PACT：循环肿瘤 DNA 分析管道。

PACT: a pipeline for analysis of circulating tumor DNA.

机构信息

McDonnell Genome Institute, Washington University in St. Louis, MO 63108, United States.

Siteman Cancer Center, Washington University in St. Louis, MO 63110, United States.

出版信息

Bioinformatics. 2023 Aug 1;39(8). doi: 10.1093/bioinformatics/btad489.

DOI:10.1093/bioinformatics/btad489

PMID:37549060

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10415172/

Abstract

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.

摘要

动机

检测循环肿瘤 DNA（ctDNA）中的基因组改变目前用于主动临床监测癌症进展和治疗反应。虽然分析小突变的方法更为发达，但检测 ctDNA 中结构变体（SV）的策略有限。此外，由于缺乏针对这些不同类别的变异的统一工具，因此在 ctDNA 中重现小范围突变、拷贝数改变和 SV 是具有挑战性的。

结果

我们开发了一种用于 ctDNA 分析的统一管道（Pipeline for the Analysis of ctDNA (PACT)]，该管道可准确检测 SV，并在应用于模拟、细胞系和临床数据时始终优于类似的工具。我们以 Common Workflow Language 管道的形式提供 PACT，该管道可以在高性能计算环境中由流行的工作流管理系统运行。