Liquid Biopsy Size Selection for Target DNA Enrichment
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Solution Overview
Problem
Current liquid biopsy methods face challenges in enriching for cell-free DNA (cfDNA) from specific sources such as fetal, cancerous, or transplanted organ tissues, due to overwhelming amounts of DNA from normal cells, making it difficult for non-invasive prenatal testing, cancer monitoring, and transplant monitoring.
Innovation Solution
A method involving the isolation of cfDNA, optional ligation of adaptors, selective enrichment of trinucleosomal, dinucleosomal, or mononucleosomal DNA, and subsequent sequencing to increase the fraction of target tissue DNA, using techniques like multiplex amplification and hybrid capture for improved diagnostic accuracy.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If conventional liquid biopsy methods are used to isolate cfDNA from biological samples, then cfDNA can be obtained for analysis, but the overwhelming majority of cfDNA comes from normal cells (maternal cells in prenatal diagnosis, host cells in transplant monitoring, normal cells in cancer monitoring), making it difficult to detect target tissue DNA
Solution Approach 1:
The patent segments cfDNA based on fragment size, recognizing that target tissue DNA (fetal, tumor, or donor-derived) produces cfDNA fragments of specific size ranges that differ from normal cell-derived fragments. By isolating and analyzing specific size fractions, the method enriches for target tissue DNA signals amidst the overwhelming background of normal cell DNA.
Solution Approach 2:
The patent applies local quality by treating different size fractions of cfDNA differently. Instead of analyzing all cfDNA uniformly, the method identifies and focuses on specific size ranges (local characteristics) that are enriched for target tissue origin, thereby improving detection precision without requiring enrichment of the entire cfDNA population.
2Measurement precision
If size selection methods are applied to enrich for specific cfDNA fragments, then the fraction of target tissue DNA increases, but the complexity of the diagnostic method increases
Solution Approach 1:
The patent changes the physical parameter of cfDNA analysis by focusing on fragment size rather than sequence content for the initial enrichment step. This parameter change allows for relatively simple size-based separation methods (such as gel electrophoresis or size-exclusion chromatography) to achieve target tissue DNA enrichment before more complex sequencing or analysis is performed.
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
This method significantly enhances the diagnostic confidence and accuracy by increasing the fraction of fetal, cancerous, or donor-derived cfDNA, enabling effective non-invasive prenatal testing, cancer monitoring, and transplant monitoring.
Implementation Method 1
selectively enriching trinucleosomal, dinucleosomal, mononucleosomal or sub-mononucleosomal DNA from the isolated cfDNA, the adaptor-ligated DNA or the amplified adaptor-ligated DNA
Data Source
AI summary
Provided herein are improved methods of determining the sequences of cell-free DNA (cfDNA). The methods in certain embodiments are used for the analysis of circulating DNA in serum samples, such as circulating fetal DNA, circulating donor derived DNA, or circulating tumor DNA. In certain embodiments, the methods include selectively enriching trinucleosomal, dinucleosomal, mononucleosomal or sub-mononucleosomal DNA from the isolated cfDNA.