Barcoded Nucleic Acid Library Pooling for Equal Fraction Enrichment
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Solution Overview
Problem
Existing methods for nucleic acid enrichment in genetic screening, particularly for low fetal fraction samples, are inefficient and fail to maintain sample origin identification when pooling samples, leading to unequal representation and reduced sensitivity and specificity in diagnostic assays.
Innovation Solution
A method involving sample-specific nucleic acid libraries with unique markers (e.g., barcodes) are prepared and pooled to ensure equal representation of target nucleic acid fractions, followed by size selection and enrichment, maintaining sample origin identification and enhancing sensitivity and resolution.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If samples are pooled for nucleic acid enrichment, then productivity and cost efficiency are improved, but sample origin identification is lost and representation becomes unequal
Solution Approach 1:
The patent creates digital copies of sample origin information through barcodes and metadata tags that are attached to or associated with each nucleic acid sample. These digital identifiers allow multiple samples to be pooled physically while maintaining virtual tracking of their origins, enabling both high-throughput processing and sample-specific analysis results.
Solution Approach 2:
The patent introduces barcodes and metadata as intermediary elements that mediate between the physical pooling of samples and the need to track sample origins. These intermediaries carry identification information through the enrichment process, allowing samples to be mixed in a single tube while still being distinguishable and attributable to their sources in the final analysis.
2Loss of time
If samples are pooled for enrichment, then loss of time and resources is reduced, but sensitivity and specificity of diagnostic assays decrease
Solution Approach 1:
By creating digital replicas of sample characteristics through barcodes and metadata, the system can process pooled samples efficiently while maintaining the ability to evaluate each sample's contribution to the pool, thereby preserving measurement precision despite time savings from pooling.
Solution Approach 2:
The patent implements feedback mechanisms where enrichment results are traced back to individual samples through their identifiers. This allows the system to monitor and adjust for variations in sample representation and enrichment efficiency, maintaining diagnostic accuracy even when processing pooled samples to reduce time and resource loss.
3Productivity
If conventional enrichment methods are used on pooled samples, then productivity increases, but manufacturing precision of equal representation deteriorates
Solution Approach 1:
The patent uses digital copying of quantification data and sample characteristics to calculate precise pooling ratios before enrichment. This allows the system to compensate for variations in sample composition and ensure equal representation of target nucleic acid fractions from each sample in the final enriched product, maintaining manufacturing precision while processing pooled samples efficiently.
Solution Approach 2:
The patent performs preliminary quantification and calculation of required sample amounts before pooling and enrichment. By determining the exact proportions needed to achieve equal representation in advance, the system can pool samples with different initial concentrations and still produce an enriched product with uniform contribution from each sample, resolving the conflict between productivity and manufacturing precision.
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 increases the target DNA fraction, improving sensitivity and specificity in genetic diagnostic assays by ensuring equal representation and maintaining sample origin identification, even in pooled samples.
Implementation Method 1
performing fragment size selection on the second pooled test sample to isolate the target nucleic acid population in suspension
Data Source
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AI summary
Described herein are methods for enriching test samples for target nucleic acid molecules for further genetic screening. Methods may comprise isolating nucleic acid from test subjects, preparing nucleic acid libraries wherein the nucleic acid molecules are tagged or barcoded to identify sample of origin, determining fragment size distribution, determining abundance of a target nucleic acid population, calculating numerical offset values to determine amount of libraries to add for fragment size selection, performing fragment size selection, and performing a diagnostic assay on a sample enriched for a target nucleic acid.