Linked Nucleic Acid Fragments for Sequencing Error Detection
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Solution Overview
Problem
High-throughput genomic sequencing platforms suffer from inaccuracies due to error propagation in nucleic acid amplification and sequencing, leading to misalignment and misidentification of mutations, with current error detection strategies being costly and resource-intensive.
Innovation Solution
The method involves linking two identical nucleic acid fragments together using a linking molecule to form a complex, which is then amplified and sequenced, allowing errors to be identified through comparison of the linked fragments during the sequencing process.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If standard barcode sequencing methods use tens to hundreds of copies of the same template or ten to hundreds of clusters to create a sample pool for comparison, then error detection capability is improved, but sequencing cost and bandwidth consumption increase
Solution Approach 1:
The patent combines multiple sequencing reads into a single consensus sequence by merging information from multiple templates. Instead of requiring tens to hundreds of separate clusters, the invention merges reads at the data processing level to achieve error detection, reducing the quantity of physical copies needed while improving reliability through consensus calling
Solution Approach 2:
The patent introduces a consensus sequence as an intermediary between raw sequencing reads and final analysis. This consensus sequence serves as a mediator that integrates information from multiple templates, allowing error detection without requiring direct comparison of numerous physical copies or clusters
2Productivity
If a single fragment seeds a cluster in amplification, then amplification efficiency is improved, but error propagation increases
Solution Approach 1:
The patent implements feedback by comparing multiple sequencing reads against a consensus sequence. Errors in individual reads are detected through deviation from the consensus, allowing correction and preventing error propagation. This feedback mechanism maintains reliability while preserving amplification efficiency
Solution Approach 2:
The patent segments the sequencing process into independent read operations, where multiple reads are generated from the same template but processed independently. This segmentation allows error detection through comparison without requiring coordinated amplification of multiple fragments, maintaining amplification efficiency while reducing error propagation
Data Source
AI summary
The invention generally relates to sequencing library preparation methods. In certain embodiments, two template nucleic acids are joined together by a linking molecule, such as a PEG derivative. The linked template nucleic acids is amplified, creating linked amplicons.