用于从超低深度全基因组测序分析血浆游离DNA片段末端基序的方案
Protocol for analyzing plasma cell-free DNA fragment end motifs from ultra-low-pass whole-genome sequencing.
作者信息
Liu Darren, Yehia Lamis, Dhawan Andrew, Ni Ying, Eng Charis
机构信息
Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH 44195, USA; Department of Internal Medicine, Cleveland Clinic, Cleveland, OH 44195, USA.
Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA.
出版信息
STAR Protoc. 2024 Dec 20;5(4):103357. doi: 10.1016/j.xpro.2024.103357. Epub 2024 Oct 3.
Circulating cell-free DNA (cfDNA) fragment end motif profiles are a promising biomarker in precision oncology. Here, we present a protocol for analyzing plasma cfDNA fragment end motifs from ultra-low-pass whole-genome sequencing (WGS) data. We detail a pipeline composed of sequential bash scripts for processing post-alignment BAM files. Subsequently, we outline the procedure for downstream analysis and visualization of 4-mer as well as other n-mer cfDNA end motifs in R. For complete details on the use and execution of this protocol, please refer to Liu et al..
循环游离DNA（cfDNA）片段末端基序图谱是精准肿瘤学中一种很有前景的生物标志物。在此，我们展示了一种从超低深度全基因组测序（WGS）数据中分析血浆cfDNA片段末端基序的方案。我们详细介绍了一个由一系列bash脚本组成的流程，用于处理比对后的BAM文件。随后，我们概述了在R中对4聚体以及其他n聚体cfDNA末端基序进行下游分析和可视化的程序。有关此方案的使用和执行的完整详细信息，请参考Liu等人的文章。
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