Nucleic Acid Pool Complexity Reduction via Segmentation
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Solution Overview
Problem
Current high-throughput sequencing methods face challenges in aligning and assembling nucleic acid sequences due to the complexity of mixed samples, particularly in identifying rare nucleic acids amidst abundant ones, which limits the accuracy and efficiency of sequence assembly and detection.
Innovation Solution
A method involving random or sequence-independent cutting of nucleic acid molecules to create subpools with a common nucleic acid feature, followed by amplification and segregation, allowing for the separation and analysis of fragments with shared characteristics, thereby reducing sequence complexity and enhancing the detection of rare nucleic acids.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Ease of manufacture
If random amplification of input DNA fragments is performed to simplify preparation, then ease of manufacture is improved, but device complexity increases due to the sheer complexity of complete sample information obtained simultaneously
Solution Approach 1:
The patent divides the complex nucleic acid sample into multiple subpools based on fragment characteristics (e.g., size, sequence features). Each subpool contains a subset of fragments with common features, reducing the complexity of information that must be processed simultaneously. This segmentation allows parallel processing of simpler subpools rather than attempting to process the entire complex sample at once.
2Measurement precision
If the number of reads is increased to improve sequence assembly quality, then measurement precision is improved, but device complexity increases due to the challenging task of assembling millions of small reads
Solution Approach 1:
By dividing reads into subpools based on shared characteristics, the patent reduces the assembly complexity from handling millions of reads simultaneously to assembling smaller subsets independently. Each subpool assembly task is computationally simpler, and the results can be integrated to reconstruct the complete sequence with high precision.
Solution Approach 2:
The patent performs preliminary grouping of reads into subpools based on common features before the assembly process. This preliminary organization simplifies subsequent assembly operations by pre-establishing relationships between reads that share characteristics, making the assembly process more efficient and accurate.
3Manufacturing precision
If rigorous dilution is used to singularize DNA molecules, then manufacturing precision is improved, but loss of substance increases due to the dilution process
Solution Approach 1:
Instead of using rigorous dilution to achieve singularization, the patent segments the sample into subpools based on fragment characteristics. This approach maintains higher concentrations of nucleic acids in each subpool while still achieving effective singularization for sequencing, thereby reducing material loss compared to dilution-based methods.
Data Source
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AI summary
The present invention relates to a method for the reduction of the complexity of nucleic acid pool(s), comprising - providing a sample with one or more nucleic acid molecules, - cutting the nucleic acid molecules by a random and/or sequence independent cutting step thereby obtaining a pool of nucleic acid fragments, - amplifying one or more fragments of said nucleic acid molecules, wherein the one or more fragments constitute at least a fraction of all fragments of the nucleic acid molecules, and wherein the amplified or amplifying one or more fragments of said fraction are divided into different subpools, and wherein the fragments of each subpool comprise a common nucleic acid feature.