duet +modC mosaic

duet +modC mosaic | biomodal
duet +modC mosaic

Every fragment.
The essential picture.

Using single-stranded ligation, read genetics, modC and fragmentomics together from the same molecule, maximizing insight from every cfDNA sample.

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Get the essential picture

Accurate genetic and complete epigenetic insights from the same sample

Individual molecular signals provide valuable insights into disease biology. Together, genetics, methylation and fragmentomics assemble a more complete picture of the biology underlying disease.

duet +modC 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 delivers high-quality modified cytosine data from the same molecules.

The result is integrated genetic, methylation and fragmentomic insight from a single workflow. duet +modC mosaic is the efficient route to multiomic cfDNA analysis when independent 5mC and 5hmC resolution is not required. It is the ideal choice for cfDNA and liquid biopsy, and a powerful option wherever sample is the limiting factor.

Why choose duet +modC mosaic?

01

Three independent pieces of the picture

Genetics, modified cytosine and fragmentomics from a single molecule, each reveal signal but are far more powerful when assembled together.

02

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.

03

High-quality methylation data

Measure modified cytosine with high sensitivity and specificity, helping identify more true methylation events while reducing false-positive calls and missed signals.

04

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 reading methylation from the same molecule.

05

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.

06

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.

SNV calling performance

Quantification of short cfDNA fragments (below ~145bp) in matched clinical cfDNA samples processed using duet +modC mosaic and a conventional end-repair and A-tailed approach shows improved capture of shorter fragments

Why it matters: More of the molecules that matter most, means a clearer picture of biology.

High sensitivity and specificity for modified cytosine detection

duet +modC mosaic detects modified cytosine with high sensitivity and specificity, reducing the false-positive calls and missed events that obscure biological signal.

modC sensitivity
modC specificity

Methylation sensitivity and specificity of duet 6-base mosaic evaluated using the included controls and compared to published or internally generated data for other epigenetic sequencing technologies. duet +modC mosaic has higher sensitivity and a 9-fold lower false positive rate than company I.

Why it matters: Better methylation data supports stronger, more reproducible biological conclusions.

Low LoD genetic variant detection

Sensitive detection of individual low-frequency variants, including biologically important C>T mutations, while maintaining high-quality methylation measurements from the same molecules.

SNV calling performance

C>T and G>A SNV calling performance in contrived samples of known VAF between 0% and 5%

Why it matters: Generate genetic and epigenetic insight without sacrificing variant-detection performance.

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.

Fragment end correlation

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 +modC mosaic WGS in real cfDNA samples

Why it matters: Fragmentomic biomarkers such as fragment-size ratios, end-motif diversity and nucleosome footprints depend on faithfully preserved fragment ends. Distorted ends from end-repair-based workflows can obscure exactly the signals these methods rely on.

Ultra-low limits of detection

Capturing more of the right molecules, plus complementary signals, plus high per-signal accuracy, together yield a lower limit of detection than single-analyte methods.

Genetic limits of detection

Genetic LoD95 derived from contrived spike in samples of known VAF

Why it matters: LoD determines whether a liquid biopsy assay can detect disease early and monitor it reliably.

Software included, analysis on your terms

Every duet +modC mosaic kit includes the duet software pipeline and modality XPLR, taking you from raw reads to 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.

duet software workflow
Why it matters: Get to biological insight faster, on your own infrastructure, with no custom pipeline to build and no data lock-in.

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
  • 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

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Catalog number Product name Product description
5301 duet +modC mosaic 8x reaction duet +modC mosaic assay, duet software, modality XPLR for pre and post-sequencing workflows for 8 reactions
5302 duet +modC mosaic 24x reaction duet +modC mosaic assay, duet software, modality XPLR for pre and post-sequencing workflows for 24 reactions
5303 duet +modC mosaic 96x reaction duet +modC 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 typecfDNA
Input requirement5–30 ng cfDNA (60 µL input volume)
WorkflowSingle-stranded, 7-step cfDNA-optimized workflow; automation-ready
Sequencing compatibilityStandard short-read sequencing platforms
Analysisduet software + modality XPLR

Software outputs • Resolved FASTQ • BAM • VCF • QC reports • Zarr file • ASM file

FAQs

What sample types is duet +modC mosaic designed for?
Optimized for cfDNA, supporting input amounts from 5–30 ng, and a powerful option wherever sample is precious or limited.
How does the single-stranded workflow help with cfDNA?
Conventional double-stranded library prep loses single-stranded and short, damaged fragments. duet mosaic's single-stranded ligation recovers both double- and single-stranded molecules, including the shorter fragments enriched for circulating tumor DNA, so you capture more of the molecules most likely to carry your signal.
What is modified cytosine (modC)?
Modified cytosine (modC) refers to methylated forms of cytosine involved in epigenetic regulation. duet +modC mosaic measures combined modC (5mC and 5hmC together) while simultaneously generating accurate genetic and fragmentomic information from the same cfDNA sample.
How does duet +modC mosaic protect genetic accuracy while reading methylation?
Like many methylation methods, duet converts unmodified cytosines to read methylation state. What is unique to duet is that its hairpin adapter first captures a complementary copy of each fragment's genetic sequence before conversion. Reading both strands lets duet reconstruct the original base, preserving C>T variant detection, while flagging sequencing and PCR errors as an N. Conversion-only methods do not do this.
How do I know the fragmentomics data is high quality?
Fragmentomics quality has two dimensions: technical usability and biological fidelity. For usability, standard QC applies: modal fragment size near 167 bp, high mapping rate, and sufficient library complexity from your input. For fidelity, the key question is whether the assay preserves native fragment ends: end-repair-based library preps rewrite fragment ends and can distort end-motif and nucleosome signals, while duet's single-stranded ligation preserves them. duet enables fragment-size distributions and end-motif frequencies that can be benchmarked against whole-genome sequencing, so you can confirm the fragmentomic signal reflects biology, not library artifact.
Does duet +modC mosaic include quality controls?
Yes. Integrated methylation controls ship with every kit, so you can confirm conversion performance and data quality in every run without sourcing your own.
What data can I generate from a single assay?
Genetic variants, combined modified cytosine (modC), and fragmentomics (fragment-length distributions, end motifs and nucleosome positioning): three independent pieces of the biological picture from the same molecules.
How is duet +modC mosaic different from duet +modC?
duet +modC mosaic is optimized for cfDNA and precious low-input samples through single-stranded ligation, improving access to rare and tumor-enriched molecules and preserving native fragmentomic information, while delivering the same combined modC and genetic measurements.
How is duet +modC mosaic different from duet 6-base mosaic?
Both recover the same molecules and deliver genetics and fragmentomics with the same single-stranded workflow. The difference is methylation resolution: duet +modC mosaic measures combined modC (5mC and 5hmC together), the efficient route when you do not need to distinguish the two; duet 6-base mosaic resolves 5mC and 5hmC as independent signals. The analysis stack is shared, so moving between them requires no change in workflow.
What is modified cytosine sequencing?
Modified cytosine sequencing measures methylated forms of cytosine, including 5mC and 5hmC together as a combined modC signal. duet +modC adds genetic variant information from the same molecules, so methylation data is interpreted alongside the original genetic sequence.
What software is included?
The duet software pipeline plus modality XPLR for biological QC, visualization, and multiomic data exploration.
Can I analyze data in my own environment?
Yes. The software supports workstation, HPC, and cloud deployments and produces community-standard file outputs.

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