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Domain-Scan: Combinatorial Sero-Diagnosis of Infectious Diseases Using Machine Learning
- Source :
- Frontiers in Immunology, Frontiers in Immunology, Vol 11 (2021)
- Publication Year :
- 2021
- Publisher :
- Frontiers Media S.A., 2021.
-
Abstract
- The presence of pathogen-specific antibodies in an individual’s blood-sample is used as an indication of previous exposure and infection to that specific pathogen (e.g., virus or bacterium). Measurement of the diagnostic antibodies is routinely achieved using solid phase immuno-assays such as ELISA tests and western blots. Here, we describe a sero-diagnostic approach based on phage-display of epitope arrays we term “Domain-Scan”. We harness Next-generation sequencing (NGS) to measure the serum binding to dozens of epitopes derived from HIV-1 and HCV simultaneously. The distinction of healthy individuals from those infected with either HIV-1 or HCV, is modeled as a machine-learning classification problem, in which each determinant (“domain”) is considered as a feature, and its NGS read-out provides values that correspond to the level of determinant-specific antibodies in the sample. We show that following training of a machine-learning model on labeled examples, we can very accurately classify unlabeled samples and pinpoint the domains that contribute most to the classification. Our experimental/computational Domain-Scan approach is general and can be adapted to other pathogens as long as sufficient training samples are provided.
- Subjects :
- lcsh:Immunologic diseases. Allergy
0301 basic medicine
Phage display
Sample (material)
Immunology
DNA barcodes
Genetic Vectors
DNA, Recombinant
HIV Core Protein p24
Oligonucleotides
HIV Infections
Computational biology
Biology
HIV Antibodies
Communicable Diseases
Polymerase Chain Reaction
DNA sequencing
Epitope
Virus
HIV Envelope Protein gp160
Antigen-Antibody Reactions
Machine Learning
03 medical and health sciences
Epitopes
0302 clinical medicine
Peptide Library
Immunology and Allergy
DNA Barcoding, Taxonomic
Humans
Serologic Tests
Amino Acid Sequence
Pathogen
Original Research
Base Sequence
AIDS Serodiagnosis
High-Throughput Nucleotide Sequencing
Hepatitis C Antibodies
sero-diagnostics
Hepatitis C
Peptide Fragments
030104 developmental biology
Feature (computer vision)
biology.protein
next-generation sequencing
phage-display
Antibody
Hepatitis C Antigens
lcsh:RC581-607
030217 neurology & neurosurgery
Subjects
Details
- Language :
- English
- ISSN :
- 16643224
- Volume :
- 11
- Database :
- OpenAIRE
- Journal :
- Frontiers in Immunology
- Accession number :
- edsair.doi.dedup.....79d5648e9e43b91dd0e9592ee0a11cf3