Nanopore Array Data Compression for High-Throughput Sequencing
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Solution Overview
Problem
Nanopore-based sequencing chips face challenges in managing the high data transmission rates generated by large arrays of sensor cells, leading to unattainable data rates due to the vast amount of data produced during nucleotide sequencing, which complicates efficient processing and analysis.
Innovation Solution
Implementing digital compression techniques and on-chip data reduction methods, such as filtering and calibration, to process and summarize the data, reducing the aggregate transmission data rate by converting raw data into more compact summaries that retain essential information for base calling, and using field programmable gate arrays or application-specific integrated circuits for data processing.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If large arrays of sensor cells are used for sequencing, then sequencing capacity and productivity are improved, but data transmission rate becomes unmanageably high
Solution Approach 1:
The patent divides the large array of sensor cells into smaller groups or blocks, processing and compressing data from each group separately before aggregation. This segmentation allows manageable data handling while maintaining overall high sequencing capacity, as each segment's data can be processed independently through compression algorithms.
Solution Approach 2:
The patent extracts and removes redundant or less critical data elements from the raw sensor output, retaining only the most essential information needed for accurate base calling. This extraction process significantly reduces the data volume transmitted from the chip while preserving sequencing accuracy.
2Loss of information
If raw data is transmitted directly from all sensor cells, then data completeness is improved, but transmission bandwidth requirements become unattainable
Solution Approach 1:
The patent transforms the data from its original high-volume format into a compressed representation with different parameters. By changing how data is encoded and aggregated, the system maintains the essential information content while dramatically reducing the transmission rate required to move data off-chip.
Solution Approach 2:
The patent performs data compression and filtering operations on-chip before data leaves the sensor array. This preliminary processing reduces the data volume that needs to be transmitted, allowing complete sequencing information to be conveyed at manageable transmission speeds.
3Quantity of substance
If data compression and filtering are applied on-chip, then data transmission rate is reduced, but processing complexity increases
Solution Approach 1:
The patent introduces intermediate processing stages within the chip architecture that bridge the simple sensor array and the external processing systems. These intermediary components perform targeted compression and filtering operations, adding necessary processing complexity only where needed to reduce transmission volume without overwhelming the system.
Solution Approach 2:
The patent combines multiple data processing functions (filtering, compression, aggregation) into integrated on-chip processing units. By merging these functions into unified processing blocks, the system reduces overall complexity compared to having separate dedicated circuits for each function, while still achieving significant data reduction.
Data Source
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AI summary
A method of exporting measurements of a nanopore sensor on a nanopore based sequencing chip is disclosed. An electrical characteristic associated with the nanopore sensor is measured. The electrical characteristic associated with the nanopore sensor is processed. A summary for the electrical characteristic and one or more previous electrical characteristics is determined. The summary for the electrical characteristic and the one or more previous electrical characteristics are exported. Determining the summary includes determining that the electrical characteristic and at least a portion of the one or more previous electrical characteristics correspond to a base call event at the nanopore sensor. The summary represents the electrical characteristic and the at least a portion of the one or more previous electrical characteristics.