Dovetail® FFPE Assay

Unlock Genomic Variants in Your FFPE Samples

Dovetail linked-read technology enables high-sensitivity, comprehensive detection of structural variants (SVs) from FFPE samples.

FFPE Services

Dovetail FFPE Kit

FFPE samples are the most abundant resource in cancer research, yet nucleic acid degradation makes them challenging for most genomic assays—especially when detecting structural variants. Dovetail FFPE Technology overcomes this challenge.

Dovetail Genomics offers an FFPE-compatible workflow for generating linked-read libraries. Dovetail linked-reads enable high sensitivity detection of SVs, including coding and non-coding genomic rearrangements, while maintaining standard short-read performance for other variant (SNV, INDEL, CNV) detection.

The Dovetail® Linked-Read Advantage

A circular diagram illustrating the process of DNA sequencing with three segments labeled 'Coding & Non-coding Rearrangements,' 'Complex Rearrangements,' and 'Comprehensive Variant Detection.'

  • Compatible with FFPE Samples – No high-molecular-weight DNA required.

  • Consistent performance – Validated across a variety of tumor types and varying DNA quality.

  • Amplifies true-variant signal – Increases SV detection sensitivity and minimizes false positives.

  • Comprehensive rearrangement profiling – Detects coding (gene fusions) and non-coding (enhancer hijacking) events.

  • Streamlines variant detection – Detects SV, SNVs, INDELs, and CNVs in a single assay.

  • Fits existing NGS infrastructure – Compatible with standard short-read platforms.

Uncover More
Uncover More

Dovetail FFPE technology is available as a kit or service- whichever works best for you.

Dovetail addresses both library preparation and downstream data analysis in a single streamlined workflow. Prepare your library, sequence, and use the The Dovetail® Analysis Portal to upload your FASTQ files and submit the analysis in just a few clicks—no bioinformatics setup required. Receive results in a conveniently packaged downloadable archive, access a summary report with AI-driven interpretation of key findings, and explore your data with interactive tools.

A Complete Solution - Sample to Insight

A detailed infographic illustrating the process flow of Dovetail linked-read shotgun sequencing, from sample preparation to report generation, including tools like library setup, sequencing, data analysis, and visualization.
Dovetail FFPE Kit
Dovetail FFPE Kit
Dovetail FFPE Services
Dovetail FFPE Services

Known Challenges With FFPE Samples

A sign titled 'DNA Quality Constraints' listing two points about DNA quality, including poor DNA translating to low coverage and fragmented DNA being incompatible with emerging technologies like long-read sequencing, OGM, and TruPath.
Information about gene fusion detection limitations, including issues with low-quality RNA results and poor RNA yields affecting sequencing library preparation and accuracy.
A sign with the title 'High False Positive SV Calls' explaining that high artificially chimatic reads and coverage drop-outs cause false positive structural variant calls in genomic data.
Dovetail FFPE Kit
Dovetail FFPE Kit


DNA Quality Constraints

Dovetail FFPE Services
Dovetail FFPE Services

· Poor DNA quality translates to low complexity libraries leading to limited achievable coverage

·  FFPE’s fragmented DNA is incompatible with emerging technologies (long-reads, OGM, TruPath)


Gene Fusion Detection Limitations

·  Low quality RNA results in fewer breakpoint spanning reads and missed fusion calls

·  Poor RNA yields often fail in RNA-seq library preparation or yield biased, high duplicate libraries


High False Positive SV Calls

·  Artifactual chimeric reads introduced during library prep are high in FFPE samples and inflate false positive SV calls

·  Coverage drop-outs and spikes, common to FFPE NGS data, confuse SV callers

The Dovetail FFPE Solution

Learn more
Learn more
Learn more
Learn more

In standard whole genome sequencing, only reads that align to structural variant (SV) breakpoints support variant calls. Insufficient breakpoint-spanning reads —an issue intensified by limited achievable coverage in FFPE samples—lead to decreased sensitivity and increased false positives.

Dovetail technology overcomes these limitations by generating libraries that leverage both breakpoint-spanning and breakpoint-flanking reads, expanding the detection window to megabase-scale regions and significantly boosting sensitivity. This enables highly sensitive SV calling while maintaining WGS-equivalent performance for small variants, including SNVs, INDELs, and CNVs.

Diagram comparing WGS and Dovetail sequencing technologies, showing genetic regions and read spans.

➜ Robust Performance

The Dovetail FFPE assay was used to prepare libraries from FFPE samples of varying quality, tumor types and fractions. Libraries were sequenced to 30X genome coverage and used to call both intra- and inter-chromosomal structural variants. Dovetail FFPE demonstrated robust performance across all sample types. Performance remained robust when the data was downsampled to 10X coverage.

Table comparing genetic features of three tumor types: Sinonasal Osteosarcoma, Serous Ovarian Adenocarcinoma, and Breast Ductal Carcinoma. Includes data on DIN score, tumor fraction, inter-chromosomal and intra-chromosomal recall, with associated visual circular genome plots for each tumor type.

➜High Concordance

0% 20% 40% 60% Fresh Frozen 0% 20% 40% 60% FFPE Structural Variant VAF Sample Breast Osteosarcoma Ovarian DIN %Tumor 6.0 5.2 2.0 98% 73% 24% r = 0.91

The tumor FFPE samples profiled above were also available as fresh frozen tissue. Libraries were prepared from the fresh frozen samples and sequenced to equivalent coverage. Structural variants were called and variant allele fraction (VAF) was assigned to inter-chromosomal calls using the Dovetail Analysis Portal. SV calls between fresh frozen and FFPE samples showed high concordance in both breakpoint precision and VAF estimation.

Your project, your way — choose between kits or services

Run Dovetail’s FFPE assay in your lab, or leverage our expert service team.

Dovetail® FFPE Kit | Full Solution Dovetail® FFPE Kit | Full Solution
Dovetail® FFPE Kit | Full Solution
$3,013.00

Please note that the earliest ship date is May 25.

PN: 20109V

Dovetail® FFPE Kit Full Solution, 8 Samples, 8 Libraries

Includes:

Dovetail® FFPE Kit

Dovetail® Library Module

Dovetail® Primer Module Set 1

Run the Dovetail® FFPE Kit in your lab

  • User Guides

  • Dovetail® FFPE Kit, 8 reactions

    Includes:

    • Dovetail® Proximity Ligation Core 

    • Dovetail® FFPE Module

    • Dovetail® FFPE Conditioning Module 

    • Dovetail® Primer Module Set 1 

    • Dovetail® Library Module 

    Gain access to our dedicated customer support team to guide your in-house workflows.

Leverage our specialist service team

Explore our optimized services to uncover critical genomic variants.

A digital rendering of a cancer cell with a spherical shape and surrounding abnormal blood vessels.
Start Your Project Today
Start Your Project Today

  • The Dovetail® FFPE Service delivers highly sensitive structural variant detection while preserving insights into all other variant types from your FFPE samples.

    You provide:
    11 × 5 µm scrolls (>20% tumor fraction)

    We provide:
    Library preparation for you to carry out sequencing in-house or a sequenced library.

    A dedicated project manager will oversee your project and ensure smooth delivery.

    Analysis is then available as a self-service option via the Dovetail Analysis Portal.

    Turnaround time:
    4 weeks

  • Flexible deliverables tailored to your workflow:

    • Prefer to sequence in-house?
      We can deliver sequencing-ready libraries to your lab.

    • Lack sequencing capacity?
      We can take your samples through sequencing and deliver raw data (FASTQ files).

    • Need downstream insights?
      Analysis is available as a self-service option via the Dovetail Analysis Portal.

Explore Our FFPE Flyer
Explore Our FFPE Flyer

Streamline Your Data Analysis
Analysis is available as a self-service option via the Dovetail Analysis Portal

Flowchart showing a process: Dovetail FFPE Linked-Read Data combined with Portal Credits, followed by Analysis, leading to Success, and then Exploring Reports with interactive data browsing. The background features abstract digital graphics.

The Dovetail Analysis Portal (DAP) offers customers instant access to streamlined, cloud-based analysis of NGS FASTQ files generated from Dovetail FFPE libraries. Accepting standard paired-end FASTQ inputs, it delivers packaged, easily downloadable results. Data analysis requires Dovetail Portal Credits.

Detect All Variant Classes

  • Identify SVs with high sensitivity

  • Alongside other variants: SNVs, INDELs, and CNVs

Access Results Easily

  • Insightful summary report

  • Data visualization

  • Downloadable outputs in standard formats for further exploration

Exploit Proprietary Analytics

  • ‍‍Single base breakpoint refinement

  • Variant allele fraction (VAF) estimation including SVs

  • ecDNA vs. HSR predictor

  • ‍‍Al-based interpretation of variant calls

Sign Up To Access The Demo Report
Sign Up To Access The Demo Report

Need our FFPE solution at scale?

Working with hundreds of samples?

Get in touch to explore partnership options.

We look forward to hearing from you!