Multiplexing Base Calling and Alignment for Nucleic Acid Sequencing
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Solution Overview
Problem
Current genome sequencing platforms are limited to sequencing a single DNA molecule per flow cell at a time, hindering speed and output, necessitating either increased sequencing speed or the number of DNA molecules per flow cell.
Innovation Solution
A system and method for multiplexing base calling and alignment by obtaining combined raw intensity outputs from multiple nucleic acid molecules, using optimized score functions and reference sequences to select base calls, allowing for simultaneous sequencing of multiple molecules on a single flow cell.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If multiple DNA molecules are sequenced simultaneously on a single flow cell, then sequencing output and speed are improved, but the complexity of base calling and data processing increases
Solution Approach 1:
The patent divides the base calling process into separate independent modules for each DNA molecule. Each module processes intensity data from its specific molecule independently, then results are combined. This segmentation allows parallel processing of multiple molecules while maintaining manageable complexity in each processing unit.
Solution Approach 2:
The patent combines base calling and alignment operations into a unified multiplexed process. Multiple base calling operations and alignment operations are merged into single integrated workflows that process multiple DNA molecules simultaneously, improving efficiency while using modular design to control complexity.
2Productivity
If the sequencing speed for each genome is increased, then productivity is improved, but accuracy may deteriorate
Solution Approach 1:
The patent performs preliminary alignment of intensity data to reference sequences before final base calling. By pre-aligning the data structure and establishing expected patterns, the system can rapidly process sequences while maintaining accuracy through the constraint of known reference alignments, enabling speed without sacrificing precision.
Solution Approach 2:
The patent incorporates iterative refinement where alignment results feed back into base calling adjustments. The system uses reference sequence alignment feedback to correct and refine base calls, ensuring accuracy is maintained even as processing speed increases through efficient feedback loops rather than exhaustive processing.
Data Source
AI summary
An exemplary system, method and computer-accessible medium for multiplexing base-calling of a plurality of nucleic acid molecules in the same flow cell is provided. When multiplexing for just two nucleic acid molecules, it can operate by selecting a first base call for a first nucleic acid molecule and a second base call for a second nucleic acid molecule, after having placed them in the same flow cell and obtaining the combined raw intensity output. It can use as prior the appropriate reference genome sequences from which the nucleic acid molecules can be derived in order to create a score function, which can additionally be constrained by various penalty functions. It can derive accuracy and speed by using a branch and bound strategy as well as by performing alignment and base-calling in one step per cycle.