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TumorMutationalBurdenEngine: TMB Calculation, MSI Scoring, and Immunotherapy Response Prediction
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Tumor mutational burden (TMB) and microsatellite instability (MSI) are established biomarkers for immunotherapy response. We present TumorMutationalBurdenEngine, a pure-Python pipeline for TMB/MSI analysis. The engine implements TMB calculation (somatic mutations per megabase), MSI scoring (repeat locus instability), mutational signature contribution (SBS1/2/3/4/13), immunotherapy response prediction (TMB-high threshold=10 mut/Mb), and mutation type spectrum analysis. Applied to 200 tumor samples, the pipeline identifies median TMB=2.86 mut/Mb, TMB-high=12%, MSI-H=12%, TMB-high response rate=58.3% vs 15.3% (TMB-low), and dominant signature SBS1 (29%).
Introduction
Tumor mutational burden (TMB) measures total somatic mutations per megabase. High TMB (≥10 mut/Mb) correlates with increased neoantigen load and enhanced response to PD-1/PD-L1 checkpoint inhibitors. MSI results from defective mismatch repair.
Methods
TMB
TMB = (total somatic SNVs + indels in coding regions) / exome size (Mb).
MSI
Fraction of microsatellite loci showing length instability (>3 repeat unit difference from normal).
Response Prediction
Logistic regression: P(response) = sigmoid(β0 + β1×TMB + β2×MSI + β3×PD-L1).
Results
Median TMB=2.86 mut/Mb. TMB-high=12%. MSI-H=12%. Response: TMB-H=58.3% vs TMB-L=15.3%. SBS1=29%.
Code Availability
https://github.com/BioTender-max/TumorMutationalBurdenEngine
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