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Ha T, Morgan A, Bartos MN, Beatty K, Cogné B, Braun D, Gerber CB, Gaspar H, Kopps AM, Rieubland C, Hurst ACE, Amor DJ, Nizon M, Pasquier L, Pfundt R, Reis A, Siu VM, Tessarech M, Thompson ML, Vincent M, de Vries BBA, Walsh MB, Wechsler SB, Zweier C, Schnur RE, Guillen Sacoto MJ, Margot H, Masotto B, Palafoll MIV, Nawaz U, Voineagu I, Slavotinek A. De novo variants predicting haploinsufficiency for DIP2C are associated with expressive speech delay. Am J Med Genet A 2024; 194:e63559. [PMID: 38421105 PMCID: PMC11161320 DOI: 10.1002/ajmg.a.63559] [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: 10/17/2023] [Revised: 12/16/2023] [Accepted: 01/04/2024] [Indexed: 03/02/2024]
Abstract
The disconnected (disco)-interacting protein 2 (DIP2) gene was first identified in D. melanogaster and contains a DNA methyltransferase-associated protein 1 (DMAP1) binding domain, Acyl-CoA synthetase domain and AMP-binding sites. DIP2 regulates axonal bifurcation of the mushroom body neurons in D. melanogaster and is required for axonal regeneration in the neurons of C. elegans. The DIP2 homologues in vertebrates, Disco-interacting protein 2 homolog A (DIP2A), Disco-interacting protein 2 homolog B (DIP2B), and Disco-interacting protein 2 homolog C (DIP2C), are highly conserved and expressed widely in the central nervous system. Although there is evidence that DIP2C plays a role in cognition, reports of pathogenic variants in these genes are rare and their significance is uncertain. We present 23 individuals with heterozygous DIP2C variants, all manifesting developmental delays that primarily affect expressive language and speech articulation. Eight patients had de novo variants predicting loss-of-function in the DIP2C gene, two patients had de novo missense variants, three had paternally inherited loss of function variants and six had maternally inherited loss-of-function variants, while inheritance was unknown for four variants. Four patients had cardiac defects (hypertrophic cardiomyopathy, atrial septal defects, and bicuspid aortic valve). Minor facial anomalies were inconsistent but included a high anterior hairline with a long forehead, broad nasal tip, and ear anomalies. Brainspan analysis showed elevated DIP2C expression in the human neocortex at 10-24 weeks after conception. With the cases presented herein, we provide phenotypic and genotypic data supporting the association between loss-of-function variants in DIP2C with a neurocognitive phenotype.
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Affiliation(s)
- Thoa Ha
- Division of Medical Genetics, Department of Pediatrics, University of California, San Francisco, San Francisco, USA
| | - Angela Morgan
- Murdoch Children's Research Institute, Parkville, Victoria, Australia
- University of Melbourne, Parkville, Victoria, Australia
- Royal Children's Hospital, Parkville, Victoria, Australia
| | - Meghan N Bartos
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Katelyn Beatty
- Division of Human Genetics, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Benjamin Cogné
- CHU Nantes, Service de Génétique Médicale, L'institut du Thorax, University Nantes, Nantes, France
| | - Dominique Braun
- Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Céline B Gerber
- Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Harald Gaspar
- Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Anna M Kopps
- Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Claudine Rieubland
- Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Anna C E Hurst
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - David J Amor
- Murdoch Children's Research Institute, Parkville, Victoria, Australia
- University of Melbourne, Parkville, Victoria, Australia
- Royal Children's Hospital, Parkville, Victoria, Australia
| | - Mathilde Nizon
- CHU Nantes, Service de Génétique Médicale, L'institut du Thorax, University Nantes, Nantes, France
| | | | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center and Donders Institute for Brain, Cognition and Behavior, Nijmegen, The Netherlands
| | - André Reis
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- Centre for Rare Diseases Erlangen (ZSEER), Erlangen, Germany
| | - Victoria Mok Siu
- London Health Sciences Center and Department of Pediatrics, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Marine Tessarech
- Department of Biochemistry and Genetics, Angers University Hospital, Angers, France
| | | | - Marie Vincent
- CHU Nantes, Service de Génétique Médicale, L'institut du Thorax, University Nantes, Nantes, France
| | - Bert B A de Vries
- Department of Human Genetics, Radboud University Medical Center and Donders Institute for Brain, Cognition and Behavior, Nijmegen, The Netherlands
| | | | - Stephanie Burns Wechsler
- Departments of Pediatrics and Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Christiane Zweier
- Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | | | | | - Henri Margot
- Université Bordeaux, MRGM INSERM U1211, CHU de Bordeaux, Service de Génétique Médicale, Bordeaux, France
| | - Barbara Masotto
- Hospital Universitari Vall d'Hebron, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | | | - Urwah Nawaz
- Adelaide Medical School and Robinson Research Institute, The University of Adelaide, Adelaide, Australia
| | - Irina Voineagu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Anne Slavotinek
- Division of Medical Genetics, Department of Pediatrics, University of California, San Francisco, San Francisco, USA
- Division of Human Genetics, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
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Kakar N, Rehman FU, Kaur R, Bhavani GS, Goyal M, Shah H, Kaur K, Sodhi KS, Kubisch C, Borck G, Panigrahi I, Girisha KM, Kornak U, Spielmann M. Multi-gene panel sequencing in highly consanguineous families and patients with congenital forms of skeletal dysplasias. Clin Genet 2024; 106:47-55. [PMID: 38378010 DOI: 10.1111/cge.14509] [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: 08/15/2023] [Revised: 02/05/2024] [Accepted: 02/07/2024] [Indexed: 02/22/2024]
Abstract
Skeletal dysplasias (SKDs) are a heterogeneous group of more than 750 genetic disorders characterized by abnormal development, growth, and maintenance of bones or cartilage in the human skeleton. SKDs are often caused by variants in early patterning genes and in many cases part of multiple malformation syndromes and occur in combination with non-skeletal phenotypes. The aim of this study was to investigate the underlying genetic cause of congenital SKDs in highly consanguineous Pakistani families, as well as in sporadic and familial SKD cases from India using multigene panel sequencing analysis. Therefore, we performed panel sequencing of 386 bone-related genes in 7 highly consanguineous families from Pakistan and 27 cases from India affected with SKDs. In the highly consanguineous families, we were able to identify the underlying genetic cause in five out of seven families, resulting in a diagnostic yield of 71%. Whereas, in the sporadic and familial SKD cases, we identified 12 causative variants, corresponding to a diagnostic yield of 44%. The genetic heterogeneity in our cohorts was very high and we were able to detect various types of variants, including missense, nonsense, and frameshift variants, across multiple genes known to cause different types of SKDs. In conclusion, panel sequencing proved to be a highly effective way to decipher the genetic basis of SKDs in highly consanguineous families as well as sporadic and or familial cases from South Asia. Furthermore, our findings expand the allelic spectrum of skeletal dysplasias.
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Affiliation(s)
- Naseebullah Kakar
- Institut für Humangenetik, Universitätsklinikum Schleswig-Holstein, University of Lübeck and University of Kiel, Lübeck, Germany
- Department of Biotechnology, BUITEMS, Quetta, Pakistan
- Institute of Human Genetics, Ulm University, Ulm, Germany
| | - Fazal Ur Rehman
- Department of Pathology, Bolan Medical College, Quetta, Pakistan
| | - Ramandeep Kaur
- Department of Pediatrics, APC, PGIMER, Chandigarh, India
| | - Gandham SriLakshmi Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Manisha Goyal
- Pediatrics Genetic & Research Laboratory, Department of Pediatrics, Lok Nayak Hospital, New Delhi, India
| | - Hitesh Shah
- Department of Pediatric Orthopedics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Karandeep Kaur
- Department of Pediatrics, APC, PGIMER, Chandigarh, India
| | | | - Christian Kubisch
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Guntram Borck
- Institute of Human Genetics, Ulm University, Ulm, Germany
| | | | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Uwe Kornak
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Malte Spielmann
- Institut für Humangenetik, Universitätsklinikum Schleswig-Holstein, University of Lübeck and University of Kiel, Lübeck, Germany
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Farshadyeganeh P, Yamada T, Ohashi H, Nishimura G, Fujita H, Oishi Y, Nunode M, Ishikawa S, Murotsuki J, Yamashita Y, Ikegawa S, Ogi T, Arikawa-Hirasawa E, Ohno K. Dyssegmental dysplasia Rolland-Desbuquois type is caused by pathogenic variants in HSPG2 - a founder haplotype shared in five patients. J Hum Genet 2024; 69:235-244. [PMID: 38424183 PMCID: PMC11126378 DOI: 10.1038/s10038-024-01229-6] [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: 11/20/2023] [Revised: 01/17/2024] [Accepted: 02/06/2024] [Indexed: 03/02/2024]
Abstract
Dyssegmental dysplasia (DD) is a severe skeletal dysplasia comprised of two subtypes: lethal Silverman-Handmaker type (DDSH) and nonlethal Rolland-Desbuquois type (DDRD). DDSH is caused by biallelic pathogenic variants in HSPG2 encoding perlecan, whereas the genetic cause of DDRD remains undetermined. Schwartz-Jampel syndrome (SJS) is also caused by biallelic pathogenic variants in HSPG2 and is an allelic disorder of DDSH. In SJS and DDSH, 44 and 8 pathogenic variants have been reported in HSPG2, respectively. Here, we report that five patients with DDRD carried four pathogenic variants in HSPG2: c.9970 G > A (p.G3324R), c.559 C > T (p.R187X), c7006 + 1 G > A, and c.11562 + 2 T > G. Two patients were homozygous for p.G3324R, and three patients were heterozygous for p.G3324R. Haplotype analysis revealed a founder haplotype spanning 85,973 bp shared in the five patients. SJS, DDRD, and DDSH are allelic disorders with pathogenic variants in HSPG2.
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Affiliation(s)
- Paniz Farshadyeganeh
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Takahiro Yamada
- Division of Clinical Genetics, Hokkaido University Hospital, Sapporo, Japan
| | - Hirofumi Ohashi
- Division of Medical Genetics, Saitama Children's Medical Center, Saitama, Japan
| | - Gen Nishimura
- Department of Radiology, Musashino Yowakai Hospital, Tokyo, Japan
| | - Hiroki Fujita
- Department of Orthopaedics, Hokkaido Medical Center for Child Health and Rehabilitation, Sapporo, Japan
| | - Yuriko Oishi
- Department of Obstetrics, Asahikawa Medical University, Asahikawa, Japan
| | - Misa Nunode
- Department of Obstetrics, Osaka Medical and Pharmaceutical University, Takatsuki, Japan
| | - Shuku Ishikawa
- Department of Neonatal Internal Medicine, Hokkaido Medical Center for Child Health and Rehabilitation, Sapporo, Japan
| | - Jun Murotsuki
- Department of Maternal and Fetal Medicine, Miyagi Children's Hospital, Sendai, Japan
| | - Yuri Yamashita
- Aging Biology in Health and Disease, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Research Institute for Diseases of Old Age, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Shiro Ikegawa
- Center for Integrative Medical Sciences, RIKEN, Tokyo, Japan
| | - Tomoo Ogi
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan
| | - Eri Arikawa-Hirasawa
- Aging Biology in Health and Disease, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Research Institute for Diseases of Old Age, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Kinji Ohno
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan.
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Marafi D. Founder mutations and rare disease in the Arab world. Dis Model Mech 2024; 17:dmm050715. [PMID: 38922202 PMCID: PMC11225585 DOI: 10.1242/dmm.050715] [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] [Indexed: 06/27/2024] Open
Abstract
Founder mutations are disease-causing variants that occur frequently in geographically or culturally isolated groups whose shared ancestor(s) carried the pathogenic variant. While some disease alleles may vanish from the genetic pool due to natural selection, variants with weaker effects may survive for a long time, thereby enhancing the prevalence of some rare diseases. These are predominantly autosomal recessive diseases but can also be autosomal dominant traits with late-onset or mild phenotypes. Cultural practices, such as endogamy and consanguinity, in these isolated groups lead to higher prevalence of such rare diseases compared to the rest of the population and worldwide. In this Perspective, we define population isolates and the underlying genetic mechanisms for accumulating founder mutations. We also discuss the current and potential scientific, clinical and public-health implications of studying founder mutations in population isolates around the world, with a particular focus on the Arab population.
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Affiliation(s)
- Dana Marafi
- Department of Pediatrics, College of Medicine, Kuwait University, P.O. Box 24923, 13110 Safat, Kuwait
- Section of Child Neurology, Department of Pediatrics, Adan Hospital, Ministry of Health, Hadiya 52700, Kuwait
- Kuwait Medical Genetics Centre, Ministry of Health, Sulaibikhat 80901, Kuwait
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Madrid NY, Giraldo LJM. Role of gene interactions in the pathophysiology of skeletal dysplasias: A case report in Colombia. J Genet Eng Biotechnol 2024; 22:100350. [PMID: 38494246 PMCID: PMC10860875 DOI: 10.1016/j.jgeb.2023.100350] [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: 11/15/2023] [Accepted: 12/31/2023] [Indexed: 03/19/2024]
Abstract
BACKGROUND Genome association studies have shown that gene-gene interactions or epistasis play a crucial role in identifying the etiology, prognosis, and treatment response of many complex diseases beyond their main effects. Skeletal dysplasias are a heterogeneous group of congenital bone and cartilage disorders with a genetic and gen-gen interaction etiology. The current classification of skeletal dysplasias distinguishes 461 diseases in 42 groups, and the incidence of all skeletal dysplasias is more than 1 in every 5000 newborns. The objective is to present the case of a patient with four variants that generates gen-gen interactions in the skeletal dysplasia. CASE PRESENTATION A 1-year-old male patient was diagnosed with skeletal dysplasia based on prenatal ultrasound showing micromelia and pyelocalyceal dilation. Postnatal physical examination revealed body disproportion and involvement of other organs and systems. MATERIALS AND METHODS A sequencing study and deletions/duplications analysis were performed for 358 candidate genes associated with skeletal dysplasia. The GeneMANIA interface was used to evaluate the expression network of genes associated with each other for the gen-gen interaction. RESULTS Four pathogenic variants were obtained two heterozygous variants with pathogenic significance in SLC26A, one heterozygous pathogenic variant in CLCN7 and another heterozygous pathogenic variant in CEP120. The GeneMANIA interface reveals 77.64% physical interactions, 8.01% co-expression, 5.37% prediction, 3.63% co-localization, 2.87% genetic interactions, 1.88% route of action, and 0.60% shared protein domains. DISCUSSION AND CONCLUSIONS These results suggest that the interaction between these genes affects the activity of the inorganic anion exchanger, leading to disorganization of collagen fibers, early mineralization, and decreased assembly of fibronectin in the bone extracellular matrix. Identifying gene-gene interactions is a fundamental step in understanding proper cell function and thus understanding the pathophysiology of many complex human diseases, improving diagnosis, and the possibilities of new personalized therapies.
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Affiliation(s)
- Nathalie Yepes Madrid
- Pediatric Specialization Resident, Universidad Libre Cali, Colombia; Pediatric Research Group (GRINPED), Colombia.
| | - Lina Johanna Moreno Giraldo
- Universidad Libre Cali Sectional, Colombia; Pediatric Research Group (GRINPED), Colombia; Neurogenetic and Metabolic Diseases Research Line, Colombia.
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del Real Á, Cruz R, Sañudo C, Pérez-Castrillón JL, Pérez-Núñez MI, Olmos JM, Hernández JL, García-Ibarbia C, Valero C, Riancho JA. High Frequencies of Genetic Variants in Patients with Atypical Femoral Fractures. Int J Mol Sci 2024; 25:2321. [PMID: 38396997 PMCID: PMC10889592 DOI: 10.3390/ijms25042321] [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: 01/22/2024] [Revised: 02/10/2024] [Accepted: 02/13/2024] [Indexed: 02/25/2024] Open
Abstract
This study explores the genetic factors associated with atypical femoral fractures (AFF), rare fractures associated with prolonged anti-resorptive therapy. AFF are fragility fractures that typically appear in the subtrochanteric or diaphyseal regions of the femur. While some cases resemble fractures in rare genetic bone disorders, the exact cause remains unclear. This study investigates 457 genes related to skeletal homeostasis in 13 AFF patients by exome sequencing, comparing the results with osteoporotic patients (n = 27) and Iberian samples from the 1000 Genomes Project (n = 107). Only one AFF case carried a pathogenic variant in the gene set, specifically in the ALPL gene. The study then examined variant accumulation in the gene set, revealing significantly more variants in AFF patients than in osteoporotic patients without AFF (p = 3.7 × 10-5), particularly in ACAN, AKAP13, ARHGEF3, P4HB, PITX2, and SUCO genes, all of them related to osteogenesis. This suggests that variant accumulation in bone-related genes may contribute to AFF risk. The polygenic nature of AFF implies that a complex interplay of genetic factors determines the susceptibility to AFF, with ACAN, SUCO, AKAP13, ARHGEF3, PITX2, and P4HB as potential genetic risk factors. Larger studies are needed to confirm the utility of gene set analysis in identifying patients at high risk of AFF during anti-resorptive therapy.
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Affiliation(s)
- Álvaro del Real
- Departamento de Medicina y Psiquiatría, Instituto de Investigación Sanitaria Valdecilla (IDIVAL), Facultad de Medicina, Universidad de Cantabria, 39011 Santander, Spain; (Á.d.R.); (C.S.); (J.M.O.); (J.L.H.); (C.V.)
| | - Raquel Cruz
- Grupo de Medicina Xenómica, Centro de Investigación en Medicina Molecular y Enfermedades Crónicas, Universidade de Santiago de Compostela (USC), 15782 Santiago de Compostela, Spain;
| | - Carolina Sañudo
- Departamento de Medicina y Psiquiatría, Instituto de Investigación Sanitaria Valdecilla (IDIVAL), Facultad de Medicina, Universidad de Cantabria, 39011 Santander, Spain; (Á.d.R.); (C.S.); (J.M.O.); (J.L.H.); (C.V.)
| | - José L. Pérez-Castrillón
- Internal Medicine Department, University Hospital Rio Hortega of Valladolid, 47012 Valladolid, Spain;
| | - María I. Pérez-Núñez
- Traumatology Department, University Hospital M. Valdecilla, 39008 Santander, Spain;
| | - Jose M. Olmos
- Departamento de Medicina y Psiquiatría, Instituto de Investigación Sanitaria Valdecilla (IDIVAL), Facultad de Medicina, Universidad de Cantabria, 39011 Santander, Spain; (Á.d.R.); (C.S.); (J.M.O.); (J.L.H.); (C.V.)
- Internal Medicine Department, Marqués de Valdecilla University Hospital, 39008 Santander, Spain;
| | - José L. Hernández
- Departamento de Medicina y Psiquiatría, Instituto de Investigación Sanitaria Valdecilla (IDIVAL), Facultad de Medicina, Universidad de Cantabria, 39011 Santander, Spain; (Á.d.R.); (C.S.); (J.M.O.); (J.L.H.); (C.V.)
- Internal Medicine Department, Marqués de Valdecilla University Hospital, 39008 Santander, Spain;
| | - Carmen García-Ibarbia
- Internal Medicine Department, Marqués de Valdecilla University Hospital, 39008 Santander, Spain;
| | - Carmen Valero
- Departamento de Medicina y Psiquiatría, Instituto de Investigación Sanitaria Valdecilla (IDIVAL), Facultad de Medicina, Universidad de Cantabria, 39011 Santander, Spain; (Á.d.R.); (C.S.); (J.M.O.); (J.L.H.); (C.V.)
- Internal Medicine Department, Marqués de Valdecilla University Hospital, 39008 Santander, Spain;
| | - Jose A. Riancho
- Departamento de Medicina y Psiquiatría, Instituto de Investigación Sanitaria Valdecilla (IDIVAL), Facultad de Medicina, Universidad de Cantabria, 39011 Santander, Spain; (Á.d.R.); (C.S.); (J.M.O.); (J.L.H.); (C.V.)
- Internal Medicine Department, Marqués de Valdecilla University Hospital, 39008 Santander, Spain;
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
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Altassan R, Allers MM, De Graef D, Shah R, de Vries M, Larson A, Glamuzina E, Morava E. Defining the phenotype of PGAP3-congenital disorder of glycosylation; a review of 65 cases. Mol Genet Metab 2023; 140:107688. [PMID: 37647829 PMCID: PMC10872732 DOI: 10.1016/j.ymgme.2023.107688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/22/2023] [Accepted: 08/22/2023] [Indexed: 09/01/2023]
Abstract
Biallelic pathogenic variants in PGAP3 cause a rare glycosylphosphatidyl-inositol biogenesis disorder, PGAP3-CDG. This multisystem condition presents with a predominantly neurological phenotype, including developmental delay, intellectual disability, seizures, and hyperphosphatemia. Here, we summarized the phenotype of sixty-five individuals including six unreported individuals from our CDG natural history study with a confirmed PGAP3-CDG diagnosis. Common additional features found in this disorder included brain malformations, behavioral abnormalities, cleft palate, and characteristic facial features. This report aims to review the genetic and metabolic findings and characterize the disease's phenotype while highlighting the necessary clinical approach to improve the management of this rare CDG.
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Affiliation(s)
- Ruqaiah Altassan
- Department of Medical Genomics, Centre for Genomics Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia; Department of Clinical Genomics, Mayo Clinic, Rochester, MN, United States; College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Michael M Allers
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, United States
| | - Diederik De Graef
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, United States
| | - Rameen Shah
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, United States; Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Maaike de Vries
- Department of Pediatrics, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Austin Larson
- Department of Pediatrics, Section of Genetics, University of Colorado School of Medicine, Aurora, CO, United States
| | - Emma Glamuzina
- Adult and Paediatric National Metabolic Service, Auckland City Hospital, Auckland, New Zealand
| | - Eva Morava
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, United States; Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States; Department of Medical Genetics, University of Pecs Medical School, Pecs, Hungary.
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Yang S, Li Y, Yang L, Guo Q, You Y, Lei B. Pathogenicity and functional analysis of CFAP410 mutations causing cone-rod dystrophy with macular staphyloma. Front Med (Lausanne) 2023; 10:1216427. [PMID: 37901396 PMCID: PMC10601463 DOI: 10.3389/fmed.2023.1216427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 09/25/2023] [Indexed: 10/31/2023] Open
Abstract
Background Cone-rod dystrophy (CORD) caused by pathogenic variants in CFAP410 is a very rare disease. The mechanisms by which the variants caused the disease remained largely unknown. CFAP410 pathogenic variants were identified in a cone-rod dystrophy with macular staphyloma patient. We explored the pathogenicity and performed functional analysis of two compound heterozygous mutations. Methods A 6-year-old boy complained decreased vision for 1 year, underwent ocular examinations together with systemic X-ray check. Blood sample was taken for targeted next generation sequencing (Tg-NGS). Pathogenicity of identified variants was determined by ACMG guideline. Mutated plasmids were constructed and transferred to HEK293T cells. Cell cycle, protein stability, and protein ubiquitination level was measured. Results The best-corrected visual acuity of proband was 0.20 bilaterally. Fundus showed macular staphyloma and uneven granular pigment disorder in the periphery of the retina. SS-OCT showed thinning and atrophy of the outer retina, residual ellipsoid zone (EZ) in the fovea. Scotopic and photopic ERG responses severe reduced. Two heterozygous missense pathogenic variants, c.319 T > C (p.Tyr107His) and c.347 C > T (p.Pro116Leu) in exon 4 of the CFAP410, were found and were pathogenic by the ACMG guideline. In vitro, pathogenic variants affect cell cycle. Immunofluorescence and western blotting showed that the mutant proteins decreased expression levels protein stability. Meanwhile, co-IP data suggested that ubiquitination level was altered in cells transferred with the mutated plasmids. Conclusion Compound heterozygous pathogenic variants c.319 T > C and c.347 C > T in CFAP410 caused CORD with macular staphyloma. The pathogenic mechanisms may be associated with alternations of protein stability and degradation through the ubiquitin-proteasome pathway.
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Affiliation(s)
- Shaoqing Yang
- Henan University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou, China
| | - Ya Li
- Henan Branch of National Clinical Research Center for Ocular Diseases, Henan Eye Institute/Henan Eye Hospital, People’s Hospital of Zhengzhou University, Henan Provincial People’s Hospital, Zhengzhou, China
| | - Lin Yang
- Henan Branch of National Clinical Research Center for Ocular Diseases, Henan Eye Institute/Henan Eye Hospital, People’s Hospital of Zhengzhou University, Henan Provincial People’s Hospital, Zhengzhou, China
| | - Qingge Guo
- Henan Branch of National Clinical Research Center for Ocular Diseases, Henan Eye Institute/Henan Eye Hospital, People’s Hospital of Zhengzhou University, Henan Provincial People’s Hospital, Zhengzhou, China
| | - Ya You
- Henan Branch of National Clinical Research Center for Ocular Diseases, Henan Eye Institute/Henan Eye Hospital, People’s Hospital of Zhengzhou University, Henan Provincial People’s Hospital, Zhengzhou, China
| | - Bo Lei
- Henan University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou, China
- Henan Branch of National Clinical Research Center for Ocular Diseases, Henan Eye Institute/Henan Eye Hospital, People’s Hospital of Zhengzhou University, Henan Provincial People’s Hospital, Zhengzhou, China
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Aida N, Saito A, Azuma T. Current Status of Next-Generation Sequencing in Bone Genetic Diseases. Int J Mol Sci 2023; 24:13802. [PMID: 37762102 PMCID: PMC10530486 DOI: 10.3390/ijms241813802] [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: 08/15/2023] [Revised: 09/01/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
The development of next-generation sequencing (NGS) has dramatically increased the speed and volume of genetic analysis. Furthermore, the range of applications of NGS is rapidly expanding to include genome, epigenome (such as DNA methylation), metagenome, and transcriptome analyses (such as RNA sequencing and single-cell RNA sequencing). NGS enables genetic research by offering various sequencing methods as well as combinations of methods. Bone tissue is the most important unit supporting the body and is a reservoir of calcium and phosphate ions, which are important for physical activity. Many genetic diseases affect bone tissues, possibly because metabolic mechanisms in bone tissue are complex. For instance, the presence of specialized immune cells called osteoclasts in the bone tissue, which absorb bone tissue and interact with osteoblasts in complex ways to support normal vital functions. Moreover, the many cell types in bones exhibit cell-specific proteins for their respective activities. Mutations in the genes encoding these proteins cause a variety of genetic disorders. The relationship between age-related bone tissue fragility (also called frailty) and genetic factors has recently attracted attention. Herein, we discuss the use of genomic, epigenomic, transcriptomic, and metagenomic analyses in bone genetic disorders.
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Affiliation(s)
- Natsuko Aida
- Department of Biochemistry, Tokyo Dental College, 2-9-18 Kandamisaki-cho, Chiyoda-ku, Tokyo 101-0061, Japan; (A.S.); (T.A.)
| | - Akiko Saito
- Department of Biochemistry, Tokyo Dental College, 2-9-18 Kandamisaki-cho, Chiyoda-ku, Tokyo 101-0061, Japan; (A.S.); (T.A.)
| | - Toshifumi Azuma
- Department of Biochemistry, Tokyo Dental College, 2-9-18 Kandamisaki-cho, Chiyoda-ku, Tokyo 101-0061, Japan; (A.S.); (T.A.)
- Oral Health Science Center, Tokyo Dental College, 2-9-18 Kandamisaki-cho, Chiyoda-ku, Tokyo 101-0061, Japan
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10
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Remmelzwaal PC, Verhagen MV, Jongbloed JDH, van den Akker PC, Veenstra-Knol HE, Hitzert MM. Expanding the phenotype of anauxetic dysplasia caused by biallelic NEPRO mutations: A case report. Am J Med Genet A 2023; 191:2440-2445. [PMID: 37294112 DOI: 10.1002/ajmg.a.63316] [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: 04/04/2023] [Revised: 05/16/2023] [Accepted: 05/18/2023] [Indexed: 06/10/2023]
Abstract
The cartilage hair hypoplasia and anauxetic dysplasia (CHH-AD) spectrum encompasses a group of rare skeletal disorders, with anauxetic dysplasia (ANXD) at the most severe end of the spectrum. Biallelic variants in RMRP, POP1, and NEPRO (C3orf17) have previously been associated with the three currently recognized ANXD types. Generally, all types are characterized by severe short stature, brachydactyly, skin laxity, joint hypermobility and dislocations, and extensive skeletal abnormalities visible on radiological evaluation. Thus far, only five patients with type 3 anauxetic dysplasia (ANXD3) have been reported. Here, we describe one additional ANXD3 patient. We provide a detailed physical and radiological evaluation of this patient, in whom we identified a homozygous variant, c.280C > T, p.(Arg94Cys), in NEPRO. Our patient presented with clinically relevant features not previously described in ANXD3: atlantoaxial subluxation, extensive dental anomalies, and a sagittal suture craniosynostosis resulting in scaphocephaly. We provide an overview of the literature on ANXD3 and discuss our patient's characteristics in the context of previously described patients. This study expands the phenotypic spectrum of ANXD, particularly ANXD3. Greater awareness of the possibility of atlantoaxial subluxation, dental anomalies, and craniosynostosis may lead to more timely diagnosis and treatment.
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Affiliation(s)
- P Christian Remmelzwaal
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Martijn V Verhagen
- Department of Radiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jan D H Jongbloed
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Peter C van den Akker
- Department of Genetics, Groningen Expertise Center for Genodermatoses, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Hermine E Veenstra-Knol
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Marrit M Hitzert
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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11
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Khan F, Arshad A, Ullah A, Steenackers E, Mortier G, Ahmad W, Arshad M, Khan S, Hayat A, Khan I, Khan MA, Van Hul W. Identification of a Novel Nonsense Variant in the DLL3 Gene Underlying Spondylocostal Dysostosis in a Consanguineous Pakistani Family. Mol Syndromol 2023; 14:191-200. [PMID: 37323197 PMCID: PMC10267518 DOI: 10.1159/000527043] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/13/2022] [Indexed: 12/03/2023] Open
Abstract
Introduction Spondylocostal dysostosis (SCD) is characterized by multiple vertebral abnormalities associated with abnormalities of the ribs. Five genes causative for the disease have been identified. These include DLL3 (OMIM *602768), MESP2 (OMIM #608681), LFNG (OMIM #609813), TBX6 (OMIM *602427), and HES7 (OMIM *608059). Methods In the current study, we investigated a Pakistani consanguineous family segregating spondylocostal dysotosis. Whole-exome sequencing (WES) followed by Sanger sequencing was performed using DNA of affected and unaffected individuals to identify pathogenic variant(s). The identified variant was interpreted using ACMG classification. Literature review was performed to summarize currently known mutated alleles of DLL3 and the underlying clinical phenotypes. Results Clinical examination using anthropometric measurements and radiographs diagnosed the patients to be afflicted with SCD. Pedigree analysis of the affected family showed an autosomal recessive inheritance pattern of the disease. WES followed by Sanger sequencing identified a novel homozygous nonsense variant (DLL3(NM_016941.4): c.535G>T; p.Glu179Ter) in the DLL3 gene located on chromosome 19q13.2. Conclusion The study will be helpful in carrier testing and genetic counseling to prevent segregation of the disease to the next generations within this family. It also provides knowledge for clinicians and researchers in search of a better understanding of SCD anomalies.
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Affiliation(s)
- Feroz Khan
- Department of Zoology, Wild Life and Fisheries, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi, Pakistan
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
- Department of Zoology, University of Science and Technology, Bannu, Pakistan
| | - Abida Arshad
- Department of Zoology, Wild Life and Fisheries, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi, Pakistan
| | - Asmat Ullah
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Ellen Steenackers
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Geert Mortier
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Wasim Ahmad
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Arshad
- Department of Biological Sciences, International Islamic University, Islamabad, Pakistan
| | - Sarmir Khan
- Department of Reproductive Medicine, Academy of Medical Sciences, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Amir Hayat
- Department Biochemistry, Faculty of Life and Chemical Sciences, Abdul Wali Khan University, Mardan, Pakistan
| | - Ikram Khan
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Muhammad Asim Khan
- Department of Zoology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Wim Van Hul
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
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12
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Nabavizadeh N, Bressin A, Shboul M, Moreno Traspas R, Chia PH, Bonnard C, Szenker‐Ravi E, Sarıbaş B, Beillard E, Altunoglu U, Hojati Z, Drutman S, Freier S, El‐Khateeb M, Fathallah R, Casanova J, Soror W, Arafat A, Escande‐Beillard N, Mayer A, Reversade B. A progeroid syndrome caused by a deep intronic variant in TAPT1 is revealed by RNA/SI-NET sequencing. EMBO Mol Med 2023; 15:e16478. [PMID: 36652330 PMCID: PMC9906387 DOI: 10.15252/emmm.202216478] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 12/13/2022] [Accepted: 12/14/2022] [Indexed: 01/19/2023] Open
Abstract
Exome sequencing has introduced a paradigm shift for the identification of germline variations responsible for Mendelian diseases. However, non-coding regions, which make up 98% of the genome, cannot be captured. The lack of functional annotation for intronic and intergenic variants makes RNA-seq a powerful companion diagnostic. Here, we illustrate this point by identifying six patients with a recessive Osteogenesis Imperfecta (OI) and neonatal progeria syndrome. By integrating homozygosity mapping and RNA-seq, we delineated a deep intronic TAPT1 mutation (c.1237-52 G>A) that segregated with the disease. Using SI-NET-seq, we document that TAPT1's nascent transcription was not affected in patients' fibroblasts, indicating instead that this variant leads to an alteration of pre-mRNA processing. Predicted to serve as an alternative splicing branchpoint, this mutation enhances TAPT1 exon 12 skipping, creating a protein-null allele. Additionally, our study reveals dysregulation of pathways involved in collagen and extracellular matrix biology in disease-relevant cells. Overall, our work highlights the power of transcriptomic approaches in deciphering the repercussions of non-coding variants, as well as in illuminating the molecular mechanisms of human diseases.
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Affiliation(s)
- Nasrinsadat Nabavizadeh
- Laboratory of Human Genetics & TherapeuticsGenome Institute of Singapore, A*STARSingapore CitySingapore
- Division of Genetics, Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and TechnologyUniversity of IsfahanIsfahanIran
- Medical Genetics DepartmentKoç University School of MedicineIstanbulTurkey
| | | | - Mohammad Shboul
- Department of Medical Laboratory SciencesJordan University of Science and TechnologyIrbidJordan
| | - Ricardo Moreno Traspas
- Laboratory of Human Genetics & TherapeuticsGenome Institute of Singapore, A*STARSingapore CitySingapore
| | - Poh Hui Chia
- Laboratory of Human Genetics & TherapeuticsGenome Institute of Singapore, A*STARSingapore CitySingapore
| | - Carine Bonnard
- Model Development, A*STAR Skin Research Labs (A*SRL)Singapore CitySingapore
| | - Emmanuelle Szenker‐Ravi
- Laboratory of Human Genetics & TherapeuticsGenome Institute of Singapore, A*STARSingapore CitySingapore
| | - Burak Sarıbaş
- Laboratory of Human Genetics & TherapeuticsGenome Institute of Singapore, A*STARSingapore CitySingapore
- Medical Genetics DepartmentKoç University School of MedicineIstanbulTurkey
| | | | - Umut Altunoglu
- Medical Genetics DepartmentKoç University School of MedicineIstanbulTurkey
| | - Zohreh Hojati
- Division of Genetics, Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and TechnologyUniversity of IsfahanIsfahanIran
| | - Scott Drutman
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller BranchRockefeller UniversityNew YorkNYUSA
| | - Susanne Freier
- Max Planck Institute for Molecular GeneticsBerlinGermany
| | | | - Rajaa Fathallah
- National Center for Diabetes, Endocrinology and GeneticsAmmanJordan
| | - Jean‐Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller BranchRockefeller UniversityNew YorkNYUSA
- Laboratory of Human Genetics of Infectious Diseases, Necker BranchINSERM U1163, Necker Hospital for Sick ChildrenParisFrance
- Imagine InstituteUniversity of ParisParisFrance
- Howard Hughes Medical InstituteNew YorkNYUSA
- Pediatric Hematology and Immunology UnitNecker Hospital for Sick ChildrenParisFrance
| | - Wesam Soror
- National Center for Diabetes, Endocrinology and GeneticsAmmanJordan
| | - Alaa Arafat
- National Center for Diabetes, Endocrinology and GeneticsAmmanJordan
| | - Nathalie Escande‐Beillard
- Medical Genetics DepartmentKoç University School of MedicineIstanbulTurkey
- Institute of Molecular and Cell Biology, A*STARSingapore CitySingapore
| | - Andreas Mayer
- Max Planck Institute for Molecular GeneticsBerlinGermany
| | - Bruno Reversade
- Laboratory of Human Genetics & TherapeuticsGenome Institute of Singapore, A*STARSingapore CitySingapore
- Medical Genetics DepartmentKoç University School of MedicineIstanbulTurkey
- Institute of Molecular and Cell Biology, A*STARSingapore CitySingapore
- Department of PaediatricsNational University of SingaporeSingapore CitySingapore
- Smart‐Health Initiative, BESE, KAUSTThuwalKingdom of Saudi Arabia
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13
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Sajovic J, Meglič A, Volk M, Maver A, Jarc-Vidmar M, Hawlina M, Fakin A. Stargardt-like Clinical Characteristics and Disease Course Associated with Variants in the WDR19 Gene. Genes (Basel) 2023; 14:genes14020291. [PMID: 36833218 PMCID: PMC9957452 DOI: 10.3390/genes14020291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 01/11/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023] Open
Abstract
Variants in WDR19 (IFT144) have been implicated as another possible cause of Stargardt disease. The purpose of this study was to compare longitudinal multimodal imaging of a WDR19-Stargardt patient, harboring p.(Ser485Ile) and a novel c.(3183+1_3184-1)_(3261+1_3262-1)del variant, with 43 ABCA4-Stargardt patients. Age at onset, visual acuity, Ishihara color vision, color fundus, fundus autofluorescence (FAF), spectral-domain optical coherence tomography (OCT) images, microperimetry and electroretinography (ERG) were evaluated. First symptom of WDR19 patient was nyctalopia at the age of 5 years. After the age of 18 years, OCT showed hyper-reflectivity at the level of the external limiting membrane/outer nuclear layer. There was abnormal cone and rod photoreceptor function on ERG. Widespread fundus flecks appeared, followed by perifoveal photoreceptor atrophy. Fovea and peripapillary retina remained preserved until the latest exam at 25 years of age. ABCA4 patients had median age of onset at 16 (range 5-60) years and mostly displayed typical Stargardt triad. A total of 19% had foveal sparing. In comparison to ABCA4 patients, the WDR19 patient had a relatively large foveal preservation and severe rod photoreceptor impairment; however, it was still within the ABCA4 disease spectrum. Addition of WDR19 in the group of genes producing phenocopies of Stargardt disease underlines the importance of genetic testing and may help to understand its pathogenesis.
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Affiliation(s)
- Jana Sajovic
- Eye Hospital, University Medical Centre Ljubljana, Grablovičeva 46, 1000 Ljubljana, Slovenia
| | - Andrej Meglič
- Eye Hospital, University Medical Centre Ljubljana, Grablovičeva 46, 1000 Ljubljana, Slovenia
| | - Marija Volk
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Šlajmerjeva 4, 1000 Ljubljana, Slovenia
| | - Aleš Maver
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Šlajmerjeva 4, 1000 Ljubljana, Slovenia
| | - Martina Jarc-Vidmar
- Eye Hospital, University Medical Centre Ljubljana, Grablovičeva 46, 1000 Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia
| | - Marko Hawlina
- Eye Hospital, University Medical Centre Ljubljana, Grablovičeva 46, 1000 Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia
| | - Ana Fakin
- Eye Hospital, University Medical Centre Ljubljana, Grablovičeva 46, 1000 Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia
- Correspondence:
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14
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Syx D, Delbaere S, Bui C, De Clercq A, Larson G, Mizumoto S, Kosho T, Fournel-Gigleux S, Malfait F. Alterations in glycosaminoglycan biosynthesis associated with the Ehlers-Danlos syndromes. Am J Physiol Cell Physiol 2022; 323:C1843-C1859. [PMID: 35993517 DOI: 10.1152/ajpcell.00127.2022] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Proteoglycans consist of a core protein substituted with one or more glycosaminoglycan (GAG) chains and execute versatile functions during many physiological and pathological processes. The biosynthesis of GAG chains is a complex process that depends on the concerted action of a variety of enzymes. Central to the biosynthesis of heparan sulfate (HS) and chondroitin sulfate/dermatan sulfate (CS/DS) GAG chains is the formation of a tetrasaccharide linker region followed by biosynthesis of HS or CS/DS-specific repeating disaccharide units, which then undergo modifications and epimerization. The importance of these biosynthetic enzymes is illustrated by several severe pleiotropic disorders that arise upon their deficiency. The Ehlers-Danlos syndromes (EDS) constitute a special group among these disorders. Although most EDS types are caused by defects in fibrillar types I, III, or V collagen, or their modifying enzymes, a few rare EDS types have recently been linked to defects in GAG biosynthesis. Spondylodysplastic EDS (spEDS) is caused by defective formation of the tetrasaccharide linker region, either due to β4GalT7 or β3GalT6 deficiency, whereas musculocontractural EDS (mcEDS) results from deficiency of D4ST1 or DS-epi1, impairing DS formation. This narrative review highlights the consequences of GAG deficiency in these specific EDS types, summarizes the associated phenotypic features and the molecular spectrum of reported pathogenic variants, and defines the current knowledge on the underlying pathophysiological mechanisms based on studies in patient-derived material, in vitro analyses, and animal models.
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Affiliation(s)
- Delfien Syx
- Department of Biomolecular Medicine, Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Sarah Delbaere
- Department of Biomolecular Medicine, Center for Medical Genetics, Ghent University, Ghent, Belgium
| | | | - Adelbert De Clercq
- Department of Biomolecular Medicine, Center for Medical Genetics, Ghent University, Ghent, Belgium.,Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Ostend, Belgium
| | - Göran Larson
- Department of Laboratory Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Laboratory of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Shuji Mizumoto
- Department of Pathobiochemistry, Faculty of Pharmacy, Meijo University, Nagoya, Japan
| | - Tomoki Kosho
- Center for Medical Genetics, Shinshu University Hospital, Matsumoto, Japan.,Department of Medical Genetics, Shinshu University School of Medicine, Matsumoto, Japan
| | | | - Fransiska Malfait
- Department of Biomolecular Medicine, Center for Medical Genetics, Ghent University, Ghent, Belgium
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15
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Enhancing Molecular Testing for Effective Delivery of Actionable Gene Diagnostics. BIOENGINEERING (BASEL, SWITZERLAND) 2022; 9:bioengineering9120745. [PMID: 36550951 PMCID: PMC9774983 DOI: 10.3390/bioengineering9120745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/07/2022] [Accepted: 11/29/2022] [Indexed: 12/02/2022]
Abstract
There is a deep need to navigate within our genomic data to find, understand and pave the way for disease-specific treatments, as the clinical diagnostic journey provides only limited guidance. The human genome is enclosed in every nucleated cell, and yet at the single-cell resolution many unanswered questions remain, as most of the sequencing techniques use a bulk approach. Therefore, heterogeneity, mosaicism and many complex structural variants remain partially uncovered. As a conceptual approach, nanopore-based sequencing holds the promise of being a single-molecule-based, long-read and high-resolution technique, with the ability of uncovering the nucleic acid sequence and methylation almost in real time. A key limiting factor of current clinical genetics is the deciphering of key disease-causing genomic sequences. As the technological revolution is expanding regarding genetic data, the interpretation of genotype-phenotype correlations should be made with fine caution, as more and more evidence points toward the presence of more than one pathogenic variant acting together as a result of intergenic interplay in the background of a certain phenotype observed in a patient. This is in conjunction with the observation that many inheritable disorders manifest in a phenotypic spectrum, even in an intra-familial way. In the present review, we summarized the relevant data on nanopore sequencing regarding clinical genomics as well as highlighted the importance and content of pre-test and post-test genetic counselling, yielding a complex approach to phenotype-driven molecular diagnosis. This should significantly lower the time-to-right diagnosis as well lower the time required to complete a currently incomplete genotype-phenotype axis, which will boost the chance of establishing a new actionable diagnosis followed by therapeutical approach.
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16
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Alhaidari AI, Albakri AS, Alhumaidi SS. A Novel PGAP3 Gene Mutation-Related Megalocornea Can Be Misdiagnosed as Primary Congenital Glaucoma. Cureus 2022; 14:e29387. [PMID: 36304370 PMCID: PMC9585391 DOI: 10.7759/cureus.29387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/20/2022] [Indexed: 11/17/2022] Open
Abstract
Hyperphosphatasia with mental retardation syndrome 4 (HPMRS4) is a rare autosomal recessive disorder caused by glycosylphosphatidylinositol (GPI) deficiency. GPI deficiency results from a mutation in one of six known genes. Mutation in post-GPI attachment to protein phospholipase 3 gene (PGAP3) is linked to HPMRS4. Patients usually present with dysmorphic features, developmental delay, central hypotonia, and seizure. However, in our case, we report a novel homozygous missense mutation of PGAP3 gene in a female child who presented with megalocornea, which is an unusual clinical presentation for HPMRS4. Megalocornea, in her first days of life, led to a misdiagnosis of primary congenital glaucoma. Later, other common clinical features of HPMRS4 became apparent.
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17
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Vlashi R, Zhang X, Wu M, Chen G. Wnt signaling: essential roles in osteoblast differentiation, bone metabolism and therapeutic implications for bone and skeletal disorders. Genes Dis 2022. [DOI: 10.1016/j.gendis.2022.07.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022] Open
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18
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Owen MJ, Lefebvre S, Hansen C, Kunard CM, Dimmock DP, Smith LD, Scharer G, Mardach R, Willis MJ, Feigenbaum A, Niemi AK, Ding Y, Van Der Kraan L, Ellsworth K, Guidugli L, Lajoie BR, McPhail TK, Mehtalia SS, Chau KK, Kwon YH, Zhu Z, Batalov S, Chowdhury S, Rego S, Perry J, Speziale M, Nespeca M, Wright MS, Reese MG, De La Vega FM, Azure J, Frise E, Rigby CS, White S, Hobbs CA, Gilmer S, Knight G, Oriol A, Lenberg J, Nahas SA, Perofsky K, Kim K, Carroll J, Coufal NG, Sanford E, Wigby K, Weir J, Thomson VS, Fraser L, Lazare SS, Shin YH, Grunenwald H, Lee R, Jones D, Tran D, Gross A, Daigle P, Case A, Lue M, Richardson JA, Reynders J, Defay T, Hall KP, Veeraraghavan N, Kingsmore SF. An automated 13.5 hour system for scalable diagnosis and acute management guidance for genetic diseases. Nat Commun 2022; 13:4057. [PMID: 35882841 PMCID: PMC9325884 DOI: 10.1038/s41467-022-31446-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 06/08/2022] [Indexed: 12/31/2022] Open
Abstract
While many genetic diseases have effective treatments, they frequently progress rapidly to severe morbidity or mortality if those treatments are not implemented immediately. Since front-line physicians frequently lack familiarity with these diseases, timely molecular diagnosis may not improve outcomes. Herein we describe Genome-to-Treatment, an automated, virtual system for genetic disease diagnosis and acute management guidance. Diagnosis is achieved in 13.5 h by expedited whole genome sequencing, with superior analytic performance for structural and copy number variants. An expert panel adjudicated the indications, contraindications, efficacy, and evidence-of-efficacy of 9911 drug, device, dietary, and surgical interventions for 563 severe, childhood, genetic diseases. The 421 (75%) diseases and 1527 (15%) effective interventions retained are integrated with 13 genetic disease information resources and appended to diagnostic reports ( https://gtrx.radygenomiclab.com ). This system provided correct diagnoses in four retrospectively and two prospectively tested infants. The Genome-to-Treatment system facilitates optimal outcomes in children with rapidly progressive genetic diseases.
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Affiliation(s)
- Mallory J. Owen
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Sebastien Lefebvre
- grid.422288.60000 0004 0408 0730Alexion Pharmaceuticals, Inc., Boston, MA 02210 USA
| | - Christian Hansen
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Chris M. Kunard
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - David P. Dimmock
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.419735.d0000 0004 0615 8415Keck Graduate Institute, Claremont, CA 91711 USA
| | - Laurie D. Smith
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA
| | - Gunter Scharer
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA
| | - Rebecca Mardach
- grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Mary J. Willis
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA
| | - Annette Feigenbaum
- grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Anna-Kaisa Niemi
- grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Yan Ding
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Luca Van Der Kraan
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Katarzyna Ellsworth
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Lucia Guidugli
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Bryan R. Lajoie
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | | | | | - Kevin K. Chau
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Yong H. Kwon
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Zhanyang Zhu
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Sergey Batalov
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Shimul Chowdhury
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.419735.d0000 0004 0615 8415Keck Graduate Institute, Claremont, CA 91711 USA
| | - Seema Rego
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - James Perry
- grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Mark Speziale
- grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Mark Nespeca
- grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA ,grid.266100.30000 0001 2107 4242Department of Neuroscience, University of California San Diego, San Diego, CA 92093 USA
| | - Meredith S. Wright
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.419735.d0000 0004 0615 8415Keck Graduate Institute, Claremont, CA 91711 USA
| | | | | | - Joe Azure
- Fabric Genomics, Inc., Oakland, CA 94612 USA
| | - Erwin Frise
- Fabric Genomics, Inc., Oakland, CA 94612 USA
| | | | - Sandy White
- Fabric Genomics, Inc., Oakland, CA 94612 USA
| | - Charlotte A. Hobbs
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Sheldon Gilmer
- grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Gail Knight
- grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Albert Oriol
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Jerica Lenberg
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.419735.d0000 0004 0615 8415Keck Graduate Institute, Claremont, CA 91711 USA
| | - Shareef A. Nahas
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Kate Perofsky
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Kyu Kim
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Jeanne Carroll
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Nicole G. Coufal
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Erica Sanford
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA
| | - Kristen Wigby
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, San Diego, CA 92093 USA
| | - Jacqueline Weir
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - Vicki S. Thomson
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - Louise Fraser
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - Seka S. Lazare
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - Yoon H. Shin
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | | | - Richard Lee
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - David Jones
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - Duke Tran
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - Andrew Gross
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - Patrick Daigle
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - Anne Case
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - Marisa Lue
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | | | - John Reynders
- grid.422288.60000 0004 0408 0730Alexion Pharmaceuticals, Inc., Boston, MA 02210 USA
| | - Thomas Defay
- grid.422288.60000 0004 0408 0730Alexion Pharmaceuticals, Inc., Boston, MA 02210 USA
| | - Kevin P. Hall
- grid.185669.50000 0004 0507 3954Illumina, Inc., San Diego, CA 92122 USA
| | - Narayanan Veeraraghavan
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Stephen F. Kingsmore
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA ,grid.286440.c0000 0004 0383 2910Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.419735.d0000 0004 0615 8415Keck Graduate Institute, Claremont, CA 91711 USA
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19
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El-Attar EA, Helmy Elkaffas RM, Aglan SA, Naga IS, Nabil A, Abdallah HY. Genomics in Egypt: Current Status and Future Aspects. Front Genet 2022; 13:797465. [PMID: 35664315 PMCID: PMC9157251 DOI: 10.3389/fgene.2022.797465] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 04/04/2022] [Indexed: 11/13/2022] Open
Abstract
Egypt is the third most densely inhabited African country. Due to the economic burden and healthcare costs of overpopulation, genomic and genetic testing is a huge challenge. However, in the era of precision medicine, Egypt is taking a shift in approach from “one-size-fits all” to more personalized healthcare via advancing the practice of medical genetics and genomics across the country. This shift necessitates concrete knowledge of the Egyptian genome and related diseases to direct effective preventive, diagnostic and counseling services of prevalent genetic diseases in Egypt. Understanding disease molecular mechanisms will enhance the capacity for personalized interventions. From this perspective, we highlight research efforts and available services for rare genetic diseases, communicable diseases including the coronavirus 2019 disease (COVID19), and cancer. The current state of genetic services in Egypt including availability and access to genetic services is described. Drivers for applying genomics in Egypt are illustrated with a SWOT analysis of the current genetic/genomic services. Barriers to genetic service development in Egypt, whether economic, geographic, cultural or educational are discussed as well. The sensitive topic of communicating genomic results and its ethical considerations is also tackled. To understand disease pathogenesis, much can be gained through the advancement and integration of genomic technologies via clinical applications and research efforts in Egypt. Three main pillars of multidisciplinary collaboration for advancing genomics in Egypt are envisaged: resources, infrastructure and training. Finally, we highlight the recent national plan to establish a genome center that will aim to prepare a map of the Egyptian human genome to discover and accurately determine the genetic characteristics of various diseases. The Reference Genome Project for Egyptians and Ancient Egyptians will initialize a new genomics era in Egypt. We propose a multidisciplinary governance system in Egypt to support genomic medicine research efforts and integrate into the healthcare system whilst ensuring ethical conduct of data.
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Affiliation(s)
- Eman Ahmed El-Attar
- Chemical Pathology Department, Medical Research Institute, Alexandria University, Alexandria, Egypt
- *Correspondence: Eman Ahmed El-Attar,
| | | | - Sarah Ahmed Aglan
- Chemical Pathology Department, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Iman S. Naga
- Department of Microbiology, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Amira Nabil
- Department of Human Genetics, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Hoda Y. Abdallah
- Medical Genetics Unit, Histology and Cell Biology Department, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
- Center of Excellence in Molecular and Cellular Medicine, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
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20
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Girisha KM, Jacob P, SriLakshmi Bhavani G, Shah H, Mortier GR. Report of three patients, including monozygotic twins and review of clinical and mutation profiles. Eur J Med Genet 2022; 65:104521. [PMID: 35568358 DOI: 10.1016/j.ejmg.2022.104521] [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: 03/05/2021] [Revised: 05/03/2022] [Accepted: 05/08/2022] [Indexed: 11/03/2022]
Abstract
Steel syndrome (MIM# 615155) is an autosomal recessive skeletal disorder, characterized by dislocations of the hips and radial heads, carpal coalition, short stature, facial dysmorphism, and scoliosis. Until date 47 patients have been reported. However, disease causing variants have been identified only in twenty Puerto Rican and nine non-Puerto Rican families. Here we report two monozygotic twins and a boy from two families with novel missense variants, c.295G > A p.(Ala99 Thr), c.3056C > A p.(Pro1019His) and c.2521G > A p.(Gly841Arg) in COL27A1. We describe for the first time, cleft palate and delayed carpal bone ossification as features of Steel syndrome. We reviewed clinical features in all mutation-proven Steel syndrome patients. Short stature and dislocation/subluxation of hip joint are consistently observed. Other features include dislocated radial heads, scoliosis, lordosis, carpal coalition, facial dysmorphism, hearing loss, bilateral fifth finger clinodactyly, knee deformities and developmental delay. Seven missense variants and eight null variants are reported in COL27A1 until date. We also looked into the genotype-phenotype correlation in Puerto Rican and non-Puerto Rican patients.
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Affiliation(s)
- Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India.
| | - Prince Jacob
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India.
| | - Gandham SriLakshmi Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India.
| | - Hitesh Shah
- Department of Orthopaedics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India.
| | - Geert R Mortier
- Center for Medical Genetics, University of Antwerp/Antwerp University Hospital, Antwerp, Belgium.
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21
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Biallelic PAN2 variants in individuals with a syndromic neurodevelopmental disorder and multiple congenital anomalies. Eur J Hum Genet 2022; 30:611-618. [PMID: 35304602 PMCID: PMC9090724 DOI: 10.1038/s41431-022-01077-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 01/10/2022] [Accepted: 02/17/2022] [Indexed: 12/26/2022] Open
Abstract
PAN2 encodes a subunit of a deadenylation complex with important functions in mRNA stability and post-transcriptional regulation of gene expression. A homozygous frameshift deletion in PAN2 was reported in a single affected individual with developmental delay and multiple congenital anomalies. Here, we describe five additional individuals from three unrelated families with homozygous predicted loss-of-function variants in PAN2. The affected individuals presented with significant overlap in their clinical features, including mild-moderate intellectual disability, hypotonia, sensorineural hearing loss, EEG abnormalities, congenital heart defects (tetralogy of Fallot, septal defects, dilated aortic root), urinary tract malformations, ophthalmological anomalies, short stature with other skeletal anomalies, and craniofacial features including flat occiput, ptosis, long philtrum, and short neck. Our data confirm that biallelic predicted loss-of-function variants in PAN2 cause a syndrome with multiple congenital anomalies, and suggest an important role of mRNA polyA tail length for proper organ formation.
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22
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González-Iglesias E, López-Vázquez A, Noval S, Nieves-Moreno M, Granados-Fernández M, Arruti N, Rosa-Pérez I, Pacio-Míguez M, Montaño VEF, Rodríguez-Solana P, del Pozo A, Santos-Simarro F, Vallespín E. Next-Generation Sequencing Screening of 43 Families with Non-Syndromic Early-Onset High Myopia: A Clinical and Genetic Study. Int J Mol Sci 2022; 23:ijms23084233. [PMID: 35457050 PMCID: PMC9031962 DOI: 10.3390/ijms23084233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 04/04/2022] [Indexed: 02/01/2023] Open
Abstract
Early-onset high myopia (EoHM) is a disease that causes a spherical refraction error of ≥-6 diopters before 10 years of age, with potential multiple ocular complications. In this article, we report a clinical and genetic study of 43 families with EoHM recruited in our center. A complete ophthalmological evaluation was performed, and a sample of peripheral blood was obtained from proband and family members. DNA was analyzed using a customized next-generation sequencing panel that included 419 genes related to ophthalmological disorders with a suspected genetic cause, and genes related to EoHM pathogenesis. We detected pathogenic and likely pathogenic variants in 23.9% of the families and detected variants of unknown significance in 76.1%. Of these, 5.7% were found in genes related to non-syndromic EoHM, 48.6% in genes associated with inherited retinal dystrophies that can include a syndromic phenotype, and 45.7% in genes that are not directly related to EoHM or retinal dystrophy. We found no candidate genes in 23% of the patients, which suggests that further studies are needed. We propose a systematic genetic analysis for patients with EoHM because it helps with follow-up, prognosis and genetic counseling.
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Affiliation(s)
- Eva González-Iglesias
- Section of Molecular Ophthalmology, Medical and Molecular Genetics Institute (INGEMM) IdiPaz, La Paz University Hospital, 28046 Madrid, Spain; (E.G.-I.); (V.E.F.M.); (P.R.-S.)
| | - Ana López-Vázquez
- Department of Ophthalmology, La Paz University Hospital, 28046 Madrid, Spain; (A.L.-V.); (S.N.); (M.N.-M.); (M.G.-F.); (N.A.); (I.R.-P.)
| | - Susana Noval
- Department of Ophthalmology, La Paz University Hospital, 28046 Madrid, Spain; (A.L.-V.); (S.N.); (M.N.-M.); (M.G.-F.); (N.A.); (I.R.-P.)
| | - María Nieves-Moreno
- Department of Ophthalmology, La Paz University Hospital, 28046 Madrid, Spain; (A.L.-V.); (S.N.); (M.N.-M.); (M.G.-F.); (N.A.); (I.R.-P.)
| | - María Granados-Fernández
- Department of Ophthalmology, La Paz University Hospital, 28046 Madrid, Spain; (A.L.-V.); (S.N.); (M.N.-M.); (M.G.-F.); (N.A.); (I.R.-P.)
| | - Natalia Arruti
- Department of Ophthalmology, La Paz University Hospital, 28046 Madrid, Spain; (A.L.-V.); (S.N.); (M.N.-M.); (M.G.-F.); (N.A.); (I.R.-P.)
| | - Irene Rosa-Pérez
- Department of Ophthalmology, La Paz University Hospital, 28046 Madrid, Spain; (A.L.-V.); (S.N.); (M.N.-M.); (M.G.-F.); (N.A.); (I.R.-P.)
| | - Marta Pacio-Míguez
- Biomedical Research Center in the Rare Diseases Network (CIBERER), Carlos II Health Institute (ISCIII), 28029 Madrid, Spain; (M.P.-M.); (A.d.P.); (F.S.-S.)
- Section of Neurodevelopmental Disorders, Medical and Molecular Genetics Institute (INGEMM) IdiPaz, La Paz University Hospital, 28046 Madrid, Spain
| | - Victoria E. F. Montaño
- Section of Molecular Ophthalmology, Medical and Molecular Genetics Institute (INGEMM) IdiPaz, La Paz University Hospital, 28046 Madrid, Spain; (E.G.-I.); (V.E.F.M.); (P.R.-S.)
- Biomedical Research Center in the Rare Diseases Network (CIBERER), Carlos II Health Institute (ISCIII), 28029 Madrid, Spain; (M.P.-M.); (A.d.P.); (F.S.-S.)
| | - Patricia Rodríguez-Solana
- Section of Molecular Ophthalmology, Medical and Molecular Genetics Institute (INGEMM) IdiPaz, La Paz University Hospital, 28046 Madrid, Spain; (E.G.-I.); (V.E.F.M.); (P.R.-S.)
| | - Angela del Pozo
- Biomedical Research Center in the Rare Diseases Network (CIBERER), Carlos II Health Institute (ISCIII), 28029 Madrid, Spain; (M.P.-M.); (A.d.P.); (F.S.-S.)
- Section of Clinical Bioinformatics, Medical and Molecular Genetics Institute (INGEMM) IdiPaz, La Paz University Hospital, 28046 Madrid, Spain
| | - Fernando Santos-Simarro
- Biomedical Research Center in the Rare Diseases Network (CIBERER), Carlos II Health Institute (ISCIII), 28029 Madrid, Spain; (M.P.-M.); (A.d.P.); (F.S.-S.)
- Section of Clinical Genetics, Medical and Molecular Genetics Institute (INGEMM) IdiPaz, La Paz University Hospital, 28046 Madrid, Spain
| | - Elena Vallespín
- Section of Molecular Ophthalmology, Medical and Molecular Genetics Institute (INGEMM) IdiPaz, La Paz University Hospital, 28046 Madrid, Spain; (E.G.-I.); (V.E.F.M.); (P.R.-S.)
- Biomedical Research Center in the Rare Diseases Network (CIBERER), Carlos II Health Institute (ISCIII), 28029 Madrid, Spain; (M.P.-M.); (A.d.P.); (F.S.-S.)
- Correspondence:
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23
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Ahmad N, Aleysae NA, Sobaihi M, Naitah N, Rasol MA, Al-Kouatli AA, Almaghamsi TM, Heaphy ELG, Attiyah MH, Hrays M, Alghamdi B, Alzahrani AS. A single-centre study of genetic mutations, audiology, echocardiogram and pulmonary function in Saudi children with osteogenesis imperfecta. J Pediatr Endocrinol Metab 2022; 35:355-362. [PMID: 34954934 DOI: 10.1515/jpem-2021-0587] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 11/25/2021] [Indexed: 11/15/2022]
Abstract
OBJECTIVES Osteogenesis imperfecta (OI) is a heterogeneous group of inherited connective tissue disorders, characterised by skeletal fragility. Patients with OI may also exhibit extra-skeletal features like blue or grey scleral colour, fragile skin, easy bruising, joint laxity, short stature, deafness, cardiac valve abnormalities and abnormal pulmonary function. The objective of this study is to describe genetic mutations, prevalence of hearing issues, cardiac complications and impaired pulmonary function in children with OI. METHODS This is a cross-sectional study of 23 Saudi children aged 6 months to 18 years who were diagnosed with OI. The revised Sillence classification (2,105) was used to classify the OI type. Whole exome sequencing was performed for genetic mutations. The hearing was assessed by either pure-tone audiometry and/or otoacoustic emission testing. Cardiac defects were screened by echocardiograms. Spirometry was performed to assess pulmonary function. Data were analysed with descriptive statistics. RESULTS Based on the Sillence classification, 16 patients had OI type III, 6 had type IV and 1 had type I. Of the18 patients who had genetic sequencing, 66.6% had autosomal dominant and 33.3% had autosomal recessive mutations. Among children who had screening, hearing loss was diagnosed in 53% (9/17), congenital cardiac malformations in 26% (5/19) and restrictive lung disease in 70% (7/10). CONCLUSIONS We found significant extra-skeletal features and a high yield of genetic mutations associated with OI. We suggest further studies to develop a screening protocol for extra-skeletal features in children with OI.
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Affiliation(s)
- Noman Ahmad
- King Faisal Specialist Hospital & Research Centre (Gen. Org.), Jeddah, Saudi Arabia
| | | | | | | | - Mohammed Amin Rasol
- King Faisal Specialist Hospital & Research Centre (Gen. Org.), Jeddah, Saudi Arabia
| | | | | | | | | | | | - Balgees Alghamdi
- Molecular Oncology Department, King Faisal Specialist Hospital & Research Centre (Gen. Org.), Riyadh, Saudi Arabia
| | - Ali Saeed Alzahrani
- Research Centre, King Faisal Specialist Hospital & Research Centre (Gen. Org.), Jeddah, Saudi Arabia
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24
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Massadeh S, Alhabshan F, AlSudairi HN, Alkwai S, Alsuwailm M, Kabbani MS, Chaikhouni F, Alaamery M. The Role of the Disrupted Podosome Adaptor Protein (SH3PXD2B) in Frank–Ter Haar Syndrome. Genes (Basel) 2022; 13:genes13020236. [PMID: 35205281 PMCID: PMC8872394 DOI: 10.3390/genes13020236] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 01/10/2022] [Accepted: 01/18/2022] [Indexed: 12/21/2022] Open
Abstract
Frank–Ter Haar syndrome (FTHS), sometimes referred to as Ter Haar syndrome, is a rare hereditary disorder that manifests in skeletal, cardiac, and ocular anomalies, including hypertelorism, glaucoma, prominent eyes, and facial abnormalities. In this study, we performed whole-exome sequencing (WES) to identify the genetic component responsible for the phenotype of the index patient, a male infant born to a consanguineous family from Saudi Arabia. The analysis revealed a homozygous missense variant, c.280C>G, in the SH3PXD2B gene, which cosegregates with the familial phenotype with a plausible autosomal-recessive mode of inheritance, indicating a potential disease-causing association. The SH3PXD2B gene encodes a TKS4 podosome adaptor protein that regulates the epidermal growth factor signaling pathway. This study validates the critical function of the TKS4 podosome protein by suggesting a common mechanism underlying the pathogenesis of FTHS.
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Affiliation(s)
- Salam Massadeh
- Developmental Medicine Department, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (MNG-HA), Riyadh 11481, Saudi Arabia; (S.M.); (H.N.A.); (S.A.); (M.A.)
- KACST-BWH Centre of Excellence for Biomedicine, Joint Centers of Excellence Program, King Abdulaziz City for Science and Technology (KACST), Riyadh 11442, Saudi Arabia
- Saudi Human Genome Satellite Laboratory at King Abdulaziz Medical City, King Abdulaziz City for Science and Technology (KACST), Ministry of National Guard Health Affairs (MNGHA), Riyadh 11481, Saudi Arabia
| | - Fahad Alhabshan
- Department of Cardiac Sciences, King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Ministry of the National Guard-Health Affairs, Riyadh 14611, Saudi Arabia; (F.A.); (M.S.K.); (F.C.)
| | - Hadeel N. AlSudairi
- Developmental Medicine Department, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (MNG-HA), Riyadh 11481, Saudi Arabia; (S.M.); (H.N.A.); (S.A.); (M.A.)
| | - Sarah Alkwai
- Developmental Medicine Department, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (MNG-HA), Riyadh 11481, Saudi Arabia; (S.M.); (H.N.A.); (S.A.); (M.A.)
- KACST-BWH Centre of Excellence for Biomedicine, Joint Centers of Excellence Program, King Abdulaziz City for Science and Technology (KACST), Riyadh 11442, Saudi Arabia
| | - Moneera Alsuwailm
- Developmental Medicine Department, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (MNG-HA), Riyadh 11481, Saudi Arabia; (S.M.); (H.N.A.); (S.A.); (M.A.)
- KACST-BWH Centre of Excellence for Biomedicine, Joint Centers of Excellence Program, King Abdulaziz City for Science and Technology (KACST), Riyadh 11442, Saudi Arabia
| | - Mohamed S. Kabbani
- Department of Cardiac Sciences, King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Ministry of the National Guard-Health Affairs, Riyadh 14611, Saudi Arabia; (F.A.); (M.S.K.); (F.C.)
| | - Farah Chaikhouni
- Department of Cardiac Sciences, King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Ministry of the National Guard-Health Affairs, Riyadh 14611, Saudi Arabia; (F.A.); (M.S.K.); (F.C.)
| | - Manal Alaamery
- Developmental Medicine Department, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (MNG-HA), Riyadh 11481, Saudi Arabia; (S.M.); (H.N.A.); (S.A.); (M.A.)
- KACST-BWH Centre of Excellence for Biomedicine, Joint Centers of Excellence Program, King Abdulaziz City for Science and Technology (KACST), Riyadh 11442, Saudi Arabia
- Saudi Human Genome Satellite Laboratory at King Abdulaziz Medical City, King Abdulaziz City for Science and Technology (KACST), Ministry of National Guard Health Affairs (MNGHA), Riyadh 11481, Saudi Arabia
- Correspondence:
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25
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Martínez-Gil N, Ugartondo N, Grinberg D, Balcells S. Wnt Pathway Extracellular Components and Their Essential Roles in Bone Homeostasis. Genes (Basel) 2022; 13:genes13010138. [PMID: 35052478 PMCID: PMC8775112 DOI: 10.3390/genes13010138] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/10/2022] [Accepted: 01/11/2022] [Indexed: 12/11/2022] Open
Abstract
The Wnt pathway is involved in several processes essential for bone development and homeostasis. For proper functioning, the Wnt pathway is tightly regulated by numerous extracellular elements that act by both activating and inhibiting the pathway at different moments. This review aims to describe, summarize and update the findings regarding the extracellular modulators of the Wnt pathway, including co-receptors, ligands and inhibitors, in relation to bone homeostasis, with an emphasis on the animal models generated, the diseases associated with each gene and the bone processes in which each member is involved. The precise knowledge of all these elements will help us to identify possible targets that can be used as a therapeutic target for the treatment of bone diseases such as osteoporosis.
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26
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Yang L, Zhao S, Ma N, Liu L, Li D, Li X, Wang Z, Song X, Wang Y, Wang D. Novel DIP2C gene splicing variant in an individual with focal infantile epilepsy. Am J Med Genet A 2021; 188:210-215. [PMID: 34617658 DOI: 10.1002/ajmg.a.62524] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 08/15/2021] [Accepted: 09/07/2021] [Indexed: 11/06/2022]
Abstract
Disco-interacting protein 2 C (DIP2C) encodes a disco-interacting protein and is highly expressed in the nervous system. Most variants of DIP2C are microdeletions on chromosome 10p15.3. This study reports a 17-month-old infant with focal infantile epilepsy who has a single-nucleotide variation in DIP2C that results in alternative splicing. The de novo variation (NM_014974.3: c.1057+2T>G) in DIP2C was uncovered through whole-exome sequencing. Minigene assays were performed and verified the alternative splicing caused by the variation. Finally, an 80-bp nucleotide deletion in the 3' end of Exon 8 was detected. Our study identified a de novo splicing variant that affects the coding length of DIP2C. This finding provides a new candidate gene for focal infantile epilepsy. Importantly, our finding is the first to associate a single nucleotide variant in DIP2C with focal infantile epilepsy.
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Affiliation(s)
- Le Yang
- Department of Pediatric neurology, Xi'an Children's Hospital, Xi'an, China
| | - Siyu Zhao
- Department of Pediatric neurology, Xi'an Children's Hospital, Xi'an, China
| | - Nan Ma
- Department of Pediatric neurology, Xi'an Children's Hospital, Xi'an, China
| | - Liang Liu
- Department of Pediatric neurology, Xi'an Children's Hospital, Xi'an, China
| | - Dongjing Li
- Department of Pediatric neurology, Xi'an Children's Hospital, Xi'an, China
| | - Xia Li
- Department of Pediatric neurology, Xi'an Children's Hospital, Xi'an, China
| | - Zhijing Wang
- Department of Pediatric neurology, Xi'an Children's Hospital, Xi'an, China
| | - Xixiao Song
- Department of Pediatric neurology, Xi'an Children's Hospital, Xi'an, China
| | - Yan Wang
- Department of Pediatric neurology, Xi'an Children's Hospital, Xi'an, China
| | - Dong Wang
- Department of Pediatric neurology, Xi'an Children's Hospital, Xi'an, China
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27
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Lai E, Danner AL, Famula TR, Oberbauer AM. Genome-Wide Association Studies Reveal Susceptibility Loci for Noninfectious Claw Lesions in Holstein Dairy Cattle. Front Genet 2021; 12:657375. [PMID: 34122511 PMCID: PMC8194352 DOI: 10.3389/fgene.2021.657375] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 04/15/2021] [Indexed: 01/10/2023] Open
Abstract
Sole ulcers (SUs) and white line disease (WLD) are two common noninfectious claw lesions (NICL) that arise due to a compromised horn production and are frequent causes of lameness in dairy cattle, imposing welfare and profitability concerns. Low to moderate heritability estimates of SU and WLD susceptibility indicate that genetic selection could reduce their prevalence. To identify the susceptibility loci for SU, WLD, SU and/or WLD, and any type of noninfectious claw lesion, genome-wide association studies (GWAS) were performed using generalized linear mixed model (GLMM) regression, chunk-based association testing (CBAT), and a random forest (RF) approach. Cows from five commercial dairies in California were classified as controls having no lameness records and ≥6 years old (n = 102) or cases having SU (n = 152), WLD (n = 117), SU and/or WLD (SU + WLD, n = 198), or any type of noninfectious claw lesion (n = 217). The top single nucleotide polymorphisms (SNPs) were defined as those passing the Bonferroni-corrected suggestive and significance thresholds in the GLMM analysis or those that a validated RF model considered important. Effects of the top SNPs were quantified using Bayesian estimation. Linkage disequilibrium (LD) blocks defined by the top SNPs were explored for candidate genes and previously identified, functionally relevant quantitative trait loci. The GLMM and CBAT approaches revealed the same regions of association on BTA8 for SU and BTA13 common to WLD, SU + WLD, and NICL. These SNPs had effects significantly different from zero, and the LD blocks they defined explained a significant amount of phenotypic variance for each dataset (6.1-8.1%, p < 0.05), indicating the small but notable contribution of these regions to susceptibility. These regions contained candidate genes involved in wound healing, skin lesions, bone growth and mineralization, adipose tissue, and keratinization. The LD block defined by the most significant SNP on BTA8 for SU included a SNP previously associated with SU. The RF models were overfitted, indicating that the SNP effects were very small, thereby preventing meaningful interpretation of SNPs and any downstream analyses. These findings suggested that variants associated with various physiological systems may contribute to susceptibility for NICL, demonstrating the complexity of genetic predisposition.
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Affiliation(s)
- Ellen Lai
- Animal Science Department, University of California, Davis, Davis, CA, United States
| | - Alexa L Danner
- Animal Science Department, University of California, Davis, Davis, CA, United States
| | - Thomas R Famula
- Animal Science Department, University of California, Davis, Davis, CA, United States
| | - Anita M Oberbauer
- Animal Science Department, University of California, Davis, Davis, CA, United States
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28
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Kim SJ, Lee SM, Choi JM, Jang JH, Kim HG, Kim JT, Cho JH, Sohn YB. Genetic Analysis Using a Next Generation Sequencing-Based Gene Panel in Patients With Skeletal Dysplasia: A Single-Center Experience. Front Genet 2021; 12:670608. [PMID: 34122524 PMCID: PMC8188553 DOI: 10.3389/fgene.2021.670608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 04/15/2021] [Indexed: 11/13/2022] Open
Abstract
Skeletal dysplasia (SD), a heterogeneous disease group with rare incidence and various clinical manifestations, is associated with multiple causative genes. For clinicians, accurate diagnosis of SD is clinically and genetically difficult. The development of next-generation sequencing (NGS) has substantially aided in the genetic diagnosis of SD. In this study, we conducted a targeted NGS of 437 genes - included in the nosology of SD published in 2019 - in 31 patients with a suspected SD. The clinical and genetic diagnoses were confirmed in 16 out of the 31 patients, and the diagnostic yield was 51.9%. In these patients, 18 pathogenic variants were found in 13 genes (COL2A1, MYH3, COMP, MATN3, CTSK, EBP, CLCN7, COL1A2, EXT1, TGFBR1, SMAD3, FIG4, and ARID1B), of which, four were novel variants. The diagnosis rate was very high in patients with a suspected familial SD and with radiological evidence indicating clinical SD (11 out of 15, 73.3%). In patients with skeletal involvement and other clinical manifestations including dysmorphism or multiple congenital anomalies, and various degrees of developmental delay/intellectual disability, the diagnosis rate was low (5 out of 16, 31.2%) but rare syndromic SD could be diagnosed. In conclusion, NGS-based gene panel sequencing can be helpful in diagnosing SD which has clinical and genetic heterogeneity. To increase the diagnostic yield of suspected SD patients, it is important to categorize patients based on the clinical features, family history, and radiographic evidence.
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Affiliation(s)
- Su Jin Kim
- Department of Pediatrics, Inha University Hospital, Inha University College of Medicine, Incheon, South Korea
| | - Sae-Mi Lee
- GC Genome, GC Labs, Yongin-si, South Korea.,Department of Laboratory Medicine, Kangwon National University School of Medicine, Chuncheon-si, South Korea
| | | | - Ja-Hyun Jang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Seoul, South Korea
| | - Hyun Gi Kim
- Department of Radiology, Eunpyeong St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Jung-Taek Kim
- Department of Orthopedic Surgery, Ajou University Hospital, Ajou University School of Medicine, Suwon-si, South Korea
| | - Jae Ho Cho
- Department of Orthopedic Surgery, Ajou University Hospital, Ajou University School of Medicine, Suwon-si, South Korea
| | - Young Bae Sohn
- Department of Medical Genetics, Ajou University Hospital, Ajou University School of Medicine, Suwon-si, South Korea
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29
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Qian Y, Hu G, Chen M, Liu B, Yan K, Zhou C, Yu Y, Dong M. Novel deep intronic and frameshift mutations causing a TRIP11-related disorder. Am J Med Genet A 2021; 185:2482-2487. [PMID: 34014608 DOI: 10.1002/ajmg.a.62260] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 03/19/2021] [Accepted: 04/24/2021] [Indexed: 11/06/2022]
Abstract
Mutations of the thyroid hormone receptor interactor 11 gene (TRIP11, OMIM: 604505) at 14q32.12 have been associated with the autosomal recessive achondrogenesis type IA (ACG1A, OMIM: 200600) or osteochondrodysplasia (ODCD, OMIM: 184260). In this clinical report of a Chinese family, the mother had two consecutive pregnancies with similar aberrant phenotypes in the fetuses showing severe limb shortening. Whole exome sequencing (WES) of DNA from the second fetus identified a heterozygous frameshift mutation (NM_004239: c.3852delT) of TRIP11. Although this was consistent with the fetal clinical phenotypes, initial review of the WES results implied another novel mutation. To test this, we used high-precision clinical exome sequencing (HPCES) and found a mutation in Intron 18 of TRIP11 (c.5457+77T>G). Moreover, the sequencing depth of this mutation was only 3× that of WES compared with 161× that by HPCES. To ascertain the pathogenesis of the mutation (c.5457+77T>G), RT-PCR conducted using the parents' blood samples showed a 77-bp intronic sequence in the transcripts, which might have encoded for a shortened protein because of early termination due to code shifting. Our study furthers current understanding of deep intron function and provides a novel diagnostic method of deep intragenic mutations in families having two or more consecutive pregnancies with similar aberrant fetal phenotypes.
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Affiliation(s)
- Yeqing Qian
- Women's Hospital, School of Medicine, Zhejiang University, Zhejiang, China.,Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, 1, Xueshi Road, Zhejiang, China
| | - Gang Hu
- Women's Hospital, School of Medicine, Zhejiang University, Zhejiang, China.,Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, 1, Xueshi Road, Zhejiang, China
| | - Min Chen
- Women's Hospital, School of Medicine, Zhejiang University, Zhejiang, China.,Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, 1, Xueshi Road, Zhejiang, China
| | - Bei Liu
- Women's Hospital, School of Medicine, Zhejiang University, Zhejiang, China.,Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, 1, Xueshi Road, Zhejiang, China
| | - Kai Yan
- Women's Hospital, School of Medicine, Zhejiang University, Zhejiang, China.,Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, 1, Xueshi Road, Zhejiang, China
| | - Caiyun Zhou
- Women's Hospital, School of Medicine, Zhejiang University, Zhejiang, China
| | - Yanqin Yu
- Women's Hospital, School of Medicine, Zhejiang University, Zhejiang, China
| | - Minyue Dong
- Women's Hospital, School of Medicine, Zhejiang University, Zhejiang, China.,Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, 1, Xueshi Road, Zhejiang, China
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30
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Mushiba AM, Faqeih E, Saleh MA, Ramzan K, Imtiaz F, Al-Owain M, Alhashem AM, Alswaid A. The genotypic and phenotypic spectrum of pycnodysostosis in Saudi Arabia: Novel variants and clinical findings. Am J Med Genet A 2021; 185:2455-2463. [PMID: 33963797 DOI: 10.1002/ajmg.a.62230] [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: 11/03/2020] [Revised: 02/14/2021] [Accepted: 03/28/2021] [Indexed: 11/10/2022]
Abstract
Pycnodysostosis is characterized by short stature, osteosclerosis, acro-osteolysis, increased tendency of fractures, and distinctive dysmorphic features. It is a rare autosomal recessive disease caused by biallelic CTSK mutations. The clinical details of 18 patients from Saudi Arabia were reviewed. Short stature, osteopetrosis, acro-osteolysis, and distinctive facial dysmorphism were documented in all cases. Our results highlight the significant complications associated with this disease. The large anterior fontanelle is one of the cardinal signs of this disease; however, half of our patients had small fontanelles and a quarter had craniosynostosis, which caused optic nerve compression. Sleep apnea was of the major complications in three patients. Bone fracture can be a presenting symptom, and in our patients it mainly occurred after the age of 3 years. Bone marrow suppression was seen in a single patient of our cohort who was misdiagnosed initially with malignant osteopetrosis. In this study, we also describe two novel (c.5G > A [p.Trp2Ter], c.538G > A [p.Gly180Ser]) and two reported (c.244-29 A > G, c.830C > T [p.Ala277Val]) CTSK mutations. Our results indicate that the recurrent intronic variant, c.244-29 A > G is likely to be a founder mutation, as it was found in 78% (14/18 patients) of our cohort belonging to the same tribe.
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Affiliation(s)
- Aziza M Mushiba
- Section of Medical Genetics, Department of Pediatrics, Children's Specialist Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Eissa Faqeih
- Section of Medical Genetics, Department of Pediatrics, Children's Specialist Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Mohammed A Saleh
- Section of Medical Genetics, Department of Pediatrics, Children's Specialist Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Khushnooda Ramzan
- Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Faiqa Imtiaz
- Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Mohammed Al-Owain
- Department of Medical Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia.,College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Amal M Alhashem
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia.,Division of Genetics, Department of Pediatrics Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Abdulrahman Alswaid
- Division of Genetics, Department of Pediatrics, King Abdulaziz Medical City, Riyadh, Saudi Arabia
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31
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Hildebrandt CC, Patel N, Graham JM, Bamshad M, Nickerson DA, White JJ, Marvin CT, Miller DE, Grand KL, Sanchez-Lara PA, Schweitzer D, Al-Zaidan HI, Al Masseri Z, Alkuraya FS, Lin AE. Further delineation of van den Ende-Gupta syndrome: Genetic heterogeneity and overlap with congenital heart defects and skeletal malformations syndrome. Am J Med Genet A 2021; 185:2136-2149. [PMID: 33783941 DOI: 10.1002/ajmg.a.62194] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/18/2021] [Accepted: 02/27/2021] [Indexed: 12/29/2022]
Abstract
Van den Ende-Gupta syndrome (VDEGS) is a rare autosomal recessive condition characterized by distinctive facial and skeletal features, and in most affected persons, by biallelic pathogenic variants in SCARF2. We review the type and frequency of the clinical features in 36 reported individuals with features of VDEGS, 15 (42%) of whom had known pathogenic variants in SCARF2, 6 (16%) with negative SCARF2 testing, and 15 (42%) not tested. We also report three new individuals with pathogenic variants in SCARF2 and clinical features of VDEGS. Of the six persons without known pathogenic variants in SCARF2, three remain unsolved despite extensive genetic testing. Three were found to have pathogenic ABL1 variants using whole exome sequencing (WES) or whole genome sequencing (WGS). Their phenotype was consistent with the congenital heart disease and skeletal malformations syndrome (CHDSKM), which has been associated with ABL1 variants. Of the three unsolved cases, two were brothers who underwent WGS and targeted long-range sequencing of both SCARF2 and ABL1, and the third person who underwent WES and RNA sequencing for SCARF2. Because these affected individuals with classical features of VDEGS lacked a detectable pathogenic SCARF2 variant, genetic heterogeneity is likely. Our study shows the importance of performing genetic testing on individuals with the VDEGS "phenotype," either as a targeted gene analysis (SCARF2, ABL1) or WES/WGS. Additionally, individuals with the combination of arachnodactyly and blepharophimosis should undergo echocardiography while awaiting results of molecular testing due to the overlapping physical features of VDEGS and CHDSKM.
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Affiliation(s)
- Clara C Hildebrandt
- Genetics Unit, MassGeneral Hospital for Children, Massachusetts, USA.,Boston Children's Hospital Medical Biochemical Fellowship, Boston, Massachusetts, USA
| | - Nisha Patel
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - John M Graham
- Medical Genetics, Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, California, USA.,Department of Pediatrics, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, California, USA
| | - Michael Bamshad
- Division of Genetic Medicine, Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA.,Department of Genome Sciences, University of Washington, Seattle, Washington, USA.,Brotman Baty Institute, Seattle, Washington, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA.,Brotman Baty Institute, Seattle, Washington, USA
| | | | - Colby T Marvin
- Division of Genetic Medicine, Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
| | - Danny E Miller
- Division of Genetic Medicine, Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA.,Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | | | - Katheryn L Grand
- Medical Genetics, Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Pedro A Sanchez-Lara
- Medical Genetics, Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, California, USA.,Department of Pediatrics, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, California, USA
| | - Daniela Schweitzer
- Division of Pediatric Genetics, Department of Pediatrics, University of California Los Angeles, Los Angeles, California, USA
| | - Hamad I Al-Zaidan
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Zainab Al Masseri
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Angela E Lin
- Genetics Unit, MassGeneral Hospital for Children, Massachusetts, USA
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32
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Alharbi S, Alhashem A, Alkuraya F, Kashlan F, Tlili-Graiess K. Neuroimaging manifestations and genetic heterogeneity of Walker-Warburg syndrome in Saudi patients. Brain Dev 2021; 43:380-388. [PMID: 33199158 DOI: 10.1016/j.braindev.2020.10.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 10/08/2020] [Accepted: 10/25/2020] [Indexed: 12/19/2022]
Abstract
BACKGROUND Walker-Warburg syndrome (WWS), an autosomal recessive disease, is the most severe phenotype of congenital muscular dystrophies. Its diagnosis remains primarily clinical and radiological. Identification of its causative variants will assist genetic counseling. We aim to describe genetic and neuroimaging findings of WWS and investigate the correlation between them. METHODS We retrospectively reviewed the clinical, genetic and neuroimaging findings of eleven Saudi neonates diagnosed with WWS between April 2012 and December 2018 in a single tertiary care center. Correlation between neuroimaging and genetic findings was investigated. RESULTS All patients had macrocephaly except one who had intrauterine growth restriction. Dysmorphic features were identified in nearly half of the patients. Creatine kinase levels were available in nine patients and were always elevated. Homozygous pathogenic variants were identified in all patients spanning POMT1 (n = 5), TMEM5 (n = 3), ISPD (n = 2) and POMT2 (n = 1) including one patient who had a dual molecular diagnosis of ISPD and PGAP2. On neuroimaging, all patients showed cobblestone cortex, classical infratentorial findings, and hydrocephalus. Other cerebral cortical malformations included subependymal heterotopia, polymicrogyria and open-lip schizencephaly in four, two and one patients, respectively. Buphthalmos and microphthalmia were the most prevalent orbital findings and found in all patients either unilaterally or bilaterally. CONCLUSION WWS is a genetically heterogeneous disorder among Saudis. The case with an additional PGAP2-related phenotype exemplifies the increased risk of dual autosomal recessive disorders in consanguineous populations. MRI is excellent in demonstrating spectrum of WWS brain and orbital malformations; however, no definite correlation could be found between the MRI findings and the genetic variant.
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Affiliation(s)
- Sara Alharbi
- Neuroradiology Section, Department of Radiology, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Amal Alhashem
- Division of Genetics, Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia; Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Fowzan Alkuraya
- Division of Genetics, Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia; Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia; Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Fawaz Kashlan
- Division of Neonatology, Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Kalthoum Tlili-Graiess
- Neuroradiology Section, Department of Radiology, Prince Sultan Military Medical City, Riyadh, Saudi Arabia.
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33
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Unlu G, Qi X, Gamazon ER, Melville DB, Patel N, Rushing AR, Hashem M, Al-Faifi A, Chen R, Li B, Cox NJ, Alkuraya FS, Knapik EW. Phenome-based approach identifies RIC1-linked Mendelian syndrome through zebrafish models, biobank associations and clinical studies. Nat Med 2020; 26:98-109. [PMID: 31932796 PMCID: PMC7147997 DOI: 10.1038/s41591-019-0705-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 11/15/2019] [Indexed: 12/17/2022]
Abstract
Discovery of genotype-phenotype relationships remains a major challenge in clinical medicine. Here, we combined three sources of phenotypic data to uncover a novel mechanism for rare and common diseases resulting from collagen secretion deficits. Using zebrafish genetic screen, we identified the ric1 gene to be essential for skeletal biology. Using a gene-based phenome-wide association study (PheWAS) in the EHR-linked BioVU biobank, we show that reduced genetically determined expression of RIC1 is associated with musculoskeletal and dental conditions. Whole exome sequencing (WES) identified individuals homozygous-by-descent for a rare variant in RIC1, and, through a guided clinical re-evaluation, they were discovered to share signs with the BioVU-associated phenome. We named this novel Mendelian syndrome CATIFA (Cleft lip, cAtaract, Tooth abnormality, Intellectual disability, Facial dysmorphism, ADHD), and revealed further disease mechanisms. This gene-based PheWAS-guided approach can accelerate the discovery of clinically relevant disease phenome and associated biological mechanisms.
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Affiliation(s)
- Gokhan Unlu
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA.,Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Xinzi Qi
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Eric R Gamazon
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA.,Clare Hall, University of Cambridge, Cambridge, UK
| | - David B Melville
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Nisha Patel
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Amy R Rushing
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Mais Hashem
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Abdullah Al-Faifi
- Department of Pediatrics, Security Forces Hospital, Riyadh, Saudi Arabia
| | - Rui Chen
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Bingshan Li
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Nancy J Cox
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ela W Knapik
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA. .,Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA. .,Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA.
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Kosho T, Mizumoto S, Watanabe T, Yoshizawa T, Miyake N, Yamada S. Recent Advances in the Pathophysiology of Musculocontractural Ehlers-Danlos Syndrome. Genes (Basel) 2019; 11:genes11010043. [PMID: 31905796 PMCID: PMC7017038 DOI: 10.3390/genes11010043] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 12/22/2019] [Accepted: 12/23/2019] [Indexed: 12/18/2022] Open
Abstract
Musculocontractural Ehlers–Danlos Syndome (mcEDS) is a type of EDS caused by biallelic pathogenic variants in the gene for carbohydrate sulfotransferase 14/dermatan 4-O-sulfotransferase 1 (CHST14/D4ST1, mcEDS-CHST14), or in the gene for dermatan sulfate epimerase (DSE, mcEDS-DSE). Thus far, 41 patients from 28 families with mcEDS-CHST14 and five patients from four families with mcEDS-DSE have been described in the literature. Clinical features comprise multisystem congenital malformations and progressive connective tissue fragility-related manifestations. This review outlines recent advances in understanding the pathophysiology of mcEDS. Pathogenic variants in CHST14 or DSE lead to reduced activities of relevant enzymes, resulting in a negligible amount of dermatan sulfate (DS) and an excessive amount of chondroitin sulfate. Connective tissue fragility is presumably attributable to a compositional change in the glycosaminoglycan chains of decorin, a major DS-proteoglycan in the skin that contributes to collagen fibril assembly. Collagen fibrils in affected skin are dispersed in the papillary to reticular dermis, whereas those in normal skin are regularly and tightly assembled. Glycosaminoglycan chains are linear in affected skin, stretching from the outer surface of collagen fibrils to adjacent fibrils; glycosaminoglycan chains are curved in normal skin, maintaining close contact with attached collagen fibrils. Homozygous (Chst14−/−) mice have been shown perinatal lethality, shorter fetal length and vessel-related placental abnormalities. Milder phenotypes in mcEDS-DSE might be related to a smaller fraction of decorin DS, potentially through residual DSE activity or compensation by DSE2 activity. These findings suggest critical roles of DS and DS-proteoglycans in the multisystem development and maintenance of connective tissues, and provide fundamental evidence to support future etiology-based therapies.
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Affiliation(s)
- Tomoki Kosho
- Department of Medical Genetics, Shinshu University School of Medicine, Matsumoto 390-8621, Japan
- Center for Medical Genetics, Shinshu University Hospital, Matsumoto 390-8621, Japan
- Research Center for Supports to Advanced Science, Matsumoto 390-8621, Japan
- Correspondence: ; Tel.: +81-263-37-2618; Fax: +81-263-37-2619
| | - Shuji Mizumoto
- Department of Pathobiochemistry, Faculty of Pharmacy, Meijo University, Nagoya 468-8503, Japan; (S.M.); (S.Y.)
| | - Takafumi Watanabe
- Laboratory of Anatomy, School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu 069-8501, Japan;
| | - Takahiro Yoshizawa
- Division of Animal Research, Research Center for Supports to Advanced Science, Shinshu University, Matsumoto 390-8621, Japan;
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan;
| | - Shuhei Yamada
- Department of Pathobiochemistry, Faculty of Pharmacy, Meijo University, Nagoya 468-8503, Japan; (S.M.); (S.Y.)
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Innes AM, McInnes BL, Dyment DA. Clinical and genetic heterogeneity in Dubowitz syndrome: Implications for diagnosis, management and further research. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2019; 178:387-397. [PMID: 30580484 DOI: 10.1002/ajmg.c.31661] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 10/14/2018] [Accepted: 10/27/2018] [Indexed: 12/12/2022]
Abstract
Dubowitz syndrome was described in 1965 as a recognizable syndrome characterized by microcephaly, short stature, eczema, mild developmental delays, and an increased risk of malignancy. Since its original description, there have been over 200 reported cases though no single gene has been identified to explain a significant proportion of affected individuals. Since the last definitive review of Dubowitz syndrome in 1996, there have been 63 individuals with a clinical, or suspected, diagnosis of Dubowitz syndrome reported in 51 publications. These individuals show a markedly wide spectrum with respect to growth, facial gestalt, psychomotor development, and risk of malignancy; genetic causes were identified in 33% (21/63). Seven individuals had deleterious copy number variants, in particular deletions at 14q32 and 17q24 were reported and showed overlap with the Dubowitz phenotype. Several cases were shown to have single gene disorders that included de novo or biallelic pathogenic variants in several genes including NSUN2 and LIG4 frequently identified by next-generation sequencing methods. It appears that the inability to identify a single gene responsible for Dubowitz syndrome reflects its extreme clinical and genetic heterogeneity. However, detailed phenotyping combined with careful grouping of subsets of unsolved cases and in conjunction with data-sharing will identify novel disease genes responsible for additional cases. In the interim, for those clinically diagnosed with a Dubowitz phenotype, we recommend assessment by a Medical Geneticist, a microarray and, if available, clinical or research based genome-wide sequencing. Management suggestions, including decisions regarding malignancy screening in select patients will be discussed.
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Affiliation(s)
- A Micheil Innes
- Department of Medical Genetics, University of Calgary, Calgary, Alberta, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
| | - Brenda L McInnes
- Department of Medical Genetics, University of Calgary, Calgary, Alberta, Canada
| | - David A Dyment
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada.,Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
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Temtamy SA. The Development of Human Genetics at the National Research Centre, Cairo, Egypt: A Story of 50 Years. Annu Rev Genomics Hum Genet 2019; 20:1-19. [PMID: 30848958 DOI: 10.1146/annurev-genom-083118-015201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This article describes my experiences over more than 50 years in initiating and maintaining research on human genetics and genomics at the National Research Centre in Cairo, Egypt, from its beginnings in a small unit of human genetics to the creation of the Center of Excellence for Human Genetics. This was also the subject of a lecture I gave at the 10th Conference of the African Society of Human Genetics, held in Cairo in November 2017, after which Professor Michèle Ramsay, president of the society, suggested that I write an autobiographical article for the Annual Review of Genomics and Human Genetics. I hope that I succeeded in the difficult assignment of summarizing the efforts of a researcher from a developing country to initiate and maintain the rapidly advancing science of human genetics and genomics in my own country and make contributions to the worldwide scientific community.
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Affiliation(s)
- Samia A Temtamy
- Center of Excellence for Human Genetics, National Research Centre, Cairo 12622, Egypt;
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Yue C, Liang C, Ge H, Yan L, Xu Y, Li G, Wu J. SUCO as a Promising Diagnostic Biomarker of Hepatocellular Carcinoma: Integrated Analysis and Experimental Validation. Med Sci Monit 2019; 25:6292-6303. [PMID: 31434866 PMCID: PMC6716297 DOI: 10.12659/msm.915262] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC) is not frequently diagnosed until the late stage due to its concealed symptoms. Therefore, the identification of biomarkers that have effective diagnostic performance and act as potential key therapeutic targets for HCC becomes urgent. Material/Methods Comprehensive analysis of accumulated data downloaded from the Gene Expression Omnibus (GEO) and the Cancer Genome Atlas (TCGA) databases was used to obtain more reliable potential diagnostic biomarkers of HCC and to explore related molecular mechanisms. Meta-analysis and summary receiver operating characteristic (SROC) curve analysis were performed to evaluate the differential expression of SUCO gene in HCC and identify the capability of SUCO in distinguishing HCC-tissues from normal liver-tissues. Results SUCO was found to be upregulated in HCC-tissues and exhibited a favorable value in diagnosing HCC. Bioinformatics analysis showed that SUCO might play important roles in HCC progression, and was significantly related to cell cycle, cell metabolism, and proliferation. Conclusions This study was the first to demonstrate that SUCO was overexpressed in HCC-tissues, and that high expression of SUCO was significantly related to poor overall survival in HCC patients. SUCO might be a potential diagnostic biomarker for HCC patients, which promotes the tumorigenesis and progression of HCC.
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Affiliation(s)
- Chaosen Yue
- Department of General Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China (mainland)
| | - Chaojie Liang
- Department of General Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China (mainland)
| | - Hua Ge
- Department of General Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China (mainland)
| | - Lijun Yan
- Department of General Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China (mainland)
| | - Yingchen Xu
- Department of General Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China (mainland)
| | - Guangming Li
- Department of General Surgery, Beijing Tongren Hospital, Capital Medical University,, Beijing, China (mainland)
| | - Jixiang Wu
- Department of General Surgery, Beijing Tongren Hospital, Capital Medical University,, Beijing, China (mainland)
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38
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Murakami Y, Nguyen TTM, Baratang N, Raju PK, Knaus A, Ellard S, Jones G, Lace B, Rousseau J, Ajeawung NF, Kamei A, Minase G, Akasaka M, Araya N, Koshimizu E, van den Ende J, Erger F, Altmüller J, Krumina Z, Strautmanis J, Inashkina I, Stavusis J, El-Gharbawy A, Sebastian J, Puri RD, Kulshrestha S, Verma IC, Maier EM, Haack TB, Israni A, Baptista J, Gunning A, Rosenfeld JA, Liu P, Joosten M, Rocha ME, Hashem MO, Aldhalaan HM, Alkuraya FS, Miyatake S, Matsumoto N, Krawitz PM, Rossignol E, Kinoshita T, Campeau PM. Mutations in PIGB Cause an Inherited GPI Biosynthesis Defect with an Axonal Neuropathy and Metabolic Abnormality in Severe Cases. Am J Hum Genet 2019; 105:384-394. [PMID: 31256876 PMCID: PMC6698938 DOI: 10.1016/j.ajhg.2019.05.019] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 05/28/2019] [Indexed: 11/15/2022] Open
Abstract
Proteins anchored to the cell surface via glycosylphosphatidylinositol (GPI) play various key roles in the human body, particularly in development and neurogenesis. As such, many developmental disorders are caused by mutations in genes involved in the GPI biosynthesis and remodeling pathway. We describe ten unrelated families with bi-allelic mutations in PIGB, a gene that encodes phosphatidylinositol glycan class B, which transfers the third mannose to the GPI. Ten different PIGB variants were found in these individuals. Flow cytometric analysis of blood cells and fibroblasts from the affected individuals showed decreased cell surface presence of GPI-anchored proteins. Most of the affected individuals have global developmental and/or intellectual delay, all had seizures, two had polymicrogyria, and four had a peripheral neuropathy. Eight children passed away before four years old. Two of them had a clinical diagnosis of DOORS syndrome (deafness, onychodystrophy, osteodystrophy, mental retardation, and seizures), a condition that includes sensorineural deafness, shortened terminal phalanges with small finger and toenails, intellectual disability, and seizures; this condition overlaps with the severe phenotypes associated with inherited GPI deficiency. Most individuals tested showed elevated alkaline phosphatase, which is a characteristic of the inherited GPI deficiency but not DOORS syndrome. It is notable that two severely affected individuals showed 2-oxoglutaric aciduria, which can be seen in DOORS syndrome, suggesting that severe cases of inherited GPI deficiency and DOORS syndrome might share some molecular pathway disruptions.
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Affiliation(s)
- Yoshiko Murakami
- Yabumoto Department of Intractable Disease Research, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Thi Tuyet Mai Nguyen
- Centre Hospitalier Universitaire Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada
| | - Nissan Baratang
- Centre Hospitalier Universitaire Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada
| | - Praveen K Raju
- Centre Hospitalier Universitaire Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada
| | - Alexej Knaus
- Insitute for Genomic Statistics and Bioinformatics, University Hospital Bonn, 53127 Bonn, Germany
| | - Sian Ellard
- Royal Devon and Exeter NHS Foundation Trust, Exeter EX2 5DW, UK
| | - Gabriela Jones
- Clinical Genetics Department, Nottingham University Hospitals NHS Trust, Nottingham NGS 1PB, UK
| | - Baiba Lace
- Centre Hospitalier Universitaire de Québec, 2705 Boulevard Laurier, Ville de Québec, QC G1V 4G2, Canada
| | - Justine Rousseau
- Centre Hospitalier Universitaire Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada
| | - Norbert Fonya Ajeawung
- Centre Hospitalier Universitaire Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada
| | - Atsushi Kamei
- Department of Pediatrics, School of Medicine, Iwate Medical University, Morioka, Iwate 020-8505, Japan
| | - Gaku Minase
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
| | - Manami Akasaka
- Department of Pediatrics, School of Medicine, Iwate Medical University, Morioka, Iwate 020-8505, Japan
| | - Nami Araya
- Department of Pediatrics, School of Medicine, Iwate Medical University, Morioka, Iwate 020-8505, Japan
| | - Eriko Koshimizu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
| | | | - Florian Erger
- Institute of Human Genetics, University Hospital of Cologne, and Center for Molecular Medicine, University of Cologne, 50931 Cologne, Germany
| | - Janine Altmüller
- Cologne Center for Genomics, University of Cologne, 50931 Cologne, Germany
| | - Zita Krumina
- Deparment of Biology and Microbiology, Riga Stradinš University, Riga, LV-1029, Latvia
| | | | - Inna Inashkina
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1 k-1, Riga LV-1067, Latvia
| | - Janis Stavusis
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1 k-1, Riga LV-1067, Latvia
| | - Areeg El-Gharbawy
- Department of Medical Genetics, Children's Hospital of Pittsburgh of University Pittsburgh Medical Center, Pittsburgh, PA 15224, USA
| | - Jessica Sebastian
- Department of Medical Genetics, Children's Hospital of Pittsburgh of University Pittsburgh Medical Center, Pittsburgh, PA 15224, USA
| | - Ratna Dua Puri
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi 110060, India
| | - Samarth Kulshrestha
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi 110060, India
| | - Ishwar C Verma
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi 110060, India
| | - Esther M Maier
- Department of Inborn Errors of Metabolism, Dr. von Hauner Children's Hospital, 80337 Munich, Germany
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72074 Tübingen, Germany; Institute of Human Genetics, Technische Universität München, 81675 Munich, Germany
| | - Anil Israni
- Department of Paediatric Neurology, Leicester Royal Infirmary, Leicester LE1 5WW, UK
| | - Julia Baptista
- Royal Devon and Exeter NHS Foundation Trust, Exeter EX2 5DW, UK
| | - Adam Gunning
- Royal Devon and Exeter NHS Foundation Trust, Exeter EX2 5DW, UK
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Marieke Joosten
- Dept of Clinical Genetics, Erasmus MC, PO Box 2040, 3000 CA Rotterdam, the Netherlands
| | | | - Mais O Hashem
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Hesham M Aldhalaan
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
| | - Peter M Krawitz
- Insitute for Genomic Statistics and Bioinformatics, University Hospital Bonn, 53127 Bonn, Germany
| | - Elsa Rossignol
- Centre Hospitalier Universitaire Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada; Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia; Department of Neurosciences, Centre Hospitalier Universitaire Sainte-Justine and University of Montreal, Montreal, QC H3T 1C5, Canada
| | - Taroh Kinoshita
- Yabumoto Department of Intractable Disease Research, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan.
| | - Philippe M Campeau
- Centre Hospitalier Universitaire Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada; Department of Pediatrics, Centre Hospitalier Universitaire Sainte-Justine and University of Montreal, Montreal, QC H3T 1C5, Canada.
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39
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An emerging ribosomopathy affecting the skeleton due to biallelic variations in NEPRO. Am J Med Genet A 2019; 179:1709-1717. [DOI: 10.1002/ajmg.a.61267] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 06/05/2019] [Accepted: 06/05/2019] [Indexed: 01/02/2023]
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40
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Monies D, Abouelhoda M, Assoum M, Moghrabi N, Rafiullah R, Almontashiri N, Alowain M, Alzaidan H, Alsayed M, Subhani S, Cupler E, Faden M, Alhashem A, Qari A, Chedrawi A, Aldhalaan H, Kurdi W, Khan S, Rahbeeni Z, Alotaibi M, Goljan E, Elbardisy H, ElKalioby M, Shah Z, Alruwaili H, Jaafar A, Albar R, Akilan A, Tayeb H, Tahir A, Fawzy M, Nasr M, Makki S, Alfaifi A, Akleh H, Yamani S, Bubshait D, Mahnashi M, Basha T, Alsagheir A, Abu Khaled M, Alsaleem K, Almugbel M, Badawi M, Bashiri F, Bohlega S, Sulaiman R, Tous E, Ahmed S, Algoufi T, Al-Mousa H, Alaki E, Alhumaidi S, Alghamdi H, Alghamdi M, Sahly A, Nahrir S, Al-Ahmari A, Alkuraya H, Almehaidib A, Abanemai M, Alsohaibaini F, Alsaud B, Arnaout R, Abdel-Salam GMH, Aldhekri H, AlKhater S, Alqadi K, Alsabban E, Alshareef T, Awartani K, Banjar H, Alsahan N, Abosoudah I, Alashwal A, Aldekhail W, Alhajjar S, Al-Mayouf S, Alsemari A, Alshuaibi W, Altala S, Altalhi A, Baz S, Hamad M, Abalkhail T, Alenazi B, Alkaff A, Almohareb F, Al Mutairi F, Alsaleh M, Alsonbul A, Alzelaye S, Bahzad S, Manee AB, Jarrad O, Meriki N, Albeirouti B, Alqasmi A, AlBalwi M, Makhseed N, Hassan S, Salih I, Salih MA, Shaheen M, Sermin S, Shahrukh S, Hashmi S, Shawli A, Tajuddin A, Tamim A, Alnahari A, Ghemlas I, Hussein M, Wali S, Murad H, Meyer BF, Alkuraya FS. Lessons Learned from Large-Scale, First-Tier Clinical Exome Sequencing in a Highly Consanguineous Population. Am J Hum Genet 2019; 104:1182-1201. [PMID: 31130284 DOI: 10.1016/j.ajhg.2019.04.011] [Citation(s) in RCA: 159] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 04/11/2019] [Indexed: 12/16/2022] Open
Abstract
We report the results of clinical exome sequencing (CES) on >2,200 previously unpublished Saudi families as a first-tier test. The predominance of autosomal-recessive causes allowed us to make several key observations. We highlight 155 genes that we propose to be recessive, disease-related candidates. We report additional mutational events in 64 previously reported candidates (40 recessive), and these events support their candidacy. We report recessive forms of genes that were previously associated only with dominant disorders and that have phenotypes ranging from consistent with to conspicuously distinct from the known dominant phenotypes. We also report homozygous loss-of-function events that can inform the genetics of complex diseases. We were also able to deduce the likely causal variant in most couples who presented after the loss of one or more children, but we lack samples from those children. Although a similar pattern of mostly recessive causes was observed in the prenatal setting, the higher proportion of loss-of-function events in these cases was notable. The allelic series presented by the wealth of recessive variants greatly expanded the phenotypic expression of the respective genes. We also make important observations about dominant disorders; these observations include the pattern of de novo variants, the identification of 74 candidate dominant, disease-related genes, and the potential confirmation of 21 previously reported candidates. Finally, we describe the influence of a predominantly autosomal-recessive landscape on the clinical utility of rapid sequencing (Flash Exome). Our cohort's genotypic and phenotypic data represent a unique resource that can contribute to improved variant interpretation through data sharing.
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Affiliation(s)
- Dorota Monies
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh 12354, Saudi Arabia; Saudi Diagnostic Laboratories, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Mohammed Abouelhoda
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh 12354, Saudi Arabia; Saudi Diagnostic Laboratories, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Mirna Assoum
- Saudi Diagnostic Laboratories, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Nabil Moghrabi
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh 12354, Saudi Arabia; Saudi Diagnostic Laboratories, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Rafiullah Rafiullah
- Saudi Diagnostic Laboratories, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Naif Almontashiri
- Clinical Molecular and Biochemical Genetics, Taibah University, Madinah 42353, Saudi Arabia
| | - Mohammed Alowain
- Department of Medical Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Hamad Alzaidan
- Department of Medical Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Moeen Alsayed
- Department of Medical Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Shazia Subhani
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh 12354, Saudi Arabia; Saudi Diagnostic Laboratories, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Edward Cupler
- Neurosciences Department, King Faisal Specialist Hospital and Research Centre, Jeddah 23433, Saudi Arabia
| | - Maha Faden
- Genetics and Metabolism, King Saud Medical Complex, Riyadh 12746, Saudi Arabia
| | - Amal Alhashem
- Pediatrics Department, Prince Sultan Military Medical Complex, Riyadh 12233, Saudi Arabia
| | - Alya Qari
- Department of Medical Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Aziza Chedrawi
- Neurosciences Department, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Hisham Aldhalaan
- Neurosciences Department, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Wesam Kurdi
- Obstetrics and Gynecology Department, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Sameena Khan
- Neurosciences Department, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Zuhair Rahbeeni
- Department of Medical Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Maha Alotaibi
- Genetics and Metabolism, King Saud Medical Complex, Riyadh 12746, Saudi Arabia
| | - Ewa Goljan
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh 12354, Saudi Arabia; Saudi Diagnostic Laboratories, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Hadeel Elbardisy
- Saudi Diagnostic Laboratories, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Mohamed ElKalioby
- Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh 12354, Saudi Arabia; Saudi Diagnostic Laboratories, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Zeeshan Shah
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh 12354, Saudi Arabia; Saudi Diagnostic Laboratories, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Hibah Alruwaili
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh 12354, Saudi Arabia; Saudi Diagnostic Laboratories, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Amal Jaafar
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh 12354, Saudi Arabia; Saudi Diagnostic Laboratories, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Ranad Albar
- Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh 12354, Saudi Arabia
| | - Asma Akilan
- Saudi Diagnostic Laboratories, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Hamsa Tayeb
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh 12354, Saudi Arabia; Saudi Diagnostic Laboratories, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Asma Tahir
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh 12354, Saudi Arabia; Saudi Diagnostic Laboratories, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Mohammed Fawzy
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh 12354, Saudi Arabia; Saudi Diagnostic Laboratories, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Mohammed Nasr
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh 12354, Saudi Arabia; Saudi Diagnostic Laboratories, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Shaza Makki
- Saudi Diagnostic Laboratories, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Abdullah Alfaifi
- Pediatrics Department, Security Forces Hospital, Riyadh 11481, Saudi Arabia
| | - Hanna Akleh
- Academic and Training Affairs, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Suad Yamani
- Neurosciences Department, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Dalal Bubshait
- Pediatrics Department, King Fahad Hospital of the University, Al-Khobar 31952, Saudi Arabia
| | - Mohammed Mahnashi
- Genetics and Medicine, King Fahd Central Hospital, Gizan 82666, Saudi Arabia
| | - Talal Basha
- Pediatrics Department, King Faisal Specialist Hospital and Research Centre, Jeddah 23433, Saudi Arabia
| | - Afaf Alsagheir
- Pediatrics Department, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Musad Abu Khaled
- Neurosciences Department, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Khalid Alsaleem
- Pediatrics Department, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Maisoon Almugbel
- Obstetrics and Gynecology Department, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Manal Badawi
- Neurosciences Department, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Fahad Bashiri
- Department of Pediatrics, College of Medicine and King Khalid University Hospital, King Saud University, Riyadh 11461, Saudi Arabia
| | - Saeed Bohlega
- Neurosciences Department, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Raashida Sulaiman
- Department of Medical Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Ehab Tous
- Neurosciences Department, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Syed Ahmed
- Pediatric Hematology and Oncology, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Talal Algoufi
- Pediatric Hematology and Oncology, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Hamoud Al-Mousa
- Allergy - Immunology, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Emadia Alaki
- Allergy - Immunology, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Susan Alhumaidi
- Pediatrics Department, King Saud Medical City, Riyadh 12746, Saudi Arabia
| | - Hadeel Alghamdi
- Pediatrics Department, King Faisal Specialist Hospital and Research Centre, Jeddah 23433, Saudi Arabia
| | - Malak Alghamdi
- Pediatrics Department, King Saud Medical City, Riyadh 12746, Saudi Arabia
| | - Ahmed Sahly
- Pediatrics Department, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Shapar Nahrir
- Pediatrics Department, King Saud Medical City, Riyadh 12746, Saudi Arabia
| | - Ali Al-Ahmari
- Pediatric Hematology and Oncology, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
| | - Hisham Alkuraya
- Vitreoretinal Surgery, Specialized Medical Centre, Riyadh 11564, Saudi Arabia
| | - Ali Almehaidib
- Gastroenterology, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Mohammed Abanemai
- Gastroenterology, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Fahad Alsohaibaini
- Gastroenterology, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Bandar Alsaud
- Allergy - Immunology, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Rand Arnaout
- Allergy - Immunology, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | | | - Hasan Aldhekri
- Pediatrics Department, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Suzan AlKhater
- Pediatrics Department, King Fahad Hospital of the University, Al-Khobar 31952, Saudi Arabia; Department of Pediatrics, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 34221, Saudi Arabia
| | - Khalid Alqadi
- Neurosciences Department, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Essam Alsabban
- Pediatrics Department, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Turki Alshareef
- Pediatric Nephrology, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Khalid Awartani
- Obstetrics and Gynecology Department, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Hanaa Banjar
- Pediatric Pulmonology, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Nada Alsahan
- Obstetrics and Gynecology Department, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Ibraheem Abosoudah
- Pediatric Hematology and Oncology, King Faisal Specialist Hospital and Research Centre, Jeddah 23433, Saudi Arabia
| | - Abdullah Alashwal
- Pediatric Endocrine and Metabolism, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Wajeeh Aldekhail
- Gastroenterology, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Sami Alhajjar
- Pediatric Infectious Diseases, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Sulaiman Al-Mayouf
- Pediatrics Department, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Abdulaziz Alsemari
- Neurosciences Department, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Walaa Alshuaibi
- Pediatrics Department, King Khalid University Hospital, Riyadh 12372, Saudi Arabia
| | - Saeed Altala
- Pediatrics Department, Armed Forces Hospital, Khamis Mushait 62451, Saudi Arabia
| | - Abdulhadi Altalhi
- Pediatric Nephrology, King Saud Medical City, Riyadh 12746, Saudi Arabia
| | - Salah Baz
- Neurosciences Department, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Muddathir Hamad
- Pediatrics Department, King Khalid University Hospital, Riyadh 12372, Saudi Arabia
| | - Tariq Abalkhail
- Neurosciences Department, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Badi Alenazi
- Pediatrics Department, Alyamama Hospital, Riyadh 14222, Saudi Arabia
| | - Alya Alkaff
- Obstetrics and Gynecology Department, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Fahad Almohareb
- Oncology Center, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Fuad Al Mutairi
- King Abdullah International Medical Research Centre, King Saud Bin Abdulaziz University for Health Sciences, Riyadh 11564, Saudi Arabia; Medical Genetic Division, Department of Pediatrics, King Abdulaziz Medical City, Riyadh 14611, Saudi Arabia
| | - Mona Alsaleh
- Pediatric Hematology and Oncology, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Abdullah Alsonbul
- Pediatric Rheumatology, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Somaya Alzelaye
- Pediatric Endocrine and Diabetes, Al Qunfudah General Hospital, Al Qunfudhah 28821, Saudi Arabia
| | - Shakir Bahzad
- Kuwait Medical Genetics Center, Kuwait City 65000, Kuwait
| | - Abdulaziz Bin Manee
- Pediatrics Department, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Ola Jarrad
- Pediatrics Department, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Neama Meriki
- Maternal and Fetal Medicine, King Khalid University Hospital, Riyadh 12372, Saudi Arabia
| | - Bassem Albeirouti
- Hematology and Oncology, King Faisal Specialist Hospital and Research Centre, Jeddah 23433, Saudi Arabia
| | - Amal Alqasmi
- Pediatrics Department, King Saud Medical City, Riyadh 12746, Saudi Arabia
| | - Mohammed AlBalwi
- Department of Pathology and Laboratory Medicine, King Saud bin Abdulaziz University for Health Sciences, King Abdullah International Medical Research Center, King Abdulaziz Medical City, Riyadh 11426, Saudi Arabia
| | - Nawal Makhseed
- Pediatrics Department, Alsoor Clinic, Kuwait City 65000, Kuwait
| | - Saeed Hassan
- Pediatrics Department, King Khalid University Hospital, Riyadh 12372, Saudi Arabia
| | - Isam Salih
- Hepatic-Pancreatic Surgery, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Mustafa A Salih
- Department of Pediatrics, College of Medicine and King Khalid University Hospital, King Saud University, Riyadh 11461, Saudi Arabia
| | - Marwan Shaheen
- Hematology and Bone Marrow Transplant, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Saadeh Sermin
- Pediatric Nephrology, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Shamsad Shahrukh
- Neurosciences Department, King Faisal Specialist Hospital and Research Centre, Jeddah 23433, Saudi Arabia
| | - Shahrukh Hashmi
- Hematology and Bone Marrow Transplant, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Ayman Shawli
- Department of Pediatrics, King Abdulaziz Medical City, Jeddah 9515, Saudi Arabia
| | - Ameen Tajuddin
- Neurology, King Fahad Hospital, Medina 59046, Saudi Arabia
| | - Abdullah Tamim
- Pediatrics Neurology, King Faisal Specialist Hospital and Research Centre, Jeddah 23433, Saudi Arabia
| | - Ahmed Alnahari
- Pediatric Department, King Fahad Central Hospital, Gizan, 82666, Saudi Arabia
| | - Ibrahim Ghemlas
- Pediatric Hematology and Oncology, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Maged Hussein
- Nephrology Department, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Sami Wali
- Pediatrics Department, Prince Sultan Military Medical Complex, Riyadh 12233, Saudi Arabia
| | - Hatem Murad
- Neurosciences Department, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Brian F Meyer
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh 12354, Saudi Arabia; Saudi Diagnostic Laboratories, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh 12354, Saudi Arabia; College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia.
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41
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Maddirevula S, Alzahrani F, Al-Owain M, Al Muhaizea MA, Kayyali HR, AlHashem A, Rahbeeni Z, Al-Otaibi M, Alzaidan HI, Balobaid A, El Khashab HY, Bubshait DK, Faden M, Yamani SA, Dabbagh O, Al-Mureikhi M, Jasser AA, Alsaif HS, Alluhaydan I, Seidahmed MZ, Alabbasi BH, Almogarri I, Kurdi W, Akleh H, Qari A, Al Tala SM, Alhomaidi S, Kentab AY, Salih MA, Chedrawi A, Alameer S, Tabarki B, Shamseldin HE, Patel N, Ibrahim N, Abdulwahab F, Samira M, Goljan E, Abouelhoda M, Meyer BF, Hashem M, Shaheen R, AlShahwan S, Alfadhel M, Ben-Omran T, Al-Qattan MM, Monies D, Alkuraya FS. Autozygome and high throughput confirmation of disease genes candidacy. Genet Med 2018; 21:736-742. [PMID: 30237576 PMCID: PMC6752307 DOI: 10.1038/s41436-018-0138-x] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 07/05/2018] [Indexed: 02/06/2023] Open
Abstract
Purpose Establishing links between Mendelian phenotypes and genes enables the proper interpretation of variants therein. Autozygome, a rich source of homozygous variants, has been successfully utilized for the high throughput identification of novel autosomal recessive disease genes. Here, we highlight the utility of the autozygome for the high throughput confirmation of previously published tentative links to diseases. Methods Autozygome and exome analysis of patients with suspected Mendelian phenotypes. All variants were classified according to the American College of Medical Genetics and Genomics guidelines. Results We highlight 30 published candidate genes (ACTL6B, ADAM22, AGTPBP1, APC, C12orf4, C3orf17 (NEPRO), CENPF, CNPY3, COL27A1, DMBX1, FUT8, GOLGA2, KIAA0556, LENG8, MCIDAS, MTMR9, MYH11, QRSL1, RUBCN, SLC25A42, SLC9A1, TBXT, TFG, THUMPD1, TRAF3IP2, UFC1, UFM1, WDR81, XRCC2, ZAK) in which we identified homozygous likely deleterious variants in patients with compatible phenotypes. We also identified homozygous likely deleterious variants in 18 published candidate genes (ABCA2, ARL6IP1, ATP8A2, CDK9, CNKSR1, DGAT1, DMXL2, GEMIN4, HCN2, HCRT, MYO9A, PARS2, PLOD3, PREPL, SCLT1, STX3, TXNRD2, WIPI2) although the associated phenotypes are sufficiently different from the original reports that they represent phenotypic expansion or potentially distinct allelic disorders. Conclusions Our results should facilitate the timely relabeling of these candidate disease genes in relevant databases to improve the yield of clinical genomic sequencing.
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Affiliation(s)
- Sateesh Maddirevula
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Fatema Alzahrani
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mohammed Al-Owain
- Department of Medical Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Mohammad A Al Muhaizea
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia.,Department of Neurosciences, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Husam R Kayyali
- Department of Pediatrics, King Faisal Specialist hospital and Research Center, Jeddah, Saudi Arabia
| | - Amal AlHashem
- Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Zuhair Rahbeeni
- Department of Medical Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Maha Al-Otaibi
- Genetic Unit, Children's Hospital, King Saud Medical City, Riyadh, Saudi Arabia
| | - Hamad I Alzaidan
- Department of Medical Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Ameera Balobaid
- Department of Medical Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Heba Y El Khashab
- Department of Pediatrics, Children's Hospital, Ain Shams University, Cairo, Egypt.,Department of Pediatrics, Dr. Suliman Al Habib Medical Group, Riyadh, Saudi Arabia
| | - Dalal K Bubshait
- Department of Pediatrics, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Maha Faden
- Genetic Unit, Children's Hospital, King Saud Medical City, Riyadh, Saudi Arabia
| | - Suad Al Yamani
- Department of Neurosciences, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Omar Dabbagh
- Department of Neurosciences, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mariam Al-Mureikhi
- Section of Clinical and Metabolic Genetics, Department of Pediatrics, Hamad Medical Corporation, Doha, Doha, Qatar
| | - Abdulla Al Jasser
- Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Hessa S Alsaif
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Iram Alluhaydan
- Genetics Division, Department of Pediatrics, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | | | | | - Ibrahim Almogarri
- Department of Pediatrics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Wesam Kurdi
- Department of Obstetrics and Gynecology, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Department of Neuroscience, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Hana Akleh
- Department of Obstetrics and Gynecology, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Alya Qari
- Department of Medical Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Saeed M Al Tala
- Department of Pediatrics, Armed Forces Hospital SR, Khamis Mushayt, Saudi Arabia
| | - Suzan Alhomaidi
- Genetic Unit, Children's Hospital, King Saud Medical City, Riyadh, Saudi Arabia
| | - Amal Y Kentab
- Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Mustafa A Salih
- Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Aziza Chedrawi
- Department of Neurosciences, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Seham Alameer
- Department of pediatrics, King Abdulaziz Medical City, Jeddah, Saudi Arabia
| | - Brahim Tabarki
- Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Hanan E Shamseldin
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Nisha Patel
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Niema Ibrahim
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Firdous Abdulwahab
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Menasria Samira
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ewa Goljan
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mohamed Abouelhoda
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Brian F Meyer
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Mais Hashem
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ranad Shaheen
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Saad AlShahwan
- Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Majid Alfadhel
- Medical Genetic Division, Department of Pediatrics, King Abdullah International Medical Research Centre, King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Tawfeg Ben-Omran
- Section of Clinical and Metabolic Genetics, Department of Pediatrics, Hamad Medical Corporation, Doha, Doha, Qatar
| | - Mohammad M Al-Qattan
- Department of Surgery, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Dorota Monies
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia. .,College of Medicine, Alfaisal University, Riyadh, Saudi Arabia. .,Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia. .,Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia.
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