Related Experiment Video
Updated: Jun 14, 2026
Target Cell Pre-enrichment and Whole Genome Amplification for Single Cell Downstream Characterization
Published on: May 15, 2018
PACT: a pipeline for analysis of circulating tumor DNA
Jace Webster1, Ha X Dang1,2,3, Pradeep S Chauhan4
1McDonnell Genome Institute, Washington University in St. Louis, MO 63108, United States.
Motivation:
Detection of genomic alterations in circulating tumor DNA (ctDNA) is currently used for active clinical monitoring of cancer progression and treatment response. While methods for analysis of small mutations are more developed, strategies for detecting structural variants (SVs) in ctDNA are limited. Additionally, reproducibly calling small-scale mutations, copy number alterations, and SVs in ctDNA is challenging due to the lack to unified tools for these different classes of variants.
Results:
We developed a unified pipeline for the analysis of ctDNA [Pipeline for the Analysis of ctDNA (PACT)] that accurately detects SVs and consistently outperformed similar tools when applied to simulated, cell line, and clinical data. We provide PACT in the form of a Common Workflow Language pipeline which can be run by popular workflow management systems in high-performance computing environments.
Availability And Implementation:
PACT is freely available at https://github.com/ChrisMaherLab/PACT.
