Y-Shaped ctDNA Adapters for Ultrasensitive Mutation Detection
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Solution Overview
Problem
Existing methods for detecting and profiling circulating tumor DNA (ctDNA) are limited by low sensitivity and inefficiency, particularly in samples with low DNA content, due to factors like recovery of cfDNA molecules and sequencing errors, complicating cancer detection and monitoring.
Innovation Solution
The use of polynucleotide adapter compositions, specifically Y-shaped adapters with unique molecular identifiers and non-degenerate sequences, enhances ligation efficiency and allows for ultrasensitive detection of ctDNA mutations by improving analytical sensitivity and reducing sequencing artifacts.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If conventional library preparation and sequencing methods are used, then the process is simple and fast, but the detection sensitivity is limited and analytical precision is poor due to recovery losses and non-biological errors
Solution Approach 1:
The patent applies preliminary action by incorporating unique molecular identifiers (UMIs) and adapter sequences during the initial library preparation stage, before sequencing. This allows for subsequent bioinformatic processing to distinguish true biological variants from artifacts introduced during library preparation, thereby improving detection sensitivity without requiring complex wet-lab procedures
Solution Approach 2:
The patent uses adapter sequences as intermediaries that ligate to cfDNA fragments and incorporate UMIs. These adapters serve as mediators between the cfDNA sample and the sequencing platform, enabling tracking of individual molecules through the library preparation process and facilitating error correction during data analysis
2Quantity of substance
If cfDNA recovery is maximized, then more DNA is available for analysis, but non-biological errors introduced during library preparation increase, reducing analytical precision
Solution Approach 1:
The patent implements feedback through the use of UMIs that allow bioinformatic processing to identify and correct non-biological errors. By comparing sequences with identical UMIs, the system can distinguish true biological variants from artifacts introduced during library preparation, providing feedback that improves analytical precision while maintaining high cfDNA recovery
Solution Approach 2:
The UMIs are incorporated during preliminary library preparation steps, enabling subsequent error correction. This preliminary tagging allows the system to trace back and identify where errors were introduced during the cfDNA recovery and library construction process
3Productivity
If standard adapter sequences are used, then the ligation process is straightforward, but ligation efficiency is insufficient for ultrasensitive ctDNA detection
Solution Approach 1:
The patent applies local quality by designing adapters with specific local characteristics - the 5' overhang sequence is optimized for high ligation efficiency with cfDNA fragments, while the body of the adapter contains UMIs for molecular tracking. This localized optimization of different regions of the adapter enables both efficient ligation and ultrasensitive detection
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
The methods provide a framework for rapid and sensitive detection of ctDNA mutations, achieving improved detection limits and generating 500-1800 single strand consensus reads from as little as 5 ng of cfDNA input, thereby enhancing cancer detection and monitoring capabilities.
Implementation Method 1
the first proximal region of the first oligonucleotide strand hybridizes with the second proximal region of the second oligonucleotide strand
Data Source
AI summary
The present technology provides polynucleotide compositions and methods of using the same to detect circulating tumor DNA (ctDNA) in a patient. Kits for use in practicing the methods are also provided.