REVIEW article
Front. Genet.
Sec. Genomic Assay Technology
Volume 16 - 2025 | doi: 10.3389/fgene.2025.1610026
Get ready for short tandem repeats analysis using long reads -The challenges and the state of the art
Provisionally accepted
Marija Chaushevska1,2*
Karmele Alapont-Celaya2Anne Kristine Schack2,3
Lukasz Krych3M. Carmen Garrido Navas4,5,6
Anastasia Krithara7
Gjorgji Madjarov1- 1Faculty of Computer Science and Engineering, Saints Cyril and Methodius University of Skopje, Skopje, North Macedonia
- 2gMendel ApS, Copenhagen, Denmark
- 3Food Microbiology and Fermentation, Department of Food Science, University of Copenhagen, Copenhagen, Denmark
- 4Center for Genomics and Oncology Research, Andalusian Autonomous Government of Genomics and Oncological Research (GENYO), Granada, Spain
- 5IBS Granada, Institute of Biomedical Research, Granada, Spain
- 6CONGEN, Genetic Counselling Services, Granada, Spain
- 7National Centre of Scientific Research Demokritos, Athens, Greece
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Short tandem repeats (STRs) are repetitive DNA sequences that contribute to genetic diversity and play a significant role in disease susceptibility. The human genome contains approximately 1.5 million STR loci, collectively covering around 3% of the total sequence. Certain repeat expansions can significantly impact cellular function by altering protein synthesis, impairing DNA repair, and leading to neurodegenerative and neuromuscular diseases. Traditional shortread sequencing struggles to accurately characterize STRs due to its limited read length, which limits the ability to resolve repeat expansions, increases mapping errors, and reduces sensitivity for detecting large insertions or interruptions. This review examines how long-read sequencing technologies, particularly Oxford Nanopore and PacBio, overcome these limitations by enabling direct sequencing of full STR regions with improved accuracy. We discuss challenges in sequencing, bioinformatics workflows, and the latest computational tools for STR detection.Additionally, we highlight the strengths and limitations of different methods, providing deeper insight into the future of STR genotyping.
Keywords: Short tandem repeats, long reads, sequencing technologies, Structural variants, Variant detection, bioinformatics tools To overcome these challenges, third-generation :::::::::::::::::: Third-generation sequencing (long-read sequencing) the diversity, Structural complexity
Received: 11 Apr 2025; Accepted: 06 Jun 2025.
Copyright: © 2025 Chaushevska, Alapont-Celaya, Schack, Krych, Garrido Navas, Krithara and Madjarov. 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: Marija Chaushevska, Faculty of Computer Science and Engineering, Saints Cyril and Methodius University of Skopje, Skopje, North Macedonia
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.