Prenatal cfDNA Enrichment Using Long Probes for Low Fetal Fraction Detection
Find Innovative SolutionsGenerate Solutions
Solution Overview
Problem
Current non-invasive prenatal tests for fetal aneuploidy and micro-deletion detection face challenges in achieving high sensitivity, particularly when the proportion of cell-free fetal DNA in maternal circulation is below 4%, and existing methods struggle to provide sufficient accuracy even with next-generation sequencing technology.
Innovation Solution
A method utilizing long capture-probes and bioinformatics approaches for double enrichment of fetal cell-free DNA fragments, focusing on hot spots of non-random fragmentation (HSNRF), and a novel bioinformatics framework to enhance the signal-to-noise ratio in DNA analysis, enabling high-sensitivity detection of fetal abnormalities.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If single normalized values derived from read-depth information are used for fetal aneuploidy detection, then the test can be implemented with existing sequencing technology, but the clinical sensitivity does not exceed more than 99% and is insufficient when cffDNA proportion is below 4%
Solution Approach 1:
The patent segments the detection approach by dividing cfDNA fragments into different size categories (short fragments 100-150bp vs long fragments 150-250bp) and applying different analytical methods to each segment. Short fragments are analyzed using a binning approach with position-specific scoring, while long fragments use a different normalization method, thereby improving overall detection sensitivity by treating different fragment types differently
Solution Approach 2:
The patent introduces a new dimension of analysis by incorporating fragment size information and position-specific scoring into the detection methodology. Instead of relying solely on read-depth normalization, the system uses a two-dimensional approach combining fragment length categorization with position-specific enrichment scores, enabling detection in low cffDNA proportion samples
2Measurement precision
If next generation sequencing technology is used to improve detection sensitivity, then higher sensitivity is achieved, but obtaining sufficient accuracy for non-invasive prenatal testing remains challenging when cffDNA proportion is below 4%
Solution Approach 1:
The patent applies local quality by implementing position-specific scoring where different genomic positions are assigned different weights based on their enrichment potential. The system identifies regions with high cffDNA enrichment (such as imprinted regions and regions with tissue-specific expression) and applies enhanced scoring to these specific locations, thereby improving detection accuracy locally where it matters most
Solution Approach 2:
The patent changes the parameter of fragment size categorization to improve detection. By separating fragments into size bins (100-150bp and 150-250bp) and applying different analytical approaches to each bin, the system optimizes detection sensitivity for the specific size distribution characteristics of cffDNA in low-proportion samples
3Measurement precision
If long DNA probes are used to capture cell-free DNA fragments and enrich for hot spots of non-random fragmentation, then the signal-to-noise ratio is increased, but the device complexity and methodology complexity increase
Solution Approach 1:
The patent applies preliminary action by pre-identifying and cataloging hot spots of non-random fragmentation (HSNRF) across the genome before sample analysis. These predetermined HSNRF locations are used to guide probe design and enrichment strategies, allowing the system to focus sequencing efforts on regions most likely to yield diagnostic information, thereby improving signal-to-noise ratio without proportionally increasing complexity
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 method significantly improves the detection of fetal chromosomal abnormalities by enhancing the signal-to-noise ratio, allowing for accurate identification of aneuploidies, microdeletions, and microduplications in mixed DNA samples with low fetal DNA concentrations.
Implementation Method 1
hybridizing one or more probes to at least one or more cfDNA fragments
Data Source
Figure 1~2
Figure 3A~3B
AI summary
The present invention relates to a method for the detection of genetic and or genomic abnormalities in a mixed sample, comprising the steps of biochemical and in-silico enrichment of a subset of cell-free DNA fragments derived from the mixed sample. The invention utilizes a pool of long DNA probes to enrich for sequences of interest in the mixed sample, followed by massive parallel sequencing and a computer-based analysis of the enriched sub-population to detect a risk of genetic and or genomic abnormalities in the said sub-population of the mixed sample. The computer-based part of the method does not necessarily require alignment on a reference genome nor calibration values using reference samples. The method also comprises a kit for performing the invention.