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

STAR Protoc. 2024 Dec 20;5(4):103357. doi: 10.1016/j.xpro.2024.103357. Epub 2024 Oct 3.

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.

Keywords: Cancer; Genomics; Sequence analysis; Sequencing.

MeSH terms

  • Cell-Free Nucleic Acids* / blood
  • Cell-Free Nucleic Acids* / genetics
  • High-Throughput Nucleotide Sequencing / methods
  • Humans
  • Nucleotide Motifs / genetics
  • Sequence Analysis, DNA / methods
  • Software
  • Whole Genome Sequencing* / methods

Substances

  • Cell-Free Nucleic Acids