Nucleic Acid Sequencing via Overlapping Read Assembly
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Solution Overview
Problem
Current nucleotide sequencing technologies are limited by long turnaround times and short read lengths, necessitating the development of methods that can rapidly generate sequence data for longer template samples.
Innovation Solution
The method involves generating overlapping sequencing reads by processing polynucleotides to produce overlapping nucleotide regions, attaching these regions to a substrate, and sequencing them to produce overlapping reads, which are then assembled to obtain a contiguous nucleotide sequence of a nucleic acid.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If current sequencing technology is used, then sequencing can be performed, but the turnaround time is long and read length is limited
Solution Approach 1:
The patent segments the nucleic acid template into multiple overlapping fragments that are processed simultaneously. By dividing the long template into smaller overlapping segments and sequencing them in parallel, the system reduces the total time required to obtain sequence data while maintaining complete coverage of the entire template.
Solution Approach 2:
The patent introduces a temporal dimension to the sequencing process by generating multiple overlapping reads at different positions along the template simultaneously. This dimensional approach allows parallel processing of sequence data from multiple locations, thereby reducing the overall turnaround time without compromising read length accuracy.
2Productivity
If current sequencing technology is used, then sequencing can be performed, but the read length is limited
Solution Approach 1:
The patent segments the sequencing process into multiple overlapping reads of moderate length that collectively cover the entire template. By generating overlapping reads from different starting positions, the system achieves effective read length extension without requiring excessively long single-read sequencing, thereby balancing read length capability with sequencing time.
Solution Approach 2:
The patent performs preliminary processing of the template to generate multiple overlapping fragments before sequencing. This preliminary segmentation and preparation allows the sequencing instrument to process shorter, manageable reads that can be assembled into longer effective read lengths, reducing the time required compared to attempting single long-read sequencing.
3Adaptability or versatility
If overlapping sequencing reads are generated and assembled, then longer template samples can be sequenced, but the process complexity increases
Solution Approach 1:
The patent segments the template into overlapping fragments and processes them through standardized sequencing and assembly steps. By using consistent segmentation protocols and overlapping read generation, the system achieves versatility in handling longer templates while managing complexity through repetitive, standardized operations rather than requiring entirely new complex processes.
Solution Approach 2:
The patent uses overlapping reads as copies of the template sequence from different positions. These overlapping copies are then assembled computationally to reconstruct the full template sequence. This copying and assembly approach enables sequencing of longer templates by combining multiple shorter reads, managing the complexity through computational assembly rather than requiring proportionally more complex experimental procedures.
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 significantly reduces the time to obtain sequence data and allows for the sequencing of longer template samples by generating overlapping reads that can be assembled into a contiguous sequence, improving the efficiency and accuracy of nucleic acid sequencing.
Implementation Method 1
providing a substrate having a surface which comprises a site having the set of overlapping nucleotide regions attached thereto
Data Source
AI summary
Disclosed herein are compositions and methods for sequencing nucleic acids.