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Vodnjov N, Zupan Mežnar A, Maver A, Dolinšek A, Peterlin B, Writzl K. Non-dilated left ventricular cardiomyopathy with arrhythmias is commonly caused by the nonsense variant DSP:c.3793G>T in Slovenian patients. Clin Genet 2024. [PMID: 38860409 DOI: 10.1111/cge.14567] [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: 03/06/2024] [Revised: 05/22/2024] [Accepted: 05/24/2024] [Indexed: 06/12/2024]
Abstract
DSP-cardiomyopathy has recently been recognised as a specific type of cardiomyopathy. Using an in-house Mendelian disease registry, we aimed to identify probands with likely pathogenic or pathogenic DSP variants. We detected these variants in 4.8% and 77.8% of genotype-positive probands referred for dilated and non-dilated left ventricular cardiomyopathy (NDLVC), respectively. We identified six Slovenian probands with the DSP:c.3793G>T and characterised them along with further eight of their relatives at the molecular and phenotypic level. Medical records revealed NDLVC with arrhythmia in six individuals (five probands, one relative; 33 ± 14 years; three males, three females). All had subepicardial late gadolinium enhancement on cardiac MRI (CMRI), and five received an ICD. Four individuals (one proband, three relatives; 48 ± 14 years; all female) had no ECG and/or cardiac abnormalities on CMRI detected. Our analysis presents a Slovenian-specific molecular pathology of DSP cardiomyopathy, delineates the clinical manifestation of DSP:c.3793C>T, and thereby improves the understanding of the clinical outcomes associated with truncating DSP variants.
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Affiliation(s)
- Nina Vodnjov
- Clinical Institute of Genomic Medicine (CIGM), University Medical Centre (UMC) Ljubljana, Ljubljana, Slovenia
- Biotechnical Faculty, University of Ljubljana (UL), Ljubljana, Slovenia
| | | | - Aleš Maver
- Clinical Institute of Genomic Medicine (CIGM), University Medical Centre (UMC) Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Ajda Dolinšek
- Institute of Radiology, UMC Ljubljana, Ljubljana, Slovenia
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine (CIGM), University Medical Centre (UMC) Ljubljana, Ljubljana, Slovenia
| | - Karin Writzl
- Clinical Institute of Genomic Medicine (CIGM), University Medical Centre (UMC) Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
- Member of the European Reference Network for Rare, Low Prevalence and Complex Diseases of the Heart-ERN GUARD- Heart, UMC Ljubljana, Ljubljana, Slovenia
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Al-Kurbi AA, Aliyev E, AlSa’afin S, Aamer W, Palaniswamy S, Al-Maraghi A, Kilani H, Akil AAS, Stotland MA, Fakhro KA. A Complex Intrachromosomal Rearrangement Disrupting IRF6 in a Family with Popliteal Pterygium and Van der Woude Syndromes. Genes (Basel) 2023; 14:genes14040849. [PMID: 37107607 PMCID: PMC10137688 DOI: 10.3390/genes14040849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 03/26/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023] Open
Abstract
Clefts of the lip and/or palate (CL/P) are considered the most common form of congenital anomalies occurring either in isolation or in association with other clinical features. Van der woude syndrome (VWS) is associated with about 2% of all CL/P cases and is further characterized by having lower lip pits. Popliteal pterygium syndrome (PPS) is a more severe form of VWS, normally characterized by orofacial clefts, lower lip pits, skin webbing, skeletal anomalies and syndactyly of toes and fingers. Both syndromes are inherited in an autosomal dominant manner, usually caused by heterozygous mutations in the Interferon Regulatory Factor 6 (IRF6) gene. Here we report the case of a two-generation family where the index presented with popliteal pterygium syndrome while both the father and sister had clinical features of van der woude syndrome, but without any point mutations detected by re-sequencing of known gene panels or microarray testing. Using whole genome sequencing (WGS) followed by local de novo assembly, we discover and validate a copy-neutral, 429 kb complex intra-chromosomal rearrangement in the long arm of chromosome 1, disrupting the IRF6 gene. This variant is copy-neutral, novel against publicly available databases, and segregates in the family in an autosomal dominant pattern. This finding suggests that missing heritability in rare diseases may be due to complex genomic rearrangements that can be resolved by WGS and de novo assembly, helping deliver answers to patients where no genetic etiology was identified by other means.
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Affiliation(s)
- Alya A. Al-Kurbi
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha 34110, Qatar
- Department of Human Genetics, Sidra Medicine, Doha 26999, Qatar
| | - Elbay Aliyev
- Department of Human Genetics, Sidra Medicine, Doha 26999, Qatar
| | - Sana AlSa’afin
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha 34110, Qatar
| | - Waleed Aamer
- Department of Human Genetics, Sidra Medicine, Doha 26999, Qatar
| | | | | | - Houda Kilani
- Division of Plastic and Craniofacial Surgery, Sidra Medicine, Doha 26999, Qatar
| | | | - Mitchell A. Stotland
- Division of Plastic and Craniofacial Surgery, Sidra Medicine, Doha 26999, Qatar
- Department of Surgery, Weill Cornell Medical College, Doha 24144, Qatar
| | - Khalid A. Fakhro
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha 34110, Qatar
- Department of Human Genetics, Sidra Medicine, Doha 26999, Qatar
- Department of Genetic Medicine, Weill Cornell Medical College, Doha 24144, Qatar
- Correspondence:
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Ferre-Fernández JJ, Muheisen S, Thompson S, Semina EV. CRISPR-Cas9-mediated functional dissection of the foxc1 genomic region in zebrafish identifies critical conserved cis-regulatory elements. Hum Genomics 2022; 16:49. [PMID: 36284357 PMCID: PMC9597995 DOI: 10.1186/s40246-022-00423-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 10/19/2022] [Indexed: 11/10/2022] Open
Abstract
FOXC1 encodes a forkhead-domain transcription factor associated with several ocular disorders. Correct FOXC1 dosage is critical to normal development, yet the mechanisms controlling its expression remain unknown. Together with FOXQ1 and FOXF2, FOXC1 is part of a cluster of FOX genes conserved in vertebrates. CRISPR-Cas9-mediated dissection of genomic sequences surrounding two zebrafish orthologs of FOXC1 was performed. This included five zebrafish-human conserved regions, three downstream of foxc1a and two remotely upstream of foxf2a/foxc1a or foxf2b/foxc1b clusters, as well as two intergenic regions between foxc1a/b and foxf2a/b lacking sequence conservation but positionally corresponding to the area encompassing a previously reported glaucoma-associated SNP in humans. Removal of downstream sequences altered foxc1a expression; moreover, zebrafish carrying deletions of two or three downstream elements demonstrated abnormal phenotypes including enlargement of the anterior chamber of the eye reminiscent of human congenital glaucoma. Deletions of distant upstream conserved elements influenced the expression of foxf2a/b or foxq1a/b but not foxc1a/b within each cluster. Removal of either intergenic sequence reduced foxc1a or foxc1b expression during late development, suggesting a role in transcriptional regulation despite the lack of conservation at the nucleotide level. Further studies of the identified regions in human patients may explain additional individuals with developmental ocular disorders.
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Affiliation(s)
- Jesús-José Ferre-Fernández
- Department of Pediatrics and Children's Research Institute, Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, WI, 53226, USA
| | - Sanaa Muheisen
- Department of Pediatrics and Children's Research Institute, Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, WI, 53226, USA
| | - Samuel Thompson
- Department of Pediatrics and Children's Research Institute, Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, WI, 53226, USA
| | - Elena V Semina
- Department of Pediatrics and Children's Research Institute, Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, WI, 53226, USA.
- Department of Ophthalmology and Visual Sciences, Medical College of Wisconsin, Milwaukee, WI, 53226, USA.
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI, 53226, USA.
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Marwaha S, Knowles JW, Ashley EA. A guide for the diagnosis of rare and undiagnosed disease: beyond the exome. Genome Med 2022; 14:23. [PMID: 35220969 PMCID: PMC8883622 DOI: 10.1186/s13073-022-01026-w] [Citation(s) in RCA: 83] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 02/10/2022] [Indexed: 02/07/2023] Open
Abstract
AbstractRare diseases affect 30 million people in the USA and more than 300–400 million worldwide, often causing chronic illness, disability, and premature death. Traditional diagnostic techniques rely heavily on heuristic approaches, coupling clinical experience from prior rare disease presentations with the medical literature. A large number of rare disease patients remain undiagnosed for years and many even die without an accurate diagnosis. In recent years, gene panels, microarrays, and exome sequencing have helped to identify the molecular cause of such rare and undiagnosed diseases. These technologies have allowed diagnoses for a sizable proportion (25–35%) of undiagnosed patients, often with actionable findings. However, a large proportion of these patients remain undiagnosed. In this review, we focus on technologies that can be adopted if exome sequencing is unrevealing. We discuss the benefits of sequencing the whole genome and the additional benefit that may be offered by long-read technology, pan-genome reference, transcriptomics, metabolomics, proteomics, and methyl profiling. We highlight computational methods to help identify regionally distant patients with similar phenotypes or similar genetic mutations. Finally, we describe approaches to automate and accelerate genomic analysis. The strategies discussed here are intended to serve as a guide for clinicians and researchers in the next steps when encountering patients with non-diagnostic exomes.
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Szűcs Z, Fitala R, Nyuzó ÁR, Fodor K, Czemmel É, Vrancsik N, Bessenyei M, Szabó T, Szakszon K, Balogh I. Four New Cases of Hypomyelinating Leukodystrophy Associated with the UFM1 c.-155_-153delTCA Founder Mutation in Pediatric Patients of Roma Descent in Hungary. Genes (Basel) 2021; 12:genes12091331. [PMID: 34573312 PMCID: PMC8471165 DOI: 10.3390/genes12091331] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 08/26/2021] [Accepted: 08/26/2021] [Indexed: 01/10/2023] Open
Abstract
Ufmylation is a relatively newly discovered type of post-translational modification when the ubiquitin-fold modifier 1 (UFM1) protein is covalently attached to its target proteins in a three-step enzymatic reaction involving an E1 activating enzyme (UBA5), E2 conjugating enzyme (UFC1), and E3 ligase enzyme (UFL1). The process of ufmylation is essential for normal brain development and function in humans. Mutations in the UFM1 gene are associated with Hypomyelinating leukodystrophy type 14, presenting with global developmental delay, failure to thrive, progressive microcephaly, refractive epilepsy, and hypomyelination, with atrophy of the basal ganglia and cerebellum phenotypes. The c.-155_-153delTCA deletion in the promoter region of UFM1 is considered to be a founding mutation in the Roma population. Here we present four index patients with homozygous UFM1:c.-155_-153delTCA mutation detected by next-generation sequencing (whole genome/exome sequencing) or Sanger sequencing. This mutation may be more common in the Roma population than previously estimated, and the targeted testing of the UFM1:c.-155_-153delTCA mutation may have an indication in cases of hypomyelination and neurodegenerative clinical course in pediatric patients of Roma descent.
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Affiliation(s)
- Zsuzsanna Szűcs
- Division of Clinical Genetics, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary;
| | - Réka Fitala
- Velkey László Child Health Center, Borsod-Abaúj-Zemplén County Central Regional Hospital and University Educational Center, 3526 Miskolc, Hungary; (R.F.); (Á.R.N.); (K.F.)
| | - Ágnes Renáta Nyuzó
- Velkey László Child Health Center, Borsod-Abaúj-Zemplén County Central Regional Hospital and University Educational Center, 3526 Miskolc, Hungary; (R.F.); (Á.R.N.); (K.F.)
| | - Krisztina Fodor
- Velkey László Child Health Center, Borsod-Abaúj-Zemplén County Central Regional Hospital and University Educational Center, 3526 Miskolc, Hungary; (R.F.); (Á.R.N.); (K.F.)
| | - Éva Czemmel
- Neurodevelopmental Ward, St. Margaret Hospital, 1032 Budapest, Hungary;
| | - Nóra Vrancsik
- Division of Radiology, Department of Medical Imaging, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary;
| | - Mónika Bessenyei
- Institute of Pediatrics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (M.B.); (T.S.); (K.S.)
| | - Tamás Szabó
- Institute of Pediatrics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (M.B.); (T.S.); (K.S.)
| | - Katalin Szakszon
- Institute of Pediatrics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (M.B.); (T.S.); (K.S.)
| | - István Balogh
- Division of Clinical Genetics, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary;
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
- Correspondence:
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