Long-Read Sequencing and Structural Variant Detection: Unlocking the Hidden Genome in Rare Genetic Disorders Article Swipe
Efthalia Moustakli
,
Panagiotis Christopoulos
,
Anastasios Potiris
,
Athanasios Zikopoulos
,
Despoina Mavrogianni
,
Grigorios Karampas
,
Nikolaos Kathopoulis
,
Ismini Anagnostaki
,
Ekaterini Domali
,
Alexandros T. Tzallas
,
Peter Drakakis
,
Sofoklis Stavros
·
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.3390/diagnostics15141803
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.3390/diagnostics15141803
Rare genetic diseases are often caused by structural variants (SVs), such as insertions, deletions, duplications, inversions, and complex rearrangements. However, due to the technical limitations of short-read sequencing, these variants remain underdiagnosed. Long-read sequencing technologies, including Oxford Nanopore and Pacific Biosciences high-fidelity (HiFi), have recently advanced to the point that they can accurately find SVs throughout the genome, including in previously unreachable areas like repetitive sequences and segmental duplications. This study underscores the transformative role of long-read sequencing in diagnosing rare diseases, emphasizing the bioinformatics tools designed for detecting and interpreting structural variants (SVs). Comprehensive methods are reviewed, including methylation profiling, RNA-seq, phasing analysis, and long-read sequencing. The effectiveness and applications of well-known tools like Sniffles2, SVIM, and cuteSV are also assessed. Case studies illustrate how this technique has revealed new pathogenic pathways and solved cases that were previously undetected. Along with outlining potential future paths like telomere-to-telomere assemblies and pan-genome integration, we also address existing issues, including cost, clinical validation, and computational complexity. For uncommon genetic illnesses, long-read sequencing has the potential to completely change the molecular diagnostic picture as it approaches clinical adoption.
Related Topics
Concepts
Computational biology
Nanopore sequencing
DNA sequencing
Structural variation
Exome sequencing
Biology
Genome
Genetics
Whole genome sequencing
Bioinformatics
Mutation
Gene
Metadata
- Type
- review
- Language
- en
- Landing Page
- https://doi.org/10.3390/diagnostics15141803
- OA Status
- gold
- Cited By
- 3
- References
- 84
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4412727383
All OpenAlex metadata
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https://doi.org/10.3390/diagnostics15141803Digital Object Identifier
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Long-Read Sequencing and Structural Variant Detection: Unlocking the Hidden Genome in Rare Genetic DisordersWork title
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reviewOpenAlex work type
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enPrimary language
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2025Year of publication
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2025-07-17Full publication date if available
- Authors
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Efthalia Moustakli, Panagiotis Christopoulos, Anastasios Potiris, Athanasios Zikopoulos, Despoina Mavrogianni, Grigorios Karampas, Nikolaos Kathopoulis, Ismini Anagnostaki, Ekaterini Domali, Alexandros T. Tzallas, Peter Drakakis, Sofoklis StavrosList of authors in order
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https://doi.org/10.3390/diagnostics15141803Publisher landing page
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YesWhether a free full text is available
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goldOpen access status per OpenAlex
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https://doi.org/10.3390/diagnostics15141803Direct OA link when available
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Computational biology, Nanopore sequencing, DNA sequencing, Structural variation, Exome sequencing, Biology, Genome, Genetics, Whole genome sequencing, Bioinformatics, Mutation, GeneTop concepts (fields/topics) attached by OpenAlex
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2025: 3Per-year citation counts (last 5 years)
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10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.Nanopore | 37 |
| abstract_inverted_index.RNA-seq, | 101 |
| abstract_inverted_index.advanced | 45 |
| abstract_inverted_index.clinical | 159, 183 |
| abstract_inverted_index.designed | 86 |
| abstract_inverted_index.diseases | 2 |
| abstract_inverted_index.existing | 155 |
| abstract_inverted_index.pathways | 132 |
| abstract_inverted_index.recently | 44 |
| abstract_inverted_index.revealed | 129 |
| abstract_inverted_index.uncommon | 165 |
| abstract_inverted_index.variants | 8, 29, 92 |
| abstract_inverted_index.Long-read | 32 |
| abstract_inverted_index.adoption. | 184 |
| abstract_inverted_index.analysis, | 103 |
| abstract_inverted_index.assessed. | 121 |
| abstract_inverted_index.detecting | 88 |
| abstract_inverted_index.diseases, | 81 |
| abstract_inverted_index.including | 35, 58, 98, 157 |
| abstract_inverted_index.long-read | 76, 105, 168 |
| abstract_inverted_index.molecular | 177 |
| abstract_inverted_index.outlining | 142 |
| abstract_inverted_index.potential | 143, 172 |
| abstract_inverted_index.reviewed, | 97 |
| abstract_inverted_index.segmental | 67 |
| abstract_inverted_index.sequences | 65 |
| abstract_inverted_index.technical | 23 |
| abstract_inverted_index.technique | 127 |
| abstract_inverted_index.Sniffles2, | 115 |
| abstract_inverted_index.accurately | 52 |
| abstract_inverted_index.approaches | 182 |
| abstract_inverted_index.assemblies | 148 |
| abstract_inverted_index.completely | 174 |
| abstract_inverted_index.deletions, | 13 |
| abstract_inverted_index.diagnosing | 79 |
| abstract_inverted_index.diagnostic | 178 |
| abstract_inverted_index.illnesses, | 167 |
| abstract_inverted_index.illustrate | 124 |
| abstract_inverted_index.pan-genome | 150 |
| abstract_inverted_index.pathogenic | 131 |
| abstract_inverted_index.previously | 60, 138 |
| abstract_inverted_index.profiling, | 100 |
| abstract_inverted_index.repetitive | 64 |
| abstract_inverted_index.sequencing | 33, 77, 169 |
| abstract_inverted_index.short-read | 26 |
| abstract_inverted_index.structural | 7, 91 |
| abstract_inverted_index.throughout | 55 |
| abstract_inverted_index.well-known | 112 |
| abstract_inverted_index.Biosciences | 40 |
| abstract_inverted_index.complexity. | 163 |
| abstract_inverted_index.emphasizing | 82 |
| abstract_inverted_index.insertions, | 12 |
| abstract_inverted_index.inversions, | 15 |
| abstract_inverted_index.limitations | 24 |
| abstract_inverted_index.methylation | 99 |
| abstract_inverted_index.sequencing, | 27 |
| abstract_inverted_index.sequencing. | 106 |
| abstract_inverted_index.underscores | 71 |
| abstract_inverted_index.undetected. | 139 |
| abstract_inverted_index.unreachable | 61 |
| abstract_inverted_index.validation, | 160 |
| abstract_inverted_index.applications | 110 |
| abstract_inverted_index.integration, | 151 |
| abstract_inverted_index.interpreting | 90 |
| abstract_inverted_index.Comprehensive | 94 |
| abstract_inverted_index.computational | 162 |
| abstract_inverted_index.duplications, | 14 |
| abstract_inverted_index.duplications. | 68 |
| abstract_inverted_index.effectiveness | 108 |
| abstract_inverted_index.high-fidelity | 41 |
| abstract_inverted_index.technologies, | 34 |
| abstract_inverted_index.bioinformatics | 84 |
| abstract_inverted_index.transformative | 73 |
| abstract_inverted_index.rearrangements. | 18 |
| abstract_inverted_index.underdiagnosed. | 31 |
| abstract_inverted_index.telomere-to-telomere | 147 |
| cited_by_percentile_year.max | 97 |
| cited_by_percentile_year.min | 96 |
| countries_distinct_count | 1 |
| institutions_distinct_count | 12 |
| citation_normalized_percentile.value | 0.97810475 |
| citation_normalized_percentile.is_in_top_1_percent | True |
| citation_normalized_percentile.is_in_top_10_percent | True |