Curriculum Modules
Click on any chapter below to explore complete code, diagnostic guidelines, and clinical reporting algorithms.
1: Clinical NGS Standards: CLIA/CAP Regulations & Analytical Validation
CLIA/CAP regulatory accreditation, diagnostic sensitivity and specificity, Limit of Detection (LoD), Genome in a Bottle (GIAB) reference standards, and analytical validation protocols.
2: Inherited Disease Genomics: Trio Exomes & Mendelian Inheritance
Autosomal dominant, recessive, and X-linked inheritance, de novo mutation discovery, parent-offspring trio exome sequencing, and candidate gene prioritization.
3: The ACMG/AMP 5-Tier Variant Classification Framework
Pathogenic, Likely Pathogenic, VUS, Likely Benign, Benign, 28 evidence criteria (PVS1 null variants, PS1-4, PM1-6, PP1-5, BA1, BS1-4, BP1-7), and Bayesian point systems.
4: Databases for Clinical Variant Interpretation: ClinVar, ClinGen & HPO
ClinVar review stars, ClinGen Expert Panels, gnomAD allele frequency thresholds for disease prevalence, and Human Phenotype Ontology (HPO) clinical match scoring.
5: Precision Oncology: Driver Mutations, Oncogenes & Tumor Suppressors
Knudson's two-hit hypothesis, activating hotspot mutations (BRAF V600E, EGFR L858R), loss-of-function tumor suppressors (TP53, PTEN), and AMP/ASCO/CAP somatic tiers.
6: Molecular Tumor Boards & Actionable Biomarker Databases
OncoKB evidence levels, CIViC open clinical interpretation, Cancer Genome Interpreter (CGI), and automated therapeutic biomarker matching.
7: Tumor Mutational Burden (TMB) & Microsatellite Instability (MSI)
Calculating TMB (mut/Mb), TMB-High cutoffs (>=10 mut/Mb) for immune checkpoint inhibitors, mismatch repair deficiency (dMMR), and MSI-H algorithms (MSIsensor-pro).
8: Liquid Biopsy: Circulating Tumor DNA (ctDNA) & Minimal Residual Disease
Cell-free DNA (cfDNA) fragmentation physics (167 bp nucleosome footprint), duplex UMIs, calling ultra-low allele frequencies (VAF < 0.1%), and monitoring MRD.
9: Pharmacogenomics (PGx): CPIC Guidelines & Drug-Gene Pairs
Cytochrome P450 enzymes (CYP2D6, CYP2C19), star allele nomenclature, CPIC and PharmGKB clinical dosing guidelines (Warfarin, Clopidogrel, TPMT 6-mercaptopurine).
10: Whole-Genome Clinical Diagnostics: Deep Intronic & Regulatory Variants
SpliceAI for cryptic splice site prediction, non-coding promoter mutations (TERT -124 C>T), enhancer disruptions, and clinical Whole-Genome Sequencing (cWGS).
11: Repeat Expansion Disorders & Mitochondrial Genome Pathogenicity
Short tandem repeat expansions (Huntington CAG, Fragile X CGG, ALS C9orf72), ExpansionHunter CLI, mitochondrial heteroplasmy thresholds, and m.3243A>G MELAS.
12: Ethical, Legal, Social Implications (ELSI) & Genetic Counseling
Secondary and incidental findings (ACMG SF v3.2 list of 81 actionable genes), patient consent, right not to know, GINA non-discrimination act, and HIPAA/GDPR clinical compliance.
13: Building an Automated Clinical NGS Variant Reporting Pipeline
End-to-end clinical workflow: VCF input -> ClinGen/gnomAD/VEP annotation -> ACMG auto-classification (InterVar / AutoPVS1) -> PDF clinical diagnostic report generation.
📚 Foundational Literature & Methodology Benchmarks
ACMG & AMP Clinical Standards
- Richards S, Aziz N, Bale S, et al. (2015). Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of ACMG and AMP. Genet Med 17(5):405–424. doi:10.1038/gim.2015.30
- Li MM, Datto M, Duncavage EJ, et al. (2017). Standards and guidelines for the interpretation and reporting of sequence variants in cancer: a joint consensus recommendation of AMP, ASCO, and CAP. J Mol Diagn 19(1):4–23. doi:10.1016/j.jmoldx.2016.10.002
- Chakravarty D, Gao J, Phillips SM, et al. (2017). OncoKB: a precision oncology knowledge base. JCO Precis Oncol 2017:PO.17.00011. doi:10.1200/PO.17.00011
Somatic Calling & Tumor Profiling
- Benjamin D, Sato T, Cibulskis K, et al. (2019). Calling somatic SNVs and indels with Mutect2. bioRxiv. doi:10.1101/861054
- Cerami E, Gao J, Dogrusoz U, et al. (2012). The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov 2(5):401–404. doi:10.1158/2159-8290.CD-12-0095
- McLaren W, Gil L, Hunt SE, et al. (2016). The Ensembl Variant Effect Predictor. Genome Biol 17(1):122. doi:10.1186/s13059-016-0974-4
Biomarkers & Pharmacogenomics
- Chalmers ZR, Connelly CF, Fabrizio D, et al. (2017). Analysis of 100,000 human cancer genomes reveals the landscape of tumor mutational burden. Genome Med 9(1):34. doi:10.1186/s13073-017-0424-2
- Bettegowda C, Sausen M, Leary RJ, et al. (2014). Detection of circulating tumor DNA in early- and late-stage human malignancies. Sci Transl Med 6(224):224ra24. doi:10.1126/scitranslmed.3007794
- Relling MV, Klein TE. (2011). CPIC: Clinical Pharmacogenetics Implementation Consortium of the Pharmacogenomics Research Network. Clin Pharmacol Ther 89(3):464–467. doi:10.1038/clpt.2010.279