ctDNA Enrichment via Size Selection for Copy Number Alteration Analysis
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Solution Overview
Problem
Current methods for enriching circulating tumor DNA (ctDNA) and circulating fetal cell-free DNA (fetal cfDNA) face challenges in distinguishing the biological signal from technical and statistical noise, requiring increased sequencing depth and advanced analytical techniques, which are not always effective for early disease detection and noninvasive diagnostics.
Innovation Solution
A method involving the selection of adapter-ligated nucleic acid fragments of specific sizes, typically less than 150 bp, to enhance the enrichment of ctDNA or fetal cfDNA, followed by sequencing and quantification of copy number alterations (CNAs) to determine disease status, using techniques such as electrophoresis, magnetic bead-based selection, or in silico size selection during sequencing data processing.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If current methodologies are used to distinguish ctDNA signal from noise, then detection accuracy may be maintained, but sequencing depth must be increased and advanced analytical techniques are required
Solution Approach 1:
The patent extracts and isolates ctDNA molecules based on their unique fragment size characteristics (typically <150bp) from the total cell-free DNA population. By size-selecting nucleic acid fragments after adapter ligation, the method enriches for tumor-derived DNA while excluding larger genomic DNA and smaller degradation products, thereby improving detection accuracy without requiring excessive sequencing depth
Solution Approach 2:
The patent applies local quality by treating different size fractions of cell-free DNA differently. Instead of uniform analysis, the method specifically targets and enriches for the size range characteristic of ctDNA (e.g., 100-150bp), applying size-selection criteria that differentiate this subpopulation from other cell-free DNA based on its unique biophysical properties
2Measurement precision
If size selection is applied to enrich ctDNA, then detection sensitivity is improved, but the method must be adapted for different fragment size ranges
Solution Approach 1:
The patent employs parameter changes by adjusting the size-selection cutoff thresholds based on the specific clinical application and sample type. For example, different fragment size ranges may be selected for early-stage cancer detection versus late-stage disease monitoring, or for fetal cfDNA versus tumor ctDNA. The method allows optimization of size-selection parameters (e.g., 100-150bp vs. 150-200bp cutoffs) to maximize sensitivity for different diagnostic scenarios
3Measurement precision
If advanced analytical techniques are used to distinguish ctDNA from noise, then detection accuracy is maintained, but the complexity and cost of the assay increases
Solution Approach 1:
The patent performs preliminary action by enriching for ctDNA through size-based selection before sequencing and analysis. This pre-enrichment step concentrates the target analyte in a size-selected fraction, reducing the background noise and improving the signal-to-noise ratio. Consequently, standard sequencing and analysis pipelines can be used without requiring complex advanced analytical techniques, thereby reducing assay complexity and cost while maintaining high detection accuracy
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 significantly enhances the detection of ctDNA and fetal cfDNA signals, improving the accuracy of early disease detection and prediction of disease progression by amplifying the amplitude of detectable autosomal copy number alterations, thereby improving noninvasive cancer diagnostics and prenatal testing.
Implementation Method 1
the adapter-ligated nucleic acid fragments can be size selected via electrophoresis
Implementation Method 2
the adapter-ligated nucleic acid fragments may be size selected via magnetic bead-based selection
Data Source
AI summary
The present disclosure relates to methods for enriching circulating tumor DNA (ctDNA) to enhance early disease detection or predictions of disease progression. The present disclosure also relates to methods for enriching circulating fetal cell free DNA (fetal cfDNA) to enhance early disease detection. In some embodiments, the method comprises enriching ctDNA or fetal cfDNA in a sample by selecting for cell-free nucleic acid fragments that are less than 150 bp prior to copy number alteration (CNA) analysis. Also disclosed are compositions, systems, and computer-program products for analyzing circulating cell free nucleic acids by any of the methods disclosed herein.