Plasma DNA Concatemerization for Nanopore Sequencing Efficiency
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Solution Overview
Problem
Current nanopore sequencing techniques are inefficient for analyzing short, low-concentration DNA fragments in plasma samples due to low sequencing accuracy and frequency of DNA molecules passing through nanopores, making non-invasive prenatal testing and other applications challenging.
Innovation Solution
The method involves concatemerization of DNA fragments to create longer molecules and concentration of DNA samples to increase the likelihood of DNA fragments interacting with nanopores, allowing for more efficient sequencing by enhancing the frequency and accuracy of DNA analysis.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Ease of manufacture
If nanopore sequencing is used for plasma DNA analysis, then the equipment cost is reduced and footprint is minimized, but the sequencing efficiency and accuracy deteriorate due to low DNA concentration and short fragment length
Solution Approach 1:
The patent applies preliminary action by performing concatemerization of DNA fragments before nanopore sequencing. This pre-processing step creates longer DNA molecules from short plasma DNA fragments, ensuring they are suitable for efficient nanopore sequencing. The concatemerization process joins multiple short DNA fragments into longer chains, which then pass through nanopores more effectively, resolving the efficiency problem while maintaining the cost advantage of nanopore technology.
2Area of stationary object
If nanopore sequencing is used for plasma DNA analysis, then the equipment footprint is minimized, but the sequencing accuracy deteriorates due to low frequency of DNA molecules passing through nanopores
Solution Approach 1:
The patent applies preliminary action by performing concatemerization of DNA fragments before nanopore sequencing. This pre-processing step creates longer DNA molecules from short plasma DNA fragments, ensuring they are suitable for efficient nanopore sequencing. The concatemerization process joins multiple short DNA fragments into longer chains, which then pass through nanopores more effectively, resolving the efficiency problem while maintaining the cost advantage of nanopore technology.
3Productivity
If DNA fragments are concatemerized to create longer molecules, then the sequencing efficiency is improved, but the sample preparation complexity increases
Solution Approach 1:
The patent applies parameter changes by modifying the physical state and length of DNA molecules through concatemerization. By changing the length parameter of DNA fragments from short individual pieces to longer concatemerized chains, the patent improves sequencing efficiency. The concatemerization process transforms the DNA sample into a form that is more suitable for nanopore sequencing, allowing longer molecules to pass through nanopores and generate sufficient signal for accurate base calling.
4Productivity
If DNA concentration is increased to improve sequencing frequency, then the sequencing efficiency is improved, but the risk of DNA degradation or contamination increases
Solution Approach 1:
The patent applies preliminary action by performing concatemerization of DNA fragments before nanopore sequencing. This pre-processing step creates longer DNA molecules from short plasma DNA fragments, ensuring they are suitable for efficient nanopore sequencing. The concatemerization process joins multiple short DNA fragments into longer chains, which then pass through nanopores more effectively, resolving the efficiency problem while maintaining the cost advantage of nanopore technology.
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 approach improves the sequencing efficiency and accuracy of short DNA fragments, enabling the detection of plasma DNA aberrations and fetal chromosomal aneuploidies, and can be applied to various medical applications such as prenatal diagnosis and cancer assessment.
Implementation Method 1
performing single-molecule sequencing of the first concatemer to obtain a first sequence of the first concatemer. In some embodiments, single-molecule sequencing may be performed using a nanopore, and the method may include passing the first concatemer through a first nanopore. A first electrical signal may then be detected as the first concatemer passes through the first nanopore.
Data Source
AI summary
Embodiments may include a method of sequencing cell-free DNA fragments. Cell-free DNA fragments may include plasma DNA fragments. The method may include receiving a biological sample including a plurality of DNA fragments. The biological sample may have a first concentration of DNA fragments. The method may also include concentrating the biological sample to have a second concentration of DNA fragments. The second concentration of DNA fragments may be 5 or more times higher than the first concentration of DNA fragments. The method may further include passing the plurality of DNA fragments through nanopores on a substrate. For each of the plurality of DNA fragments, electrical signals may be detected as the DNA fragment passes through a nanopore. The electrical signals may correspond to the sequence of the DNA fragment. Systems for analyzing DNA fragments are also described.