Circulating Nucleosome Isolation Using Linker DNA Separation

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Solution Overview

Problem

Current methods for analyzing circulating tumor DNA (ctDNA) and nucleosomes in cancer patients face challenges due to low mutant allele fraction (MAF) and interference from non-tumor-derived DNA, leading to poor quality samples and limited clinical applicability of ctDNA-based tests.

Innovation Solution

A method for separating circulating cell-free nucleosomes based on the presence or absence of linker DNA using binding agents such as histone H1, chromatin binding proteins, or antibodies that target linker DNA, allowing for the isolation of tumor-derived nucleosomes.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Measurement precision

If circulating cell-free nucleosomes are isolated from biological fluid samples for cancer detection, then tumor-derived nucleosomes can be detected, but non-tumor nucleosomes interfere with the analysis reducing detection sensitivity

Engineering Contradiction:

Improvedetection sensitivityVSAvoidinterference from non-tumor nucleosomes

Core Design Contradiction:

Measurement precisionVSObject-affected harmful factors

Solution Approach 1:

The patent segments circulating nucleosomes into two distinct groups based on the presence or absence of linker DNA: tumor-derived nucleosomes (without linker DNA, ~146 bp) and non-tumor nucleosomes (with linker DNA, >150 bp). This segmentation enables selective isolation and analysis of tumor-derived nucleosomes by targeting specific structural characteristics, thereby eliminating interference from non-tumor nucleosomes and improving detection sensitivity.

Inventive Principle:

Principle #1Segmentation

Solution Approach 2:

The patent extracts and isolates tumor-derived nucleosomes from the complex mixture of circulating nucleosomes by using binding agents that specifically recognize and bind to nucleosomes lacking linker DNA. This extraction process separates the target analyte (tumor-derived nucleosomes) from interfering substances (non-tumor nucleosomes with linker DNA), enabling precise detection and analysis of tumor-derived material in liquid biopsies.

Inventive Principle:

Principle #2Taking out (Extraction)

2Reliability

If circulating tumor DNA is analyzed directly from patient samples, then cancer detection is possible, but low mutant allele fraction limits test reliability

Engineering Contradiction:

Improvetest reliabilityVSAvoidmutant allele fraction

Core Design Contradiction:

ReliabilityVSQuantity of substance

Solution Approach 1:

The patent changes the analytical parameter from detecting mutant alleles in bulk circulating tumor DNA to detecting the specific structural parameter of linker DNA absence in nucleosomes. By focusing on the physical structure (146 bp vs. >150 bp) rather than genetic mutations, the method achieves higher reliability because the structural parameter is more abundant and easier to detect than low-frequency mutant alleles, thereby improving test reliability without being limited by low mutant allele fraction.

Inventive Principle:

Principle #35Parameter changes

3Quantity of substance

If nucleosomes with and without linker DNA are analyzed together, then all circulating nucleosomes are captured, but sample quality is reduced due to mixture of tumor and non-tumor origin

Engineering Contradiction:

Improvetotal nucleosome captureVSAvoidsample quality

Core Design Contradiction:

Quantity of substanceVSManufacturing precision

Solution Approach 1:

Instead of trying to directly isolate tumor-derived nucleosomes through positive selection, the patent uses negative selection by targeting and removing non-tumor nucleosomes that contain linker DNA. By inverting the approach and eliminating the unwanted fraction first, the remaining sample becomes enriched for tumor-derived nucleosomes, thereby improving sample quality while maintaining comprehensive capture of circulating nucleosomes.

Inventive Principle:

Principle #13The other way round (Inversion)

Applied Scientific Principles

This section explains which scientific principles are used to turn an abstract innovation direction into a practical engineering solution.

Function Achieved in This Case

Enhances the purity and quality of tumor-derived nucleosomes and DNA for analysis, improving the detection and monitoring of cancer by reducing interference from non-tumor nucleosomes and enhancing the sensitivity of ctDNA tests.

Implementation Method 1

contacting the sample with a binding agent which binds to: (a) nucleosome associated linker DNA; (b) a chromatin binding protein which binds to linker DNA

Methodology Applied

Scientific EffectDNA-protein binding:

Implementation Method 2

contacting the sample with a binding agent which binds to a clipped histone molecule from which all or part of the histone tail is absent

Methodology Applied

Scientific EffectAntigen-antibody binding:

Data Source

PatentUS12571051B2Method of isolating circulating nucleosomes

Publication Date: 2026.03.10 BELGIAN VOLITION SRL

AI summary

The invention relates to methods for separating circulating cell free nucleosomes comprising linker DNA from a biological fluid sample, in particular nucleosomes of disease origin. Such methods allow for improved analysis of genetic and epigenetic markers associated with nucleosomes of disease origin.