Scholarlink

<p>Fragmentomics based analysis of cell-free DNA (cfDNA) has recently emerged as a method to infer epigenetic and transcriptional data. Many of these reports analyze whole genome sequencing (WGS) which is not readily available clinically. Targeted exon panels are used for clinical cfDNA variant calling. In this report, we conduct an investigation of multiple published fragmentomics methods for WGS, but on cancer exon panels. We find that strategies utilizing normalized depth metrics, as well as all exons present on the panel, generally allow for better prediction of cancer phenotypes across a range of tumor fractions, though other metrics work particularly well in specific applications. Additionally, genes from commercial clinical targeted sequencing panels could be similarly employed for cancer phenotyping with a minimal decrease in performance despite their smaller genomic coverage. These results suggest that fragmentomics-based analysis of cfDNA can utilize targeted sequencing panels and does not necessarily require additional WGS.</p>

错误：搜索内容不能为空，请输入英文关键词
错误：关键词超出字数限制，请精简
高级检索

Analysis of cfDNA fragmentomics metrics and commercial targeted sequencing panels

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2025年10月14日

查看全文
  • Kyle T. Helzer,
  • Marina N. Sharifi,
  • Jamie M. Sperger,
  • Matthew R. Chrostek,
  • Matthew L. Bootsma,
  • Shannon R. Reese,
  • Amy Taylor,
  • Katie R. Kaufmann,
  • Hannah Krause,
  • Jennifer Schehr,
  • Nan Sethakorn,
  • David Kosoff,
  • Christos E. Kyriakopoulos,
  • Michael Bassetti,
  • Grace Blitzer,
  • John Floberg,
  • Martin Sjöström,
  • Andrew J. Armstrong,
  • Himisha Beltran,
  • Rana R. McKay,
  • Felix Y. Feng,
  • Ruth O’Regan,
  • Kari B. Wisinski,
  • Hamid Emamekhoo,
  • Alex W. Wyatt,
  • Joshua M. Lang,
  • Shuang G. Zhao

摘要

Fragmentomics based analysis of cell-free DNA (cfDNA) has recently emerged as a method to infer epigenetic and transcriptional data. Many of these reports analyze whole genome sequencing (WGS) which is not readily available clinically. Targeted exon panels are used for clinical cfDNA variant calling. In this report, we conduct an investigation of multiple published fragmentomics methods for WGS, but on cancer exon panels. We find that strategies utilizing normalized depth metrics, as well as all exons present on the panel, generally allow for better prediction of cancer phenotypes across a range of tumor fractions, though other metrics work particularly well in specific applications. Additionally, genes from commercial clinical targeted sequencing panels could be similarly employed for cancer phenotyping with a minimal decrease in performance despite their smaller genomic coverage. These results suggest that fragmentomics-based analysis of cfDNA can utilize targeted sequencing panels and does not necessarily require additional WGS.