RNA fragmentomics
Data analysis for a new kind of liquid biopsy: reading not only how much RNA there is, but how it is fragmented.
What it is
Blood contains cell-free RNA released from cells throughout the body, including tumour cells. By the time it is sampled, that RNA has been cut into fragments.
Conventional analysis counts how much of each RNA is present. Fragmentomics also looks at the fragments themselves: their length, where along a transcript they begin and end, and the sequence at their ends. These patterns reflect how and where the RNA was processed and degraded, and can differ between healthy and diseased tissue, and before and after treatment.
RNA fragmentomics is a young field. The aim is more sensitive detection of disease and closer monitoring of how a patient responds to therapy, from a blood sample.
What we analyse
Each sample is described by a set of fragment features that are combined with expression data and clinical variables.
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Fragment length
The distribution of fragment sizes per sample and per gene, and how it shifts between groups.
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End motifs
The short sequences at fragment ends, which reflect the enzymes and processes that cut the RNA.
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Positional coverage
Where along each transcript fragments start and stop, revealing protected regions and cleavage hot spots.
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Expression and clinical data
Conventional quantitative measures and patient information, analysed together with the fragment features.
How a project runs
We can take a study from design to report, or step in where you need us.
Scoping
We discuss your clinical or biological question, samples and existing data, and agree on scope, deliverables and timeline.
Study design
Group sizes, controls, pre-analytical handling and sequencing depth, planned so the data can answer the question.
Quality control
Alignment, deduplication and QC adapted to short, degraded cell-free RNA, with a clear decision on which samples go forward.
Fragment profiling
Length distributions, end motifs and positional coverage for every sample and gene.
Modelling
Biomarker discovery and predictive models combining fragment features with clinical data, validated with resampling and independent data where available.
Report and handover
Figures, tables and methods text ready for publication or regulatory documentation, and if you want it, the pipeline itself with training for your team.
Our work in the field
MultiD develops analysis methods for RNA fragmentomics together with academic and industrial partners.
Ultrasensitive diagnostics using RNA fragmentomics
A Vinnova-funded project (2024–2026) coordinated by the University of Gothenburg with MultiD and RealSeq Biosciences, described by the partners as Europe’s first RNA fragmentomics study in cancer. RealSeq provided the fragmentomics technology, the University of Gothenburg ran a pilot study on blood samples from sarcoma patients, and MultiD developed the data analysis pipeline.
Industry PhD in data-driven precision medicine
Within the SciLifeLab and Wallenberg national programme for Data-Driven Life Science (DDLS), MultiD and the University of Gothenburg are developing bioinformatics and machine-learning methods for RNA fragmentomics, aimed at improving cancer diagnostics and treatment monitoring.
Who it is for
- Diagnostics companies developing liquid biopsy assays who need fragment-level analysis and validated models.
- Translational and clinical research groups exploring new biomarkers for treatment response or relapse.
- Technology providers who want an analysis pipeline to offer alongside their library preparation or sequencing.
Planning a fragmentomics study?
Tell us about your samples and your question, even at an early stage.