DNA-Barcoded Digital Serotyping Assay for Population-Scale Profiling
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Solution Overview
Problem
Current serotyping assays have limited throughput, preventing timely collection of population-scale data on pathogen exposure, which is critical for managing pandemics like COVID-19, and do not effectively differentiate between neutralizing and enhancing antibodies.
Innovation Solution
A high-throughput Digital Serotyping (DST) assay using next-generation sequencing (NGS) to measure serotyping profiles of barcoded subject serum antibodies against DNA-tagged pathogen-derived antigens, allowing simultaneous assessment of multiple antibodies and antigens, with minimal sample input requirements.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If current serotyping assays are used, then the assay can detect antibody presence, but the throughput is limited and cannot handle population-scale data collection
Solution Approach 1:
The assay segments the detection process by using DNA-barcoded antigens that can be simultaneously processed. Each antigen is tagged with a unique DNA barcode, allowing multiple antigens to be tested in parallel through next-generation sequencing, thereby dramatically increasing throughput while reducing the time required for population-scale serotyping.
Solution Approach 2:
The invention creates a universal platform that can detect antibodies against multiple different pathogens and antigens using a single assay system. The DNA-barcoded antigen approach allows the same methodology to be applied across various pathogens, enabling multi-functional capability that increases productivity without proportionally increasing time investment.
2Measurement precision
If current serotyping assays are used, then the assay can provide serotyping data, but the data quality is insufficient for population-wide assessment
Solution Approach 1:
The invention introduces DNA barcodes as an intermediary between the antigen and the detection system. These barcodes enable precise identification of which antibodies bind to which antigens through next-generation sequencing, providing high measurement precision. Simultaneously, the intermediary allows for high-throughput processing by enabling parallel analysis of multiple antigen-antibody interactions in a single experiment.
3Loss of information
If current serotyping assays are used, then the assay can detect antibodies, but it cannot effectively differentiate between neutralizing and enhancing antibodies
Solution Approach 1:
The assay segments the antibody population by using a library of peptides representing different epitopes. By testing binding to multiple epitope-specific peptides, the system can differentiate antibody specificities and infer functional characteristics (neutralizing vs. enhancing) based on binding patterns to specific epitopes, thereby reducing information loss without excessively increasing assay complexity.
4Productivity
If high-throughput methods are implemented, then productivity increases, but the sample input requirements and resource consumption increase
Solution Approach 1:
The invention uses DNA barcodes as information copies that can be amplified and sequenced. Instead of requiring large amounts of physical antigen samples for each test, the system creates informational copies through DNA sequencing, allowing high-throughput analysis with minimal physical sample consumption. The DNA-barcoded antigens enable parallel processing that increases productivity without proportionally increasing sample input requirements.
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
Enables comprehensive, accurate, and rapid population-wide serotyping and antibody profiling, capable of scaling to monitor pathogen mutation spectra, and applicable to various sample types and applications including cancer immunology and veterinary medicine.
Implementation Method 1
contacting a sample with a binding element configured to bind to a plurality of different antibodies in the sample, thereby obtaining binding element-antibody conjugates
Implementation Method 2
allowing transfer of identifying information between the coding tag and the recording tag of the bead, thereby generating an extended coding tag or an extended recording tag, wherein the transfer occurs through a primer extension reaction
Data Source
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AI summary
Provided herein are high-throughput, population-wide serotyping and antibody profiling assays. Disclosed variants of a Digital Serotyping assay employ next generation sequencing to measure the "serotyping profile" of barcoded subject serum antibodies tested against a range of DNA-tagged pathogen-derived antigens. The disclosed assay setup enables multiplexing in both the sample and antigen dimensions, generating a large multi-dimensional serotyping data set for more comprehensive serotyping profiling of large populations across a large number of antigens and possible pathogens. Moreover, the ability to easily scale and multiplex the number of peptide epitopes allows rapid updating of the assay content to monitor the ever-changing spectrum of pathogens. Additional applications of this technology include cancer immunology and autoimmune conditions (e.g., neoantigen or autoimmune profiling), screening for toxins, antibody therapeutics development, biosecurity, and veterinary medicine.