Amplicon Sequencing Analysis Pipeline Using Segmented Modules
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Solution Overview
Problem
Medical and biological research using DNA sequencing is complex due to the need for interpreting large amounts of sequencing data from various sources, with existing technologies struggling to efficiently process and analyze amplicon sequencing data to identify genetic characteristics and interpret results accurately.
Innovation Solution
The Amplicon Sequencing Analysis Pipeline (ASAP) system processes amplicon sequencing data by receiving assay configuration data that associates reference sequences with genetic characteristics, comparing the data to identify target genetic features, and generating interpretation metrics such as read depth and quality, facilitating easier analysis of genetic samples.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If traditional DNA sequencing analysis methods are used to process large amounts of sequencing data from multiple sources, then comprehensive genetic characterization can be achieved, but the complexity of data interpretation increases significantly
Solution Approach 1:
The patent segments the complex sequencing data analysis into distinct functional modules: quality control module, alignment module, variant calling module, and interpretation module. Each module processes specific aspects of the data independently, reducing overall system complexity while maintaining comprehensive genetic characterization capability.
Solution Approach 2:
The patent introduces standardized intermediate data formats and reference genomes as mediators between raw sequencing data and final interpretation. These intermediaries normalize data from multiple sources, enabling consistent analysis without requiring complex custom processing for each data type.
2Measurement precision
If multiple reference sequences are used to identify genetic characteristics, then the accuracy of genetic feature identification improves, but the processing time and computational resources increase
Solution Approach 1:
The patent performs preliminary filtering and pre-alignment of sequencing reads against multiple reference sequences before full analysis. This preliminary action identifies obvious matches and filters out reads that clearly don't belong to certain references, reducing the computational burden of exhaustive multi-reference comparison.
Solution Approach 2:
The patent applies different processing strategies to different regions of the genome based on their characteristics. High-identity regions use faster alignment algorithms, while variable regions receive more intensive analysis. This local optimization maintains accuracy where needed while reducing overall processing time.
3Quantity of substance
If extensive amplicon sequencing data is generated to cover all target regions, then comprehensive genetic coverage is achieved, but the difficulty of data analysis and interpretation increases
Solution Approach 1:
The patent extracts and separates critical quality metrics (alignment quality, base quality, coverage depth) from the bulk sequencing data. These extracted metrics are presented as distinct, easily interpretable values that indicate data quality without requiring analysis of the entire raw dataset.
Solution Approach 2:
The patent uses visual indicators (such as color-coded quality scores and coverage representations) to convey complex data quality information in an intuitively understandable format. Different colors represent different quality levels, allowing rapid assessment of data reliability without detailed numerical analysis.
Data Source
AI summary
An Amplicon Sequencing Analysis Pipeline (ASAP) system (120, 600) characterizes a genetic sample. The ASAP system (120, 600) receives assay configuration data individually associating reference sequences and genetic characteristics. The ASAP system (120, 600) processes amplicon sequencing data and the reference sequences to characterize the genetic sample based on the individual associations between the reference sequences and the genetic characteristics in the assay configuration data. The ASAP (120, 600) system transfers genetic data indicating the genetic characteristics for the genetic sample and indicating interpretation metrics for amplicon sequencing read depth and quality related to the genetic characteristics.