PACT

PACT detects and integrates small-scale mutations, copy number alterations, and structural variants in circulating tumor DNA (ctDNA) to enable comprehensive genomic profiling for cancer monitoring and treatment response assessment.

Key Features:

• Unified variant detection: Detects small-scale mutations, copy number alterations, and structural variants (SVs) in circulating tumor DNA (ctDNA) within a single pipeline.
• Structural variant detection: Accurately detects structural variants in ctDNA, addressing challenges in SV identification from fragmented circulating DNA.
• Small mutation detection: Identifies small-scale somatic mutations from ctDNA sequencing data.
• Copy number alteration detection: Calls copy number alterations from ctDNA-derived genomic data.
• Reproducibility and benchmarking: Demonstrates consistent performance across simulated data, cell line samples, and clinical specimens.
• CWL implementation and workflow compatibility: Implemented as a Common Workflow Language (CWL) pipeline and executable within workflow management systems and high-performance computing environments.

Scientific Applications:

• Cancer monitoring: Enables longitudinal monitoring of cancer progression through detection of ctDNA genomic alterations.
• Treatment response assessment: Supports assessment of therapeutic response by tracking somatic variants in ctDNA.
• Comprehensive ctDNA profiling: Provides integrated analysis of small mutations, copy number alterations, and structural variants for clinical and research genomic studies.

Methodology:

Implemented as a Common Workflow Language (CWL) pipeline that integrates detection of small mutations, copy number alterations, and structural variants; evaluated on simulated data, cell line samples, and clinical specimens; and executable within workflow management systems and high-performance computing environments.