Heterozygosity (LOH).
Module 4: Oncology File Formats, Phred Scores & Alignment Concepts: FASTQ, BAM & VCF
Anatomy of raw sequencing formats (FASTQ Phred+33), coordinate-sorted BAM/CRAM alignment flags, VCF 4.2 architecture, INFO and FORMAT field parsing, and quality metrics.
Module 5: Somatic Variant Calling Paradigms: Mutect2, Panel of Normals & Low-VAF Detection
Tumor-normal paired vs tumor-only calling, GATK Mutect2 architecture, generating a Panel of Normals (PoN), filtering FFPE deamination, and detecting low-VAF subclonal mutations.
Module 6: Read-Level Verification & Visualizing Somatic Hotspots in IGV
Navigating BAM alignments in the Integrative Genomics Viewer (IGV), inspecting diagnostic cancer hotspots (EGFR L858R, KRAS G13D, TP53), and identifying alignment red flags.
Module 7: Hands-On Somatic Pipeline Execution: FastQC, BWA-MEM & Picard Deduplication
Step-by-step guided execution of an end-to-end somatic bioinformatics pipeline in Galaxy: quality trimming with fastp, BWA-MEM alignment, and Picard MarkDuplicates.
Module 8: Somatic Mutation Discovery: GATK Mutect2 & FilterMutectCalls
Executing Mutect2 on target capture BED regions, integrating Panel of Normals (PoN), calculating contamination with GetPileupSummaries, and executing FilterMutectCalls.
Module 9: Somatic Variant Annotation & Filtering: VEP, SnpEff, gnomAD & COSMIC
Functional annotation using Ensembl VEP and SnpEff, integrating somatic (COSMIC), population (gnomAD), and clinical (ClinVar, OncoKB) databases, and exporting filtered mutation tables.
Module 10: Somatic Interpretation Frameworks: AMP/ASCO/CAP Tiers & ClinGen Criteria
Clinical classification of somatic variants under AMP/ASCO/CAP 2017 guidelines (Tiers I–IV, Evidence Levels A–D), ClinGen/CGC/VICC oncogenicity specifications, and managing VUSs.
Module 11: Complex Alterations: Gene Fusions, Amplifications & Immunotherapy Eligibility
Detecting actionable oncogenic gene fusions (ALK, ROS1, NTRK), focal gene amplifications (ERBB2, MET), and integrating TMB/MSI for immune checkpoint inhibitor selection.
Module 12: Molecular Tumor Board (MDT) Simulation: Real Patient Cases & Clinical Reporting
Presenting real lung, colon, and breast cancer cases to a Multidisciplinary Tumor Board (MDT), resolving co-mutations and resistance mechanisms, and drafting clinical reports.