Cell-Free DNA (cfDNA) & Fragmentomics
What Is Cell-Free DNA (cfDNA) & Fragmentomics?
Cell-free DNA (cfDNA) fragmentomics is an emerging approach that analyzes the fragmentation patterns of cfDNA in the bloodstream to gain insights into its tissue of origin, chromatin structure, and disease-associated alterations.
cfDNA fragments are released into circulation through apoptosis, necrosis, and other cellular processes. These fragments carry not only genetic information (mutations, copy number changes) but also structural features—such as fragment size distributions, end motifs, and nucleosome footprints—that reflect the epigenetic landscape of the originating tissue.
Unlike traditional cfDNA mutation analysis, fragmentomics provides a multi-dimensional view of cfDNA, combining fragment size, end chemistry, and coverage patterns to enhance liquid biopsy sensitivity and tissue-of-origin detection. AUGenomics integrates high-coverage sequencing with bioinformatics pipelines specifically tuned to extract and interpret these fragmentomic signals.
Advantages of cfDNA & Fragmentomics
01
Tissue-of-Origin Profiling: Infers the source tissue by analyzing nucleosome patterns and fragmentation signatures.
02
Enhanced Liquid Biopsy Sensitivity: Detects cancer signals even at very low tumor fractions.
03
Multi-Dimensional Analysis: Uses fragment size, end motifs, and coverage patterns to generate richer data than mutation-only approaches.
04
Integration with cfDNA Mutation and Methylation Data: Combines fragmentomics with genetic and epigenetic profiling for comprehensive analysis.
05
Low Input Requirements: Optimized for the small, fragmented DNA typical of plasma samples.
06
Non-Invasive Sampling: Uses simple blood draws for real-time monitoring.
07
Applicable to Multiple Diseases: Cancer, prenatal, transplant, and other conditions.
08
Customizable Workflows: Supports both research discovery and translational studies.
cfDNA fragmentomics is driving a new wave of liquid biopsy research, enabling sensitive detection and classification of disease from a simple blood sample. Applications include:
-
Early Cancer Detection: Identifying tumor-associated fragmentation patterns at early stages.
-
Tumor Tissue-of-Origin Assignment: Determining which organ the tumor-derived cfDNA originates from.
-
Minimal Residual Disease (MRD) Monitoring: Detecting traces of cancer post-treatment.
-
Transplant Monitoring: Assessing graft injury and rejection through donor-derived cfDNA fragment patterns.
-
Prenatal Testing: Analyzing placental cfDNA to monitor fetal health.
-
Epigenetic Research: Using nucleosome positioning data to study chromatin architecture in health and disease.
-
Multi-Omic Liquid Biopsy: Combining fragmentomics with methylation and mutation analysis for improved diagnostic performance.
What is cfDNA & Fragmentomics Used For?
cfDNA & Fragmentomics with AUGenomics
Sample Submission
500–1,000 µL of plasma or serum (EDTA tubes recommended). Extracted RNA should be ≥10 ng with minimal degradation. Store plasma samples at –80°C.
Please refer to our Shipping Guidelines for project-specific guidance.
Turnaround Time
Typical turnaround for plasma cfRNA projects is 12–16 business days from sample receipt. Expedited options are available depending on project scope and sequencing depth.
Frequently Asked Questions (FAQs)
Q: How is fragmentomics different from standard cfDNA sequencing?
A: Standard cfDNA sequencing focuses on detecting mutations or methylation. Fragmentomics analyzes physical properties of cfDNA fragments—such as size patterns, end motifs, and nucleosome positioning—providing additional diagnostic signals.
Q: What sample type is required?
A: Plasma collected using cfDNA stabilization tubes is recommended to prevent degradation and contamination.
Q: How much input DNA is needed?
A: Our workflows generate robust data from as little as 10–20 ng cfDNA, depending on assay design.
Q: Can fragmentomics be combined with other analyses?
A: Yes. We frequently integrate fragmentomics with mutation and methylation profiling to create multi-omic liquid biopsy datasets.
Q: What is the turnaround time?
A: Standard turnaround is 2–3 weeks, with expedited options available for urgent studies.
Q: Is this service clinically validated?
A: Our cfDNA fragmentomics service is for research use only (RUO) but generates high-quality data applicable to translational research and biomarker development.
Got more questions? Contact our team and get a free consultation anytime. info@augenomics.com
Glossary of Terms
-
cfRNA: Cell-free RNA fragments circulating in blood or other fluids
-
Transcriptome: The full set of RNA transcripts produced in a cell or tissue
-
Liquid biopsy: A non-invasive method of testing for disease biomarkers using blood or other fluids
-
EDTA: A type of anticoagulant used in blood collection tubes
