Noninvasive Prenatal CNV Detection via GC Bias Correction
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Solution Overview
Problem
Current methods for noninvasive prenatal diagnosis of copy number variations (CNVs) face challenges such as reduced signal-to-noise ratio in fraternal multiple pregnancies and limitations in detecting Y chromosome-based diagnoses due to lower coverage and repeated sequences.
Innovation Solution
The method involves receiving sequence reads from cell-free DNA, aligning them to a reference genome, determining coverage, and adjusting it using expected coverages from unaffected training samples to evaluate copy number variations, particularly in sub-chromosomal regions associated with genetic syndromes.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If conventional invasive procedures (amniocentesis, cordocentesis, CVS) are used to obtain cells for karyotype analysis, then diagnostic accuracy is improved, but patient safety deteriorates due to invasive risks
Solution Approach 1:
The patent uses cell-free DNA (cfDNA) circulating in maternal plasma as an intermediary substance to obtain fetal genetic information without direct invasive access to fetal cells. The cfDNA serves as a mediator that carries fetal genetic material that can be analyzed noninvasively, resolving the contradiction between diagnostic accuracy and patient safety
Solution Approach 2:
The patent replaces mechanical invasive procedures (needle puncture, surgical sampling) with molecular biological methods (DNA extraction, sequencing, and analysis). This substitution eliminates the physical trauma and infection risks associated with invasive procedures while maintaining diagnostic capability through genetic analysis
2Productivity
If molecular-cytogenetic methods (FISH, QF-PCR, array-CGH) are used for rapid testing without cell culture, then testing speed is improved, but detection precision deteriorates for sub-chromosomal aneuploidies
Solution Approach 1:
The patent changes the parameter of DNA fragment analysis from targeted specific loci (as in FISH, QF-PCR) to comprehensive whole-genome sequencing. By sequencing and analyzing copy number variations across the entire genome, the method achieves both rapid testing and high detection precision for sub-chromosomal aneuploidies that were previously difficult to detect
Solution Approach 2:
The patent employs a universal whole-genome sequencing approach that can simultaneously detect various types of copy number variations including sub-chromosomal aneuploidies, microdeletions, and microduplications. This multi-functional method replaces multiple specialized tests with a single comprehensive analysis
3Adaptability or versatility
If Y chromosome based diagnosis is used for gender identification, then diagnostic capability is improved, but measurement precision deteriorates due to lower coverage and repeated sequences
Solution Approach 1:
The patent segments the Y chromosome into multiple small bins or regions for individual analysis. By dividing the Y chromosome into numerous small segments and analyzing copy number variations in each segment, the method overcomes the problems of low overall coverage and repeated sequences, achieving more precise gender identification and detection of Y chromosome abnormalities
4Productivity
If ultra-short reads (25mer reads and tags) are used in sequencing protocols, then sequencing speed is improved, but alignment precision deteriorates due to repeated sequences
Solution Approach 1:
The patent segments the genome into small bins and analyzes copy number variations at the bin level rather than requiring precise alignment of individual short reads. This segmentation approach allows the use of ultra-short reads for rapid sequencing while avoiding the alignment precision problems by aggregating signal at the bin level
Data Source
AI summary
Disclosed are methods for determining copy number variation (CNV) known or suspected to be associated with a variety of medical conditions, including syndromes related to CNV of subchromosomal regions. In some embodiments, methods are provided for determining CNV of fetuses using maternal samples comprising maternal and fetal cell free DNA. Some embodiments disclosed herein provide methods to improve the sensitivity and/or specificity of sequence data analysis by removing within-sample GC-content bias. In some embodiments, removal of within-sample GC-content bias is based on sequence data corrected for systematic variation common across unaffected training samples. In some embodiments, syndrome related biases in sample data are also removed to increase signal to noise ratio. Also disclosed are systems for evaluation of CNV of sequences of interest.