REVIEW article
Front. Genet.
Sec. Genomic Assay Technology
This article is part of the Research TopicAdvancements in Sequencing Technologies for Epigenomic and Transcriptomic Analysis: From Bulk to Single-Cell ResolutionView all 5 articles
Single-Cell Sequencing in Molecular Diagnostics: Transformative Yet Untapped Potential
Provisionally accepted
Duaa El Sheikh1Nour Farchoukh1Reema El-Hassan1Sara Al-Marzooqi1Waad Rashid Alateeq2
Haissam Abou-Saleh1
Amal Al-Haidose1
Hatem Zayed1
Atiyeh M Abdallah1,3*- 1Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, Doha, Qatar, Doha, Qatar
- 2Forensic DNA and Biology laboratory, Ministry of Interior,, Doha, Qatar
- 3Department of Biomedical Sciences, College of Health Sciences, Qatar University, Doha, Qatar
Select one of your emails
You have multiple emails registered with Frontiers:
Notify me on publication
Please enter your email address:
If you already have an account, please login
You don't have a Frontiers account ? You can register here
Single-cell sequencing (SCS) techniques have the potential to offer precise insights into cellular diversity by revealing unique genetic and transcriptomic profiles at the single-cell level. This advanced technology has been used extensively in research, but it has still not translated to clinical diagnostics, despite its potential. SCS provides more accurate granular information about heterogeneous cell populations and the creation of personalized treatment strategies. However, the integration of SCS into clinical practice is challenging. This review discusses the potential of SCS technologies in improving clinical molecular diagnostics in various clinical areas including oncology, genetics and rare diseases, infectious diseases, and autoimmune disorders and inflammation. We review recent advances, current uses, integration challenges, and their contribution to the development of these fields. SCS provides significant opportunities in oncology to analyze tumor heterogeneity and develop personalized treatments. In autoimmune and rare diseases, SCS has helped to define novel biomarkers and understand complex immune pathways. SCS has also been used to understand pathogen diversity and host-pathogen interactions in the context of infectious diseases, leading to targeted therapeutic approaches. Despite this progress, there remain challenges in data analysis, standardization, and routine clinical application. The future of SCS in clinical molecular diagnostics is promising. Further technological and research developments in SCS are expected to increase the precision and personalization of medical diagnostics and treatment. To overcome current limitations, interdisciplinary cooperation and innovative approaches to data analysis are needed.
Keywords: single-cell sequencing, Clinical molecular diagnostics, personalized treatment, Data analysis challenges, omics
Received: 30 Apr 2025; Accepted: 04 Nov 2025.
Copyright: © 2025 El Sheikh, Farchoukh, El-Hassan, Al-Marzooqi, Alateeq, Abou-Saleh, Al-Haidose, Zayed and Abdallah. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Atiyeh M Abdallah, aabdallah@qu.edu.qa
Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.