Whole Genome Sequencing, Focused Assays and Functional Studies Increasing Understanding in Cryptic Inherited Retinal Dystrophies
The inherited retinal dystrophies (IRDs) are a clinically and genetically complex group of disorders primarily affecting the rod and cone photoreceptors or other retinal neuronal layers, with emerging therapies heralding the need for accurate molecular diagnosis. Targeted capture and panel-based str...
| Main Authors: | , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-03-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/23/7/3905 |
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| author | Benjamin M. Nash Alan Ma Gladys Ho Elizabeth Farnsworth Andre E. Minoche Mark J. Cowley Christopher Barnett Janine M. Smith To Ha Loi Karen Wong Luke St Heaps Dale Wright Marcel E. Dinger Bruce Bennetts John R. Grigg Robyn V. Jamieson |
| author_facet | Benjamin M. Nash Alan Ma Gladys Ho Elizabeth Farnsworth Andre E. Minoche Mark J. Cowley Christopher Barnett Janine M. Smith To Ha Loi Karen Wong Luke St Heaps Dale Wright Marcel E. Dinger Bruce Bennetts John R. Grigg Robyn V. Jamieson |
| author_sort | Benjamin M. Nash |
| collection | DOAJ |
| description | The inherited retinal dystrophies (IRDs) are a clinically and genetically complex group of disorders primarily affecting the rod and cone photoreceptors or other retinal neuronal layers, with emerging therapies heralding the need for accurate molecular diagnosis. Targeted capture and panel-based strategies examining the partial or full exome deliver molecular diagnoses in many IRD families tested. However, approximately one in three families remain unsolved and unable to obtain personalised recurrence risk or access to new clinical trials or therapy. In this study, we investigated whole genome sequencing (WGS), focused assays and functional studies to assist with unsolved IRD cases and facilitate integration of these approaches to a broad molecular diagnostic clinical service. The WGS approach identified variants not covered or underinvestigated by targeted capture panel-based clinical testing strategies in six families. This included structural variants, with notable benefit of the WGS approach in repetitive regions demonstrated by a family with a hybrid gene and hemizygous missense variant involving the opsin genes, <i>OPN1LW</i> and <i>OPN1MW</i>. There was also benefit in investigation of the repetitive GC-rich ORF15 region of <i>RPGR</i>. Further molecular investigations were facilitated by focused assays in these regions. Deep intronic variants were identified in <i>IQCB1</i> and <i>ABCA4</i>, with functional RNA based studies of the <i>IQCB1</i> variant revealing activation of a cryptic splice acceptor site. While targeted capture panel-based methods are successful in achieving an efficient molecular diagnosis in a proportion of cases, this study highlights the additional benefit and clinical value that may be derived from WGS, focused assays and functional genomics in the highly heterogeneous IRDs. |
| first_indexed | 2024-03-09T11:45:08Z |
| format | Article |
| id | doaj.art-0cebdd4d5ce8417199fe976e77ef071a |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-09T11:45:08Z |
| publishDate | 2022-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-0cebdd4d5ce8417199fe976e77ef071a2023-11-30T23:23:50ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672022-03-01237390510.3390/ijms23073905Whole Genome Sequencing, Focused Assays and Functional Studies Increasing Understanding in Cryptic Inherited Retinal DystrophiesBenjamin M. Nash0Alan Ma1Gladys Ho2Elizabeth Farnsworth3Andre E. Minoche4Mark J. Cowley5Christopher Barnett6Janine M. Smith7To Ha Loi8Karen Wong9Luke St Heaps10Dale Wright11Marcel E. Dinger12Bruce Bennetts13John R. Grigg14Robyn V. Jamieson15Eye Genetics Research Unit, Sydney Children’s Hospitals Network, Save Sight Institute, Children’s Medical Research Institute, University of Sydney, Sydney, NSW 2000, AustraliaEye Genetics Research Unit, Sydney Children’s Hospitals Network, Save Sight Institute, Children’s Medical Research Institute, University of Sydney, Sydney, NSW 2000, AustraliaSpecialty of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2000, AustraliaSpecialty of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2000, AustraliaKinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, AustraliaKinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, AustraliaSouth Australian Clinical Genetics Service, Women’s and Children’s Hospital, North Adelaide, SA 5006, AustraliaSpecialty of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2000, AustraliaEye Genetics Research Unit, Sydney Children’s Hospitals Network, Save Sight Institute, Children’s Medical Research Institute, University of Sydney, Sydney, NSW 2000, AustraliaSydney Genome Diagnostics, Western Sydney Genetics Program, Sydney Children’s Hospitals Network, Westmead, NSW 2145, AustraliaSpecialty of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2000, AustraliaSpecialty of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2000, AustraliaSchool of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Randwick, NSW 2031, AustraliaSpecialty of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2000, AustraliaEye Genetics Research Unit, Sydney Children’s Hospitals Network, Save Sight Institute, Children’s Medical Research Institute, University of Sydney, Sydney, NSW 2000, AustraliaEye Genetics Research Unit, Sydney Children’s Hospitals Network, Save Sight Institute, Children’s Medical Research Institute, University of Sydney, Sydney, NSW 2000, AustraliaThe inherited retinal dystrophies (IRDs) are a clinically and genetically complex group of disorders primarily affecting the rod and cone photoreceptors or other retinal neuronal layers, with emerging therapies heralding the need for accurate molecular diagnosis. Targeted capture and panel-based strategies examining the partial or full exome deliver molecular diagnoses in many IRD families tested. However, approximately one in three families remain unsolved and unable to obtain personalised recurrence risk or access to new clinical trials or therapy. In this study, we investigated whole genome sequencing (WGS), focused assays and functional studies to assist with unsolved IRD cases and facilitate integration of these approaches to a broad molecular diagnostic clinical service. The WGS approach identified variants not covered or underinvestigated by targeted capture panel-based clinical testing strategies in six families. This included structural variants, with notable benefit of the WGS approach in repetitive regions demonstrated by a family with a hybrid gene and hemizygous missense variant involving the opsin genes, <i>OPN1LW</i> and <i>OPN1MW</i>. There was also benefit in investigation of the repetitive GC-rich ORF15 region of <i>RPGR</i>. Further molecular investigations were facilitated by focused assays in these regions. Deep intronic variants were identified in <i>IQCB1</i> and <i>ABCA4</i>, with functional RNA based studies of the <i>IQCB1</i> variant revealing activation of a cryptic splice acceptor site. While targeted capture panel-based methods are successful in achieving an efficient molecular diagnosis in a proportion of cases, this study highlights the additional benefit and clinical value that may be derived from WGS, focused assays and functional genomics in the highly heterogeneous IRDs.https://www.mdpi.com/1422-0067/23/7/3905inherited retinal dystrophywhole genome sequencinggene panelsRNA analysis |
| spellingShingle | Benjamin M. Nash Alan Ma Gladys Ho Elizabeth Farnsworth Andre E. Minoche Mark J. Cowley Christopher Barnett Janine M. Smith To Ha Loi Karen Wong Luke St Heaps Dale Wright Marcel E. Dinger Bruce Bennetts John R. Grigg Robyn V. Jamieson Whole Genome Sequencing, Focused Assays and Functional Studies Increasing Understanding in Cryptic Inherited Retinal Dystrophies International Journal of Molecular Sciences inherited retinal dystrophy whole genome sequencing gene panels RNA analysis |
| title | Whole Genome Sequencing, Focused Assays and Functional Studies Increasing Understanding in Cryptic Inherited Retinal Dystrophies |
| title_full | Whole Genome Sequencing, Focused Assays and Functional Studies Increasing Understanding in Cryptic Inherited Retinal Dystrophies |
| title_fullStr | Whole Genome Sequencing, Focused Assays and Functional Studies Increasing Understanding in Cryptic Inherited Retinal Dystrophies |
| title_full_unstemmed | Whole Genome Sequencing, Focused Assays and Functional Studies Increasing Understanding in Cryptic Inherited Retinal Dystrophies |
| title_short | Whole Genome Sequencing, Focused Assays and Functional Studies Increasing Understanding in Cryptic Inherited Retinal Dystrophies |
| title_sort | whole genome sequencing focused assays and functional studies increasing understanding in cryptic inherited retinal dystrophies |
| topic | inherited retinal dystrophy whole genome sequencing gene panels RNA analysis |
| url | https://www.mdpi.com/1422-0067/23/7/3905 |
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