Get ready for short tandem repeats analysis using long reads-the challenges and the state of the art
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 sign...
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Frontiers Media S.A.
2025-07-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2025.1610026/full |
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| author | Marija Chaushevska Marija Chaushevska Karmele Alapont-Celaya Anne Kristine Schack Anne Kristine Schack Lukasz Krych M. Carmen Garrido Navas M. Carmen Garrido Navas M. Carmen Garrido Navas Anastasia Krithara Gjorgji Madjarov Gjorgji Madjarov |
| author_facet | Marija Chaushevska Marija Chaushevska Karmele Alapont-Celaya Anne Kristine Schack Anne Kristine Schack Lukasz Krych M. Carmen Garrido Navas M. Carmen Garrido Navas M. Carmen Garrido Navas Anastasia Krithara Gjorgji Madjarov Gjorgji Madjarov |
| author_sort | Marija Chaushevska |
| collection | DOAJ |
| description | 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 short-read 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. |
| format | Article |
| id | doaj-art-7cc58943663d4f83881eea67eb789f10 |
| institution | Kabale University |
| issn | 1664-8021 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj-art-7cc58943663d4f83881eea67eb789f102025-08-20T03:33:02ZengFrontiers Media S.A.Frontiers in Genetics1664-80212025-07-011610.3389/fgene.2025.16100261610026Get ready for short tandem repeats analysis using long reads-the challenges and the state of the artMarija Chaushevska0Marija Chaushevska1Karmele Alapont-Celaya2Anne Kristine Schack3Anne Kristine Schack4Lukasz Krych5M. Carmen Garrido Navas6M. Carmen Garrido Navas7M. Carmen Garrido Navas8Anastasia Krithara9Gjorgji Madjarov10Gjorgji Madjarov11Faculty of Computer Science and Engineering, University Saints Cyril and Methodius, Skopje, North MacedoniagMendel ApS, Copenhagen, DenmarkgMendel ApS, Copenhagen, DenmarkgMendel ApS, Copenhagen, DenmarkFood Microbiology and Fermentation, Department of Food Science, University of Copenhagen, Copenhagen, DenmarkFood Microbiology and Fermentation, Department of Food Science, University of Copenhagen, Copenhagen, DenmarkgMendel ApS, Copenhagen, DenmarkCardiovascular Development Group, Department of Experimental Biology, University of Jaen, Jaen, SpainGENetic COUNselling (CONGEN), Genetic Counselling Services, Granada, SpainInstitute of Informatics and Telecommunications, National Centre of Scientific Research “Demokritos”, Athens, GreeceFaculty of Computer Science and Engineering, University Saints Cyril and Methodius, Skopje, North MacedoniagMendel ApS, Copenhagen, DenmarkShort 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 short-read 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.https://www.frontiersin.org/articles/10.3389/fgene.2025.1610026/fullshort tandem repeatslong readssequencing technologiesstructural variantsvariant detectionbioinformatics tools |
| spellingShingle | Marija Chaushevska Marija Chaushevska Karmele Alapont-Celaya Anne Kristine Schack Anne Kristine Schack Lukasz Krych M. Carmen Garrido Navas M. Carmen Garrido Navas M. Carmen Garrido Navas Anastasia Krithara Gjorgji Madjarov Gjorgji Madjarov Get ready for short tandem repeats analysis using long reads-the challenges and the state of the art Frontiers in Genetics short tandem repeats long reads sequencing technologies structural variants variant detection bioinformatics tools |
| title | Get ready for short tandem repeats analysis using long reads-the challenges and the state of the art |
| title_full | Get ready for short tandem repeats analysis using long reads-the challenges and the state of the art |
| title_fullStr | Get ready for short tandem repeats analysis using long reads-the challenges and the state of the art |
| title_full_unstemmed | Get ready for short tandem repeats analysis using long reads-the challenges and the state of the art |
| title_short | Get ready for short tandem repeats analysis using long reads-the challenges and the state of the art |
| title_sort | get ready for short tandem repeats analysis using long reads the challenges and the state of the art |
| topic | short tandem repeats long reads sequencing technologies structural variants variant detection bioinformatics tools |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2025.1610026/full |
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