Hairpin Adapter Duplex Sequencing for Low-Prevalence Mutation Detection
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Solution Overview
Problem
Current DNA sequencing technologies face limitations in detecting low-prevalence mutations due to high error rates, leading to increased costs and reduced scalability, making them impractical for routine clinical use in precision medicine.
Innovation Solution
The method involves preparing a double-stranded nucleic acid molecule with complementary strands joined by a hairpin adapter for self-correction of sequencing errors, reducing the need for redundant sequencing and enabling efficient detection of genetic variants with minimal sequencing reads.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If conventional NGS methods are used, then sequencing can be performed with standard protocols, but error rates remain high leading to poor sensitivity for detecting low-prevalence mutations
Solution Approach 1:
The patent introduces UMID tags as intermediary molecular identifiers that are attached to DNA fragments during library preparation. These UMID tags serve as mediators to group and track individual original DNA molecules through the sequencing process, enabling error correction by comparing multiple reads from the same original molecule. This intermediary tagging system allows distinction between true low-prevalence mutations and sequencing errors.
2Measurement precision
If UMID-mediated duplex sequencing is used to correct sequencing errors, then detection sensitivity improves, but read depth requirements and sequencing costs increase excessively
Solution Approach 1:
The patent applies partial action by implementing error correction only where necessary - using UMID-mediated consensus calling specifically for low-prevalence mutation detection while maintaining standard sequencing for other applications. The method performs targeted error correction on reads containing UMID tags that indicate potential low-frequency variants, rather than applying exhaustive error correction to all sequencing data, thereby reducing overall read depth requirements.
Solution Approach 2:
The patent changes the parameter of sequencing depth requirements by introducing UMID-based molecular tagging that enables error correction through consensus calling. This parameter change allows the system to achieve high detection sensitivity at lower sequencing depths because the UMID tags provide a mechanism to distinguish true variants from errors without requiring excessive redundant sequencing of every fragment.
3Measurement precision
If high-depth redundant sequencing is performed to achieve error correction, then mutation detection accuracy improves, but sequencing costs and processing time increase
Solution Approach 1:
The patent applies preliminary action by attaching UMID tags to DNA fragments during the library preparation stage, before sequencing occurs. This preliminary tagging enables subsequent error correction through consensus calling without requiring additional time-consuming processing steps after sequencing. The UMID information is embedded upfront, allowing efficient grouping and analysis of reads during data processing.
4Adaptability or versatility
If standard NGS protocols are used, then the method is simple and cost-effective, but scalability to examine large numbers of genomic targets is limited
Solution Approach 1:
The patent applies universality by designing a UMID-based error correction framework that can be integrated into existing standard NGS workflows and applied across multiple genomic targets simultaneously. The UMID tagging and consensus calling approach serves multiple functions: error correction, low-prevalence mutation detection, and scalable application across different gene panels and genomic regions, all within a unified methodology that maintains compatibility with standard sequencing protocols.
Data Source
AI summary
Embodiments of the present disclosure provide a method for detecting one or more genetic variants in a biological sample. Embodiments of the method include preparing an error-corrected nucleic library for sequencing, wherein the nucleic acid library comprises a double stranded nucleic molecule comprising a hairpin adapter, wherein the hairpin adapter covalently joins each strand of the double stranded nucleic molecule into a single covalently linked duplex strand for self-correction of sequencing errors.