FFPE Nucleic Acid Prep for Chromosome Rearrangement Detection

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Solution Overview

Problem

Formalin-fixed paraffin-embedded (FFPE) samples are typically not successfully prepared using standard nucleic acid sequencing protocols, leading to a loss of spatial-proximal contiguity information necessary for genomic rearrangement detection and other applications.

Innovation Solution

A method for preparing nucleic acids from FFPE samples that involves de-waxing, rehydrating, and contacting the sample with denaturing detergent at elevated temperatures, followed by the use of reagents that preserve spatial-proximal contiguity information, optionally with extracellular matrix protease treatment.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Reliability

If standard nucleic acid sequencing protocols are used on FFPE samples, then the samples can be processed through the sequencing workflow, but spatial-proximal contiguity information is lost

Engineering Contradiction:

Improvespatial-proximal contiguity information preservationVSAvoidsample preparation success

Core Design Contradiction:

ReliabilityVSEase of manufacture

Solution Approach 1:

The patent modifies the sample preparation parameters by using elevated temperature (65-95°C) treatment with denaturing detergent, which changes the physical state of the FFPE sample to enable chromatin decompaction while preserving spatial-proximal contiguity information that would otherwise be lost in standard protocols

Inventive Principle:

Principle #35Parameter changes

Solution Approach 2:

The patent introduces an intermediary treatment step involving denaturing detergent and protease that acts as a mediator between the fixed FFPE sample and the sequencing process, enabling the release and preservation of spatial-proximal contiguity information without direct application of standard protocols

Inventive Principle:

Principle #24Intermediary (Mediator)

2Measurement precision

If FFPE samples undergo standard preparation protocols, then processing can proceed, but genomic rearrangement detection capability is lost

Engineering Contradiction:

Improvegenomic rearrangement detectionVSAvoidspatial-proximal contiguity information

Core Design Contradiction:

Measurement precisionVSLoss of information

Solution Approach 1:

The patent performs preliminary action by treating the FFPE sample with denaturing detergent and protease before sequencing to pre-preserve spatial-proximal contiguity information, ensuring that the chromatin structure maintains its spatial relationships necessary for accurate genomic rearrangement detection

Inventive Principle:

Principle #10Preliminary action

Solution Approach 2:

The patent changes the temperature parameter to elevated levels (65-95°C) during sample preparation, which prevents the loss of spatial-proximal contiguity information and thereby enables precise genomic rearrangement detection that would otherwise be impossible with standard protocols

Inventive Principle:

Principle #35Parameter changes

3Manufacturing precision

If conventional sample preparation is used on FFPE samples, then the workflow can continue, but long-range sequence contiguity information is degraded

Engineering Contradiction:

Improvelong-range sequence contiguityVSAvoidspatial-proximal contiguity preservation

Core Design Contradiction:

Manufacturing precisionVSReliability

Solution Approach 1:

The patent elevates the temperature parameter to 65-95°C during sample preparation, which maintains the reliability of spatial-proximal contiguity preservation and thereby ensures high manufacturing precision in long-range sequence contiguity for downstream sequencing applications

Inventive Principle:

Principle #35Parameter changes

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

Preserves spatial-proximal contiguity information, enabling comprehensive genomic analysis, including genomic rearrangement detection, even from low-input and long-archival-period samples, using short-read or long-read sequencing.

Implementation Method 1

contacting the dewaxed/rehydrated sample with denaturing detergent at a temperature greater than 65° C., thereby generating a solubilized and decompacted sample

Methodology Applied

Scientific EffectThermal denaturation: Heating

Implementation Method 2

the dewaxed/rehydrated sample is contacted with an extracellular matrix protease prior to contact with lysis buffer

Methodology Applied

Scientific EffectProteolytic degradation: Enzyme

Data Source

PatentUS12534490B2Methods for detecting the presence or absence of a chromosome rearrangement in a formalin-fixed paraffin embedded (FFPE) sample with no detectable genomic variant associated with cancer

Publication Date: 2026.01.27 ARIMA GENOMICS INC

AI summary

Provided herein are methods for detecting the presence or absence of a chromosome rearrangement in a formalin-fixed paraffin embedded (FFPE) sample with no detectable genomic variant associated with cancer. In certain embodiments, the methods include selecting a sample and performing a nucleic acid analysis on the selected sample and detecting whether a chromosome rearrangement is present or absent in the selected sample according to the nucleic acid analysis. In preferred embodiments, the nucleic acid analysis is a method that preserves spatial-proximal contiguity information.