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Updated: Aug 5, 2026
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Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells
Published on: April 4, 2016
Assessing Reporting Quality and Pre-Analytical Standards in Extrachromosomal Circular DNA Studies in Cancer: A
Felishia Tian1, Sarah Soyeon Oh2, Chul S Hyun3
1College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI 48109, USA.
Cancers
|July 28, 2026
Summary
Standardizing pre-analytical methods in extracellular circular DNA (eccDNA) studies is crucial for reliable cancer biomarker development. Inconsistent reporting of sample handling procedures hinders eccDNA research reproducibility and clinical translation.
Area of Science:
- Molecular Biology
- Biochemistry
- Oncology
- Biomarker Discovery
Background:
- Extracellular circular DNA (eccDNA) shows promise as a cancer biomarker in liquid biopsies.
- Reliability and reproducibility of eccDNA studies depend on standardized pre-analytical handling and transparent reporting.
- Existing guidelines for cell-free DNA handling exist, but adherence in eccDNA research is unclear.
Purpose of the Study:
- To systematically review the reporting and adherence to pre-analytical procedures in published eccDNA studies.
- To identify common gaps and deviations from established guidelines in eccDNA sample processing.
- To propose a reporting checklist to enhance transparency and standardization in eccDNA research.
Main Methods:
- Systematic review of 14 eccDNA studies published between 2017 and 2025.
- Evaluation of studies against 22 checklist items from the NCI Biospecimen Collection and Processing Guideline.
- Categorization of items into biospecimen collection, blood processing, and eccDNA processing; calculation of missing/deviation rates.
Main Results:
- Widespread reporting gaps were observed, with 100% missing data for venipuncture site, freeze-thaw cycles, and pre-assay QC.
- Key missing elements included blood volume, collection tube type, time from draw to processing, and storage details.
- Extraction method reporting was consistent, but quantification reporting had gaps; deviations from guidelines were infrequent when reported.
Conclusions:
- Inconsistent reporting of pre-analytical procedures impedes the reproducibility, transparency, and clinical translation of eccDNA research.
- A concise reporting checklist, based on the NCI guideline and focusing on underreported aspects, is proposed.
- The proposed checklist aims to provide an efficient framework to enhance transparency and promote standardization in future eccDNA studies.
