Nonspecific Amplification Sequence Identification in Lymphoma NGS
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Solution Overview
Problem
In lymphoma diagnosis using Next-Generation Sequencing (NGS) technology, the high variability of gene clusters leads to nonspecific amplification, resulting in low data efficiency, with less than 50% target fragments in multiplexed amplification sequencing data, and existing methods do not effectively address this issue.
Innovation Solution
A method is provided to identify the source primer of nonspecific amplification sequences by aligning amplification sequence data to source gene sequence data, identifying nonspecific amplification sequences, and then aligning these to primer sequence data to determine the amplification source primer, which involves acquiring and processing sequence data through modules for alignment and de-redundancy processing.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Adaptability or versatility
If multiplexed amplification is performed on DNA fragments using conventional methods, then the amplification coverage is increased, but nonspecific amplification occurs leading to low data efficiency
Solution Approach 1:
The patent performs preliminary alignment of amplification sequence data to source gene sequence data before final analysis, identifying nonspecific amplification sequences in advance. This preliminary action allows for the detection and exclusion of nonspecific amplification products, thereby improving data efficiency while maintaining amplification coverage
Solution Approach 2:
The patent introduces an intermediary alignment process between amplification and final sequencing analysis. By using alignment algorithms to compare amplification sequences against known source gene sequences, the system acts as an intermediary filter that separates specific from nonsspecific amplification, resolving the contradiction between coverage and efficiency
2Ease of operation
If conventional amplification methods are used without identification of nonsspecific sequences, then the process is simple, but the proportion of target fragments remains less than 50%
Solution Approach 1:
The system performs self-service by automatically aligning amplification sequences to source gene sequences and identifying nonsspecific amplification products without manual intervention. The alignment module autonomously processes the data, compares sequences, and flags nonsspecific amplification, improving target fragment proportion while maintaining operational simplicity through automation
Solution Approach 2:
The patent replaces manual analysis of amplification sequences with computational alignment algorithms. Instead of mechanically examining each sequence, the system uses bioinformatics tools to automatically identify nonsspecific amplification, significantly improving target fragment proportion while keeping the process simple through computerized automation
Data Source
AI summary
A method, an apparatus and a device for identifying a source primer of a nonspecific amplification sequence are provided in the present disclosure, which belongs to the technical field of gene detection. The method includes: acquiring amplification sequence data of an amplified gene obtained by primer amplification of a target gene fragment, source gene sequence data of a source gene to which the target gene fragment belongs, and primer sequence data used in the primer amplification; aligning the amplification sequence data to the source gene sequence data, and taking the amplification sequence data that does not match the source gene sequence data as nonspecific amplification sequence data; and aligning the nonspecific amplification sequence data to the primer sequence data, and taking a primer with primer sequence data being matched with the nonspecific amplification sequence data as an amplification source primer of the nonspecific amplification sequence.