Nanopore Signal Compression for High-Throughput DNA Sequencing
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Solution Overview
Problem
Nanopore-based DNA sequencing systems generate large amounts of data that overwhelm processing capabilities, necessitating a more efficient data compression and processing method to manage the vast amount of information from parallel sequencing sensor cells.
Innovation Solution
Implementing a pre-processing circuit to extract relevant information from data generated by sequencing sensor cells, reducing the data transferred to a processor by only sending extracted information for further processing, and adapting this extraction based on system requests during different phases of cell formation, calibration, and sequencing.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Loss of information
If all data from 100,000 or more parallel sequencing sensor cells is transmitted for processing, then complete sequencing information is available, but data transfer volume and processing load become overwhelming
Solution Approach 1:
The patent extracts only the essential sequencing information from the raw data generated by sensor cells, discarding redundant data. The pre-processing circuit identifies and extracts only the critical signal features needed for base determination, significantly reducing data volume while maintaining sequencing accuracy.
Solution Approach 2:
The patent segments the data processing into two distinct stages: pre-processing at the sensor cell level and final processing at the controller level. This segmentation allows local extraction of essential information before transmission, reducing the burden on the central processing system while preserving complete sequencing capability.
2Productivity
If a pre-processing circuit extracts only relevant information from sensor cell data, then data transfer volume is reduced, but risk of information loss increases
Solution Approach 1:
The pre-processing circuit incorporates feedback mechanisms to verify that extracted information contains all necessary sequencing data. The system monitors extraction quality and adjusts parameters to ensure no critical information is lost during the compression process, maintaining sequencing accuracy while reducing data volume.
Solution Approach 2:
The pre-processing circuit performs preliminary extraction and validation of sequencing information before data transmission. By pre-identifying and verifying essential data elements upfront, the system ensures that only necessary information is transmitted while guaranteeing sequencing accuracy is maintained.
3Adaptability or versatility
If the pre-processing circuit adaptively extracts different information during different phases, then system flexibility and calibration accuracy improve, but circuit complexity increases
Solution Approach 1:
The pre-processing circuit is designed with dynamic capabilities to adapt its extraction parameters based on the operational phase (formation, calibration, or sequencing). The circuit automatically adjusts its processing mode according to real-time system state, enabling phase-specific optimization without requiring multiple separate circuits.
Data Source
AI summary
Techniques described herein relate to systems and methods for parallel DNA molecules sequencing. A preprocessor can receive raw data frames from a sensor chip including 100,000 or more cells, where each raw data frame can include detection signals from the 100,000 or more cells at a given time during the formation of the 100,000 or more cells or during the DNA molecules sequencing using the 100,000 or more cells. The preprocessor can then extract relevant information for determining states of the cells from the raw data frames, generate one or more digested frames that includes the extracted information, and send the digested frames to a processor for processing, such as base determination. Because the number of digested frames sent to the processor is less than a number of the raw data frames and the digested frames include preprocessed data, the amount of data being transferred to the processor and the amount of data processing by the processor can be reduced.