Context-Aware Base Calling for Homopolymer Sequencing
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Solution Overview
Problem
Current nucleic acid sequencing methods face challenges in accurate base calling, particularly with sequences containing homopolymers, due to random and unpredictable systematic variations in signal levels and context-dependent signals, leading to errors in quantifying homopolymer lengths.
Innovation Solution
The method involves generating sequence signals from nucleic acid molecules, determining base calls based on these signals and quantified context dependency, and processing the signals to remove systematic errors and determine homopolymer lengths, using techniques such as imputed sequences, HpN truncated sequences, and context-specific mappings to align and quantify signals.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If base calling is performed based on quantified characteristic signals indicating nucleotide incorporation, then sequencing speed and throughput are improved, but sequencing accuracy deteriorates due to random and unpredictable systematic variations in signal levels and context dependent signals
Solution Approach 1:
The patent employs feedback mechanisms by using quantified context dependency values derived from known sequences to adjust and refine base calling decisions. The system continuously refines its understanding of context-dependent signal variations and applies this knowledge to correct base calling errors in real-time, improving accuracy without sacrificing throughput
Solution Approach 2:
The patent changes the parameter space by introducing quantified context dependency as an additional dimension for base calling. Instead of relying solely on raw signal intensity, the system incorporates context-dependent correction factors that adjust signal interpretation based on local sequence context, thereby resolving the accuracy-throughput tradeoff
2Reliability
If sequencing methods quantify homopolymer lengths based on signal levels, then homopolymer detection capability is improved, but measurement precision deteriorates due to context dependent signals varying for every sequence
Solution Approach 1:
The patent introduces quantified context dependency values as an intermediary that mediates between raw signal levels and homopolymer length determination. This intermediary layer corrects for context-dependent signal variations by comparing observed signals against expected signals derived from known sequences, thereby enabling accurate homopolymer length quantification despite signal variability
Solution Approach 2:
The patent performs preliminary action by pre-characterizing context-dependent signal variations using known sequences before actual sequencing. This pre-established context dependency information is then applied to correct and refine homopolymer length measurements during sequencing, improving precision without reducing detection capability
Data Source
AI summary
The present disclosure provides methods and systems for accurate and efficient context-aware base calling of sequences. In an aspect, disclosed herein is a method for sequencing a nucleic acid molecule, comprising: (a) sequencing the nucleic acid molecule to generate a plurality of sequence signals; and (b) determining base calls of the nucleic acid molecule based at least in part on (i) the plurality of sequence signals and (ii) quantified context dependency for at least a portion of the plurality of sequence signals.