cfDNA Methylation Detection for Native Organ Damage Monitoring
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Solution Overview
Problem
Existing methods for detecting organ-specific cell-free DNA (cfDNA) are limited in their applicability, particularly for monitoring native organs, and there is a need for methods and compositions that can identify and monitor tissue- or organ-specific cfDNA beyond situations of chimerism, such as in organ transplant recipients.
Innovation Solution
The use of epigenetic markers, specifically DNA methylation signatures, to identify and detect organ damage by analyzing cfDNA obtained from a biological sample, utilizing techniques like bisulfite treatment and PCR amplification to detect differentially methylated regions in kidney cells.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If Y-chromosomal markers or donor-specific alleles are used to detect organ-specific cfDNA, then detection accuracy for transplant rejection is improved, but applicability is limited only to chimerism situations such as organ transplant recipients
Solution Approach 1:
The patent applies universality by using epigenetic markers (DNA methylation patterns) that are tissue-specific and can identify cfDNA origin from any organ in both transplant and non-transplant scenarios. This replaces the limited Y-chromosomal markers with a universal system that works across all organs and patient types, enabling detection of organ damage in native organs, transplanted organs, and other conditions without requiring chimerism
Solution Approach 2:
The patent changes the detection parameter from genetic markers (Y-chromosome, donor-specific alleles) to epigenetic markers (DNA methylation patterns). This parameter change enables the detection system to work with autologous DNA from any tissue source, transforming the assay from transplant-specific to universally applicable for organ damage detection
2Measurement precision
If massively parallel sequencing methods are used to identify donor-specific alleles, then detection specificity is improved, but method complexity and cost increase
Solution Approach 1:
The patent extracts only the tissue-specific epigenetic marker information from cfDNA using targeted approaches such as methylation-specific PCR or targeted sequencing of differentially methylated regions. This extraction of specific markers rather than whole-genome analysis reduces method complexity and cost while maintaining detection specificity for organ damage
Solution Approach 2:
The patent uses copying by creating amplified copies of specific differentially methylated regions through PCR techniques. This allows detection of tissue-specific epigenetic markers without requiring whole-genome sequencing, simplifying the methodology while preserving detection specificity
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
Enables the detection of organ damage, including kidney damage, through the identification of specific epigenetic markers, providing a method for effective detection of acute kidney injury and chronic kidney disease, and other conditions.
Implementation Method 1
treating the cfDNA with bisulfite to obtain bisulfite converted cfDNA
Implementation Method 2
identifying the at least one methylated region by PCR amplification of the bisulfite converted cfDNA with primers that selectively amplify the at least one methylated region
Data Source
AI summary
Epigenetic modifications play an important role in regulating cell-specific expression patterns. Different DNA methylation signatures, for example, can be found in different tissues and even between different cell types within a particular tissue. In work leading to the present invention, the inventors found that these methylation signatures can be used to identify cfDNA tissue of origin. Moreover, these novel methylation markers can be used to detect cell, tissue or organ damage, including autologous cell, tissue or organ damage.