Cell-Free DNA Jagged-End Analysis for Accurate Condition Classification
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Solution Overview
Problem
Existing nucleic acid analysis methods for cell-free DNA do not effectively utilize the characteristics of jagged ends in DNA fragments, leading to inaccuracies in diagnosing conditions such as cancer and transplant rejection.
Innovation Solution
Analyze the degree, density, and periodicity of jagged ends in cell-free DNA fragments, particularly in urine samples, by avoiding trimming of 3′ overhanging ends to improve the accuracy of DNA analysis, using techniques like bisulfite sequencing and adaptor-based sequencing to measure 5′ overhanging ends.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Ease of manufacture
If 3′ overhanging ends are trimmed in DNA analysis, then the analysis process is simplified, but the accuracy of measuring 5′ overhanging ends deteriorates
Solution Approach 1:
The patent segments the DNA analysis process into distinct steps: (1) analyzing 5′ overhanging ends without trimming 3′ ends to obtain accurate measurements, (2) optionally trimming 3′ ends only after 5′ end analysis is complete, and (3) using the preserved 3′ end information to verify or supplement 5′ end measurements. This segmentation allows the methodology to achieve both measurement accuracy and process simplicity.
2Ease of operation
If existing nucleic acid analysis methods are used, then the analysis is straightforward, but the diagnostic accuracy for conditions like cancer and transplant rejection is insufficient
Solution Approach 1:
The patent introduces jagged end characteristics as an intermediary measurement that bridges the gap between simple DNA analysis and accurate disease diagnosis. By measuring the length and density of 5′ overhanging ends (jagged ends) as an intermediate parameter, the methodology transforms straightforward DNA fragment analysis into a powerful diagnostic tool that can distinguish between different disease states with high accuracy.
3Measurement precision
If 3′ overhanging ends are preserved for accurate 5′ end analysis, then measurement accuracy improves, but the complexity of the analysis process increases
Solution Approach 1:
The patent applies preliminary action by performing the 5′ overhanging end analysis first, before any 3′ end trimming occurs. This preliminary measurement captures the authentic jagged end characteristics without interference from subsequent processing steps. Only after this critical preliminary analysis is complete does the methodology proceed to optional 3′ end trimming, thereby maintaining accuracy while managing process complexity.
Data Source
AI summary
The ends of cell-free DNA fragments may be used for analysis of a biological sample. In some embodiments, DNA from a urine sample may be analyzed. Cell-free DNA fragments often include jagged ends, where one end of one strand of double-stranded DNA extends beyond the other end of the other strand. The length and amount of these jagged ends may be used to determine a level of a condition of an individual. The density of ends of fragments in certain regions may also be used in classifying the level of a condition. Additionally, DNA fragments may show a periodic pattern with the amount of DNA fragments corresponding to a length of the overhang. The periodicity may be analyzed to determine properties of a biological sample. Jagged ends may also be analyzed with a technique that avoids trimming overhanging 3′ ends of a double-stranded DNA.