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Published on: July 7, 2023
Protocol for analyzing plasma cell-free DNA fragment end motifs from ultra-low-pass whole-genome sequencing
Darren Liu1, Lamis Yehia2, Andrew Dhawan3
1Genomic 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.
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.
