Long-Read Sequencing and Structural Variant Detection: Unlocking the Hidden Genome in Rare Genetic Disorders
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
Affiliations
Efthalia Moustakli
Laboratory of Medical Genetics, Faculty of Medicine, School of Health Sciences, University of Ioannina, 451 10 Ioannina, Greece
Panagiotis Christopoulos
Second Department of Obstetrics and Gynecology, University Hospital “Aretaieion”, Medical School, National and Kapodistrian University of Athens, 115 28 Athens, Greece
Anastasios Potiris
Third Department of Obstetrics and Gynecology, University General Hospital “ATTIKON”, Medical School, National and Kapodistrian University of Athens, 124 62 Athens, Greece
Athanasios Zikopoulos
Third Department of Obstetrics and Gynecology, University General Hospital “ATTIKON”, Medical School, National and Kapodistrian University of Athens, 124 62 Athens, Greece
Despoina Mavrogianni
First Department of Obstetrics and Gynecology, Alexandra Hospital, Medical School, National and Kapodistrian University of Athens, 115 28 Athens, Greece
Grigorios Karampas
Second Department of Obstetrics and Gynecology, University Hospital “Aretaieion”, Medical School, National and Kapodistrian University of Athens, 115 28 Athens, Greece
Nikolaos Kathopoulis
First Department of Obstetrics and Gynecology, Alexandra Hospital, Medical School, National and Kapodistrian University of Athens, 115 28 Athens, Greece
Ismini Anagnostaki
Third Department of Obstetrics and Gynecology, University General Hospital “ATTIKON”, Medical School, National and Kapodistrian University of Athens, 124 62 Athens, Greece
Ekaterini Domali
First Department of Obstetrics and Gynecology, Alexandra Hospital, Medical School, National and Kapodistrian University of Athens, 115 28 Athens, Greece
Alexandros T. Tzallas
Department of Informatics and Telecommunications, University of Ioannina, Kostakioi, 471 50 Arta, Greece
Peter Drakakis
Third Department of Obstetrics and Gynecology, University General Hospital “ATTIKON”, Medical School, National and Kapodistrian University of Athens, 124 62 Athens, Greece
Sofoklis Stavros
Third Department of Obstetrics and Gynecology, University General Hospital “ATTIKON”, Medical School, National and Kapodistrian University of Athens, 124 62 Athens, Greece
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.
