Fetal DNA Sequence Imbalance Detection Using Digital PCR Cutoffs
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Solution Overview
Problem
Conventional prenatal diagnostic methods for fetal chromosomal aneuploidies, such as Down syndrome, face challenges due to invasive procedures with fetal loss risks and suboptimal accuracy of non-invasive methods, particularly in detecting fetal nucleic acid imbalances amidst maternal background interference, and are limited by the need for genetic polymorphisms.
Innovation Solution
A method using digital PCR and sequential probability ratio testing (SPRT) to determine nucleic acid sequence imbalances in maternal plasma by setting cutoff values based on fetal sequence percentages and average concentrations, independent of genetic polymorphisms, allowing precise classification of fetal genotypes.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If invasive procedures such as amniocentesis or chorionic villus sampling are used for prenatal diagnosis, then diagnostic accuracy is improved, but fetal loss risk increases
Solution Approach 1:
The invention extracts fetal nucleic acids from maternal plasma, separating the diagnostic target from the invasive procedure requirement. By detecting fetal DNA fragments circulating in maternal blood, the method eliminates the need for invasive sampling while maintaining diagnostic capability for chromosomal aneuploidies
Solution Approach 2:
The invention uses maternal plasma as an intermediary medium to access fetal genetic information. Instead of directly sampling fetal tissues, the method detects fetal nucleic acids that naturally circulate in the maternal circulation, providing an indirect but safe route to prenatal diagnosis
2Object-affected harmful factors
If non-invasive screening methods such as ultrasonography and biochemical markers are used, then fetal loss risk is reduced, but diagnostic accuracy deteriorates
Solution Approach 1:
The invention replaces mechanical and biochemical screening methods (ultrasonography, serum marker measurement) with molecular genetic analysis. By using DNA-based detection methods on maternal plasma samples, the system achieves high diagnostic accuracy while maintaining the non-invasive advantage of blood sampling
Solution Approach 2:
The invention changes the detection parameter from indirect phenotypic markers (ultrasound measurements, biochemical substances) to direct genotypic information (fetal nucleic acid sequences). This parameter change enables accurate detection of chromosomal aneuploidies through sequence analysis rather than indirect screening
3Object-affected harmful factors
If methods detecting fetal-specific nucleic acids in maternal plasma are used, then non-invasive detection is enabled, but maternal background interference increases measurement difficulty
Solution Approach 1:
The invention applies local quality by targeting specific fetal nucleic acid sequences with unique characteristics (such as paternal alleles or fetus-specific mutations) that differ from maternal sequences. This localized targeting within the complex maternal plasma background enables specific detection despite the overwhelming maternal DNA presence
Solution Approach 2:
The method uses excessive action by analyzing multiple genetic markers and sequences to overcome the background interference. By examining numerous loci and using statistical analysis of multiple data points, the method achieves reliable detection despite the challenging signal-to-noise ratio in maternal plasma
4Object-affected harmful factors
If fetal nucleic acids are analyzed in cell-free form in maternal plasma, then non-invasive sampling is achieved, but derivation of dosage information becomes difficult
Solution Approach 1:
The invention uses feedback by comparing the detected fetal nucleic acid ratios against expected reference ranges for normal diploid fetuses. By analyzing the proportion of different allele combinations and comparing them to established patterns, the system derives dosage information and determines chromosomal status despite the cell-free nature of the samples
Data Source
AI summary
Methods, systems, and apparatus are provided for determining whether a nucleic acid sequence imbalance exists within a biological sample. One or more cutoff values for determining an imbalance of, for example, the ratio of the two sequences (or sets of sequences) are chosen. The cutoff value may be determined based at least in part on the percentage of fetal DNA in a sample, such as maternal plasma, containing a background of maternal nucleic acid sequences. The percentage of fetal DNA can be calculated from the same or different data used to determine the cutoff value, and can use a locus where the mother is homozygous and the fetus is heterozygous. The cutoff value may be determined using many different types of methods, such as sequential probability ratio testing (SPRT).