Sequencing Base Calling With Two-Stage Phasing and Prephasing
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Solution Overview
Problem
Existing sequencing technologies face challenges in accurately correcting phasing and prephasing errors in DNA sequencing, leading to reduced accuracy in base calling due to unsynchronized sequencing signals from clustered DNA fragments.
Innovation Solution
A two-stage correction process utilizing phasing and prephasing information from previous and subsequent sequencing cycles, combined with penalty functions, to correct image intensities in polonies or clusters, allowing for accurate base calling even in low or unbalanced diversity samples.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If phasing and prephasing correction is performed using existing methods, then base calling accuracy is improved, but computational complexity increases and processing efficiency decreases
Solution Approach 1:
The correction process is divided into distinct stages: estimating phasing/prephasing parameters from current cycle data, applying corrections using these parameters, and optionally refining with subsequent cycle information. This segmentation allows the complex correction task to be broken into manageable computational steps, reducing overall complexity while maintaining accuracy
Solution Approach 2:
The method performs preliminary estimation of phasing and prephasing parameters using only current cycle data before applying corrections. This preliminary action enables the system to address the majority of synchronization errors without requiring complex iterative processing of multiple cycles, thereby reducing computational burden
2Measurement precision
If phasing and prephasing correction uses multiple sequencing cycles, then correction accuracy is improved, but processing time increases
Solution Approach 1:
The system performs preliminary correction using current cycle data immediately, providing timely base calling results. Subsequent cycle information is then used to refine these corrections, allowing the system to deliver accurate results without waiting for complete multi-cycle data accumulation, thus reducing processing time
Solution Approach 2:
The method uses feedback from subsequent sequencing cycles to refine initial correction estimates. After preliminary base calling is performed using current cycle data, information from subsequent cycles feeds back to adjust and improve the correction accuracy, achieving high precision without excessive processing delays
3Reliability
If existing phasing correction methods are applied, then synchronization errors are reduced, but the method fails to handle low diversity samples effectively
Solution Approach 1:
The method dynamically adjusts correction parameters based on the observed diversity characteristics of the sequencing sample. For low diversity samples, the algorithm modifies its parameter estimation approach to account for limited base variation, ensuring reliable correction across diverse sample types without requiring sample-specific preprocessing
Solution Approach 2:
The correction method is designed to universally handle different sample diversity levels through a unified algorithmic framework. By incorporating adaptive parameter estimation that works with both high and low diversity samples, the system achieves multi-functionality without requiring separate correction protocols for different sample types
Data Source
AI summary
The present disclosure includes methods, systems, and media for performing a phasing and prephasing correction in sequencing analysis, comprising: determining corrected image intensities of a plurality of polonies, Ipc(N), based on a cycle N−1 phasing coefficient, pN−1, a cycle N−1 prephasing coefficient, ppN−1, or both; obtaining base calls in the cycle N based on the corrected image intensities of the plurality of polonies in the cycle N, Ipc(N); selecting, by the processor, polonies from the plurality of polonies based on the base calls; determining a cycle N phasing coefficient, pN, a cycle N prephasing coefficient, ppN, or both; and updating image intensities of the plurality of polonies in cycle N, I(N), using updated and corrected image intensities, Ipc_n(N), wherein Ipc_n(N) is obtained based on the cycle N phasing coefficient, pN, the cycle N prephasing coefficient, ppN, or both.