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Systematic biases in reference-based plasma cell-free DNA fragmentomic profiling.
Liu, Xiaoyi; Yang, Mengqi; Hu, Dingxue; An, Yunyun; Wang, Wanqiu; Lin, Huizhen; Pan, Yuqi; Ju, Jia; Sun, Kun.
Afiliación
  • Liu X; Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, China.
  • Yang M; Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, China; Department of Chemical and Biological Engineering, Division of Life Science, Hong Kong University of Science and Technology, Hong Kong SAR 999077, China.
  • Hu D; Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, China; Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China.
  • An Y; Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, China.
  • Wang W; Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, China; Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China.
  • Lin H; Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, China.
  • Pan Y; Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, China; Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China.
  • Ju J; Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, China; Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China.
  • Sun K; Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, China. Electronic address: sunkun@szbl.ac.cn.
Cell Rep Methods ; 4(6): 100793, 2024 Jun 17.
Article en En | MEDLINE | ID: mdl-38866008
ABSTRACT
Plasma cell-free DNA (cfDNA) fragmentation patterns are emerging directions in cancer liquid biopsy with high translational significance. Conventionally, the cfDNA sequencing reads are aligned to a reference genome to extract their fragmentomic features. In this study, through cfDNA fragmentomics profiling using different reference genomes on the same datasets in parallel, we report systematic biases in such conventional reference-based approaches. The biases in cfDNA fragmentomic features vary among races in a sample-dependent manner and therefore might adversely affect the performances of cancer diagnosis assays across multiple clinical centers. In addition, to circumvent the analytical biases, we develop Freefly, a reference-free approach for cfDNA fragmentomics profiling. Freefly runs ∼60-fold faster than the conventional reference-based approach while generating highly consistent results. Moreover, cfDNA fragmentomic features reported by Freefly can be directly used for cancer diagnosis. Hence, Freefly possesses translational merit toward the rapid and unbiased measurement of cfDNA fragmentomics.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Ácidos Nucleicos Libres de Células Límite: Humans Idioma: En Revista: Cell Rep Methods Año: 2024 Tipo del documento: Article País de afiliación: China Pais de publicación: Estados Unidos
Texto completo
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XML
PubMed Links
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Ácidos Nucleicos Libres de Células Límite: Humans Idioma: En Revista: Cell Rep Methods Año: 2024 Tipo del documento: Article País de afiliación: China Pais de publicación: Estados Unidos