1
|
Pei Y, Tanguy M, Giess A, Dixit A, Wilson LC, Gibbons RJ, Twigg SRF, Elgar G, Wilkie AOM. A Comparison of Structural Variant Calling from Short-Read and Nanopore-Based Whole-Genome Sequencing Using Optical Genome Mapping as a Benchmark. Genes (Basel) 2024; 15:925. [PMID: 39062704 PMCID: PMC11276380 DOI: 10.3390/genes15070925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 07/03/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024] Open
Abstract
The identification of structural variants (SVs) in genomic data represents an ongoing challenge because of difficulties in reliable SV calling leading to reduced sensitivity and specificity. We prepared high-quality DNA from 9 parent-child trios, who had previously undergone short-read whole-genome sequencing (Illumina platform) as part of the Genomics England 100,000 Genomes Project. We reanalysed the genomes using both Bionano optical genome mapping (OGM; 8 probands and one trio) and Nanopore long-read sequencing (Oxford Nanopore Technologies [ONT] platform; all samples). To establish a "truth" dataset, we asked whether rare proband SV calls (n = 234) made by the Bionano Access (version 1.6.1)/Solve software (version 3.6.1_11162020) could be verified by individual visualisation using the Integrative Genomics Viewer with either or both of the Illumina and ONT raw sequence. Of these, 222 calls were verified, indicating that Bionano OGM calls have high precision (positive predictive value 95%). We then asked what proportion of the 222 true Bionano SVs had been identified by SV callers in the other two datasets. In the Illumina dataset, sensitivity varied according to variant type, being high for deletions (115/134; 86%) but poor for insertions (13/58; 22%). In the ONT dataset, sensitivity was generally poor using the original Sniffles variant caller (48% overall) but improved substantially with use of Sniffles2 (36/40; 90% and 17/23; 74% for deletions and insertions, respectively). In summary, we show that the precision of OGM is very high. In addition, when applying the Sniffles2 caller, the sensitivity of SV calling using ONT long-read sequence data outperforms Illumina sequencing for most SV types.
Collapse
Affiliation(s)
- Yang Pei
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; (Y.P.); (S.R.F.T.)
| | - Melanie Tanguy
- Genomics England Limited, One Canada Square, London E14 5AB, UK
| | - Adam Giess
- Genomics England Limited, One Canada Square, London E14 5AB, UK
| | - Abhijit Dixit
- Clinical Genetics Service, Nottingham University Hospitals NHS Foundation Trust, City Hospital, Nottingham NG5 1PB, UK
| | - Louise C. Wilson
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, Great Ormond Street Hospital, London WC1N 3JH, UK
| | - Richard J. Gibbons
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Stephen R. F. Twigg
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; (Y.P.); (S.R.F.T.)
| | - Greg Elgar
- Genomics England Limited, One Canada Square, London E14 5AB, UK
| | - Andrew O. M. Wilkie
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; (Y.P.); (S.R.F.T.)
| |
Collapse
|
2
|
Watts LM, Bertoli M, Attie-Bitach T, Roux N, Rausell A, Paschal CR, Zambonin JL, Curry CJ, Martin B, Tooze RS, Hawkes L, Kini U, Twigg SRF, Wilkie AOM. The phenotype of MEGF8-related Carpenter syndrome (CRPT2) is refined through the identification of eight new patients. Eur J Hum Genet 2024; 32:864-870. [PMID: 38760421 PMCID: PMC11220001 DOI: 10.1038/s41431-024-01624-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 03/31/2024] [Accepted: 04/25/2024] [Indexed: 05/19/2024] Open
Abstract
Carpenter syndrome (CRPTS) is a rare autosomal recessive condition caused by biallelic variants in genes that encode negative regulators of hedgehog signalling (RAB23 [CRPT1] or, more rarely, MEGF8 [CRPT2]), and is characterised by craniosynostosis, polysyndactyly, and other congenital abnormalities. We describe a further six families comprising eight individuals with MEGF8-associated CRPT2, increasing the total number of reported cases to fifteen, and refine the phenotype of CRPT2 compared to CRPT1. The core features of craniosynostosis, polysyndactyly and (in males) cryptorchidism are almost universal in both CRPT1 and CRPT2. However, laterality defects are present in nearly half of those with MEGF8-associated CRPT2, but are rare in RAB23-associated CRPT1. Craniosynostosis in CRPT2 commonly involves a single midline suture in comparison to the multi-suture craniosynostosis characteristic of CRPT1. No patient to date has carried two MEGF8 gene alterations that are both predicted to lead to complete loss-of-function, suggesting that a variable degree of residual MEGF8 activity may be essential for viability and potentially contributing to variable phenotypic severity. These data refine the phenotypic spectrum of CRPT2 in comparison to CRPT1 and more than double the number of likely pathogenic MEGF8 variants in this rare disorder.
Collapse
Affiliation(s)
- Laura M Watts
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Marta Bertoli
- Northern Genetics Service, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Tania Attie-Bitach
- Service de Médecine Génomique des Maladies Rares, Hôpital Necker-Enfants Malades, Paris, France
- Laboratoire de biologie médicale multisites SeqOIA, Paris, France
| | - Natalie Roux
- Service de Médecine Génomique des Maladies Rares, Hôpital Necker-Enfants Malades, Paris, France
| | - Antonio Rausell
- Service de Médecine Génomique des Maladies Rares, Hôpital Necker-Enfants Malades, Paris, France
- Laboratoire de biologie médicale multisites SeqOIA, Paris, France
| | | | - Jessica L Zambonin
- Provincial Medical Genetics Program, BC Women's Hospital and Health Centre, Vancouver, BC, Canada
| | - Cynthia J Curry
- University of California San Francisco/Fresno, Fresno, CA, USA
- Genetic Medicine, Community Regional Medical Center, Fresno, CA, USA
| | - Blanche Martin
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
- Institut de Pathologie et de Génétique, Gosselies, Belgium
| | - Rebecca S Tooze
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Lara Hawkes
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Usha Kini
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Stephen R F Twigg
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Andrew O M Wilkie
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK.
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK.
| |
Collapse
|
3
|
Pagnamenta AT, Yu J, Walker S, Noble AJ, Lord J, Dutta P, Hashim M, Camps C, Green H, Devaiah S, Nashef L, Parr J, Fratter C, Ibnouf Hussein R, Lindsay SJ, Lalloo F, Banos-Pinero B, Evans D, Mallin L, Waite A, Evans J, Newman A, Allen Z, Perez-Becerril C, Ryan G, Hart R, Taylor J, Bedenham T, Clement E, Blair E, Hay E, Forzano F, Higgs J, Canham N, Majumdar A, McEntagart M, Lahiri N, Stewart H, Smithson S, Calpena E, Jackson A, Banka S, Titheradge H, McGowan R, Rankin J, Shaw-Smith C, Evans DG, Burghel GJ, Smith MJ, Anderson E, Madhu R, Firth H, Ellard S, Brennan P, Anderson C, Taupin D, Rogers MT, Cook JA, Durkie M, East JE, Fowler D, Wilson L, Igbokwe R, Gardham A, Tomlinson I, Baralle D, Uhlig HH, Taylor JC. The impact of inversions across 33,924 families with rare disease from a national genome sequencing project. Am J Hum Genet 2024; 111:1140-1164. [PMID: 38776926 PMCID: PMC11179413 DOI: 10.1016/j.ajhg.2024.04.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 04/25/2024] [Accepted: 04/25/2024] [Indexed: 05/25/2024] Open
Abstract
Detection of structural variants (SVs) is currently biased toward those that alter copy number. The relative contribution of inversions toward genetic disease is unclear. In this study, we analyzed genome sequencing data for 33,924 families with rare disease from the 100,000 Genomes Project. From a database hosting >500 million SVs, we focused on 351 genes where haploinsufficiency is a confirmed disease mechanism and identified 47 ultra-rare rearrangements that included an inversion (24 bp to 36.4 Mb, 20/47 de novo). Validation utilized a number of orthogonal approaches, including retrospective exome analysis. RNA-seq data supported the respective diagnoses for six participants. Phenotypic blending was apparent in four probands. Diagnostic odysseys were a common theme (>50 years for one individual), and targeted analysis for the specific gene had already been performed for 30% of these individuals but with no findings. We provide formal confirmation of a European founder origin for an intragenic MSH2 inversion. For two individuals with complex SVs involving the MECP2 mutational hotspot, ambiguous SV structures were resolved using long-read sequencing, influencing clinical interpretation. A de novo inversion of HOXD11-13 was uncovered in a family with Kantaputra-type mesomelic dysplasia. Lastly, a complex translocation disrupting APC and involving nine rearranged segments confirmed a clinical diagnosis for three family members and resolved a conundrum for a sibling with a single polyp. Overall, inversions play a small but notable role in rare disease, likely explaining the etiology in around 1/750 families across heterogeneous clinical cohorts.
Collapse
Affiliation(s)
- Alistair T Pagnamenta
- Oxford Biomedical Research Centre, Centre for Human Genetics, University of Oxford, Oxford, UK.
| | - Jing Yu
- Oxford Biomedical Research Centre, Centre for Human Genetics, University of Oxford, Oxford, UK; Novo Nordisk Oxford Research Centre, Oxford, UK
| | | | - Alexandra J Noble
- Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford, UK
| | - Jenny Lord
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK; Sheffield Institute for Translational Neuroscience, The University of Sheffield, Sheffield, UK
| | - Prasun Dutta
- Oxford Biomedical Research Centre, Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Mona Hashim
- Oxford Biomedical Research Centre, Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Carme Camps
- Oxford Biomedical Research Centre, Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Hannah Green
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Smrithi Devaiah
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Lina Nashef
- Department of Neurology, King's College Hospital, London, UK
| | - Jason Parr
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Carl Fratter
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Rana Ibnouf Hussein
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Sarah J Lindsay
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Fiona Lalloo
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Benito Banos-Pinero
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - David Evans
- Exeter Genomics Laboratory, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
| | - Lucy Mallin
- Exeter Genomics Laboratory, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
| | - Adrian Waite
- Bristol Genetics Laboratory, North Bristol NHS Trust, Bristol, UK
| | - Julie Evans
- Bristol Genetics Laboratory, North Bristol NHS Trust, Bristol, UK
| | - Andrew Newman
- The All Wales Medical Genomics Service, University Hospital of Wales, Cardiff, UK
| | - Zoe Allen
- North Thames Rare and Inherited Disease Laboratory, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Cristina Perez-Becerril
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Gavin Ryan
- West Midlands Regional Genetics Laboratory, Central and South Genomic Laboratory Hub, Birmingham, UK
| | - Rachel Hart
- Liverpool Centre for Genomic Medicine, Liverpool Women's NHS Foundation Trust, Liverpool, UK
| | - John Taylor
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Tina Bedenham
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Emma Clement
- North East Thames Regional Genetic Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Ed Blair
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Eleanor Hay
- North East Thames Regional Genetic Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Francesca Forzano
- Clinical Genetics Department, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Jenny Higgs
- Liverpool Centre for Genomic Medicine, Liverpool Women's NHS Foundation Trust, Liverpool, UK
| | - Natalie Canham
- Liverpool Centre for Genomic Medicine, Liverpool Women's NHS Foundation Trust, Liverpool, UK
| | - Anirban Majumdar
- Department of Paediatric Neurology, Bristol Children's Hospital, Bristol, UK
| | - Meriel McEntagart
- SW Thames Centre for Genomic Medicine, University of London & St George's University Hospitals NHS Foundation Trust, St George's, London, UK
| | - Nayana Lahiri
- SW Thames Centre for Genomic Medicine, University of London & St George's University Hospitals NHS Foundation Trust, St George's, London, UK
| | - Helen Stewart
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Sarah Smithson
- Department of Clinical Genetics, University Hospitals Bristol NHS Foundation Trust, Bristol, UK
| | - Eduardo Calpena
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Grupo de Investigación en Biomedicina Molecular, Celular y Genómica, Unidad CIBERER (CB06/07/1030), Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain
| | - Adam Jackson
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Health Innovation Manchester, Manchester, UK; Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Siddharth Banka
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Health Innovation Manchester, Manchester, UK; Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Hannah Titheradge
- Department of Clinical Genetics, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Ruth McGowan
- West of Scotland Centre for Genomic Medicine, Glasgow, UK
| | - Julia Rankin
- Department of Clinical Genetics, Royal Devon University Healthcare NHS Trust, Exeter, UK
| | - Charles Shaw-Smith
- Department of Clinical Genetics, Royal Devon University Healthcare NHS Trust, Exeter, UK
| | - D Gareth Evans
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Health Innovation Manchester, Manchester, UK; Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - George J Burghel
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Miriam J Smith
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Emily Anderson
- Liverpool Centre for Genomic Medicine, Liverpool Women's NHS Foundation Trust, Liverpool, UK
| | - Rajesh Madhu
- Paediatric Neurosciences Department, Alder Hey Children's Hospital NHS Foundation Trust, Liverpool, UK
| | - Helen Firth
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Sian Ellard
- Exeter Genomics Laboratory, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
| | - Paul Brennan
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Newcastle University, Newcastle, UK
| | - Claire Anderson
- Canberra Clinical Genomics, Canberra Health Services and The Australian National University, Canberra, ACT, Australia
| | - Doug Taupin
- Cancer Research, Canberra Hospital, Canberra, ACT, Australia
| | - Mark T Rogers
- The All Wales Medical Genomics Service, University Hospital of Wales, Cardiff, UK
| | - Jackie A Cook
- Department of Clinical Genetics, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - Miranda Durkie
- Sheffield Diagnostic Genetics Service, Sheffield Children's NHS Foundation Trust, North East and Yorkshire Genomic Laboratory Hub, Sheffield, UK
| | - James E East
- Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford, UK
| | - Darren Fowler
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Louise Wilson
- North East Thames Regional Genetic Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Rebecca Igbokwe
- Department of Clinical Genetics, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Alice Gardham
- North East Thames Regional Genetic Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Ian Tomlinson
- Department of Oncology, University of Oxford, Oxford, UK
| | - Diana Baralle
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Holm H Uhlig
- Oxford Biomedical Research Centre, Centre for Human Genetics, University of Oxford, Oxford, UK; Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford, UK
| | - Jenny C Taylor
- Oxford Biomedical Research Centre, Centre for Human Genetics, University of Oxford, Oxford, UK.
| |
Collapse
|
4
|
Al-Saei O, Malka S, Owen N, Aliyev E, Vempalli FR, Ocieczek P, Al-Khathlan B, Fakhro K, Moosajee M. Increasing the diagnostic yield of childhood glaucoma cases recruited into the 100,000 Genomes Project. BMC Genomics 2024; 25:484. [PMID: 38755526 PMCID: PMC11097485 DOI: 10.1186/s12864-024-10353-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 04/25/2024] [Indexed: 05/18/2024] Open
Abstract
Childhood glaucoma (CG) encompasses a heterogeneous group of genetic eye disorders that is responsible for approximately 5% of childhood blindness worldwide. Understanding the molecular aetiology is key to improving diagnosis, prognosis and unlocking the potential for optimising clinical management. In this study, we investigated 86 CG cases from 78 unrelated families of diverse ethnic backgrounds, recruited into the Genomics England 100,000 Genomes Project (GE100KGP) rare disease cohort, to improve the genetic diagnostic yield. Using the Genomics England/Genomic Medicine Centres (GE/GMC) diagnostic pipeline, 13 unrelated families were solved (13/78, 17%). Further interrogation using an expanded gene panel yielded a molecular diagnosis in 7 more unrelated families (7/78, 9%). This analysis effectively raises the total number of solved CG families in the GE100KGP to 26% (20/78 families). Twenty-five percent (5/20) of the solved families had primary congenital glaucoma (PCG), while 75% (15/20) had secondary CG; 53% of this group had non-acquired ocular anomalies (including iris hypoplasia, megalocornea, ectopia pupillae, retinal dystrophy, and refractive errors) and 47% had non-acquired systemic diseases such as cardiac abnormalities, hearing impairment, and developmental delay. CYP1B1 was the most frequently implicated gene, accounting for 55% (11/20) of the solved families. We identified two novel likely pathogenic variants in the TEK gene, in addition to one novel pathogenic copy number variant (CNV) in FOXC1. Variants that passed undetected in the GE100KGP diagnostic pipeline were likely due to limitations of the tiering process, the use of smaller gene panels during analysis, and the prioritisation of coding SNVs and indels over larger structural variants, CNVs, and non-coding variants.
Collapse
Affiliation(s)
- Omayma Al-Saei
- Institute of Ophthalmology, University College London, London, EC1V 9EL, UK
- Department of Human Genetics, Sidra Medicine, PO Box 26999, Doha, Qatar
| | - Samantha Malka
- Moorfields Eye Hospital NHS Foundation Trust, London, EC1V 2PD, UK
| | - Nicholas Owen
- Institute of Ophthalmology, University College London, London, EC1V 9EL, UK
| | - Elbay Aliyev
- Department of Human Genetics, Sidra Medicine, PO Box 26999, Doha, Qatar
| | | | - Paulina Ocieczek
- Moorfields Eye Hospital NHS Foundation Trust, London, EC1V 2PD, UK
| | | | - Khalid Fakhro
- Department of Human Genetics, Sidra Medicine, PO Box 26999, Doha, Qatar
| | - Mariya Moosajee
- Institute of Ophthalmology, University College London, London, EC1V 9EL, UK.
- Moorfields Eye Hospital NHS Foundation Trust, London, EC1V 2PD, UK.
- The Francis Crick Institute, London, NW1 1AT, UK.
| |
Collapse
|
5
|
Topa A, Rohlin A, Fehr A, Lovmar L, Stenman G, Tarnow P, Maltese G, Bhatti-Søfteland M, Kölby L. The value of genome-wide analysis in craniosynostosis. Front Genet 2024; 14:1322462. [PMID: 38318288 PMCID: PMC10839781 DOI: 10.3389/fgene.2023.1322462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 12/19/2023] [Indexed: 02/07/2024] Open
Abstract
Background: This study assessed the diagnostic yield of high-throughput sequencing methods in a cohort of craniosynostosis (CS) patients not presenting causal variants identified through previous targeted analysis. Methods: Whole-genome or whole-exome sequencing (WGS/WES) was performed in a cohort of 59 patients (from 57 families) assessed by retrospective phenotyping as having syndromic or nonsyndromic CS. Results: A syndromic form was identified in 51% of the unrelated cases. A genetic cause was identified in 38% of syndromic cases, with novel variants detected in FGFR2 (a rare Alu insertion), TWIST1, TCF12, KIAA0586, HDAC9, FOXP1, and NSD2. Additionally, we report two patients with rare recurrent variants in KAT6A and YY1 as well as two patients with structural genomic aberrations: one with a 22q13 duplication and one with a complex rearrangement involving chromosome 2 (2p25 duplication including SOX11 and deletion of 2q22). Moreover, we identified potentially relevant variants in 87% of the remaining families with no previously detected causal variants, including novel variants in ADAMTSL4, ASH1L, ATRX, C2CD3, CHD5, ERF, H4C5, IFT122, IFT140, KDM6B, KMT2D, LTBP1, MAP3K7, NOTCH2, NSD1, SOS1, SPRY1, POLR2A, PRRX1, RECQL4, TAB2, TAOK1, TET3, TGFBR1, TCF20, and ZBTB20. Conclusion: These results confirm WGS/WES as a powerful diagnostic tool capable of either targeted in silico or broad genomic analysis depending on phenotypic presentation (e.g., classical or unusual forms of syndromic CS).
Collapse
Affiliation(s)
- Alexandra Topa
- Department of Laboratory Medicine, University of Gothenburg, Sahlgrenska Academy, Gothenburg, Sweden
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Anna Rohlin
- Department of Laboratory Medicine, University of Gothenburg, Sahlgrenska Academy, Gothenburg, Sweden
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - André Fehr
- Department of Laboratory Medicine, University of Gothenburg, Sahlgrenska Academy, Gothenburg, Sweden
- Department of Pathology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Lovisa Lovmar
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Göran Stenman
- Department of Laboratory Medicine, University of Gothenburg, Sahlgrenska Academy, Gothenburg, Sweden
- Department of Pathology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Peter Tarnow
- Department of Plastic Surgery, University of Gothenburg, Sahlgrenska Academy, Gothenburg, Sweden
| | - Giovanni Maltese
- Department of Plastic Surgery, University of Gothenburg, Sahlgrenska Academy, Gothenburg, Sweden
| | - Madiha Bhatti-Søfteland
- Department of Plastic Surgery, University of Gothenburg, Sahlgrenska Academy, Gothenburg, Sweden
| | - Lars Kölby
- Department of Plastic Surgery, University of Gothenburg, Sahlgrenska Academy, Gothenburg, Sweden
| |
Collapse
|
6
|
Pagnamenta AT, Camps C, Giacopuzzi E, Taylor JM, Hashim M, Calpena E, Kaisaki PJ, Hashimoto A, Yu J, Sanders E, Schwessinger R, Hughes JR, Lunter G, Dreau H, Ferla M, Lange L, Kesim Y, Ragoussis V, Vavoulis DV, Allroggen H, Ansorge O, Babbs C, Banka S, Baños-Piñero B, Beeson D, Ben-Ami T, Bennett DL, Bento C, Blair E, Brasch-Andersen C, Bull KR, Cario H, Cilliers D, Conti V, Davies EG, Dhalla F, Dacal BD, Dong Y, Dunford JE, Guerrini R, Harris AL, Hartley J, Hollander G, Javaid K, Kane M, Kelly D, Kelly D, Knight SJL, Kreins AY, Kvikstad EM, Langman CB, Lester T, Lines KE, Lord SR, Lu X, Mansour S, Manzur A, Maroofian R, Marsden B, Mason J, McGowan SJ, Mei D, Mlcochova H, Murakami Y, Németh AH, Okoli S, Ormondroyd E, Ousager LB, Palace J, Patel SY, Pentony MM, Pugh C, Rad A, Ramesh A, Riva SG, Roberts I, Roy N, Salminen O, Schilling KD, Scott C, Sen A, Smith C, Stevenson M, Thakker RV, Twigg SRF, Uhlig HH, van Wijk R, Vona B, Wall S, Wang J, Watkins H, Zak J, Schuh AH, Kini U, Wilkie AOM, Popitsch N, Taylor JC. Structural and non-coding variants increase the diagnostic yield of clinical whole genome sequencing for rare diseases. Genome Med 2023; 15:94. [PMID: 37946251 PMCID: PMC10636885 DOI: 10.1186/s13073-023-01240-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 09/27/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND Whole genome sequencing is increasingly being used for the diagnosis of patients with rare diseases. However, the diagnostic yields of many studies, particularly those conducted in a healthcare setting, are often disappointingly low, at 25-30%. This is in part because although entire genomes are sequenced, analysis is often confined to in silico gene panels or coding regions of the genome. METHODS We undertook WGS on a cohort of 122 unrelated rare disease patients and their relatives (300 genomes) who had been pre-screened by gene panels or arrays. Patients were recruited from a broad spectrum of clinical specialties. We applied a bioinformatics pipeline that would allow comprehensive analysis of all variant types. We combined established bioinformatics tools for phenotypic and genomic analysis with our novel algorithms (SVRare, ALTSPLICE and GREEN-DB) to detect and annotate structural, splice site and non-coding variants. RESULTS Our diagnostic yield was 43/122 cases (35%), although 47/122 cases (39%) were considered solved when considering novel candidate genes with supporting functional data into account. Structural, splice site and deep intronic variants contributed to 20/47 (43%) of our solved cases. Five genes that are novel, or were novel at the time of discovery, were identified, whilst a further three genes are putative novel disease genes with evidence of causality. We identified variants of uncertain significance in a further fourteen candidate genes. The phenotypic spectrum associated with RMND1 was expanded to include polymicrogyria. Two patients with secondary findings in FBN1 and KCNQ1 were confirmed to have previously unidentified Marfan and long QT syndromes, respectively, and were referred for further clinical interventions. Clinical diagnoses were changed in six patients and treatment adjustments made for eight individuals, which for five patients was considered life-saving. CONCLUSIONS Genome sequencing is increasingly being considered as a first-line genetic test in routine clinical settings and can make a substantial contribution to rapidly identifying a causal aetiology for many patients, shortening their diagnostic odyssey. We have demonstrated that structural, splice site and intronic variants make a significant contribution to diagnostic yield and that comprehensive analysis of the entire genome is essential to maximise the value of clinical genome sequencing.
Collapse
Affiliation(s)
- Alistair T Pagnamenta
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Carme Camps
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Edoardo Giacopuzzi
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Human Technopole, Viale Rita Levi Montalcini 1, 20157, Milan, Italy
| | - John M Taylor
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Old Road, Oxford, OX3 7LE, UK
| | - Mona Hashim
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Eduardo Calpena
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Pamela J Kaisaki
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Akiko Hashimoto
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Jing Yu
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Edward Sanders
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Ron Schwessinger
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Jim R Hughes
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Gerton Lunter
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
- University Medical Center Groningen, Groningen University, PO Box 72, 9700 AB, Groningen, The Netherlands
| | - Helene Dreau
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Department of Oncology, Oxford Molecular Diagnostics Centre, University of Oxford, Level 4, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK
| | - Matteo Ferla
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Lukas Lange
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Yesim Kesim
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Vassilis Ragoussis
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Dimitrios V Vavoulis
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Department of Oncology, Oxford Molecular Diagnostics Centre, University of Oxford, Level 4, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK
| | - Holger Allroggen
- Neurosciences Department, UHCW NHS Trust, Clifford Bridge Road, Coventry, CV2 2DX, UK
| | - Olaf Ansorge
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Christian Babbs
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Siddharth Banka
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Oxford Road, Manchester, M13 9WL, UK
| | - Benito Baños-Piñero
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Old Road, Oxford, OX3 7LE, UK
| | - David Beeson
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Tal Ben-Ami
- Pediatric Hematology-Oncology Unit, Kaplan Medical Center, Rehovot, Israel
| | - David L Bennett
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Celeste Bento
- Hematology Department, Hospitais da Universidade de Coimbra, Coimbra, Portugal
| | - Edward Blair
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 7LE, UK
| | - Charlotte Brasch-Andersen
- Department of Clinical Genetics, Odense University Hospital and Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Katherine R Bull
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
| | - Holger Cario
- Department of Pediatrics and Adolescent Medicine, University Medical Center, Eythstrasse 24, 89075, Ulm, Germany
| | - Deirdre Cilliers
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 7LE, UK
| | - Valerio Conti
- Neuroscience Department, Meyer Children's Hospital IRCCS, Viale Pieraccini 24, 50139, Florence, Italy
| | - E Graham Davies
- Department of Immunology, Great Ormond Street Hospital for Children NHS Trust and UCL Great Ormond Street Institute of Child Health, Zayed Centre for Research, 2Nd Floor, 20C Guilford Street, London, WC1N 1DZ, UK
| | - Fatima Dhalla
- Department of Paediatrics, Institute of Developmental and Regenerative Medicine, IMS-Tetsuya Nakamura Building, Old Road Campus, Roosevelt Drive, Oxford, OX3 7TY, UK
| | - Beatriz Diez Dacal
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Old Road, Oxford, OX3 7LE, UK
| | - Yin Dong
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - James E Dunford
- Oxford NIHR Musculoskeletal BRC and Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Nuffield Orthopaedic Centre, Old Road, Oxford, OX3 7HE, UK
| | - Renzo Guerrini
- Neuroscience Department, Meyer Children's Hospital IRCCS, Viale Pieraccini 24, 50139, Florence, Italy
| | - Adrian L Harris
- Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
| | - Jane Hartley
- Liver Unit, Birmingham Women's & Children's Hospital and University of Birmingham, Steelhouse Lane, Birmingham, B4 6NH, UK
| | - Georg Hollander
- Department of Paediatrics, University of Oxford, Level 2, Children's Hospital, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Kassim Javaid
- Oxford NIHR Musculoskeletal BRC and Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Nuffield Orthopaedic Centre, Old Road, Oxford, OX3 7HE, UK
| | - Maureen Kane
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Pharmacy Hall North, Room 731, 20 N. Pine Street, Baltimore, MD, 21201, USA
| | - Deirdre Kelly
- Liver Unit, Birmingham Women's & Children's Hospital and University of Birmingham, Steelhouse Lane, Birmingham, B4 6NH, UK
| | - Dominic Kelly
- Children's Hospital, OUH NHS Foundation Trust, NIHR Oxford BRC, Headley Way, Oxford, OX3 9DU, UK
| | - Samantha J L Knight
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Alexandra Y Kreins
- Department of Immunology, Great Ormond Street Hospital for Children NHS Trust and UCL Great Ormond Street Institute of Child Health, Zayed Centre for Research, 2Nd Floor, 20C Guilford Street, London, WC1N 1DZ, UK
| | - Erika M Kvikstad
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Craig B Langman
- Feinberg School of Medicine, Northwestern University, 211 E Chicago Avenue, Chicago, IL, MS37, USA
| | - Tracy Lester
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Old Road, Oxford, OX3 7LE, UK
| | - Kate E Lines
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- University of Oxford, Academic Endocrine Unit, OCDEM, Churchill Hospital, Oxford, OX3 7LJ, UK
| | - Simon R Lord
- Early Phase Clinical Trials Unit, Department of Oncology, University of Oxford, Cancer and Haematology Centre, Level 2 Administration Area, Churchill Hospital, Oxford, OX3 7LJ, UK
| | - Xin Lu
- Nuffield Department of Clinical Medicine, Ludwig Institute for Cancer Research, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
| | - Sahar Mansour
- St George's University Hospitals NHS Foundation Trust, Blackshore Road, Tooting, London, SW17 0QT, UK
| | - Adnan Manzur
- MRC Centre for Neuromuscular Diseases, National Hospital for Neurology and Neurosurgery, Queen Square, London, WC1N 3BG, UK
| | - Reza Maroofian
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, WC1N 3BG, UK
| | - Brian Marsden
- Nuffield Department of Medicine, Kennedy Institute, University of Oxford, Oxford, OX3 7BN, UK
| | - Joanne Mason
- Yourgene Health Headquarters, Skelton House, Lloyd Street North, Manchester Science Park, Manchester, M15 6SH, UK
| | - Simon J McGowan
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Davide Mei
- Neuroscience Department, Meyer Children's Hospital IRCCS, Viale Pieraccini 24, 50139, Florence, Italy
| | - Hana Mlcochova
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Yoshiko Murakami
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Andrea H Németh
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 7LE, UK
| | - Steven Okoli
- Imperial College NHS Trust, Department of Haematology, Hammersmith Hospital, Du Cane Road, London, W12 0HS, UK
| | - Elizabeth Ormondroyd
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- University of Oxford, Level 6 West Wing, Oxford, OX3 9DU, JR, UK
| | - Lilian Bomme Ousager
- Department of Clinical Genetics, Odense University Hospital and Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Jacqueline Palace
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Smita Y Patel
- Clinical Immunology, John Radcliffe Hospital, Level 4A, Oxford, OX3 9DU, UK
| | - Melissa M Pentony
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Chris Pugh
- Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
| | - Aboulfazl Rad
- Department of Otolaryngology-Head & Neck Surgery, Tübingen Hearing Research Centre, Eberhard Karls University, Elfriede-Aulhorn-Str. 5, 72076, Tübingen, Germany
| | - Archana Ramesh
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Simone G Riva
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Irene Roberts
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
- Department of Paediatrics, University of Oxford, Level 2, Children's Hospital, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Noémi Roy
- Department of Haematology, Oxford University Hospitals NHS Foundation Trust, Level 4, Haematology, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Outi Salminen
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Department of Oncology, Oxford Molecular Diagnostics Centre, University of Oxford, Level 4, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK
| | - Kyleen D Schilling
- Ann & Robert H. Lurie Children's Hospital of Chicago, 225 E Chicago Avenue, Chicago, IL, 60611, USA
| | - Caroline Scott
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Arjune Sen
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Conrad Smith
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Old Road, Oxford, OX3 7LE, UK
| | - Mark Stevenson
- University of Oxford, Academic Endocrine Unit, OCDEM, Churchill Hospital, Oxford, OX3 7LJ, UK
| | - Rajesh V Thakker
- University of Oxford, Academic Endocrine Unit, OCDEM, Churchill Hospital, Oxford, OX3 7LJ, UK
| | - Stephen R F Twigg
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Holm H Uhlig
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Department of Paediatrics, University of Oxford, Level 2, Children's Hospital, John Radcliffe Hospital, Oxford, OX3 9DU, UK
- Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Richard van Wijk
- UMC Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Barbara Vona
- Department of Otolaryngology-Head & Neck Surgery, Tübingen Hearing Research Centre, Eberhard Karls University, Elfriede-Aulhorn-Str. 5, 72076, Tübingen, Germany
- Institute of Human Genetics, University Medical Center Göttingen, Heinrich-Düker-Weg 12, 37073, Göttingen, Germany
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany
| | - Steven Wall
- Oxford Craniofacial Unit, John Radcliffe Hospital, Level LG1, West Wing, Oxford, OX3 9DU, UK
| | - Jing Wang
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Hugh Watkins
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- University of Oxford, Level 6 West Wing, Oxford, OX3 9DU, JR, UK
| | - Jaroslav Zak
- Nuffield Department of Clinical Medicine, Ludwig Institute for Cancer Research, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
- Department of Immunology and Microbiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Anna H Schuh
- Department of Oncology, Oxford Molecular Diagnostics Centre, University of Oxford, Level 4, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK
| | - Usha Kini
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 7LE, UK
| | - Andrew O M Wilkie
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Niko Popitsch
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter(VBC), Dr.-Bohr-Gasse 9, 1030, Vienna, Austria
| | - Jenny C Taylor
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK.
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK.
| |
Collapse
|
7
|
Gaillard L, Goverde A, Weerts MJA, de Klein A, Mathijssen IMJ, Van Dooren MF. Genetic diagnostic yield in an 11-year cohort of craniosynostosis patients. Eur J Med Genet 2023; 66:104843. [PMID: 37716645 DOI: 10.1016/j.ejmg.2023.104843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 08/08/2023] [Accepted: 09/11/2023] [Indexed: 09/18/2023]
Abstract
Craniosynostosis may present in isolation, 'non-syndromic', or with additional congenital anomalies/neurodevelopmental disorders, 'syndromic'. Clinical focus shifted from confirming classical syndromic cases to offering genetic testing to all craniosynostosis patients. This retrospective study assesses diagnostic yield of molecular testing by investigating prevalences of chromosomal and monogenic (likely) pathogenic variants in an 11-year cohort of 1020 craniosynostosis patients. 502 children underwent genetic testing. Pathogenic variants were identified in 174 patients (35%). Diagnostic yield was significantly higher in syndromic craniosynostosis (62%) than in non-syndromic craniosynostosis (6%). Before whole exome sequencing (WES) emerged, single-gene testing was performed using Sanger sequencing or multiplex ligation-dependent probe amplification (MLPA). Diagnostic yield was 11% and was highest for EFNB1, FGFR2, FGFR3, and IL11RA. Diagnostic yield for copy number variant analysis using microarray was 8%. From 2015 onwards, the WES craniosynostosis panel was implemented, with a yield of 10%. In unsolved, mainly syndromic, cases suspected of a genetic cause, additional WES panels (multiple congenital anomalies (MCA)/intellectual disability (ID)) or open exome analysis were performed with an 18% diagnostic yield. To conclude, microarray and the WES craniosynostosis panel are key to identifying pathogenic variants. in craniosynostosis patients. Given the advances in genetic diagnostics, we should look beyond the scope of the WES craniosynostosis panel and consider extensive genetic diagnostics (e.g. open exome sequencing, whole genome sequencing, RNA sequencing and episignature analysis) if no diagnosis is obtained through microarray and/or WES craniosynostosis panel. If parents are uncomfortable with more extensive diagnostics, MCA or ID panels may be considered.
Collapse
Affiliation(s)
- Linda Gaillard
- Erasmus MC - Sophia Children's Hospital, University Medical Center Rotterdam, Department of Plastic and Reconstructive Surgery and Hand Surgery, Rotterdam, the Netherlands.
| | - Anne Goverde
- Erasmus MC, University Medical Center Rotterdam, Department of Clinical Genetics, Rotterdam, the Netherlands
| | - Marjolein J A Weerts
- Erasmus MC, University Medical Center Rotterdam, Department of Clinical Genetics, Rotterdam, the Netherlands
| | - Annelies de Klein
- Erasmus MC, University Medical Center Rotterdam, Department of Clinical Genetics, Rotterdam, the Netherlands
| | - Irene M J Mathijssen
- Erasmus MC - Sophia Children's Hospital, University Medical Center Rotterdam, Department of Plastic and Reconstructive Surgery and Hand Surgery, Rotterdam, the Netherlands
| | - Marieke F Van Dooren
- Erasmus MC, University Medical Center Rotterdam, Department of Clinical Genetics, Rotterdam, the Netherlands
| |
Collapse
|
8
|
Tooze RS, Calpena E, Twigg SRF, D'Arco F, Wakeling EL, Wilkie AOM. Craniosynostosis, inner ear, and renal anomalies in a child with complete loss of SPRY1 (sprouty homolog 1) function. J Med Genet 2023; 60:712-716. [PMID: 36543535 PMCID: PMC10359576 DOI: 10.1136/jmg-2022-108946] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 11/11/2022] [Indexed: 12/24/2022]
Abstract
INTRODUCTION SPRY1 encodes protein sprouty homolog 1 (Spry-1), a negative regulator of receptor tyrosine kinase signalling. Null mutant mice display kidney/urinary tract abnormalities and altered size of the skull; complete loss-of-function of Spry-1 in humans has not been reported. METHODS Analysis of whole-genome sequencing data from individuals with craniosynostosis enrolled in the 100,000 Genomes Project identified a likely pathogenic variant within SPRY1. Reverse-transcriptase PCR and western blot analysis were used to investigate the effect of the variant on SPRY1 mRNA and protein, in lymphoblastoid cell lines from the patient and both parents. RESULTS A nonsense variant in SPRY1, encoding p.(Leu27*), was confirmed to be heterozygous in the unaffected parents and homozygous in the child. The child's phenotype, which included sagittal craniosynostosis, subcutaneous cystic lesions overlying the lambdoid sutures, hearing loss associated with bilateral cochlear and vestibular dysplasia and a unilateral renal cyst, overlapped the features reported in Spry1-/- null mice. Functional studies supported escape from nonsense-mediated decay, but western blot analysis demonstrated complete absence of full-length protein in the affected child and a marked reduction in both parents. CONCLUSION This is the first report of complete loss of Spry-1 function in humans, associated with abnormalities of the cranial sutures, inner ear, and kidneys.
Collapse
Affiliation(s)
- Rebecca S Tooze
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Eduardo Calpena
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Stephen R F Twigg
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Felice D'Arco
- Department of Radiology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Emma L Wakeling
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Andrew O M Wilkie
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| |
Collapse
|
9
|
Tooze RS, Calpena E, Weber A, Wilson LC, Twigg SRF, Wilkie AOM. Review of Recurrently Mutated Genes in Craniosynostosis Supports Expansion of Diagnostic Gene Panels. Genes (Basel) 2023; 14:615. [PMID: 36980886 PMCID: PMC10048212 DOI: 10.3390/genes14030615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 02/17/2023] [Accepted: 02/23/2023] [Indexed: 03/05/2023] Open
Abstract
Craniosynostosis, the premature fusion of the cranial sutures, affects ~1 in 2000 children. Although many patients with a genetically determined cause harbor a variant in one of just seven genes or have a chromosomal abnormality, over 60 genes are known to be recurrently mutated, thus comprising a long tail of rarer diagnoses. Genome sequencing for the diagnosis of rare diseases is increasingly used in clinical settings, but analysis of the data is labor intensive and involves a trade-off between achieving high sensitivity or high precision. PanelApp, a crowd-sourced disease-focused set of gene panels, was designed to enable prioritization of variants in known disease genes for a given pathology, allowing enhanced identification of true-positives. For heterogeneous disorders like craniosynostosis, these panels must be regularly updated to ensure that diagnoses are not being missed. We provide a systematic review of genetic literature on craniosynostosis over the last 5 years, including additional results from resequencing a 42-gene panel in 617 affected individuals. We identify 16 genes (representing a 25% uplift) that should be added to the list of bona fide craniosynostosis disease genes and discuss the insights that these new genes provide into pathophysiological mechanisms of craniosynostosis.
Collapse
Affiliation(s)
- Rebecca S. Tooze
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Eduardo Calpena
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Astrid Weber
- Liverpool Centre for Genomic Medicine, Liverpool Women’s NHS Foundation Trust, Liverpool L8 7SS, UK
| | - Louise C. Wilson
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Stephen R. F. Twigg
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Andrew O. M. Wilkie
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| |
Collapse
|
10
|
Diaz-Gonzalez F, Sacedo-Gutiérrez JM, Twigg SRF, Calpena E, Carceller-Benito FE, Parrón-Pajares M, Santos-Simarro F, Heath KE. Case report: A third variant in the 5' UTR of TWIST1 creates a novel upstream translation initiation site in a child with Saethre-Chotzen syndrome. Front Genet 2023; 13:1089417. [PMID: 36685936 PMCID: PMC9845400 DOI: 10.3389/fgene.2022.1089417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 12/05/2022] [Indexed: 01/06/2023] Open
Abstract
Introduction: Saethre-Chotzen syndrome, a craniosynostosis syndrome characterized by the premature closure of the coronal sutures, dysmorphic facial features and limb anomalies, is caused by haploinsufficiency of TWIST1. Although the majority of variants localize in the coding region of the gene, two variants in the 5' UTR have been recently reported to generate novel upstream initiation codons. Methods: Skeletal dysplasia Next-generation sequencing (NGS) panel was used for genetic analysis in a patient with bicoronal synostosis, facial dysmorphisms and limb anomalies. The variant pathogenicity was assessed by a luciferase reporter promoter assay. Results: Here, we describe the identification of a third ATG-creating de novo variant, c.-18C>T, in the 5' UTR of TWIST1 in the patient with a clinical diagnosis of Saethre-Chotzen syndrome. It was predicted to create an out-of-frame new upstream translation initiation codon resulting in a 40 amino acid larger functionally inactive protein. We performed luciferase reporter promoter assays to demonstrate that the variant does indeed reduce translation from the main open reading frame. Conclusion: This is the third variant identified in this region and confirms the introduction of upstream ATGs in the 5' UTR of TWIST1 as a pathogenic mechanism in Saethre-Chotzen syndrome. This case report shows the necessity for performing functional characterization of variants of unknown significance within national health services.
Collapse
Affiliation(s)
- Francisca Diaz-Gonzalez
- Institute of Medical & Molecular Genetics (INGEMM), Hospital Universitario La Paz, Universidad Autónoma de Madrid, IdiPAZ, Madrid, Spain,Skeletal Dysplasia Multidisciplinary Unit (UMDE) and ERN-BOND, Hospital Universitario La Paz, Madrid, Spain
| | - Javier M. Sacedo-Gutiérrez
- Skeletal Dysplasia Multidisciplinary Unit (UMDE) and ERN-BOND, Hospital Universitario La Paz, Madrid, Spain,Department of Neurosurgery, Hospital Universitario la Paz, Universidad Autónoma de Madrid, IdiPAZ, Madrid, Spain
| | - Stephen R. F. Twigg
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Eduardo Calpena
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Fernando E. Carceller-Benito
- Skeletal Dysplasia Multidisciplinary Unit (UMDE) and ERN-BOND, Hospital Universitario La Paz, Madrid, Spain,Department of Neurosurgery, Hospital Universitario la Paz, Universidad Autónoma de Madrid, IdiPAZ, Madrid, Spain
| | - Manuel Parrón-Pajares
- Skeletal Dysplasia Multidisciplinary Unit (UMDE) and ERN-BOND, Hospital Universitario La Paz, Madrid, Spain,Department of Radiology, Hospital Universitario La Paz, Universidad Autónoma de Madrid, Madrid, Spain
| | - Fernando Santos-Simarro
- Institute of Medical & Molecular Genetics (INGEMM), Hospital Universitario La Paz, Universidad Autónoma de Madrid, IdiPAZ, Madrid, Spain,Skeletal Dysplasia Multidisciplinary Unit (UMDE) and ERN-BOND, Hospital Universitario La Paz, Madrid, Spain,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER, U753), Instituto Carlos III, Madrid, Spain
| | - Karen E. Heath
- Institute of Medical & Molecular Genetics (INGEMM), Hospital Universitario La Paz, Universidad Autónoma de Madrid, IdiPAZ, Madrid, Spain,Skeletal Dysplasia Multidisciplinary Unit (UMDE) and ERN-BOND, Hospital Universitario La Paz, Madrid, Spain,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER, U753), Instituto Carlos III, Madrid, Spain,*Correspondence: Karen E. Heath,
| |
Collapse
|
11
|
Pagnamenta AT, Yu J, Evans J, Twiss P, Offiah AC, Wafik M, Mehta SG, Javaid MK, Smithson SF, Taylor JC. Conclusion of diagnostic odysseys due to inversions disrupting GLI3 and FBN1. J Med Genet 2022; 60:505-510. [PMID: 36411030 PMCID: PMC10176330 DOI: 10.1136/jmg-2022-108753] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 10/14/2022] [Indexed: 11/22/2022]
Abstract
Many genetic testing methodologies are biased towards picking up structural variants (SVs) that alter copy number. Copy-neutral rearrangements such as inversions are therefore likely to suffer from underascertainment. In this study, manual review prompted by a virtual multidisciplinary team meeting and subsequent bioinformatic prioritisation of data from the 100K Genomes Project was performed across 43 genes linked to well-characterised skeletal disorders. Ten individuals from three independent families were found to harbour diagnostic inversions. In two families, inverted segments of 1.2/14.8 Mb unequivocally disrupted GLI3 and segregated with skeletal features consistent with Greig cephalopolysyndactyly syndrome. For one family, phenotypic blending was due to the opposing breakpoint lying ~45 kb from HOXA13 In the third family, long suspected to have Marfan syndrome, a 2.0 Mb inversion disrupting FBN1 was identified. These findings resolved lengthy diagnostic odysseys of 9-20 years and highlight the importance of direct interaction between clinicians and data-analysts. These exemplars of a rare mutational class inform future SV prioritisation strategies within the NHS Genomic Medicine Service and similar genome sequencing initiatives. In over 30 years since these two disease-gene associations were identified, large inversions have yet to be described and so our results extend the mutational spectra linked to these conditions.
Collapse
Affiliation(s)
- Alistair T Pagnamenta
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, Oxfordshire, UK .,Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford, Oxfordshire, UK
| | - Jing Yu
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, Oxfordshire, UK.,Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, Oxfordshire, UK
| | - Julie Evans
- Bristol Genetics Laboratory, North Bristol NHS Trust, Bristol, UK
| | - Philip Twiss
- Cambridge Genomics Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, Cambridgeshire, UK
| | | | | | - Amaka C Offiah
- Academic Unit of Child Health, The University of Sheffield, Sheffield, UK
| | - Mohamed Wafik
- Department of Clinical Genetics, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Sarju G Mehta
- Department of Clinical Genetics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, Cambridgeshire, UK
| | - Mohammed K Javaid
- Nuffield Department of Orthopaedics, Rheumatology and Orthopaedic Sciences, University of Oxford, Oxford, Oxfordshire, UK
| | - Sarah F Smithson
- Department of Clinical Genetics, University Hospitals Bristol NHS Foundation Trust, Bristol, UK
| | - Jenny C Taylor
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, Oxfordshire, UK.,Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford, Oxfordshire, UK
| |
Collapse
|
12
|
Macken WL, Falabella M, McKittrick C, Pizzamiglio C, Ellmers R, Eggleton K, Woodward CE, Patel Y, Labrum R, Phadke R, Reilly MM, DeVile C, Sarkozy A, Footitt E, Davison J, Rahman S, Houlden H, Bugiardini E, Quinlivan R, Hanna MG, Vandrovcova J, Pitceathly RDS. Specialist multidisciplinary input maximises rare disease diagnoses from whole genome sequencing. Nat Commun 2022; 13:6324. [PMID: 36344503 PMCID: PMC9640711 DOI: 10.1038/s41467-022-32908-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 08/24/2022] [Indexed: 11/09/2022] Open
Abstract
Diagnostic whole genome sequencing (WGS) is increasingly used in rare diseases. However, standard, semi-automated WGS analysis may overlook diagnoses in complex disorders. Here, we show that specialist multidisciplinary analysis of WGS, following an initial 'no primary findings' (NPF) report, improves diagnostic rates and alters management. We undertook WGS in 102 adults with diagnostically challenging primary mitochondrial disease phenotypes. NPF cases were reviewed by a genomic medicine team, thus enabling bespoke informatic approaches, co-ordinated phenotypic validation, and functional work. We enhanced the diagnostic rate from 16.7% to 31.4%, with management implications for all new diagnoses, and detected strong candidate disease-causing variants in a further 3.9% of patients. This approach presents a standardised model of care that supports mainstream clinicians and enhances diagnostic equity for complex disorders, thereby facilitating access to the potential benefits of genomic healthcare. This research was made possible through access to the data and findings generated by the 100,000 Genomes Project: http://www.genomicsengland.co.uk .
Collapse
Affiliation(s)
- William L Macken
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK
| | - Micol Falabella
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Caroline McKittrick
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Chiara Pizzamiglio
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK
| | - Rebecca Ellmers
- Neurogenetics Unit, Rare and Inherited Disease Laboratory, North Thames Genomic Laboratory Hub, London, UK
| | - Kelly Eggleton
- Neurogenetics Unit, Rare and Inherited Disease Laboratory, North Thames Genomic Laboratory Hub, London, UK
| | - Cathy E Woodward
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK
- Neurogenetics Unit, Rare and Inherited Disease Laboratory, North Thames Genomic Laboratory Hub, London, UK
| | - Yogen Patel
- Neurogenetics Unit, Rare and Inherited Disease Laboratory, North Thames Genomic Laboratory Hub, London, UK
| | - Robyn Labrum
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK
- Neurogenetics Unit, Rare and Inherited Disease Laboratory, North Thames Genomic Laboratory Hub, London, UK
| | - Rahul Phadke
- Dubowitz Neuromuscular Centre, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Mary M Reilly
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Catherine DeVile
- Department of Neurosciences, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Anna Sarkozy
- Dubowitz Neuromuscular Centre, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Emma Footitt
- Metabolic Unit, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - James Davison
- Metabolic Unit, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
- National Institute for Health and Care Research Great Ormond Street Hospital Biomedical Research Centre, London, UK
| | - Shamima Rahman
- Metabolic Unit, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
- Mitochondrial Research Group, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Enrico Bugiardini
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK
| | - Rosaline Quinlivan
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK
- Dubowitz Neuromuscular Centre, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Michael G Hanna
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK
| | - Jana Vandrovcova
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK.
| | - Robert D S Pitceathly
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK.
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK.
| |
Collapse
|
13
|
Chen J, Zhang P, Peng M, Liu B, Wang X, Du S, Lu Y, Mu X, Lu Y, Wang S, Wu Y. An additional whole-exome sequencing study in 102 panel-undiagnosed patients: A retrospective study in a Chinese craniosynostosis cohort. Front Genet 2022; 13:967688. [PMID: 36118902 PMCID: PMC9481236 DOI: 10.3389/fgene.2022.967688] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 08/01/2022] [Indexed: 11/13/2022] Open
Abstract
Craniosynostosis (CRS) is a disease with prematurely fused cranial sutures. In the last decade, the whole-exome sequencing (WES) was widely used in Caucasian populations. The WES largely contributed in genetic diagnosis and exploration on new genetic mechanisms of CRS. In this study, we enrolled 264 CRS patients in China. After a 17-gene-panel sequencing designed in the previous study, 139 patients were identified with pathogenic/likely pathogenic (P/LP) variants according to the ACMG guideline as positive genetic diagnosis. WES was then performed on 102 patients with negative genetic diagnosis by panel. Ten P/LP variants were additionally identified in ten patients, increasing the genetic diagnostic yield by 3.8% (10/264). The novel variants in ANKH, H1-4, EIF5A, SOX6, and ARID1B expanded the mutation spectra of CRS. Then we designed a compatible research pipeline (RP) for further exploration. The RP could detect all seven P/LP SNVs and InDels identified above, in addition to 15 candidate variants found in 13 patients with worthy of further study. In sum, the 17-gene panel and WES identified positive genetic diagnosis for 56.4% patients (149/264) in 16 genes. At last, in our estimation, the genetic testing strategy of “Panel-first” saves 24.3% of the cost compared with “WES only”, suggesting the “Panel-first” is an economical strategy.
Collapse
Affiliation(s)
- Jieyi Chen
- Department of Plastic Surgery, Huashan Hospital, Fudan University, Shanghai, China
- State Key Laboratory of Genetic Engineering at School of Life Sciences, Fudan University, Shanghai, China
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ping Zhang
- Center for Molecular Medicine, Pediatrics Research Institute, Children’s Hospital of Fudan University, Shanghai, China
| | - Meifang Peng
- The Core Laboratory in Medical Center of Clinical Research, Department of Molecular Diagnostics & Endocrinology, Shanghai Ninth People’s Hospital, State Key Laboratory of Medical Genomics, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bo Liu
- Center for Molecular Medicine, Pediatrics Research Institute, Children’s Hospital of Fudan University, Shanghai, China
| | - Xiao Wang
- Center for Molecular Medicine, Pediatrics Research Institute, Children’s Hospital of Fudan University, Shanghai, China
| | - Siyuan Du
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yao Lu
- School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Xiongzheng Mu
- Department of Plastic Surgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Yulan Lu
- Center for Molecular Medicine, Pediatrics Research Institute, Children’s Hospital of Fudan University, Shanghai, China
- *Correspondence: Yingzhi Wu, ; Sijia Wang, ; Yulan Lu,
| | - Sijia Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- *Correspondence: Yingzhi Wu, ; Sijia Wang, ; Yulan Lu,
| | - Yingzhi Wu
- Department of Plastic Surgery, Huashan Hospital, Fudan University, Shanghai, China
- *Correspondence: Yingzhi Wu, ; Sijia Wang, ; Yulan Lu,
| |
Collapse
|
14
|
Blakes AJM, Wai HA, Davies I, Moledina HE, Ruiz A, Thomas T, Bunyan D, Thomas NS, Burren CP, Greenhalgh L, Lees M, Pichini A, Smithson SF, Taylor Tavares AL, O'Donovan P, Douglas AGL, Whiffin N, Baralle D, Lord J. A systematic analysis of splicing variants identifies new diagnoses in the 100,000 Genomes Project. Genome Med 2022; 14:79. [PMID: 35883178 PMCID: PMC9327385 DOI: 10.1186/s13073-022-01087-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 07/13/2022] [Indexed: 11/24/2022] Open
Abstract
Background Genomic variants which disrupt splicing are a major cause of rare genetic diseases. However, variants which lie outside of the canonical splice sites are difficult to interpret clinically. Improving the clinical interpretation of non-canonical splicing variants offers a major opportunity to uplift diagnostic yields from whole genome sequencing data. Methods Here, we examine the landscape of splicing variants in whole-genome sequencing data from 38,688 individuals in the 100,000 Genomes Project and assess the contribution of non-canonical splicing variants to rare genetic diseases. We use a variant-level constraint metric (the mutability-adjusted proportion of singletons) to identify constrained functional variant classes near exon–intron junctions and at putative splicing branchpoints. To identify new diagnoses for individuals with unsolved rare diseases in the 100,000 Genomes Project, we identified individuals with de novo single-nucleotide variants near exon–intron boundaries and at putative splicing branchpoints in known disease genes. We identified candidate diagnostic variants through manual phenotype matching and confirmed new molecular diagnoses through clinical variant interpretation and functional RNA studies. Results We show that near-splice positions and splicing branchpoints are highly constrained by purifying selection and harbour potentially damaging non-coding variants which are amenable to systematic analysis in sequencing data. From 258 de novo splicing variants in known rare disease genes, we identify 35 new likely diagnoses in probands with an unsolved rare disease. To date, we have confirmed a new diagnosis for six individuals, including four in whom RNA studies were performed. Conclusions Overall, we demonstrate the clinical value of examining non-canonical splicing variants in individuals with unsolved rare diseases. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-022-01087-x.
Collapse
Affiliation(s)
- Alexander J M Blakes
- Faculty of Medicine, Human Development and Health, University of Southampton, Southampton, UK.,Faculty of Medicine, National Heart and Lung Institute, Imperial College London, London, UK
| | - Htoo A Wai
- Faculty of Medicine, Human Development and Health, University of Southampton, Southampton, UK
| | - Ian Davies
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Hassan E Moledina
- Faculty of Medicine, Human Development and Health, University of Southampton, Southampton, UK
| | - April Ruiz
- Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, UK
| | - Tessy Thomas
- Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, UK
| | - David Bunyan
- Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury, UK.,Faculty of Medicine, University of Southampton, Southampton, UK
| | - N Simon Thomas
- Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury, UK.,Faculty of Medicine, University of Southampton, Southampton, UK
| | - Christine P Burren
- Department of Paediatric Endocrinology and Diabetes, University Hospitals Bristol and Weston NHS Foundation Trust, Bristol, UK.,Bristol Medical School, Department of Translational Health Sciences, University of Bristol, Bristol, UK
| | - Lynn Greenhalgh
- Liverpool Centre for Genomic Medicine, Crown Street, Liverpool, UK
| | - Melissa Lees
- North East Thames Regional Genomics Service, Great Ormond Street Hospital, London, UK
| | - Amanda Pichini
- Department of Clinical Genetics, University Hospitals Bristol and Weston Foundation Trust, Bristol, UK.,Genomics England, Dawson Hall, Charterhouse Square, London, UK
| | - Sarah F Smithson
- Department of Clinical Genetics, University Hospitals Bristol and Weston Foundation Trust, Bristol, UK
| | - Ana Lisa Taylor Tavares
- Genomics England, Dawson Hall, Charterhouse Square, London, UK.,Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Hills Road, Cambridge, UK
| | - Peter O'Donovan
- Genomics England, Dawson Hall, Charterhouse Square, London, UK
| | - Andrew G L Douglas
- Faculty of Medicine, Human Development and Health, University of Southampton, Southampton, UK.,Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | | | - Nicola Whiffin
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Diana Baralle
- Faculty of Medicine, Human Development and Health, University of Southampton, Southampton, UK.,Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, UK
| | - Jenny Lord
- Faculty of Medicine, Human Development and Health, University of Southampton, Southampton, UK.
| |
Collapse
|
15
|
Navigating an early career in genomics and data science, written from the perspective of a current PhD student. PATTERNS 2022; 3:100548. [PMID: 35845831 PMCID: PMC9278496 DOI: 10.1016/j.patter.2022.100548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Rebecca Tooze, a PhD student in the Oxford Clinical Genetics’ group, discusses the importance and application for data science in her field. Using bioinformatic approaches, she analyzes whole-genome sequencing data from patients with craniosynostosis. In this paper, she comments on her current research and her opportunity as an editorial intern with Patterns.
Collapse
|