Variant Specific Primers for Homopolymer Sequencing Validation
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Solution Overview
Problem
Current nucleic acid sequencing technologies face challenges in validating sequencing results, particularly in identifying and verifying sequence variations such as homopolymer regions, which can lead to false positives and false negatives due to the complexity of sequencing longer homopolymer stretches.
Innovation Solution
The implementation of a system and method using variant specific primers with barcode regions, left and right anchor regions, and query regions to identify and verify homopolymer variants, allowing for the generation of amplicons that correspond to specific homopolymer lengths, thereby distinguishing between correct and incorrect sequencing data.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If sequencing technologies attempt to sequence longer homopolymer stretches to capture complete genetic information, then the coverage and completeness of sequencing increases, but the accuracy decreases leading to false positives and false negatives
Solution Approach 1:
The patent segments the sequencing process by using variant-specific primers that target and amplify only specific regions containing potential variants. This segmentation allows the system to focus computational and experimental resources on problematic regions rather than attempting to sequence entire long homopolymer stretches, thereby improving accuracy without proportionally increasing overall system complexity
Solution Approach 2:
The patent introduces an intermediary validation step using variant-specific primers and barcode regions. These intermediaries act as mediators between the initial sequencing data and the final variant calls, providing an additional layer of verification that reduces false positives and negatives without requiring the primary sequencing system to be fundamentally redesigned
2Productivity
If conventional sequencing methods are used to process large numbers of reads quickly, then productivity increases, but measurement precision decreases making it difficult to validate sequencing results
Solution Approach 1:
The patent performs preliminary actions by designing and preparing variant-specific primers and barcode sequences before the actual sequencing process. This preliminary preparation enables rapid validation during the sequencing workflow without compromising the high throughput of the primary sequencing operation, thus maintaining productivity while improving measurement precision
Solution Approach 2:
The patent implements a feedback mechanism where variant-specific primers and barcode regions provide validation information that feeds back into the variant calling process. This feedback loop allows the system to quickly identify and correct potential errors in high-throughput sequencing data, improving measurement precision without significantly reducing productivity
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 the accuracy of sequencing by providing a method to uniquely identify and verify homopolymer regions, reducing false positives and negatives, and ensuring reliable sequence validation.
Implementation Method 1
The implementation of a system and method using variant specific primers with barcode regions, left and right anchor regions, and query regions to identify and verify homopolymer variants
Data Source
AI summary
Systems and method for validation of sequencing results can amplify a target region of a nucleic acid sample in the presence of a primer pool including target specific and variant specific primers. The variant specific primers can include variant specific barcodes and variant specific sequences. An amplicon can be sequenced to determine the sequence of the variant specific barcode. The variant can be identified based on the sequence of the variant specific barcode, and the location of the variant can be determined by mapping the amplicon to a reference sequence.