cfDNA Fragment Size Selection for Cancer Screening
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Solution Overview
Problem
Current methods for analyzing circulating cell-free DNA (cfDNA) lack precision in determining the size distribution of cfDNA fragments, which is crucial for sensitive and specific detection of rare genetic alterations, particularly in cancer diagnosis, due to uncertainties in release mechanisms and contamination factors.
Innovation Solution
A method involving the extraction and denaturation of single-stranded DNA fragments from cfDNA, followed by quantification of specific size ranges (20-400 nucleotides) to differentiate between healthy and cancerous samples by comparing fragment levels to predetermined reference values.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If conventional NGS methods or electrophoretic mobility methods (PAGE, Agilent platform) are used to analyze cfDNA, then the analysis can be performed with standard techniques, but the size distribution measurement lacks precision due to contamination from blood-cell degradation and uncertainty in release mechanisms
Solution Approach 1:
The patent extracts and analyzes only the shortest cfDNA fragments (≤145 bp) by size-selection, separating them from longer fragments that may originate from blood-cell degradation. This extraction of the specific size range eliminates contamination factors and provides reliable size distribution data for cancer detection.
Solution Approach 2:
The patent applies different analysis criteria to different size ranges of cfDNA fragments. By focusing specifically on the ≤145 bp fragment range and using size-selected libraries, the method optimizes measurement precision for the relevant cancer-associated fragments while excluding confounding longer fragments.
2Ease of manufacture
If cfDNA analysis is performed without size definition, then the analysis process is simplified, but sensitivity and specificity for detecting rare genetic alterations cannot be achieved
Solution Approach 1:
The patent performs size-selection and normalization of cfDNA fragment libraries before sequencing. This preliminary action ensures that only fragments of the relevant size range (≤145 bp) are analyzed, providing the measurement precision needed for detecting rare genetic alterations while maintaining a streamlined workflow.
Solution Approach 2:
The patent changes the size parameter of cfDNA fragments by creating size-selected libraries with defined fragment length distributions. This parameter control enables both ease of analysis and high detection sensitivity by focusing on the diagnostic-relevant size range.
3Quantity of substance
If all cfDNA fragments are analyzed without size selection, then the total cfDNA information is captured, but the signal from cancer-associated fragments is diluted by non-informative fragments
Solution Approach 1:
The patent extracts and analyzes only the shortest cfDNA fragments (≤145 bp) by size-selection, separating them from longer fragments that may originate from blood-cell degradation. This extraction of the specific size range eliminates contamination factors and provides reliable size distribution data for cancer detection.
Solution Approach 2:
The patent analyzes only a specific portion of the cfDNA size distribution (the shortest fragments ≤145 bp) rather than all fragments. This partial action concentrates the analysis on the most diagnostic-relevant fragments, improving the signal-to-noise ratio for cancer 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
This approach allows for accurate discrimination between healthy and cancerous subjects based on distinct ratios of single-stranded DNA fragments, enhancing the sensitivity and specificity of cancer screening tests.
Implementation Method 1
denaturating the cell free nucleic acids to obtain single stranded DNA fragments
Data Source
AI summary
The present invention relates to the diagnostic of cancerous subject. Indeed, the inventors observed by using a Q-PCR based methods and sequencing methods that quantification of specific single stranded DNA fragments obtained from cell free nucleic acids (cfDNA) may discriminate cfDNA from healthy and cancer derived subjects. Single stranded DNA fragments obtained from CfDNA or specific range of single stranded DNA fragments are rather lower or higher when derived from healthy subject than from cancer subject. More, specific ratios for different size or range of single stranded DNA fragments varies between cancer subjects and healthy individuals. These values are sufficiently and significantly different to be used as values to determine whether a human subject may have cancer or not as a screening test. Thus, the invention relates to a method for screening a subject for a cancer comprising the steps of extracting and denaturing cfDNA, determining the single strand fragment level upon their size distribution, and calculate these former values to screen an individual for cancer.