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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).
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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
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Serpieri V, Mortarini G, Loucks H, Biagini T, Micalizzi A, Palmieri I, Dempsey JC, D'Abrusco F, Mazzotta C, Battini R, Bertini ES, Boltshauser E, Borgatti R, Brockmann K, D'Arrigo S, Nardocci N, Fischetto R, Agolini E, Novelli A, Romano A, Romaniello R, Stanzial F, Signorini S, Strisciuglio P, Gana S, Mazza T, Doherty D, Valente EM. Recurrent, founder and hypomorphic variants contribute to the genetic landscape of Joubert syndrome. J Med Genet 2023; 60:885-893. [PMID: 36788019 PMCID: PMC10447400 DOI: 10.1136/jmg-2022-108725] [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: 05/24/2022] [Accepted: 01/08/2023] [Indexed: 02/16/2023]
Abstract
BACKGROUND Joubert syndrome (JS) is a neurodevelopmental ciliopathy characterised by a distinctive mid-hindbrain malformation, the 'molar tooth sign'. Over 40 JS-associated genes are known, accounting for two-thirds of cases. METHODS While most variants are novel or extremely rare, we report on 11 recurring variants in seven genes, including three known 'founder variants' in the Ashkenazi Jewish, Hutterite and Finnish populations. We evaluated variant frequencies in ~550 European patients with JS and compared them with controls (>15 000 Italian plus gnomAD), and with an independent cohort of ~600 JS probands from the USA. RESULTS All variants were markedly enriched in the European JS cohort compared with controls. When comparing allele frequencies in the two JS cohorts, the Ashkenazim founder variant (TMEM216 c.218G>T) was significantly enriched in American compared with European patients with JS, while MKS1 c.1476T>G was about 10 times more frequent among European JS. Frequencies of other variants were comparable in the two cohorts. Genotyping of several markers identified four novel European founder haplotypes.Two recurrent variants (MKS1 c.1476T>G and KIAA0586 c.428delG), have been detected in homozygosity in unaffected individuals, suggesting they could act as hypomorphic variants. However, while fibroblasts from a MKS1 c.1476T>G healthy homozygote showed impaired ability to form primary cilia and mildly reduced ciliary length, ciliary parameters were normal in cells from a KIAA0586 c.428delG healthy homozygote. CONCLUSION This study contributes to understand the complex genetic landscape of JS, explain its variable prevalence in distinct geographical areas and characterise two recurrent hypomorphic variants.
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Affiliation(s)
| | - Giulia Mortarini
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Hailey Loucks
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - Tommaso Biagini
- Bioinformatics Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, S. Giovanni Rotondo, Foggia, Italy
| | - Alessia Micalizzi
- Laboratory of Medical Genetics, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Ilaria Palmieri
- Neurogenetics Research Centre, IRCCS Mondino Foundation, Pavia, Italy
| | - Jennifer C Dempsey
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - Fulvio D'Abrusco
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | | | - Roberta Battini
- Department of Neuroscience, IRCCS Stella Maris Foundation, Pisa, Italy
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Enrico Silvio Bertini
- Unit of Neuromuscular and Neurodegenerative Disorders, IRCCS Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Eugen Boltshauser
- Departement of Pediatric Neurology, University Children's Hospital Zürich, Zurich, Switzerland
| | - Renato Borgatti
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
- Child Neurology and Psychiatry Unit, IRCCS Mondino Foundation, Pavia, Italy
| | - Knut Brockmann
- Interdisciplinary Pediatric Centre for Children with Developmental Disabilities and Severe Chronic Disorders, University Medical Centre, Georg August University, Göttingen, Germany
| | - Stefano D'Arrigo
- Department of Pediatric Neuroscience, Fondazione IRCCS Istituto Neurologico "C Besta", Milan, Italy
| | - Nardo Nardocci
- Department of Pediatric Neuroscience, Fondazione IRCCS Istituto Neurologico "C Besta", Milan, Italy
| | - Rita Fischetto
- Clinical Genetics Unit, Department of Pediatric Medicine, Giovanni XXIII Children's Hospital, Bari, Italy
| | - Emanuele Agolini
- Laboratory of Medical Genetics, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Antonio Novelli
- Laboratory of Medical Genetics, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Alfonso Romano
- Section of Pediatrics, Department of Medical Translational Sciences, University of Naples Federico II, Naples, Italy
| | - Romina Romaniello
- Child Neurology and Psychiatry Unit, IRCCS Mondino Foundation, Pavia, Italy
| | - Franco Stanzial
- Genetic Counseling Service, Department of Pediatrics, Regional Hospital of Bozen, Bozen, Italy
| | - Sabrina Signorini
- Child Neurology and Psychiatry Unit, IRCCS Mondino Foundation, Pavia, Italy
| | - Pietro Strisciuglio
- Section of Pediatrics, Department of Medical Translational Sciences, University of Naples Federico II, Naples, Italy
| | - Simone Gana
- Neurogenetics Research Centre, IRCCS Mondino Foundation, Pavia, Italy
| | - Tommaso Mazza
- Bioinformatics Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, S. Giovanni Rotondo, Foggia, Italy
| | - Dan Doherty
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - Enza Maria Valente
- Neurogenetics Research Centre, IRCCS Mondino Foundation, Pavia, Italy
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
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3
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Schröder S, Yigit G, Li Y, Altmüller J, Büttel HM, Fiedler B, Kretzschmar C, Nürnberg P, Seeger J, Serpieri V, Valente EM, Wollnik B, Boltshauser E, Brockmann K. The genetic spectrum of congenital ocular motor apraxia type Cogan: an observational study, continued. Orphanet J Rare Dis 2023; 18:101. [PMID: 37131188 PMCID: PMC10155342 DOI: 10.1186/s13023-023-02706-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 04/20/2023] [Indexed: 05/04/2023] Open
Abstract
BACKGROUND The term congenital ocular motor apraxia (COMA), coined by Cogan in 1952, designates the incapacity to initiate voluntary eye movements performing rapid gaze shift, so called saccades. While regarded as a nosological entity by some authors, there is growing evidence that COMA designates merely a neurological symptom with etiologic heterogeneity. In 2016, we reported an observational study in a cohort of 21 patients diagnosed as having COMA. Thorough re-evaluation of the neuroimaging features of these 21 subjects revealed a previously not recognized molar tooth sign (MTS) in 11 of them, thus leading to a diagnostic reassignment as Joubert syndrome (JBTS). Specific MRI features in two further individuals indicated a Poretti-Boltshauser syndrome (PTBHS) and a tubulinopathy. In eight patients, a more precise diagnosis was not achieved. We pursued this cohort aiming at clarification of the definite genetic basis of COMA in each patient. RESULTS Using a candidate gene approach, molecular genetic panels or exome sequencing, we detected causative molecular genetic variants in 17 of 21 patients with COMA. In nine of those 11 subjects diagnosed with JBTS due to newly recognized MTS on neuroimaging, we found pathogenic mutations in five different genes known to be associated with JBTS, including KIAA0586, NPHP1, CC2D2A, MKS1, and TMEM67. In two individuals without MTS on MRI, pathogenic variants were detected in NPHP1 and KIAA0586, arriving at a diagnosis of JBTS type 4 and 23, respectively. Three patients carried heterozygous truncating variants in SUFU, representing the first description of a newly identified forme fruste of JBTS. The clinical diagnoses of PTBHS and tubulinopathy were confirmed by detection of causative variants in LAMA1 and TUBA1A, respectively. In one patient with normal MRI, biallelic pathogenic variants in ATM indicated variant ataxia telangiectasia. Exome sequencing failed to reveal causative genetic variants in the remaining four subjects, two of them with clear MTS on MRI. CONCLUSIONS Our findings indicate marked etiologic heterogeneity in COMA with detection of causative mutations in 81% (17/21) in our cohort and nine different genes being affected, mostly genes associated with JBTS. We provide a diagnostic algorithm for COMA.
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Affiliation(s)
- Simone Schröder
- Interdisciplinary Pediatric Center for Children with Developmental Disabilities and Severe Chronic Disorders, Department of Pediatrics and Adolescent Medicine, University Medical Center, Göttingen, Germany
| | - Gökhan Yigit
- Institute of Human Genetics, University Medical Center, Göttingen, Germany
| | - Yun Li
- Institute of Human Genetics, University Medical Center, Göttingen, Germany
| | - Janine Altmüller
- Cologne Center for Genomics (CCG) and Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Core Facility Genomics, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | | | - Barbara Fiedler
- Division of Neuropediatrics, Department of General Pediatrics, University Hospital Münster, Münster, Germany
| | | | - Peter Nürnberg
- Cologne Center for Genomics (CCG) and Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Jürgen Seeger
- Center of Developmental Neurology (SPZ Frankfurt Mitte), Frankfurt, Germany
| | | | - Enza Maria Valente
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Neurogenetics Research Center, IRCCS Mondino Foundation, Pavia, Italy
| | - Bernd Wollnik
- Institute of Human Genetics, University Medical Center, Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
| | - Eugen Boltshauser
- Department of Pediatric Neurology (Emeritus), University Children's Hospital, Zurich, Switzerland
| | - Knut Brockmann
- Interdisciplinary Pediatric Center for Children with Developmental Disabilities and Severe Chronic Disorders, Department of Pediatrics and Adolescent Medicine, University Medical Center, Göttingen, Germany.
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Zlotogora J, Harel T, Meiner V. Explanations for the discrepancy between variant frequency and homozygous disease occurrence: Lessons from Ashkenazi Jewish data. Eur J Med Genet 2023; 66:104765. [PMID: 37028505 DOI: 10.1016/j.ejmg.2023.104765] [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: 09/05/2022] [Revised: 12/28/2022] [Accepted: 04/03/2023] [Indexed: 04/09/2023]
Abstract
Ample data on recessive disorders among Ashkenazi Jews has been gathered and published through the years. The opportunity to integrate molecular records analyzed in actual affected individuals with data derived from population-documented frequencies enables to compare these figures. We reviewed assumed pathogenic variants reported among patients in the Israeli medical genetic database (IMGD) with a carrier frequency of 1% or more among Ashkenazi Jews in gnomAD. Among the 60 assumed pathogenic variants recorded in IMGD, 15 (25%) had either a disease incidence considerably lower than expected by the calculated carrier frequency (12 variants), or the variant was not characterized in Ashkenazi Jewish patients (three variants). Possible explanations for the rarity or absence of affected individuals despite high carrier frequency include embryonic lethality, clinical variability, and incomplete and age-related penetrance, in addition to the existence of additional assumed pathogenic variants on the founder haplotype, hypomorphic variants or digenic inheritance. The discrepancy in actual versus expected number of patients calls for caution upon designing and choosing targeted genes and recessive mutations for carrier screening.
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Affiliation(s)
- Joël Zlotogora
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, 9112001, Israel.
| | - Tamar Harel
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, 9112001, Israel; Department of Genetics, Hadassah Medical Organization, Jerusalem, 9112001, Israel
| | - Vardiella Meiner
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, 9112001, Israel; Department of Genetics, Hadassah Medical Organization, Jerusalem, 9112001, Israel
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5
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Spahiu L, Behluli E, Grajçevci-Uka V, Liehr T, Temaj G. Joubert syndrome: Molecular basis and treatment. JOURNAL OF MOTHER AND CHILD 2022; 26:118-123. [PMID: 36803942 PMCID: PMC10032320 DOI: 10.34763/jmotherandchild.20222601.d-22-00034] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 09/30/2022] [Indexed: 02/23/2023]
Abstract
Joubert syndrome (JS; MIM PS213300) is a rare genetic autosomal recessive disease characterized by cerebellar vermis hypoplasia, a distinctive malformation of the cerebellum and the so-called "molar tooth sign." Other characteristic features are hypotonia with lateral ataxia, intellectual disability/mental retardation, oculomotor apraxia, retinal dystrophy, abnormalities in the respiratory system, renal cysts, hepatic fibrosis, and skeletal changes. Such pleiotropic characteristics are typical of many disorders involving primary cilium aberrations, providing a significant overlap between JS and other ciliopathies such as nephronophthisis, Meckel syndrome, and Bardet-Biedl syndrome. This review will describe some characteristics of JS associated with changes in 35 genes, and will also address subtypes of JS, clinical diagnosis, and the future of therapeutic developments.
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Affiliation(s)
- Lidvana Spahiu
- Department of Pediatrics, University of Prishtina, Prishtina, Kosovo
| | - Emir Behluli
- Department of Pediatrics, University of Prishtina, Prishtina, Kosovo
| | | | - Thomas Liehr
- Institut für Humangenetik, Universitätsklinikum Jena, Friedrich Schiller Universität, Jena, Germany
| | - Gazmend Temaj
- Human Genetics, College UBT, Faculty of Pharmacy Prishtina, PrishtinaKosovo
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6
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Gana S, Serpieri V, Valente EM. Genotype-phenotype correlates in Joubert syndrome: A review. AMERICAN JOURNAL OF MEDICAL GENETICS. PART C, SEMINARS IN MEDICAL GENETICS 2022; 190:72-88. [PMID: 35238134 PMCID: PMC9314610 DOI: 10.1002/ajmg.c.31963] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/04/2022] [Accepted: 02/15/2022] [Indexed: 01/20/2023]
Abstract
Joubert syndrome (JS) is a genetically heterogeneous primary ciliopathy characterized by a pathognomonic cerebellar and brainstem malformation, the “molar tooth sign,” and variable organ involvement. Over 40 causative genes have been identified to date, explaining up to 94% of cases. To date, gene‐phenotype correlates have been delineated only for a handful of genes, directly translating into improved counseling and clinical care. For instance, JS individuals harboring pathogenic variants in TMEM67 have a significantly higher risk of liver fibrosis, while pathogenic variants in NPHP1, RPGRIP1L, and TMEM237 are frequently associated to JS with renal involvement, requiring a closer monitoring of liver parameters, or renal functioning. On the other hand, individuals with causal variants in the CEP290 or AHI1 need a closer surveillance for retinal dystrophy and, in case of CEP290, also for chronic kidney disease. These examples highlight how an accurate description of the range of clinical symptoms associated with defects in each causative gene, including the rare ones, would better address prognosis and help guiding a personalized management. This review proposes to address this issue by assessing the available literature, to confirm known, as well as to propose rare gene‐phenotype correlates in JS.
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Affiliation(s)
- Simone Gana
- Neurogenetics Research Center, IRCCS Mondino Foundation, Pavia, Italy
| | | | - Enza Maria Valente
- Neurogenetics Research Center, IRCCS Mondino Foundation, Pavia, Italy.,Department of Molecular Medicine, University of Pavia, Pavia, Italy
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7
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Barroso‐Gil M, Olinger E, Ramsbottom SA, Molinari E, Miles CG, Sayer JA. Update of genetic variants in CEP120 and CC2D2A-With an emphasis on genotype-phenotype correlations, tissue specific transcripts and exploring mutation specific exon skipping therapies. Mol Genet Genomic Med 2021; 9:e1603. [PMID: 33486889 PMCID: PMC8683696 DOI: 10.1002/mgg3.1603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 12/18/2020] [Accepted: 01/04/2021] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Mutations in ciliary genes cause a spectrum of both overlapping and distinct clinical syndromes (ciliopathies). CEP120 and CC2D2A are paradigmatic examples for this genetic heterogeneity and pleiotropy as mutations in both cause Joubert syndrome but are also associated with skeletal ciliopathies and Meckel syndrome, respectively. The molecular basis for this phenotypical variability is not understood but basal exon skipping likely contributes to tolerance for deleterious mutations via tissue-specific preservation of the amount of expressed functional protein. METHODS We systematically reviewed and annotated genetic variants and clinical presentations reported in CEP120- and CC2D2A-associated disease and we combined in silico and ex vivo approaches to study tissue-specific transcripts and identify molecular targets for exon skipping. RESULTS We confirmed more severe clinical presentations associated with truncating CC2D2A mutations. We identified and confirmed basal exon skipping in the kidney, with possible relevance for organ-specific disease manifestations. Finally, we proposed a multimodal approach to classify exons amenable to exon skipping. By mapping reported variants, 14 truncating mutations in 7 CC2D2A exons were identified as potentially rescuable by targeted exon skipping, an approach that is already in clinical use for other inherited human diseases. CONCLUSION Genotype-phenotype correlations for CC2D2A support the deleteriousness of null alleles and CC2D2A, but not CEP120, offers potential for therapeutic exon skipping approaches.
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Affiliation(s)
- Miguel Barroso‐Gil
- Translational and Clinical Research InstituteFaculty of Medical SciencesNewcastle UniversityNewcastle Upon TyneUK
| | - Eric Olinger
- Translational and Clinical Research InstituteFaculty of Medical SciencesNewcastle UniversityNewcastle Upon TyneUK
| | - Simon A. Ramsbottom
- Translational and Clinical Research InstituteFaculty of Medical SciencesNewcastle UniversityNewcastle Upon TyneUK
| | - Elisa Molinari
- Translational and Clinical Research InstituteFaculty of Medical SciencesNewcastle UniversityNewcastle Upon TyneUK
| | - Colin G. Miles
- Translational and Clinical Research InstituteFaculty of Medical SciencesNewcastle UniversityNewcastle Upon TyneUK
| | - John A. Sayer
- Translational and Clinical Research InstituteFaculty of Medical SciencesNewcastle UniversityNewcastle Upon TyneUK
- Renal ServicesThe Newcastle upon Tyne Hospitals NHS Foundation TrustNewcastle Upon TyneUK
- NIHR Newcastle Biomedical Research CentreNewcastle UniversityNewcastle Upon TyneUK
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8
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Al Alawi I, Al Riyami M, Barroso-Gil M, Powell L, Olinger E, Al Salmi I, Sayer JA. The diagnostic yield of whole exome sequencing as a first approach in consanguineous Omani renal ciliopathy syndrome patients. F1000Res 2021; 10:207. [PMID: 34354814 PMCID: PMC8290205 DOI: 10.12688/f1000research.40338.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/01/2021] [Indexed: 02/05/2023] Open
Abstract
Background: Whole exome sequencing (WES) is becoming part of routine clinical and diagnostic practice. In the investigation of inherited cystic kidney disease and renal ciliopathy syndromes, WES has been extensively applied in research studies as well as for diagnostic utility to detect various novel genes and variants. The yield of WES critically depends on the characteristics of the patient population. Methods: In this study, we selected 8 unrelated Omani children, presenting with renal ciliopathy syndromes with a positive family history and originating from consanguineous families. We performed WES in affected children to determine the genetic cause of disease and to test the yield of this approach, coupled with homozygosity mapping, in this highly selected population. DNA library construction and WES was carried out using SureSelect Human All Exon V6 Enrichment Kit and Illumina HiSeq platform. For variants filtering and annotation Qiagen Variant Ingenuity tool was used. Nexus copy number software from BioDiscovery was used for evaluation of copy number variants and whole gene deletions. Patient and parental DNA was used to confirm mutations and the segregation of alleles using Sanger sequencing. Results: Genetic analysis identified 4 potential causative homozygous variants each confirmed by Sanger sequencing in 4 clinically relevant ciliopathy syndrome genes, ( TMEM231, TMEM138, WDR19 and BBS9), leading to an overall diagnostic yield of 50%. Conclusions: WES coupled with homozygosity mapping provided a diagnostic yield of 50% in this selected population. This genetic approach needs to be embedded into clinical practise to allow confirmation of clinical diagnosis, to inform genetic screening as well as family planning decisions. Half of the patients remain without diagnosis highlighting the technical and interpretational hurdles that need to be overcome in the future.
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Affiliation(s)
- Intisar Al Alawi
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, Tyne and Wear, NE13BZ, UK
- National Genetic Center, Ministry of Health, Muscat, Oman
| | - Mohammed Al Riyami
- Pediatric Nephrology Unit, Department of Child Health, Royal Hospital, Ministry of Health, Muscat, Oman
| | - Miguel Barroso-Gil
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, Tyne and Wear, NE13BZ, UK
| | - Laura Powell
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, Tyne and Wear, NE13BZ, UK
| | - Eric Olinger
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, Tyne and Wear, NE13BZ, UK
| | - Issa Al Salmi
- Renal Medicine Department, Royal Hospital, Ministry of Health, Muscat, Oman
- Oman Medical Speciality Board, Muscat, Oman
| | - John A. Sayer
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, Tyne and Wear, NE13BZ, UK
- Oman Medical Speciality Board, Muscat, Oman
- Newcastle Biomedical Research Centre, NIHR, Newcastle upon Tyne, Tyne and Wear, NE45PL, UK
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9
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Al Alawi I, Al Riyami M, Barroso-Gil M, Powell L, Olinger E, Al Salmi I, Sayer JA. The diagnostic yield of whole exome sequencing as a first approach in consanguineous Omani renal ciliopathy syndrome patients. F1000Res 2021; 10:207. [PMID: 34354814 PMCID: PMC8290205 DOI: 10.12688/f1000research.40338.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/17/2021] [Indexed: 02/05/2023] Open
Abstract
Background: Whole exome sequencing (WES) is becoming part of routine clinical and diagnostic practice. In the investigation of inherited cystic kidney disease and renal ciliopathy syndromes, WES has been extensively applied in research studies as well as for diagnostic utility to detect various novel genes and variants. The yield of WES critically depends on the characteristics of the patient population. Methods: In this study, we selected 8 unrelated Omani children, presenting with renal ciliopathy syndromes with a positive family history and originating from consanguineous families. We performed WES in affected children to determine the genetic cause of disease and to test the yield of this approach, coupled with homozygosity mapping, in this highly selected population. DNA library construction and WES was carried out using SureSelect Human All Exon V6 Enrichment Kit and Illumina HiSeq platform. For variants filtering and annotation Qiagen Variant Ingenuity tool was used. Nexus copy number software from BioDiscovery was used for evaluation of copy number variants and whole gene deletions. Patient and parental DNA was used to confirm mutations and the segregation of alleles using Sanger sequencing. Results: Genetic analysis identified 4 potential causative homozygous variants each confirmed by Sanger sequencing in 4 clinically relevant ciliopathy syndrome genes, ( TMEM231, TMEM138, WDR19 and BBS9), leading to an overall diagnostic yield of 50%. Conclusions: WES coupled with homozygosity mapping provided a diagnostic yield of 50% in this selected population. This genetic approach needs to be embedded into clinical practise to allow confirmation of clinical diagnosis, to inform genetic screening as well as family planning decisions. Half of the patients remain without diagnosis highlighting the technical and interpretational hurdles that need to be overcome in the future.
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Affiliation(s)
- Intisar Al Alawi
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, Tyne and Wear, NE13BZ, UK
- National Genetic Center, Ministry of Health, Muscat, Oman
| | - Mohammed Al Riyami
- Pediatric Nephrology Unit, Department of Child Health, Royal Hospital, Ministry of Health, Muscat, Oman
| | - Miguel Barroso-Gil
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, Tyne and Wear, NE13BZ, UK
| | - Laura Powell
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, Tyne and Wear, NE13BZ, UK
| | - Eric Olinger
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, Tyne and Wear, NE13BZ, UK
| | - Issa Al Salmi
- Renal Medicine Department, Royal Hospital, Ministry of Health, Muscat, Oman
- Oman Medical Speciality Board, Muscat, Oman
| | - John A. Sayer
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, Tyne and Wear, NE13BZ, UK
- Oman Medical Speciality Board, Muscat, Oman
- Newcastle Biomedical Research Centre, NIHR, Newcastle upon Tyne, Tyne and Wear, NE45PL, UK
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10
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Barroso-Gil M, Powell L, Sayer JA. RE: Clinical and Molecular Diagnosis of Joubert Syndrome and Related Disorders. Pediatr Neurol 2020; 112:10. [PMID: 32827857 DOI: 10.1016/j.pediatrneurol.2020.07.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 07/21/2020] [Indexed: 10/23/2022]
Affiliation(s)
- Miguel Barroso-Gil
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Laura Powell
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - John A Sayer
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK; NHS Foundation Trust, Newcastle upon Tyne Hospitals, Renal Services, Newcastle upon Tyne, UK; National Institute for Health Research Newcastle Biomedical Research Centre, Newcastle University, Newcastle upon Tyne, UK.
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11
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Sumathipala D, Strømme P, Gilissen C, Einarsen IH, Bjørndalen HJ, Server A, Corominas J, Hassel B, Fannemel M, Misceo D, Frengen E. Sudden death in epilepsy and ectopic neurohypophysis in Joubert syndrome 23 diagnosed using SNVs/indels and structural variants pipelines on WGS data: a case report. BMC MEDICAL GENETICS 2020; 21:96. [PMID: 32381069 PMCID: PMC7204034 DOI: 10.1186/s12881-020-01024-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 04/12/2020] [Indexed: 02/06/2023]
Abstract
Background Joubert syndrome (JBTS) is a genetically heterogeneous group of neurodevelopmental syndromes caused by primary cilia dysfunction. Usually the neurological presentation starts with abnormal neonatal breathing followed by muscular hypotonia, psychomotor delay, and cerebellar ataxia. Cerebral MRI shows mid- and hindbrain anomalies including the molar tooth sign. We report a male patient with atypical presentation of Joubert syndrome type 23, thus expanding the phenotype. Case presentation Clinical features were consistent with JBTS already from infancy, yet the syndrome was not suspected before cerebral MRI later in childhood showed the characteristic molar tooth sign and ectopic neurohypophysis. From age 11 years seizures developed and after few years became increasingly difficult to treat, also related to inadequate compliance to therapy. He died at 23 years of sudden unexpected death in epilepsy (SUDEP). The genetic diagnosis remained elusive for many years, despite extensive genetic testing. We reached the genetic diagnosis by performing whole genome sequencing of the family trio and analyzing the data with the combination of one analysis pipeline for single nucleotide variants (SNVs)/indels and one for structural variants (SVs). This lead to the identification of the most common variant detected in patients with JBTS23 (OMIM# 616490), rs534542684, in compound heterozygosity with a 8.3 kb deletion in KIAA0586, not previously reported. Conclusions We describe for the first time ectopic neurohypophysis and SUDEP in JBTS23, expanding the phenotype of this condition and raising the attention on the possible severity of the epilepsy in this disease. We also highlight the diagnostic power of WGS, which efficiently detects SNVs/indels and in addition allows the identification of SVs.
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Affiliation(s)
- Dulika Sumathipala
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Petter Strømme
- Division of Pediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway.,Faculty of Medicine, University of Oslo, Oslo, Norway
| | | | - Ingunn Holm Einarsen
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Hilde J Bjørndalen
- Division of Pediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
| | - Andrés Server
- Section of Neuroradiology, Department of Radiology and Nuclear Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Jordi Corominas
- Department of Human Genetics, Radboud UMC, Nijmegen, The Netherlands
| | - Bjørnar Hassel
- Faculty of Medicine, University of Oslo, Oslo, Norway.,Department of Neurohabilitation and Complex Neurology, Oslo University Hospital, Ullevål, Oslo, Norway
| | - Madeleine Fannemel
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Doriana Misceo
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway.
| | - Eirik Frengen
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
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12
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Zlotogora J. The Israeli national population program of genetic carrier screening for reproductive purposes. How should it be continued? Isr J Health Policy Res 2019; 8:73. [PMID: 31839005 PMCID: PMC6912952 DOI: 10.1186/s13584-019-0345-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 09/26/2019] [Indexed: 12/20/2022] Open
Abstract
The Israeli population genetic screening program for reproductive purposes, is a population-specific screening that includes all known, severe diseases and relatively frequent in a specific population (carrier frequency at or above 1:60 and/or disease frequency at or above 1 in 15,000 live births). The carrier screening program is free of charge and offers testing according to disease frequency in the different groups within the population. The extraordinary technical changes that occurred in the last decade as well as the changes in the type of marriages within the Israeli population necessitate a revision in the basis of the program. The screening should include instead of only the relatively frequent variants, all the variants that were reported among patients causing a severe disease for which the natural history is well known without regard of their frequency. The population-specific screening that determine which variants are included according to the origin of the couple should be abandoned for a general screening including either all the Jewish population or all the Israeli Arab population.
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Affiliation(s)
- Joël Zlotogora
- Hadassah Medical School, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.
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Affiliation(s)
- Hanno J. Bolz
- Aff1 Senckenberg Zentrum für Humangenetik Frankfurt am Main Deutschland
| | - Alexander Hoischen
- Aff2 0000 0004 0444 9382 grid.10417.33 Department of Human Genetics & Department of Internal Medicine, Radboud Institute of Medical Life Sciences Radboud University Medical Center Nijmegen Niederlande
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Fraser AM, Davey MG. TALPID3 in Joubert syndrome and related ciliopathy disorders. Curr Opin Genet Dev 2019; 56:41-48. [DOI: 10.1016/j.gde.2019.06.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Revised: 05/27/2019] [Accepted: 06/16/2019] [Indexed: 12/18/2022]
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