Domain-Scan: Combinatorial Sero-Diagnosis of Infectious Diseases Using Machine Learning

Smadar Hada-Neeman, Yael Weiss-Ottolenghi, Naama Wagner, Oren Avram, Haim Ashkenazy, Yaakov Maor, Ella H. Sklan, Dmitry Shcherbakov, Tal Pupko*, Jonathan M. Gershoni*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

7 Scopus citations

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.

Original languageEnglish
Article number619896
JournalFrontiers in Immunology
Volume11
DOIs
StatePublished - 10 Feb 2021

Funding

FundersFunder number
Dalia and Eli Hurvitz Foundation
Edmond J. Safra Center for Bioinformatics
Alexander von Humboldt-Stiftung
Israel Science Foundation
Tel Aviv University

    Keywords

    • DNA barcodes
    • machine learning
    • next-generation sequencing
    • phage-display
    • sero-diagnostics

    Fingerprint

    Dive into the research topics of 'Domain-Scan: Combinatorial Sero-Diagnosis of Infectious Diseases Using Machine Learning'. Together they form a unique fingerprint.

    Cite this