Cell-Free DNA Sequencing (cfDNA)
What Is Cell-Free DNA Sequencing (cfDNA)?
Cell-Free DNA Sequencing (cfDNA sequencing) is a highly sensitive next-generation sequencing approach used to analyze DNA circulating freely in bodily fluids, such as plasma, serum, urine, and cerebrospinal fluid. These 150–200 bp fragments originate from apoptotic cells, tumors (circulating tumor DNA, ctDNA), the fetus (cf fetal DNA), or transplanted organs. At AUGenomics, our advanced cfDNA sequencing workflows provide ultra-sensitive genomic insights ideal for oncology research, non-invasive diagnostics, and precision medicine.
Advantages of cfDNA
01
Ultra-Sensitive Variant Calling: Duplex UMIs and error-suppression reduce noise, detecting single-nucleotide variants (SNVs) and indels at <0.1% allele frequency.
02
Broad & Flexible Workflows: Choose shallow whole-genome (0.5×–2×) for CNV and fragmentation analysis, deep targeted panels (10,000×–20,000×) for hotspot variants, or methylation capture for tissue-of-origin and epigenetic profiling.
03
Low-Input & Challenging Samples: Optimize for 5–10 ng cfDNA, FFPE-derived cfDNA, urine, saliva, or CSF.
04
High Throughput & Cost Efficiency: Multiplex up to 96 samples per run; reduce per-sample cost by focusing reads on informative regions.
05
Comprehensive Insights: Combine SNV/indel calls, copy-number variation (CNV), fragmentomics (size, end motifs), and methylation signatures in one assay.
cfDNA sequencing is ideal for:
-
Liquid biopsy applications for cancer detection and monitoring
-
Early detection of minimal residual disease (MRD)
-
Non-invasive prenatal testing (NIPT)
-
Detection of transplant rejection through donor-derived cfDNA
-
Epigenetic studies and methylation profiling
-
Disease progression and therapeutic response monitoring and prediction
-
Personalized therapy guidance
-
Mosaic & rare variant detection
-
Tissue-of-origin analysis
-
High-throughput CNV & variant screening
Our expertise in ultra-low-input sequencing ensures accurate and reliable cfDNA analysis, even with challenging or limited samples.
What is cfDNA Used For?
Cell-Free DNA Sequencing with AUGenomics
Sample Submission
-
Accepted Sample Types: Plasma, serum, urine, cerebrospinal fluid (CSF)
-
Input Requirement: ≥10 ng of cfDNA (ultra-low input protocols available for <10 ng)
-
Sequencing Recommendations:
-
Typical coverage: ~0.5x to 2x for CNV; 10,000x–20,000x+ for targeted variant detection
-
Library preparation optimized for fragmented and low-yield samples
-
Multiplexing available for large cohort studies
-
Please refer to our Shipping Guidelines for project-specific guidance.
Turnaround Time
Typical turnaround time is 7-10 business days from sample receipt. Expedited options are available depending on project scope and sequencing depth.
Frequently Asked Questions (FAQs)
Q: What makes cfDNA sequencing different from regular DNA sequencing?
A: cfDNA sequencing targets short DNA fragments circulating freely in bodily fluids, enabling non-invasive analysis. This contrasts with traditional genomic sequencing, which typically uses cellular DNA from blood or tissue samples.
Q: Can cfDNA sequencing detect early-stage cancers?
A: Yes, cfDNA sequencing can detect genetic mutations, CNVs, and epigenetic changes indicative of early-stage cancer, aiding in early intervention and treatment monitoring.
Q: Is cfDNA sequencing suitable for large-scale studies?
A: Absolutely. Our workflow supports high-throughput cfDNA sequencing for large clinical trials or cohort studies, providing cost-effective scalability.
Got more questions? Contact our team and get a free consultation anytime. info@augenomics.com
Glossary of Terms
-
cfDNA: Cell-free DNA, extracellular DNA circulating in bodily fluids
-
Liquid Biopsy: Non-invasive technique for sampling cfDNA from fluids
-
Minimal Residual Disease (MRD): Small number of cancer cells remaining after treatment
-
CNV: Copy Number Variation, changes in the number of copies of DNA segments
