TMBur

TMBur estimates tumor mutation burden (TMB) from whole genome sequencing (WGS) fastq data to provide consistent and reproducible TMB measurements for informing immune checkpoint inhibitor (ICI) response and clinical stratification.

Key Features:

• Nextflow implementation: Pipeline implemented in Nextflow to execute the analysis from raw fastq files to TMB estimation.
• Somatic variant calling: Integrates Manta, Strelka2, and Mutect2 for somatic mutation detection.
• Microsatellite instability profiling: Incorporates MSISensor for MSI assessment.
• Singularity containerization: Uses Singularity containers to enable consistent execution across computing environments.
• Reproducibility testing: Replicate runs on WGS data from COLO829 and COLO829BL across multiple research centers produced identical TMB estimates.

Scientific Applications:

• Clinical treatment selection: Provides WGS-derived TMB estimates used to stratify patients for immune checkpoint inhibitor therapy, with validation using a 90-patient advanced metastatic cancer cohort and a TMB threshold of 10 mutations per megabase (Mb).
• Prognostic association: Supported evidence that patients with genomic TMB ≥ 10/Mb have improved time to progression (reported HR = 0.39, p = 0.012) in the validated cohort.
• Multi-center standardization: Standardizes TMB calculation across research centers to support multi-center studies and harmonized comparison of WGS-derived TMB.

Methodology:

Implemented as a Nextflow pipeline processing raw fastq WGS input, performing somatic variant calling with Manta, Strelka2 and Mutect2, MSI profiling with MSISensor, and packaged in Singularity containers to produce whole genome-derived TMB estimates; reproducibility assessed via replicate runs on COLO829 and COLO829BL WGS data.