Full characterization of unresolved structural variation through long-read sequencing and optical genome mapping
Abstract Structural variants (SVs) are important contributors to human disease. Their characterization remains however difficult due to their size and association with repetitive regions. Long-read sequencing (LRS) and optical genome mapping (OGM) can aid as their molecules span multiple kilobases a...
Saved in:
| Main Authors: | , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2024-11-01
|
| Series: | Scientific Reports |
| Subjects: | |
| Online Access: | https://doi.org/10.1038/s41598-024-80068-z |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1846147922323832832 |
|---|---|
| author | Griet De Clercq Lies Vantomme Barbara Dewaele Bert Callewaert Olivier Vanakker Sandra Janssens Bart Loeys Mojca Strazisar Wouter De Coster Joris Robert Vermeesch Annelies Dheedene Björn Menten |
| author_facet | Griet De Clercq Lies Vantomme Barbara Dewaele Bert Callewaert Olivier Vanakker Sandra Janssens Bart Loeys Mojca Strazisar Wouter De Coster Joris Robert Vermeesch Annelies Dheedene Björn Menten |
| author_sort | Griet De Clercq |
| collection | DOAJ |
| description | Abstract Structural variants (SVs) are important contributors to human disease. Their characterization remains however difficult due to their size and association with repetitive regions. Long-read sequencing (LRS) and optical genome mapping (OGM) can aid as their molecules span multiple kilobases and capture SVs in full. In this study, we selected six individuals who presented with unresolved SVs. We applied LRS onto all individuals and OGM to a subset of three complex cases. LRS detected and fully resolved the interrogated SV in all samples. This enabled a precise molecular diagnosis in two individuals. Overall, LRS identified 100% of the junctions at single-basepair level, providing valuable insights into their formation mechanisms without need for additional data sources. Application of OGM added straightforward variant phasing, aiding in the unravelment of complex rearrangements. These results highlight the potential of LRS and OGM as follow-up molecular tests for complete SV characterization. We show that they can assess clinically relevant structural variation at unprecedented resolution. Additionally, they detect (complex) cryptic rearrangements missed by conventional methods. This ultimately leads to an increased diagnostic yield, emphasizing their added benefit in a diagnostic setting. To aid their rapid adoption, we provide detailed laboratory and bioinformatics workflows in this manuscript. |
| format | Article |
| id | doaj-art-ddf31f2fa73e4d6bbc89654922dff66c |
| institution | Kabale University |
| issn | 2045-2322 |
| language | English |
| publishDate | 2024-11-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj-art-ddf31f2fa73e4d6bbc89654922dff66c2024-12-01T12:20:33ZengNature PortfolioScientific Reports2045-23222024-11-0114111210.1038/s41598-024-80068-zFull characterization of unresolved structural variation through long-read sequencing and optical genome mappingGriet De Clercq0Lies Vantomme1Barbara Dewaele2Bert Callewaert3Olivier Vanakker4Sandra Janssens5Bart Loeys6Mojca Strazisar7Wouter De Coster8Joris Robert Vermeesch9Annelies Dheedene10Björn Menten11Department of Biomolecular Medicine, Ghent UniversityDepartment of Biomolecular Medicine, Ghent UniversityCenter for Human Genetics Leuven, University Hospital LeuvenDepartment of Biomolecular Medicine, Ghent UniversityDepartment of Biomolecular Medicine, Ghent UniversityDepartment of Biomolecular Medicine, Ghent UniversityCenter for Medical Genetics Antwerp, University of Antwerp, Antwerp University HospitalNeuromics Support Facility, VIB Center for Molecular Neurology, VIBDepartment of Biomedical Sciences, University of AntwerpCenter for Human Genetics Leuven, University Hospital LeuvenCenter for Medical Genetics Ghent, Ghent University HospitalDepartment of Biomolecular Medicine, Ghent UniversityAbstract Structural variants (SVs) are important contributors to human disease. Their characterization remains however difficult due to their size and association with repetitive regions. Long-read sequencing (LRS) and optical genome mapping (OGM) can aid as their molecules span multiple kilobases and capture SVs in full. In this study, we selected six individuals who presented with unresolved SVs. We applied LRS onto all individuals and OGM to a subset of three complex cases. LRS detected and fully resolved the interrogated SV in all samples. This enabled a precise molecular diagnosis in two individuals. Overall, LRS identified 100% of the junctions at single-basepair level, providing valuable insights into their formation mechanisms without need for additional data sources. Application of OGM added straightforward variant phasing, aiding in the unravelment of complex rearrangements. These results highlight the potential of LRS and OGM as follow-up molecular tests for complete SV characterization. We show that they can assess clinically relevant structural variation at unprecedented resolution. Additionally, they detect (complex) cryptic rearrangements missed by conventional methods. This ultimately leads to an increased diagnostic yield, emphasizing their added benefit in a diagnostic setting. To aid their rapid adoption, we provide detailed laboratory and bioinformatics workflows in this manuscript.https://doi.org/10.1038/s41598-024-80068-zLong-read sequencingOptical genome mappingStructural variationClinical genomicsChromothripsisComplex genomic rearrangements |
| spellingShingle | Griet De Clercq Lies Vantomme Barbara Dewaele Bert Callewaert Olivier Vanakker Sandra Janssens Bart Loeys Mojca Strazisar Wouter De Coster Joris Robert Vermeesch Annelies Dheedene Björn Menten Full characterization of unresolved structural variation through long-read sequencing and optical genome mapping Scientific Reports Long-read sequencing Optical genome mapping Structural variation Clinical genomics Chromothripsis Complex genomic rearrangements |
| title | Full characterization of unresolved structural variation through long-read sequencing and optical genome mapping |
| title_full | Full characterization of unresolved structural variation through long-read sequencing and optical genome mapping |
| title_fullStr | Full characterization of unresolved structural variation through long-read sequencing and optical genome mapping |
| title_full_unstemmed | Full characterization of unresolved structural variation through long-read sequencing and optical genome mapping |
| title_short | Full characterization of unresolved structural variation through long-read sequencing and optical genome mapping |
| title_sort | full characterization of unresolved structural variation through long read sequencing and optical genome mapping |
| topic | Long-read sequencing Optical genome mapping Structural variation Clinical genomics Chromothripsis Complex genomic rearrangements |
| url | https://doi.org/10.1038/s41598-024-80068-z |
| work_keys_str_mv | AT grietdeclercq fullcharacterizationofunresolvedstructuralvariationthroughlongreadsequencingandopticalgenomemapping AT liesvantomme fullcharacterizationofunresolvedstructuralvariationthroughlongreadsequencingandopticalgenomemapping AT barbaradewaele fullcharacterizationofunresolvedstructuralvariationthroughlongreadsequencingandopticalgenomemapping AT bertcallewaert fullcharacterizationofunresolvedstructuralvariationthroughlongreadsequencingandopticalgenomemapping AT oliviervanakker fullcharacterizationofunresolvedstructuralvariationthroughlongreadsequencingandopticalgenomemapping AT sandrajanssens fullcharacterizationofunresolvedstructuralvariationthroughlongreadsequencingandopticalgenomemapping AT bartloeys fullcharacterizationofunresolvedstructuralvariationthroughlongreadsequencingandopticalgenomemapping AT mojcastrazisar fullcharacterizationofunresolvedstructuralvariationthroughlongreadsequencingandopticalgenomemapping AT wouterdecoster fullcharacterizationofunresolvedstructuralvariationthroughlongreadsequencingandopticalgenomemapping AT jorisrobertvermeesch fullcharacterizationofunresolvedstructuralvariationthroughlongreadsequencingandopticalgenomemapping AT anneliesdheedene fullcharacterizationofunresolvedstructuralvariationthroughlongreadsequencingandopticalgenomemapping AT bjornmenten fullcharacterizationofunresolvedstructuralvariationthroughlongreadsequencingandopticalgenomemapping |