Nucleic Acid Sequencing Error Filtering via Tag Segmentation
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Solution Overview
Problem
Next Generation Sequencers (NGS) often exclude sequence information containing errors in the tag portion from analysis, leading to reduced accuracy and coverage rates in nucleic acid sequencing.
Innovation Solution
A method that includes preparing a pool of amplicons with tagged primers, sequencing, and determining the target nucleic acid sequence by comparing sequence information from error-free and error-containing amplicons, allowing for the inclusion of sequence information from amplicons with errors to improve coverage and accuracy.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If sequence information containing errors in the tag portion is excluded from analysis, then measurement precision is improved, but productivity deteriorates
Solution Approach 1:
The patent divides the sequence information into two parts: the tag portion (which may contain errors) and the target sequence portion (which is accurate). By segmenting the analysis approach, the patent excludes only the erroneous tag portion from analysis while retaining the accurate target sequence portion, thus resolving the contradiction between measurement precision and productivity
Solution Approach 2:
The patent extracts and removes the problematic tag portion from the sequence information before analysis. By taking out the erroneous elements (tag sequences with insertion/deletion errors) while preserving the useful target sequence data, the patent improves coverage rate without sacrificing analysis accuracy
2Productivity
If sequence information containing errors in the tag portion is included in analysis, then productivity is improved, but measurement precision deteriorates
Solution Approach 1:
The patent converts the potentially harmful effect of tag sequence errors into a beneficial filtering process. By using the known structure of the tag sequence as a reference, the patent identifies and excludes only the erroneous reads, transforming what would be noise into a useful quality control mechanism that enables broader data inclusion
3Measurement precision
If conventional sequencing analysis is performed excluding error-containing sequences, then measurement precision is maintained, but loss of information increases
Solution Approach 1:
The patent introduces an intermediary filtering step that compares the tag portion of each sequence against the known tag sequence structure. This intermediary process acts as a gatekeeper, allowing accurate sequences to pass through while blocking erroneous ones, thereby preventing information loss without compromising measurement precision
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 enhances the accuracy and depth of sequencing coverage by utilizing sequence information from both error-free and error-containing amplicons, thereby improving the reliability of nucleic acid sequence analysis.
Implementation Method 1
amplifying the tagged nucleotide by PCR using a universal primer which hybridizes to the universal primer section
Implementation Method 2
a universal primer which hybridizes to the universal primer section
Data Source
AI summary
The present invention relates to a method for determining a nucleotide sequence of a target nucleic acid. The method comprises: providing a pool of amplicons; sequencing each amplicon in the pool of amplicons to obtain sequence information of each amplicon; comparing a part of the sequence information of each amplicon with at least a part of the sequence of the target specific primer section, wherein the part of the sequence information of each amplicon is a sequence starting from position X+1; determining whether the part of the sequence information of each amplicon comprises at least the part of the sequence of the target specific primer section; and determining accurate sequence of the target region using sequence information which comprises at least the part of the sequence of the target-specific primer section.