> For the complete documentation index, see [llms.txt](https://book.ncrnalab.org/teaching/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://book.ncrnalab.org/teaching/part-iii.-ngs-data-analyses/8.cfdna.md).

# 8.cfDNA

Previous cfDNA studies have demonstrated that various features could be derived from cfDNA-seq and cfDNA methylation (cfDNAmet) sequencing data for diagnostic measurement. These features include:

* **cfDNAmet-seq**
  * methylation level at promoter region
  * methylation level at gene body level
  * ...
* **cfDNA-seq**
  * Mutation (requires deep sequencing depth)
  * CNV
  * Nucleosome occupancy footprint (scores: ration/CPM/WPS) ([**Pipelines**](https://cloud.tsinghua.edu.cn/f/779f7fd90bb349bfa6cb/) by *Y Li*)
  * Fragment size profile
  * End motif pattern
  * ...

> - **Instructions**: [**Analyze cfDNA features**](https://github.com/HUNNNGRY/cfDNA-NGS-analysis) and [**Related cfDNA publications**](https://docs.qq.com/sheet/DT0RCdEt0V3pQeVRj?tab=BB08J2) by *PF Bao*
> - **Literatures**: [cfDNA-seq Analysis - Lu Lab Docs](https://docs.ncrnalab.org/docs/literature-reading/med/2.-data-mining/cfDNA)