{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T13:12:15Z","timestamp":1792069935835,"version":"4.4.0"},"reference-count":119,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,11,19]],"date-time":"2025-11-19T00:00:00Z","timestamp":1763510400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Genet."],"abstract":"<jats:p>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.<\/jats:p>","DOI":"10.3389\/fgene.2025.1621081","type":"journal-article","created":{"date-parts":[[2025,11,18]],"date-time":"2025-11-18T22:10:24Z","timestamp":1763503824000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":2,"title":["Single-cell sequencing in molecular diagnostics: Transformative yet untapped potential"],"prefix":"10.3389","volume":"16","author":[{"given":"Duaa","family":"Elshiekh","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nour","family":"Farchoukh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Reema","family":"El Hassan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sara","family":"Al-Marzooqi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Waad Rashed","family":"Aldosari","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haissam","family":"Abou-Saleh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amal","family":"Al-Haidose","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hatem","family":"Zayed","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Atiyeh M.","family":"Abdallah","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2025,11,19]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"e50176","DOI":"10.7759\/cureus.50176","article-title":"Liquid biopsy: an evolving paradigm for non-invasive disease diagnosis and monitoring in medicine","volume":"15","author":"Adhit","year":"2023","journal-title":"Cureus"},{"key":"B2","doi-asserted-by":"publisher","first-page":"591122","DOI":"10.3389\/fnins.2021.591122","article-title":"Single-cell transcriptomics: current methods and challenges in data acquisition and analysis","volume":"15","author":"Adil","year":"2021","journal-title":"Front. 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