Nucleic Acid Sequencing via Barcode Adapter Assembly
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Solution Overview
Problem
Current nucleic acid sequencing methods generate short reads that require computational reassembly, which is time-consuming, laborious, and computationally demanding, often losing crucial haplotype information and being unsuitable for complex genomes, especially due to the strain of large sequencing datasets on computer clusters.
Innovation Solution
A method that assembles intermediate and long nucleic acid sequences from short sequences by attaching barcode adapters, replicating, breaking, and circularizing nucleic acid fragments to bring barcode regions into proximity with unknown sequences, allowing for the assembly of longer sequences through sequencing and sorting by shared barcodes.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If traditional Sanger-style sequencing methods are used, then sequencing accuracy is maintained, but sequencing cost and time increase significantly
Solution Approach 1:
The patent segments the sequencing process by using multiple sequencing primers that bind to different regions of the target nucleic acid, allowing parallel sequencing of multiple segments simultaneously. This maintains accuracy through controlled primer-specific sequencing while improving throughput by processing multiple segments in parallel rather than sequentially
2Productivity
If next-generation sequencing methods are used, then sequencing speed and throughput increase, but computational requirements and data processing time increase significantly
Solution Approach 1:
The patent performs preliminary action by incorporating unique identifiers (barcodes) during the sequencing preparation stage, which pre-organizes the data structure for efficient downstream processing. This preliminary tagging allows for rapid computational reassembly without the need for complex de novo assembly algorithms, significantly reducing computational reassembly time while maintaining high throughput
3Loss of information
If computational reassembly of short reads is performed, then full sequences can be reconstructed, but haplotype information is lost and computational resources are heavily strained
Solution Approach 1:
The patent introduces unique identifiers (barcodes) as intermediary elements that link short reads to their parental haplotype. These barcodes serve as mediators that preserve haplotype information through the sequencing and assembly process without requiring complex computational methods. The barcodes enable simple grouping and assignment of reads to haplotypes, dramatically reducing computational resource requirements while preserving crucial haplotype data
4Reliability
If large sequencing datasets are processed on computer clusters, then assembly completeness improves, but system strain and processing time increase
Solution Approach 1:
The patent performs preliminary organization by tagging reads with barcodes during library preparation, which pre-structures the data for efficient processing. This preliminary action allows complete assembly to be achieved with minimal computational effort during the actual assembly phase, as reads can be quickly grouped and assembled without requiring intensive computational resources or large-scale cluster processing
Data Source
AI summary
The disclosure relates to methods for obtaining nucleic acid sequence information by constructing a nucleic acid library and reconstructing longer nucleic acid sequences by assembling a series of shorter nucleic acid sequences.