Real-time Sequencing Data Streaming for Clinical Analysis
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Solution Overview
Problem
Next-generation sequencing (NGS) is a costly and time-consuming process, limiting its clinical utility due to the slow generation of sequencing data, which hinders real-time analysis and decision-making in clinical settings.
Innovation Solution
A system that generates sequencing signals from nucleic acid molecules, samples them at the Nyquist rate, packages them with base pair read numbers and timestamps into data packets, and transmits these packets in real-time to a remote system for analysis, enabling real-time or near real-time processing and annotation, and sends commands back to the sequencing platform for adjustments.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If traditional NGS processing methods are used to generate complete genome representation before analysis, then sequencing accuracy is improved, but analysis time and turnaround time are significantly increased
Solution Approach 1:
The patent applies preliminary action by performing real-time analysis on incoming sequencing data streams before the complete genome representation is generated. The system processes data as it arrives, allowing preliminary identification and analysis without waiting for full sequencing completion, thus reducing turnaround time while maintaining sufficient accuracy for clinical decisions
Solution Approach 2:
The system implements partial action by analyzing only the portion of sequencing data that has been generated at any given moment, rather than requiring complete genome representation. This allows continuous analysis and identification based on available data, reducing the time loss without compromising the ability to make accurate clinical decisions
2Loss of time
If real-time sequencing analysis is implemented, then turnaround time for clinical decisions is improved, but sequencing speed becomes a limiting factor
Solution Approach 1:
The system performs preliminary processing and analysis of sequencing data as it is being generated, rather than waiting for complete sequencing. This allows clinical decisions to be prepared in advance based on available data, effectively reducing turnaround time without requiring faster sequencing hardware
Solution Approach 2:
The patent implements continuous analysis of the sequencing data stream as it is generated, maintaining uninterrupted processing throughout the sequencing operation. This continuous useful action ensures that no time is lost between data generation and analysis, maximizing the efficiency of the available sequencing speed
3Measurement precision
If complete genome representation is generated before analysis, then data accuracy is improved, but the complexity of data processing and storage is increased
Solution Approach 1:
The patent divides the sequencing data into continuous segments or streams that are processed independently as they arrive. This segmentation allows real-time analysis of data chunks without requiring the complexity of managing and processing complete genome representations, reducing data processing complexity while maintaining accuracy through systematic segment-by-segment analysis
Solution Approach 2:
The system performs analysis on partial data sets that are sufficient for identification purposes, rather than processing complete genome representations. This partial action reduces the complexity of data processing and storage requirements while maintaining the accuracy needed for clinical decision-making
Data Source
AI summary
A method for processing sequencing data, including: (i) generating, by a sequencing platform, a plurality of sequencing signals from a sequencing operation, each of the plurality of sequencing signals representing a genetic sequence; (ii) sampling, by a controller, each of the plurality of sequencing signals at a Nyquist rate of the sequencing platform to generate an upsampled signal; (iii) receiving, for each of the plurality of sequencing signals, the respective upsampled signal and information associated with the respective sequencing signal, comprising a base pair read number and a time stamp for the respective sequencing signal; (iv) packaging, by the controller for each sequencing signal, the received upsampled signal, base pair read number, and time stamp into a data packet; (v) organizing the packaged data packets into a multiplexed single data stream; and (vi) transmitting the multiplexed single data stream to a remote system.