Protocol for the analysis of cell-free DNA end characteristics for accurate cancer diagnosis
Summary: Fragmentation patterns of plasma cell-free DNA (cfDNA) are promising biomarkers in cancer diagnosis. Here, we present a protocol to enrich tumor-derived cfDNA molecules through end selection. We describe steps for installing software, aligning plasma cfDNA data to the reference genome, and...
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| Format: | Article |
| Language: | English |
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Elsevier
2025-06-01
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| Series: | STAR Protocols |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666166725001637 |
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| author | Xiaoyi Liu Fanglei Gong Huizhen Lin Yunyun An Kun Sun |
| author_facet | Xiaoyi Liu Fanglei Gong Huizhen Lin Yunyun An Kun Sun |
| author_sort | Xiaoyi Liu |
| collection | DOAJ |
| description | Summary: Fragmentation patterns of plasma cell-free DNA (cfDNA) are promising biomarkers in cancer diagnosis. Here, we present a protocol to enrich tumor-derived cfDNA molecules through end selection. We describe steps for installing software, aligning plasma cfDNA data to the reference genome, and performing end selection on cfDNA. We then detail procedures for building cancer diagnostic models with artificial intelligence. Overall, we provide commands to align cfDNA whole-genome sequencing data starting from raw reads, then extract fragmentomic features, and finally build diagnostic models with performance evaluations.For complete information on the generation and use of this protocol, please refer to Ju et al.1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. |
| format | Article |
| id | doaj-art-23342ddd976e467095fcc237a06d34a8 |
| institution | DOAJ |
| issn | 2666-1667 |
| language | English |
| publishDate | 2025-06-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj-art-23342ddd976e467095fcc237a06d34a82025-08-20T03:09:01ZengElsevierSTAR Protocols2666-16672025-06-016210375710.1016/j.xpro.2025.103757Protocol for the analysis of cell-free DNA end characteristics for accurate cancer diagnosisXiaoyi Liu0Fanglei Gong1Huizhen Lin2Yunyun An3Kun Sun4Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, ChinaInstitute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, China; Shenzhen Medical Academy of Research and Translation, Shenzhen 518107, China; School of Life Sciences, Westlake University, Hangzhou 310030, ChinaInstitute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, China; Shenzhen Medical Academy of Research and Translation, Shenzhen 518107, China; School of Life Sciences, Westlake University, Hangzhou 310030, ChinaInstitute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, China; Corresponding authorInstitute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, China; Shenzhen Medical Academy of Research and Translation, Shenzhen 518107, China; Corresponding authorSummary: Fragmentation patterns of plasma cell-free DNA (cfDNA) are promising biomarkers in cancer diagnosis. Here, we present a protocol to enrich tumor-derived cfDNA molecules through end selection. We describe steps for installing software, aligning plasma cfDNA data to the reference genome, and performing end selection on cfDNA. We then detail procedures for building cancer diagnostic models with artificial intelligence. Overall, we provide commands to align cfDNA whole-genome sequencing data starting from raw reads, then extract fragmentomic features, and finally build diagnostic models with performance evaluations.For complete information on the generation and use of this protocol, please refer to Ju et al.1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.http://www.sciencedirect.com/science/article/pii/S2666166725001637Sequence analysisCancerGenomics |
| spellingShingle | Xiaoyi Liu Fanglei Gong Huizhen Lin Yunyun An Kun Sun Protocol for the analysis of cell-free DNA end characteristics for accurate cancer diagnosis STAR Protocols Sequence analysis Cancer Genomics |
| title | Protocol for the analysis of cell-free DNA end characteristics for accurate cancer diagnosis |
| title_full | Protocol for the analysis of cell-free DNA end characteristics for accurate cancer diagnosis |
| title_fullStr | Protocol for the analysis of cell-free DNA end characteristics for accurate cancer diagnosis |
| title_full_unstemmed | Protocol for the analysis of cell-free DNA end characteristics for accurate cancer diagnosis |
| title_short | Protocol for the analysis of cell-free DNA end characteristics for accurate cancer diagnosis |
| title_sort | protocol for the analysis of cell free dna end characteristics for accurate cancer diagnosis |
| topic | Sequence analysis Cancer Genomics |
| url | http://www.sciencedirect.com/science/article/pii/S2666166725001637 |
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