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Protocol for analyzing plasma cell-free DNA fragment end motifs from ultra-low-pass whole-genome sequencing.

ABSTRACT: 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.1.

SUBMITTER: Liu D 

PROVIDER: S-EPMC11489062 | biostudies-literature | 2024 Dec

REPOSITORIES: biostudies-literature

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Protocol for analyzing plasma cell-free DNA fragment end motifs from ultra-low-pass whole-genome sequencing.

Liu Darren D   Yehia Lamis L   Dhawan Andrew A   Ni Ying Y   Eng Charis C  

STAR protocols 20241003 4

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  ...[more]

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