From every fragment,
the full picture
Maximize insight from every precious sample by using single-stranded ligation to read genetics, 5mC, 5hmC and fragmentomics from the same molecule. Ideal for cfDNA and liquid biopsy.
Why the complete picture wins
Genetics, epigenetics and fragmentomics each reveal different aspects of disease biology. Viewed independently, they provide valuable insight. Combined, they create a more complete understanding of biological activity, regulation and change.
duet 6-base mosaic is designed to bring those pieces together. A single-stranded ligation workflow captures short and damaged cfDNA fragments that carry important disease signal, while duet's hairpin architecture preserves confident variant detection and independently resolves 5mC and 5hmC from the same molecules.
The result is integrated genetic, complete epigenetic and fragmentomic insight from a single workflow. It is the ideal choice for cfDNA and liquid biopsy, and a powerful option for wherever sample is the limiting factor.
Why choose duet 6-base mosaic?
Four independent pieces of the picture
Genetics, 5mC, 5hmC, and fragmentomics from a single molecule, each able to reveal signal on its own, and far more powerful assembled together.
Capture more of the molecules that matter
A single-stranded ligation workflow recovers both double- and single-stranded fragments, including the short, damaged, tumor-enriched molecules conventional double-stranded workflows miss. More of the right pieces to complete the picture.
Resolve 5mC and 5hmC with high sensitivity and specificity
Read 5mC and 5hmC as distinct signals, each at ~98% sensitivity with ~99.9% specificity, revealing powerful biomarkers and regulatory biology that other methods cannot separate, even from limited input.
High-confidence genetic variant detection
duet's hairpin approach copies and retains the original genetic sequence before conversion, delivering confident C>T variant detection, including low-frequency variants, while resolving methylation from the same molecule.
Native fragmentomics
Single-stranded ligation preserves native fragment ends instead of rewriting them through end-repair so fragment-length, end-motif, and nucleosome-positioning signals are captured faithfully, not distorted. Fragmentomics is enabled alongside genetics and epigenetics
Built-in error correction
Because duet reads both the original and copy strands, its read-resolution software flags implausible strand pairings as an N, filtering out sequencing and PCR errors that traditional methods carry through.
Performance data
Capture more of the informative molecules
Single-stranded ligation recovers double- and single-stranded fragments, including the short, damaged molecules enriched for circulating tumor DNA that conventional double-stranded workflows leave behind.
Quantification of short cfDNA fragments (below ~145bp) in matched clinical cfDNA samples processed using duet 6-base mosaic and a conventional end-repair and A-tailed approach shows improved capture of shorter fragments
Resolve 5mC and 5hmC with high sensitivity and specificity
High sensitivity and specificity reduce false-positive methylation calls and missed events, helping researchers focus on real biological signal rather than analytical noise.
Methylation sensitivity and specificity of duet 6-base mosaic evaluated using the included controls and compared to published data for other epigenetic sequencing technologies. duet 6-base mosaic has higher sensitivity and a 6-fold lower false positive rate than company I.
Low LoD genetic variant detection
Sensitive detection of individual low-frequency variants, including biologically important C>T mutations, while maintaining high-quality epigenetic measurements from the same molecules.
C>T and G>A SNV calling performance in contrived samples of known VAF between 0% and 5%
Native fragmentomics
Fragmentomics features are only as good as the fidelity with which fragment ends are captured. Because duet's single-stranded ligation preserves native fragment ends, rather than repairing and rewriting them, as conventional double-stranded workflows do, it faithfully recovers the fragment-length distribution, end-motif frequencies, and nucleosome-positioning signals used in fragmentomic analysis. Fidelity is measured as concordance with whole-genome sequencing: end-motif frequencies correlate closely with WGS from matched samples.
Correlation between the frequency of calling A (dark teal), T (coral), G (light teal) or C (green) at the 5' fragment end between conventional 4-base and duet 6-base mosaic WGS in real cfDNA samples
Ultra-low limits of detection
Capturing more of the right molecules, plus multiple independent signals, plus high per-signal accuracy, together yield a lower limit of detection than single-analyte methods.
| LoD95 | |
|---|---|
| Hypermethylation | 6.65 ppm |
| Hypomethylation | 12.34 ppm |
| Genetics | 0.561% |
Methylation and genetic LoD95 derived from contrived spike in samples of known VAF or methylated/unmethylated concentrations.
The complete picture through multiomic integration
When independent signals are assembled, they detect what any single piece misses. In a Stage I CRC cfDNA study, a duet multiomic classifier integrating genetics, methylation, and fragmentomics reclassified six samples that a methylation-only model missed, including two Stage I patients.
Multiomic integration gave stepwise improvements to balanced accuracy (the average of sensitivity and specificity) when distinguishing cancer cfDNA samples from healthy controls (published data from EACR)
Software included, analysis on your terms
Every duet 6-base mosaic kit includes the duet software pipeline and modality XPLR, taking you from raw reads to resolved genetics, methylation, and fragmentomics without assembling your own pipeline. Run it on your HPC or the cloud, and explore multiomic results on your laptop with no dedicated bioinformatician required. Analysis tools come standard, and your data stays yours.
Applications
- Aging studies
- Allele-specific methylation analysis
- Biomarker discovery
- Cancer research
- Differential methylation analysis
- Epigenotyping
- Fragmentomics
- Liquid biopsy (cfDNA/ctDNA) studies
- Minimal residual disease (MRD) assay development
- Multi-cancer early detection (MCED) assay development
- Neurodegenerative research
- Neuroscience and developmental biology
- Population studies, including epigenome-wide association studies (EWAS)
- Simultaneous detection of genetic variants and methylation
- Tumor profiling, including FFPE
- Whole-genome or targeted methylation sequencing
Ordering information
Request quote| Catalog number | Product name | Product description |
|---|---|---|
| 6301 | duet 6-base mosaic 8x reaction | duet 6-base mosaic assay, duet software, modality XPLR for pre and post-sequencing workflows for 8 reactions |
| 6302 | duet 6-base mosaic 24x reaction | duet 6-base mosaic assay, duet software, modality XPLR for pre and post-sequencing workflows for 24 reactions |
| 6303 | duet 6-base mosaic 96x reaction | duet 6-base mosaic assay, duet software, modality XPLR for pre and post-sequencing workflows for 96 reactions |
| 4103 | UDI 8x reactions | Unique dual indices for 8 reactions |
| 4102 | UDI 24x reactions | Unique dual indices for 24 reactions |
| 4104 | UDI 96x reactions | Unique dual indices for 96 reactions |
| 4001 | Magnetic beads mosaic 8 reaction | Magnetic beads for 8 reactions |
| 4002 | Magnetic beads mosaic 24 reaction | Magnetic beads for 24 reactions |
| 4003 | Magnetic beads mosaic 96 reaction | Magnetic beads for 96 reactions |
| Specifications | |
|---|---|
| Sample type | cfDNA |
| Input requirement | 5–30 ng cfDNA (60 µL input volume) |
| Workflow | Single-stranded, 8-step cfDNA-optimized workflow; automation-ready |
| Sequencing compatibility | Standard short-read sequencing platforms |
| Analysis | duet software + modality XPLR |
Software outputs • Resolved FASTQ • BAM • VCF • QC reports • Zarr file • ASM file