# ECLIPSE (subclone tracking from ctDNA)

Source: https://onco.cc/technologies/eclipse-subclone-ctdna/  
OnCo record `eclipse-subclone-ctdna` (Technology). Data CC BY-NC 4.0, attribute "Data from OnCo (onco.cc)"; commercial use needs a licence.

## TL;DR

A research method from the TRACERx lung cancer study that estimates which branches of a tumour's family tree are present in a blood sample, but only when there is enough tumour DNA in the blood.

## Summary

ECLIPSE is the bioinformatic tool the TRACERx team built to call the presence or absence of individual tumour subclones in plasma and estimate their cancer cell fractions from low-tumour-content cell-free DNA (Abbosh et al., Nature 2023). It uses a background error estimate for each sample and copy number from multi-region tumour sequencing, and was applied to anchored multiplex PCR panels tracking a median of 200 mutations per patient, with up to 4 mL of plasma per case.

Its stated operating point is the most useful single number on how far subclone attribution reaches: plasma with a clonal ctDNA level of 0.1 per cent (1,000 parts per million) had an estimated minimally detectable cancer cell fraction of 20 per cent for a representative subclone, and simulated subclones built from the assay's dilution validation data gave 94 per cent detection sensitivity for a 20 per cent subclone at that level with four tracked mutations and 10 ng of DNA. Detection fell below 10 ng, so only samples with at least 0.1 per cent clonal ctDNA and 10 ng input were analysed for clonal composition. ECLIPSE found patients with polyclonal metastatic dissemination, which carried a worse outcome, and subclones that later seeded metastases were more expanded in preoperative plasma.

## Fields

- Kind: Technology
- Status: emerging
- Last checked: 2026-11-04
- Also known as: ECLIPSE; ECLIPSE subclone deconvolution
- Principle: Each tracked mutation is assigned to a clone from multi-region tumour sequencing; plasma read counts for each clone's mutations are compared with a per-sample background error rate and corrected for copy number and mutation multiplicity to estimate that clone's cancer cell fraction.
- Since: 2023
- Strengths: Names the subclone, not only the presence of tumour DNA; Corrects for copy number, which a simple ratio of allele fractions does not; Validated against multi-region tumour sequencing in TRACERx
- Limitations: Works at 0.1 per cent clonal ctDNA and above, about a hundred times above the levels ultrasensitive tests now report; Needs multi-region tumour sequencing and tissue copy number; Published in non-small cell lung cancer only; no breast cancer application was found; Research tool, not a clinical test

## Sources

- Abbosh et al., Nature 2023 (TRACERx ctDNA and ECLIPSE): https://doi.org/10.1038/s41586-023-05776-4

## Connected records

- cancers: [Non-small-cell lung cancer](https://onco.cc/cancers/nsclc/)
- fronts: [Diagnostics & Biomarkers](https://onco.cc/fronts/diagnostics/)
- technologies: [MRD / molecular residual disease testing](https://onco.cc/technologies/mrd-testing/), [Tumour clonal evolution tracking](https://onco.cc/technologies/clonal-evolution-tracking/)
- terms: [Circulating tumour DNA (ctDNA)](https://onco.cc/terms/ctdna/), [Minimal / molecular residual disease (MRD)](https://onco.cc/terms/mrd/)
- trials: [TRACERx](https://onco.cc/trials/tracerx/)
- bottlenecks: [Naming which clone or phenotype is left after treatment](https://onco.cc/bottlenecks/b-subclone-attribution-residual-disease/)
- key papers: [Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution](https://onco.cc/key-papers/paper-abbosh-phylogenetic-ctdna-lung-cancer-nature-2017/), [Tracking early lung cancer metastatic dissemination in TRACERx using ctDNA](https://onco.cc/key-papers/paper-abbosh-tracerx-ctdna-relapse-nature-2023/)
- ideas: [Read methylation and mutation on the same cell-free DNA fragment to tell what kind of cancer is left](https://onco.cc/ideas/idea-same-fragment-methylation-and-mutation/)

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