Plasma Cell-Free DNA Methylome Profiling for Noninvasive Tumor Detection
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Solution Overview
Problem
There is no practical means to study the fetal or tumor methylome noninvasively, hindering the monitoring of dynamic changes throughout pregnancy or during disease processes such as malignancies.
Innovation Solution
A method for determining methylation profiles using genome-wide bisulfite sequencing of cell-free DNA in maternal plasma, allowing for the noninvasive analysis of fetal or tumor methylomes by comparing methylation patterns with maternal profiles, and utilizing fetal-specific alleles or size parameters to identify DNA fragments.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If invasive procedures are used to obtain fetal or tumor tissue for methylome analysis, then measurement precision is improved, but ease of operation deteriorates
Solution Approach 1:
The patent uses maternal plasma as an intermediary medium that contains cell-free fetal DNA, allowing indirect access to fetal methylome without directly sampling fetal tissue. This mediator enables the analysis of fetal epigenetic markers through a non-invasive blood draw from the mother, resolving the contradiction between obtaining precise fetal methylome data and avoiding invasive procedures
Solution Approach 2:
The patent analyzes copies of fetal DNA that are present in maternal plasma rather than the original fetal tissue. The cell-free fetal DNA in plasma serves as a molecular copy that retains the epigenetic methylation patterns of the fetal genome, enabling methylome analysis through non-invasive sampling while maintaining measurement precision
2Measurement precision
If genome-wide bisulfite sequencing is performed on mixed DNA samples, then measurement precision is improved, but device complexity increases
Solution Approach 1:
The patent segments the mixed DNA population by identifying and analyzing only those DNA fragments that contain fetal-specific alleles. This segmentation approach isolates the fetal-derived methylome signal from the maternal background, enabling precise fetal methylome analysis through standard sequencing technology without requiring complex specialized equipment
Solution Approach 2:
The patent applies local quality analysis by focusing methylation analysis specifically on genomic regions containing fetal-specific single nucleotide polymorphisms (SNPs). Rather than uniformly analyzing the entire genome, the method concentrates computational and analytical resources on loci where fetal DNA can be distinguished from maternal DNA, improving precision while managing complexity
3Measurement precision
If fetal-specific alleles are used to identify fetal DNA in maternal plasma, then measurement precision is improved, but difficulty of detecting and measuring increases
Solution Approach 1:
The patent performs preliminary genotyping of both mother and fetus to identify fetal-specific alleles before conducting the methylome analysis. This preliminary action establishes a reference set of discriminatory markers that simplify the subsequent detection process, allowing straightforward identification of fetal DNA fragments in the plasma sample based on the presence of these pre-identified alleles
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 noninvasive, comprehensive, and serial monitoring of fetal or tumor methylomes, facilitating early detection, monitoring, and prognostication of pregnancy-related pathologies and cancers, including various types of malignancies.
Implementation Method 1
genome-wide bisulfite sequencing of cell-free DNA
Data Source
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AI summary
Systems, methods, and apparatuses can determine and use methylation profiles of various tissues and samples. Examples are provided. A methylation profile can be deduced for fetal/tumor tissue based on a comparison of plasma methylation (or other sample with cell-free DNA) to a methylation profile of the mother/patient. A methylation profile can be determined for fetal/tumor tissue using tissue-specific alleles to identify DNA from the fetus/tumor when the sample has a mixture of DNA. A methylation profile can be used to determine copy number variations in genome of a fetus/tumor. Methylation markers for a fetus have been identified via various techniques. The methylation profile can be determined by determining a size parameter of a size distribution of DNA fragments, where reference values for the size parameter can be used to determine methylation levels. Additionally, a methylation level can be used to determine a level of cancer.