Protocol for analyzing plasma cell-free DNA fragment end motifs from ultra-low-pass whole-genome sequencing
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.<sup>1</sup>.
Authors
- Lamis Yehia (ORCID: https://orcid.org/0000-0002-6389-3059)
- Charis Eng (ORCID: https://orcid.org/0000-0002-3693-5145)
- Andrew Dhawan (ORCID: https://orcid.org/0000-0002-5027-1277)
- Darren Liu (ORCID: https://orcid.org/0000-0002-6703-1843)
- Ying Ni (ORCID: https://orcid.org/0000-0002-0338-5239)
Institutions
- Cleveland Clinic (US)
- Cleveland Clinic Lerner College of Medicine (US)
Publication Details
- Journal
- STAR Protocols
- Published
- 2024-10-03
- DOI
- https://doi.org/10.1016/j.xpro.2024.103357
- Primary Topic
- Cancer Genomics and Diagnostics
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- American Academy of Neurology
- Cleveland Clinic
- Cleveland Clinic Foundation
- PTEN Research