73-DIP Multiplex PCR Detection for East Asian Ancestry Inference
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Solution Overview
Problem
Existing forensic DNA analysis methods face challenges in accurately identifying and inferring biogeographical ancestry, particularly for East Asian populations, due to limited loci in multiplex amplification systems and the need for improved genetic markers and machine learning methodologies to handle high-dimensional and sparse data.
Innovation Solution
A system and kit for multiplex amplification and detection targeting 73 DIP loci, utilizing a set of primers and amplification premix composition, combined with six-dye fluorescent labeling and machine learning algorithms, to simultaneously detect these loci in a single reaction, enabling precise biogeographical ancestry inference for major intercontinental and intra-East Asian populations.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If the number of DIP loci in multiplex amplification system is increased, then the biogeographical ancestry inference accuracy is improved, but the system complexity and difficulty of detecting and measuring increase
Solution Approach 1:
The patent divides the detection system into modular components: 73 DIP loci are segmented into multiple groups, each detected by specific primer pairs and fluorescent dyes. The amplification system is segmented into multiple reactions that can be processed simultaneously, reducing the complexity of handling each individual locus while maintaining high overall accuracy for biogeographical ancestry inference.
Solution Approach 2:
The patent optimizes detection parameters including fluorescent dye selection, primer concentrations, and amplification conditions to enable simultaneous detection of multiple DIP loci. By carefully adjusting these parameters, the system achieves high measurement precision for ancestry inference while controlling system complexity through standardized protocols.
2Productivity
If the number of DIP loci detected simultaneously is increased, then the productivity is improved, but the difficulty of detecting and measuring increases
Solution Approach 1:
The patent merges multiple DIP locus detections into a single multiplex amplification reaction system. By combining 73 loci into one integrated detection workflow using fluorescent labeling and capillary electrophoresis, the system achieves high productivity while managing detection difficulty through unified protocol standardization and automated analysis.
Solution Approach 2:
The detection system is designed with universal applicability through the use of standardized fluorescent dyes and primer pairs that can detect multiple DIP loci simultaneously. This multi-functional approach allows the same system to handle diverse genetic markers without requiring separate detection protocols for each locus, thereby improving productivity.
3Reliability
If traditional PCR-CE platform is used with six-dye fluorescence detection, then the manufacturing precision and reliability are improved, but the device complexity increases
Solution Approach 1:
The patent utilizes six-dye fluorescent labeling to encode multiple DIP loci with distinct fluorescent signals, enabling reliable simultaneous detection. By optimizing dye selection and concentration parameters, the system achieves high reliability for ancestry inference while managing device complexity through standardized fluorescent detection protocols compatible with existing capillary electrophoresis equipment.
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
The system achieves high-performance biogeographical ancestry inference, accurately distinguishing between African, European, South Asian, and South American populations, and further subdividing East Asian populations into Han Chinese, Southeast Asian, and Japanese groups, with an average accuracy rate of over 90% through capillary electrophoresis and machine learning models.
Implementation Method 1
a system for multiplex amplification and detection targeting 73 DIP (Deletion/Insertion Polymorphism) loci
Implementation Method 2
The detection of DIP marker is applicable to both the next-generation sequencing platform and the capillary electrophoresis (CE) platform
Implementation Method 3
With the introduction of the six-dye fluorescence detection protocol in 2014, the number of loci capable of simultaneous capillary separation has been greatly increased
Data Source
AI summary
A system for multiplex amplification and detection targeting 73 DIP loci and an application thereof. The system includes a set of primers and an amplification premix composition, wherein the set of primers target each of 73 DIP loci. The present system is capable of simultaneously detecting 73 DIP loci in a single reaction on various types of samples, and thus provides a high-performance novel solution for biogeographical ancestry inference of the five major intercontinental populations including African, European, East Asian, South Asian and Native American populations other than American Mestizos and the intra-East Asian populations including Han Chinese, Southeast Asian and Japanese populations.