Sequence Information Classification for Co-Localized Nucleobase Signals
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Solution Overview
Problem
Existing next-generation sequencing (NGS) technologies face challenges in increasing sequencing throughput and efficiently determining sequence information from multiple polynucleotide sequence portions within a single sequencing run, particularly when these portions are not spatially resolvable.
Innovation Solution
A method is developed to determine sequence information from two or more polynucleotide sequence portions by obtaining intensity data from combined signals of respective nucleobases and selecting classifications based on these intensities, allowing for simultaneous determination of matches or mismatches between the sequences, even when they are co-localized within the same nucleic acid cluster.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If multiple polynucleotide sequence portions are sequenced simultaneously in a single run, then sequencing throughput is improved, but the complexity of determining sequence information from co-localized, non-spatially-resolvable portions increases
Solution Approach 1:
The patent segments the sequence determination problem by classifying signal intensity combinations into distinct categories (e.g., high-high, high-low, low-high, low-low intensity patterns). This segmentation allows the system to handle multiple sequence portions simultaneously while maintaining manageable complexity through systematic classification of signal patterns.
Solution Approach 2:
The patent introduces a classification dimension to the sequence determination process. By adding the dimension of signal intensity classification (first classification for matching nucleobases, second classification for mismatching nucleobases), the system transforms a complex multi-dimensional problem into a more manageable framework that enables simultaneous sequencing of multiple portions.
2Productivity
If combined signal intensity data is used to determine sequence information from co-localized sequence portions, then sequencing efficiency is improved, but measurement precision challenges arise from signal overlap
Solution Approach 1:
The patent changes the parameter approach by using combined signal intensity data rather than attempting to resolve individual signals spatially. By transforming the measurement approach from spatial resolution to intensity-based classification, the system achieves efficient simultaneous sequencing while managing precision challenges through systematic intensity thresholds and categories.
Solution Approach 2:
The patent introduces classification categories as intermediaries between the raw combined signal data and the final sequence information. These intermediate classifications (first and second classification categories) serve as mediators that simplify the relationship between overlapping signals and sequence determinations, enabling efficient processing while maintaining acceptable precision.
3Loss of information
If classifications representing multiple possible nucleobase combinations are used, then sequence information can be determined from ambiguous signals, but the reliability of individual base calls may be reduced
Solution Approach 1:
The patent applies partial action by accepting that some signal combinations cannot be resolved to specific nucleobase pairs and instead classifies them into broader categories. This partial resolution approach recovers sequence information where possible while honestly representing uncertainty in ambiguous cases, balancing information recovery with reliability through transparent classification categories.
Applied Scientific Principles
This section explains which scientific principles are used to turn an abstract innovation direction into a practical engineering solution.
Function Achieved in This Case
This approach enhances sequencing efficiency by enabling the simultaneous determination of sequence information from multiple polynucleotide sequence portions, including identification of modifications and errors, thereby improving the throughput and accuracy of sequencing workflows.
Implementation Method 1
deoxyribonucleic acid analogs conjugated to fluorescent labels are hybridized to the template nucleic acids, and excitation light sources are used to excite the fluorescent labels on the deoxyribonucleic acid analogs. Detectors capture fluorescent emissions from the fluorescent labels
Data Source
AI summary
A method of determining sequence information from two or more polynucleotide sequence portions, the method comprising: selecting one of a plurality of classifications based on first and second intensity data, wherein each classification represents one or more possible combinations of respective nucleobases of the two or more polynucleotide sequence portions, and wherein at least one classification represents more than one possible combination of respective nucleobases.