1
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Furia F, Levy AM, Theunis M, Bamshad MJ, Bartos MN, Bijlsma EK, Brancati F, Cejudo L, Chong JX, De Luca C, Dean SJ, Egense A, Goel H, Guenzel AJ, Hüffmeier U, Legius E, Mancini GMS, Marcos-Alcalde I, Niclass T, Planes M, Redon S, Ros-Pardo D, Rouault K, Schot R, Schuhmann S, Shen JJ, Tao AM, Thiffault I, Van Esch H, Wentzensen IM, Barakat TS, Møller RS, Gomez-Puertas P, Chung WK, Gardella E, Tümer Z. The phenotypic and genotypic spectrum of individuals with mono- or biallelic ANK3 variants. Clin Genet 2024; 106:574-584. [PMID: 38988293 PMCID: PMC11444875 DOI: 10.1111/cge.14587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 06/25/2024] [Accepted: 06/28/2024] [Indexed: 07/12/2024]
Abstract
ANK3 encodes ankyrin-G, a protein involved in neuronal development and signaling. Alternative splicing gives rise to three ankyrin-G isoforms comprising different domains with distinct expression patterns. Mono- or biallelic ANK3 variants are associated with non-specific syndromic intellectual disability in 14 individuals (seven with monoallelic and seven with biallelic variants). In this study, we describe the clinical features of 13 additional individuals and review the data on a total of 27 individuals (16 individuals with monoallelic and 11 with biallelic ANK3 variants) and demonstrate that the phenotype for biallelic variants is more severe. The phenotypic features include language delay (92%), autism spectrum disorder (76%), intellectual disability (78%), hypotonia (65%), motor delay (68%), attention deficit disorder (ADD) or attention deficit hyperactivity disorder (ADHD) (57%), sleep disturbances (50%), aggressivity/self-injury (37.5%), and epilepsy (35%). A notable phenotypic difference was presence of ataxia in three individuals with biallelic variants, but in none of the individuals with monoallelic variants. While the majority of the monoallelic variants are predicted to result in a truncated protein, biallelic variants are almost exclusively missense. Moreover, mono- and biallelic variants appear to be localized differently across the three different ankyrin-G isoforms, suggesting isoform-specific pathological mechanisms.
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Affiliation(s)
- Francesca Furia
- Department of Epilepsy Genetics and Personalized Treatment, The Danish Epilepsy Centre, Dianalund, Denmark
- Faculty of Health Science, University of Southern Denmark (SDU), Odense, Denmark
| | - Amanda M Levy
- Department of Clinical Genetics, Kennedy Center, Copenhagen University Hospital, Copenhagen, Denmark
| | - Miel Theunis
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Michael J Bamshad
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, Washington, USA
- Brotman-Baty Institute for Precision Medicine, University of Washington, Seattle, Washington, USA
- Department of Pediatrics, Division of Genetic Medicine, Seattle Children's Hospital, Seattle, Washington, USA
| | - Meghan N Bartos
- Department of Genetics, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Emilia K Bijlsma
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Francesco Brancati
- Human Genetics, Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
- Human Functional Genetics Laboratory, Istituto di Ricovero e Cura a Carattere Scientifico San Raffaele Roma, Rome, Italy
| | - Lucile Cejudo
- CHU de Poitiers, Service de Génétique, Poitiers, France
| | - Jessica X Chong
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, Washington, USA
- Brotman-Baty Institute for Precision Medicine, University of Washington, Seattle, Washington, USA
| | - Chiara De Luca
- Human Genetics, Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Sarah Joy Dean
- Department of Genetics, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Alena Egense
- Division of Genomic Medicine, Department of Pediatrics, University of California Davis, Sacramento, California, USA
| | - Himanshu Goel
- General Genetics Service, Hunter Genetics, Waratah, New South Wales, Australia
- School of Medicine and Public Health, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
| | | | - Ulrike Hüffmeier
- Institute of Human Genetics, Universitätsklinikum Erlangen, FAU Erlangen-Nürnberg, Erlangen, Germany
| | - Eric Legius
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Grazia M S Mancini
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
- ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Iñigo Marcos-Alcalde
- Molecular Modeling Group, Centro de Biología Molecular Severo Ochoa (CBM, CSIC-UAM), Madrid, Spain
| | | | - Marc Planes
- Service de Génétique Clinique, CHRU de Brest, Brest, France
| | - Sylvia Redon
- Service de Génétique Médicale et Biologie de la Reproduction, CHU de Brest, Brest, France
- Université de Brest, INSERM, Etablissement Français du Sang, UMR 1078, Brest, France
| | - David Ros-Pardo
- Molecular Modeling Group, Centro de Biología Molecular Severo Ochoa (CBM, CSIC-UAM), Madrid, Spain
| | - Karen Rouault
- Service de Génétique Médicale et Biologie de la Reproduction, CHU de Brest, Brest, France
- Université de Brest, INSERM, Etablissement Français du Sang, UMR 1078, Brest, France
| | - Rachel Schot
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
- Discovery Unit, Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Sarah Schuhmann
- Institute of Human Genetics, Universitätsklinikum Erlangen, FAU Erlangen-Nürnberg, Erlangen, Germany
| | - Joseph J Shen
- Division of Genomic Medicine, Department of Pediatrics, University of California Davis, Sacramento, California, USA
| | - Alice M Tao
- Vagelos School of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Isabelle Thiffault
- Department of Pathology, Children's Mercy Kansas City, Kansas City, Missouri, USA
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, Missouri, USA
| | - Hilde Van Esch
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
- Laboratory for the Genetics of Cognition, KU Leuven, Leuven, Belgium
| | | | - Tahsin Stefan Barakat
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
- ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC University Medical Center, Rotterdam, The Netherlands
- Discovery Unit, Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Rikke S Møller
- Department of Epilepsy Genetics and Personalized Treatment, The Danish Epilepsy Centre, Dianalund, Denmark
- Faculty of Health Science, University of Southern Denmark (SDU), Odense, Denmark
| | - Paulino Gomez-Puertas
- Molecular Modeling Group, Centro de Biología Molecular Severo Ochoa (CBM, CSIC-UAM), Madrid, Spain
| | - Wendy K Chung
- Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts, USA
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Elena Gardella
- Department of Epilepsy Genetics and Personalized Treatment, The Danish Epilepsy Centre, Dianalund, Denmark
- Faculty of Health Science, University of Southern Denmark (SDU), Odense, Denmark
- Department of Neurophysiology, The Danish Epilepsy Centre, Dianalund, Denmark
| | - Zeynep Tümer
- Department of Clinical Genetics, Kennedy Center, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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2
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Al-Dewik N, Abuarja T, Younes S, Nasrallah G, Alsharshani M, Ibrahim FE, Samara M, Farrell T, Abdulrouf PV, Qoronfleh MW, Rifai HA. Precision medicine activities and opportunities for shaping maternal and neonatal health in Qatar. Per Med 2024:1-21. [PMID: 39347749 DOI: 10.1080/17410541.2024.2394397] [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: 10/17/2023] [Accepted: 08/16/2024] [Indexed: 10/01/2024]
Abstract
Precision Medicine (PM) is a transformative clinical medicine strategy that aims to revolutionize healthcare by leveraging biological information and biomarkers. In the context of maternal and neonatal health, PM enables personalized care from preconception through the postnatal period. Qatar has emerged as a key player in PM research, with dedicated programs driving advancements and translating cutting-edge research into clinical applications. This article delves into neonatal and maternal health in Qatar, emphasizing PM programs and initiatives that have been implemented. It also features noteworthy clinical cases that demonstrate the effectiveness of precision interventions. Furthermore, the article highlights the role of pharmacogenomics in addressing various maternal health conditions. The review further explores potential advancements in the application of PM in maternal and neonatal healthcare in Qatar.
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Affiliation(s)
- Nader Al-Dewik
- Department of Research & Translational & Precision Medicine Research Lab, Women's Wellness & Research Center (WWRC), Hamad Medical Corporation (HMC), Doha, 3050, Qatar
- Department of Neonatology, Neonatal Intensive Care Unit, Newborn Screening Unit, Women's Wellness & Research Center, Hamad Medical Corporation, Doha, 3050, Qatar
- Translational Research Institute (TRI), Hamad Medical Corporation (HMC), Doha, 3050, Qatar
- Genomics & Precision Medicine (GPM), College of Health & Life Science (CHLS), Hamad Bin Khalifa University (HBKU), Doha, 34110, Qatar
| | - Tala Abuarja
- Department of Research & Translational & Precision Medicine Research Lab, Women's Wellness & Research Center (WWRC), Hamad Medical Corporation (HMC), Doha, 3050, Qatar
| | - Salma Younes
- Department of Biomedical Science, College of Health Sciences, Member of QU Health, Qatar University (QU), Doha, 2713, Qatar
| | - Gheyath Nasrallah
- Department of Biomedical Science, College of Health Sciences, Member of QU Health, Qatar University (QU), Doha, 2713, Qatar
| | - Mohamed Alsharshani
- Diagnostic Genetics Division (DGD), Department of Laboratory Medicine & Pathology (DLMP), Hamad Medical Corporation (HMC), Doha, 3050, Qatar
| | - Faisal E Ibrahim
- Department of Research & Translational & Precision Medicine Research Lab, Women's Wellness & Research Center (WWRC), Hamad Medical Corporation (HMC), Doha, 3050, Qatar
| | - Muthanna Samara
- Department of Psychology, Kingston University London, Kingston upon Thames, London, KT1 2EE, United Kingdom
| | - Thomas Farrell
- Department of Research & Translational & Precision Medicine Research Lab, Women's Wellness & Research Center (WWRC), Hamad Medical Corporation (HMC), Doha, 3050, Qatar
| | - Palli Valapila Abdulrouf
- Department of Research & Translational & Precision Medicine Research Lab, Women's Wellness & Research Center (WWRC), Hamad Medical Corporation (HMC), Doha, 3050, Qatar
| | - M Walid Qoronfleh
- Q3 Research Institute (QRI), Healthcare Research & Policy Division, 7227 Rachel Drive, Ypsilanti, MI 48917, USA
| | - Hilal Al Rifai
- Department of Research & Translational & Precision Medicine Research Lab, Women's Wellness & Research Center (WWRC), Hamad Medical Corporation (HMC), Doha, 3050, Qatar
- Department of Neonatology, Neonatal Intensive Care Unit, Newborn Screening Unit, Women's Wellness & Research Center, Hamad Medical Corporation, Doha, 3050, Qatar
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Aamer W, Al-Maraghi A, Syed N, Gandhi GD, Aliyev E, Al-Kurbi AA, Al-Saei O, Kohailan M, Krishnamoorthy N, Palaniswamy S, Al-Malki K, Abbasi S, Agrebi N, Abbaszadeh F, Akil ASAS, Badii R, Ben-Omran T, Lo B, Mokrab Y, Fakhro KA. Burden of Mendelian disorders in a large Middle Eastern biobank. Genome Med 2024; 16:46. [PMID: 38584274 PMCID: PMC11000384 DOI: 10.1186/s13073-024-01307-6] [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: 07/01/2023] [Accepted: 02/19/2024] [Indexed: 04/09/2024] Open
Abstract
BACKGROUND Genome sequencing of large biobanks from under-represented ancestries provides a valuable resource for the interrogation of Mendelian disease burden at world population level, complementing small-scale familial studies. METHODS Here, we interrogate 6045 whole genomes from Qatar-a Middle Eastern population with high consanguinity and understudied mutational burden-enrolled at the national Biobank and phenotyped for 58 clinically-relevant quantitative traits. We examine a curated set of 2648 Mendelian genes from 20 panels, annotating known and novel pathogenic variants and assessing their penetrance and impact on the measured traits. RESULTS We find that 62.5% of participants are carriers of at least 1 known pathogenic variant relating to recessive conditions, with homozygosity observed in 1 in 150 subjects (0.6%) for which Peninsular Arabs are particularly enriched versus other ancestries (5.8-fold). On average, 52.3 loss-of-function variants were found per genome, 6.5 of which affect a known Mendelian gene. Several variants annotated in ClinVar/HGMD as pathogenic appeared at intermediate frequencies in this cohort (1-3%), highlighting Arab founder effect, while others have exceedingly high frequencies (> 5%) prompting reconsideration as benign. Furthermore, cumulative gene burden analysis revealed 56 genes having gene carrier frequency > 1/50, including 5 ACMG Tier 3 panel genes which would be candidates for adding to newborn screening in the country. Additionally, leveraging 58 biobank traits, we systematically assess the impact of novel/rare variants on phenotypes and discover 39 candidate large-effect variants associating with extreme quantitative traits. Furthermore, through rare variant burden testing, we discover 13 genes with high mutational load, including 5 with impact on traits relevant to disease conditions, including metabolic disorder and type 2 diabetes, consistent with the high prevalence of these conditions in the region. CONCLUSIONS This study on the first phase of the growing Qatar Genome Program cohort provides a comprehensive resource from a Middle Eastern population to understand the global mutational burden in Mendelian genes and their impact on traits in seemingly healthy individuals in high consanguinity settings.
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Affiliation(s)
- Waleed Aamer
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | | | - Najeeb Syed
- Applied Bioinformatics Core, Sidra Medicine, Doha, Qatar
| | | | - Elbay Aliyev
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | | | - Omayma Al-Saei
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | | | | | | | | | - Saleha Abbasi
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | - Nourhen Agrebi
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | | | | | - Ramin Badii
- Diagnostic Genomic Division, Hamad Medical Corporation, Doha, Qatar
| | - Tawfeg Ben-Omran
- Section of Clinical and Metabolic Genetics, Department of pediatrics, Hamad Medical Corporation, Doha, Qatar
- Department of Pediatric, Weill Cornell Medical College, Doha, Qatar
- Division of Genetic & Genomics Medicine, Sidra Medicine, Doha, Qatar
| | - Bernice Lo
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Younes Mokrab
- Department of Human Genetics, Sidra Medicine, Doha, Qatar.
- Department of Genetic Medicine, Weill Cornell Medicine-Qatar, Doha, Qatar.
- College of Health Sciences, Qatar University, Doha, Qatar.
| | - Khalid A Fakhro
- Department of Human Genetics, Sidra Medicine, Doha, Qatar.
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar.
- Department of Genetic Medicine, Weill Cornell Medicine-Qatar, Doha, Qatar.
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4
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Abolhassani A, Fattahi Z, Beheshtian M, Fadaee M, Vazehan R, Ahangari F, Dehdahsi S, Faraji Zonooz M, Parsimehr E, Kalhor Z, Peymani F, Mozaffarpour Nouri M, Babanejad M, Noudehi K, Fatehi F, Zamanian Najafabadi S, Afroozan F, Yazdan H, Bozorgmehr B, Azarkeivan A, Sadat Mahdavi S, Nikuei P, Fatehi F, Jamali P, Ashrafi MR, Karimzadeh P, Habibi H, Kahrizi K, Nafissi S, Kariminejad A, Najmabadi H. Clinical application of next generation sequencing for Mendelian disease diagnosis in the Iranian population. NPJ Genom Med 2024; 9:12. [PMID: 38374194 PMCID: PMC10876633 DOI: 10.1038/s41525-024-00393-0] [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: 05/08/2023] [Accepted: 01/29/2024] [Indexed: 02/21/2024] Open
Abstract
Next-generation sequencing (NGS) has been proven to be one of the most powerful diagnostic tools for rare Mendelian disorders. Several studies on the clinical application of NGS in unselected cohorts of Middle Eastern patients have reported a high diagnostic yield of up to 48%, correlated with a high level of consanguinity in these populations. We evaluated the diagnostic utility of NGS-based testing across different clinical indications in 1436 patients from Iran, representing the first study of its kind in this highly consanguineous population. A total of 1075 exome sequencing and 361 targeted gene panel sequencing were performed over 8 years at a single clinical genetics laboratory, with the majority of cases tested as proband-only (91.6%). The overall diagnostic rate was 46.7%, ranging from 24% in patients with an abnormality of prenatal development to over 67% in patients with an abnormality of the skin. We identified 660 pathogenic or likely pathogenic variants, including 241 novel variants, associated with over 342 known genetic conditions. The highly consanguineous nature of this cohort led to the diagnosis of autosomal recessive disorders in the majority of patients (79.1%) and allowed us to determine the shared carrier status of couples for suspected recessive phenotypes in their deceased child(ren) when direct testing was not possible. We also highlight the observations of recessive inheritance of genes previously associated only with dominant disorders and provide an expanded genotype-phenotype spectrum for multiple less-characterized genes. We present the largest mutational spectrum of known Mendelian disease, including possible founder variants, throughout the Iranian population, which can serve as a unique resource for clinical genomic studies locally and beyond.
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Affiliation(s)
- Ayda Abolhassani
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Zohreh Fattahi
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | | | - Mahsa Fadaee
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Raheleh Vazehan
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Fatemeh Ahangari
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Shima Dehdahsi
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | | | - Elham Parsimehr
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Zahra Kalhor
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Fatemeh Peymani
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | | | - Mojgan Babanejad
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Khadijeh Noudehi
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Fatemeh Fatehi
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | | | - Fariba Afroozan
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Hilda Yazdan
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Bita Bozorgmehr
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Azita Azarkeivan
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | | | - Pooneh Nikuei
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
- Nasle Salem Genetic Counseling Center, Bandar Abbas, Iran
| | - Farzad Fatehi
- Department of Neurology, Neuromuscular Research Center, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Payman Jamali
- Genetic Counseling Center, Shahroud Welfare Organization, Semnan, Iran
| | | | - Parvaneh Karimzadeh
- Pediatric Neurology Department, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Haleh Habibi
- Hamedan University of Medical Science, Hamedan, Iran
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Shahriar Nafissi
- Department of Neurology, Neuromuscular Research Center, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Hossein Najmabadi
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran.
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
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5
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Su L, Peng M, Chen X, Wu S, Liu L. Severe Zellweger spectrum disorder due to a novel missense variant in the PEX13 gene: A case report and the literature review. Mol Genet Genomic Med 2024; 12:e2315. [PMID: 37962062 PMCID: PMC10767603 DOI: 10.1002/mgg3.2315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 10/08/2023] [Accepted: 10/13/2023] [Indexed: 11/15/2023] Open
Abstract
BACKGROUND Peroxisome biogenesis disorders (PBDs) are caused by variants in PEX genes that impair peroxisome function. Zellweger spectrum disorders (ZSDs) are the most severe and common subtype of PBDs, affecting multiple organ systems due to peroxisomal involvement in various metabolic functions. PEX13 gene variants are rare causes of ZSDs, with only 21 cases reported worldwide and none in China. METHODS We describe an infant with biochemically and molecularly confirmed ZSDs due to variants in the PEX13 gene, identified by whole exome sequencing and validated by Sanger sequencing. The patient's treatment and prognosis were followed up. We also reviewed the literature on previously reported cases with PEX13 variants. RESULTS The patient had severe hypotonia, seizures, hepatic dysfunction, failure to thrive, and dysmorphic features. Serum analysis revealed elevated levels of very long-chain fatty acids (VLCFA), phytanic acid, and pipecolic acid. We detected a novel homozygous missense variant c.493G>C (p. Ala165Pro) in the PEX13 gene (NM_002618.3), which caused severe clinical manifestations and was inherited from the consanguineous parents. The patient died at the age of 14 months. CONCLUSION We report the first case of ZSDs due to the PEX13 variant in China. Our findings broaden the mutational spectrum of the PEX13 gene and indicate that missense variants can lead to severe ZSDs phenotypes, which has implications for genotype-phenotype correlations and genetic counseling.
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Affiliation(s)
- Ling Su
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical CenterGuangzhou Medical UniversityGuangzhouP. R. China
| | - Min‐Zhi Peng
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical CenterGuangzhou Medical UniversityGuangzhouP. R. China
| | - Xiao‐Dan Chen
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical CenterGuangzhou Medical UniversityGuangzhouP. R. China
| | - Shuang Wu
- School of PediatricsGuangzhou Medical UniversityGuangzhouP. R. China
| | - Li Liu
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical CenterGuangzhou Medical UniversityGuangzhouP. R. China
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6
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Misceo D, Senaratne LDS, Mero IL, Sundaram AYM, Bjørnstad PM, Szczałuba K, Gasperowicz P, Kamien B, Nedregaard B, Holmgren A, Strømme P, Frengen E. Novel Loss of Function Variants in CENPF Including a Large Intragenic Deletion in Patients with Strømme Syndrome. Genes (Basel) 2023; 14:1985. [PMID: 38002928 PMCID: PMC10671177 DOI: 10.3390/genes14111985] [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: 09/28/2023] [Revised: 10/19/2023] [Accepted: 10/23/2023] [Indexed: 11/26/2023] Open
Abstract
Strømme syndrome is an ultra-rare primary ciliopathy with clinical variability. The syndrome is caused by bi-allelic variants in CENPF, a protein with key roles in both chromosomal segregation and ciliogenesis. We report three unrelated patients with Strømme syndrome and, using high-throughput sequencing approaches, we identified novel pathogenic variants in CENPF, including one structural variant, giving a genetic diagnosis to the patients. Patient 1 was a premature baby who died at 26 days with congenital malformations affecting many organs including the brain, eyes, and intestine. She was homozygous for a donor splice variant in CENPF, NM_016343.3:c.1068+1G>A, causing skipping of exon 7, resulting in a frameshift. Patient 2 was a female with intestinal atresia, microcephaly, and a Peters anomaly. She had normal developmental milestones at the age of 7 years. She is compound heterozygous for CENPF NM_016343.3:c.5920dup and c.8991del, both frameshift. Patient 3 was a male with anomalies of the brain, eye, intestine, and kidneys. He was compound heterozygous for CENPF p.(Glu298Ter), and a 5323 bp deletion covering exon 1. CENPF exon 1 is flanked by repetitive sequences that may represent a site of a recurrent structural variation, which should be a focus in patients with Strømme syndrome of unknown etiology.
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Affiliation(s)
- Doriana Misceo
- Department of Medical Genetics, Oslo University Hospital, 0450 Oslo, Norway; (D.M.); (L.D.S.S.); (I.-L.M.); (A.Y.M.S.); (A.H.)
- Faculty of Medicine, University of Oslo, 0450 Oslo, Norway;
| | - Lokuliyanage Dona Samudita Senaratne
- Department of Medical Genetics, Oslo University Hospital, 0450 Oslo, Norway; (D.M.); (L.D.S.S.); (I.-L.M.); (A.Y.M.S.); (A.H.)
- Faculty of Medicine, University of Oslo, 0450 Oslo, Norway;
| | - Inger-Lise Mero
- Department of Medical Genetics, Oslo University Hospital, 0450 Oslo, Norway; (D.M.); (L.D.S.S.); (I.-L.M.); (A.Y.M.S.); (A.H.)
| | - Arvind Y. M. Sundaram
- Department of Medical Genetics, Oslo University Hospital, 0450 Oslo, Norway; (D.M.); (L.D.S.S.); (I.-L.M.); (A.Y.M.S.); (A.H.)
- Faculty of Medicine, University of Oslo, 0450 Oslo, Norway;
| | - Pål Marius Bjørnstad
- Department of Medical Genetics, Oslo University Hospital, 0450 Oslo, Norway; (D.M.); (L.D.S.S.); (I.-L.M.); (A.Y.M.S.); (A.H.)
- Faculty of Medicine, University of Oslo, 0450 Oslo, Norway;
| | - Krzysztof Szczałuba
- Department of Medical Genetics, Medical University of Warsaw, Żwirki i Wigury 61, 02-091 Warszawa, Poland; (K.S.)
| | - Piotr Gasperowicz
- Department of Medical Genetics, Medical University of Warsaw, Żwirki i Wigury 61, 02-091 Warszawa, Poland; (K.S.)
| | - Benjamin Kamien
- Genetic Services of Western Australia, King Edward Memorial Hospital, 374 Bagot Rd, Subiaco, WA 6008, Australia;
| | - Bård Nedregaard
- Department of Radiology and Nuclear Medicine, Section of Neuroradiology, Oslo University Hospital, 0450 Oslo, Norway;
| | - Asbjørn Holmgren
- Department of Medical Genetics, Oslo University Hospital, 0450 Oslo, Norway; (D.M.); (L.D.S.S.); (I.-L.M.); (A.Y.M.S.); (A.H.)
- Faculty of Medicine, University of Oslo, 0450 Oslo, Norway;
| | - Petter Strømme
- Faculty of Medicine, University of Oslo, 0450 Oslo, Norway;
- Division of Pediatric and Adolescent Medicine, Oslo University Hospital, 0450 Oslo, Norway
| | - Eirik Frengen
- Department of Medical Genetics, Oslo University Hospital, 0450 Oslo, Norway; (D.M.); (L.D.S.S.); (I.-L.M.); (A.Y.M.S.); (A.H.)
- Faculty of Medicine, University of Oslo, 0450 Oslo, Norway;
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7
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Bartolomaeus T, Hentschel J, Jamra RA, Popp B. Re-evaluation and re-analysis of 152 research exomes five years after the initial report reveals clinically relevant changes in 18. Eur J Hum Genet 2023; 31:1154-1164. [PMID: 37460657 PMCID: PMC10545662 DOI: 10.1038/s41431-023-01425-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 06/16/2023] [Accepted: 06/28/2023] [Indexed: 07/22/2023] Open
Abstract
Iterative re-analysis of NGS results is not well investigated for published research cohorts of rare diseases. We revisited a cohort of 152 consanguineous families with developmental disorders (NDD) reported five years ago. We re-evaluated all reported variants according to diagnostic classification guidelines or our candidate gene scoring system (AutoCaSc) and systematically scored the validity of gene-disease associations (GDA). Sequencing data was re-processed using an up-to-date pipeline for case-level re-analysis. In 28/152 (18%) families, we identified a clinically relevant change. Ten previously reported (likely) pathogenic variants were re-classified as VUS/benign. In one case, the GDA (TSEN15) validity was judged as limited, and in five cases GDAs are meanwhile established. We identified 12 new disease causing variants. Two previously reported variants were missed by our updated pipeline due to alignment or reference issues. Our results support the need to re-evaluate screening studies, not only the negative cases but including supposedly solved ones. This also applies in a diagnostic setting. We highlight that the complexity of computational re-analysis for old data should be weighed against the decreasing re-testing costs. Since extensive re-analysis per case is beyond the resources of most institutions, we recommend a screening procedure that would quickly identify the majority (83%) of new variants.
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Affiliation(s)
- Tobias Bartolomaeus
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, 04103, Germany
| | - Julia Hentschel
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, 04103, Germany
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, 04103, Germany.
| | - Bernt Popp
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, 04103, Germany.
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Center of Functional Genomics, Hessische Straße 4A, 10115, Berlin, Germany.
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8
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Alqahtani AS, Alotibi RS, Aloraini T, Almsned F, Alassali Y, Alfares A, Alhaddad B, Al Eissa MM. Prospect of genetic disorders in Saudi Arabia. Front Genet 2023; 14:1243518. [PMID: 37799141 PMCID: PMC10548463 DOI: 10.3389/fgene.2023.1243518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 08/30/2023] [Indexed: 10/07/2023] Open
Abstract
Introduction: Rare diseases (RDs) create a massive burden for governments and families because sufferers of these diseases are required to undergo long-term treatment or rehabilitation to maintain a normal life. In Saudi Arabia (SA), the prevalence of RDs is high as a result of cultural and socio-economic factors. This study, however, aims to shed light on the genetic component of the prevalence of RDs in SA. Methodology: A retrospective study was conducted between September 2020 and December 2021 at King Saud Medical City, a tertiary hospital of the Ministry of Health (MOH), SA. A total of 1080 individuals with 544 potentially relevant variants were included. The index was 738, and the samples were tested in a commercialized laboratory using different molecular techniques, including next-generation sequencing. Result: A total of 867 molecular genetics tests were conducted on 738 probands. These tests included 610 exome sequencing (ES) tests, four genome sequencing (GS) tests, 82 molecular panels, 106 single nucleotide polymorphism (SNP) array, four methylation studies, 58 single-gene studies and three mitochondrial genome sequencing tests. The diagnostic yield among molecular genetics studies was 41.8% in ES, 24% in panels, 12% in SNP array and 24% in single gene studies. The majority of the identified potential variants (68%) were single nucleotide variants (SNV). Other ascertained variants included frameshift (11%), deletion (10%), duplication (5%), splicing (9%), in-frame deletion (3%) and indels (1%). The rate of positive consanguinity was 56%, and the autosomal recessive accounted for 54%. We found a significant correlation between the ES detection rate and positive consanguinity. We illustrated the presence of rare treatable conditions in DNAJC12, SLC19A3, and ALDH7A1, and the presence of the founder effect variant in SKIC2. Neurodevelopmental disorders were the main phenotype for which genetics studies were required (35.7%). Conclusion: This is the sixth-largest local study reporting next-generation sequencing. The results indicate the influence of consanguineous marriages on genetic disease and the burden it causes for the Kingdom of SA. This study highlights the need to enrich our society's knowledge of genetic disorders. We recommend utilising ES as a first-tier test to establish genetic diagnosis in a highly consanguineous population.
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Affiliation(s)
- Amerh S. Alqahtani
- Medical Genetics Department, King Saud Medical City, Riyadh, Saudi Arabia
| | - Raniah S. Alotibi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud bin Abdulaziz University for Health Sciences, King Abdullah International Medical Research Centre (KAIMRC), Riyadh, Saudi Arabia
- Division of Translational Pathology, Department of Laboratory Medicine, King Abdulaziz Medical City, Department of Genetics, King Abdullah Specialized Children Hospital, MNGHA, Riyadh, Saudi Arabia
| | - Taghrid Aloraini
- Division of Translational Pathology, Department of Laboratory Medicine, King Abdulaziz Medical City, Riyadh, Saudi Arabia
- Department of Genetics, King Abdullah Specialized Children Hospital, MNGHA, Riyadh, Saudi Arabia
| | - Fahad Almsned
- Research Centre, King Fahad Specialist Hospital in Dammam (KFSH-D), Dammam, Saudi Arabia
- Population Health Management, Eastern Health Cluster, Dammam, Saudi Arabia
- Research and Development Department, NovoGenomics, Riyadh, Saudi Arabia
| | - Yara Alassali
- Medical School, AlFaisal University, Riyadh, Saudi Arabia
| | - Ahmed Alfares
- Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Bader Alhaddad
- Molecular Genetics Department, King Saud Medical City, Riyadh, Saudi Arabia
- Laboratory Medicine Department, King Fahd Hospital of the University, Imam Abdulrahman Bin Faisal University, Al Khobar, Saudi Arabia
| | - Mariam M. Al Eissa
- Medical School, AlFaisal University, Riyadh, Saudi Arabia
- Public Health Authority, Public Health Lab, Molecular Genetics Laboratory, Riyadh, Saudi Arabia
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9
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Chung CCY, Hue SPY, Ng NYT, Doong PHL, Chu ATW, Chung BHY. Meta-analysis of the diagnostic and clinical utility of exome and genome sequencing in pediatric and adult patients with rare diseases across diverse populations. Genet Med 2023; 25:100896. [PMID: 37191093 DOI: 10.1016/j.gim.2023.100896] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 05/07/2023] [Accepted: 05/10/2023] [Indexed: 05/17/2023] Open
Abstract
PURPOSE This meta-analysis aims to compare the diagnostic and clinical utility of exome sequencing (ES) vs genome sequencing (GS) in pediatric and adult patients with rare diseases across diverse populations. METHODS A meta-analysis was conducted to identify studies from 2011 to 2021. RESULTS One hundred sixty-one studies across 31 countries/regions were eligible, featuring 50,417 probands of diverse populations. Diagnostic rates of ES (0.38, 95% CI 0.36-0.40) and GS (0.34, 95% CI 0.30-0.38) were similar (P = .1). Within-cohort comparison illustrated 1.2-times odds of diagnosis by GS over ES (95% CI 0.79-1.83, P = .38). GS studies discovered a higher range of novel genes than ES studies; yet, the rate of variant of unknown significance did not differ (P = .78). Among high-quality studies, clinical utility of GS (0.77, 95% CI 0.64-0.90) was higher than that of ES (0.44, 95% CI 0.30-0.58) (P < .01). CONCLUSION This meta-analysis provides an important update to demonstrate the similar diagnostic rates between ES and GS and the higher clinical utility of GS over ES. With the newly published recommendations for clinical interpretation of variants found in noncoding regions of the genome and the trend of decreasing variant of unknown significance and GS cost, it is expected that GS will be more widely used in clinical settings.
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Affiliation(s)
| | - Shirley P Y Hue
- Hong Kong Genome Institute, Hong Kong Special Administrative Region
| | - Nicole Y T Ng
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Phoenix H L Doong
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Annie T W Chu
- Hong Kong Genome Institute, Hong Kong Special Administrative Region.
| | - Brian H Y Chung
- Hong Kong Genome Institute, Hong Kong Special Administrative Region; Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region.
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10
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Gorukmez O, Gorukmez O, Topak A. Clinical exome sequencing findings in 1589 patients. Am J Med Genet A 2023; 191:1557-1564. [PMID: 36964972 DOI: 10.1002/ajmg.a.63190] [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: 08/25/2022] [Revised: 01/31/2023] [Accepted: 03/15/2023] [Indexed: 03/27/2023]
Abstract
Clinical exome sequencing (CES) is important for the diagnosis of Mendelian diseases, which are clinically and etiologically heterogeneous. Sharing of large amounts of CES data associated with clinical findings will increase the accuracy of variant interpretation. We performed a retrospective study to state the diagnostic yield of CES in 1589 patients with a wide phenotypic spectrum. CES was performed using the Sophia Clinical Exome Sequencing Kit with 4493 genes, followed by sequencing on a NextSeq 500 system. The diagnosis rate was 36.8% when only pathogenic and likely pathogenic variants were included. Consanguineous unions and positive family history were associated with a high diagnostic yield. The neurological disease group had the highest number of patients. The groups with high diagnosis rates were ear, eye, and muscle disease groups. Seven candidate genes (EFHC2, HSPB3, FAAH2, ITGB1, GYG2, CD177, and CSTF2T) that are not yet associated with human diseases were identified. Owing to the high diagnostic yield of CES compared with that of other genetic tests, it can be used as a standard diagnostic test in patients with rare genetic disorders that require a wide differential diagnosis, especially in laboratories with limited resources.
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Affiliation(s)
- Ozlem Gorukmez
- Department of Medical Genetics, Bursa Yüksek İhtisas Training and Research Hospital, Bursa, Turkey
| | - Orhan Gorukmez
- Department of Medical Genetics, Bursa Yüksek İhtisas Training and Research Hospital, Bursa, Turkey
| | - Ali Topak
- Department of Medical Genetics, Bursa Yüksek İhtisas Training and Research Hospital, Bursa, Turkey
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11
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Alix T, Chéry C, Josse T, Bronowicki JP, Feillet F, Guéant-Rodriguez RM, Namour F, Guéant JL, Oussalah A. Predictors of the utility of clinical exome sequencing as a first-tier genetic test in patients with Mendelian phenotypes: results from a referral center study on 603 consecutive cases. Hum Genomics 2023; 17:5. [PMID: 36740706 PMCID: PMC9899384 DOI: 10.1186/s40246-023-00455-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 01/28/2023] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Clinical exome sequencing (CES) provides a comprehensive and effective analysis of relevant disease-associated genes in a cost-effective manner compared to whole exome sequencing. Although several studies have focused on the diagnostic yield of CES, no study has assessed predictors of CES utility among patients with various Mendelian phenotypes. We assessed the effectiveness of CES as a first-level genetic test for molecular diagnosis in patients with a Mendelian phenotype and explored independent predictors of the clinical utility of CES. RESULTS Between January 2016 and December 2019, 603 patients (426 probands and 177 siblings) underwent CES at the Department of Molecular Medicine of the University Hospital of Nancy. The median age of the probands was 34 years (IQR, 12-48), and the proportion of males was 46.9% (200/426). Adults and children represented 64.8% (276/426) and 35.2% (150/426), respectively. The median test-to-report time was 5.6 months (IQR, 4.1-7.2). CES revealed 203 pathogenic or likely pathogenic variants in 160 patients, corresponding to a diagnostic yield of 37.6% (160/426). Independent predictors of CES utility were criteria strongly suggestive of an extreme phenotype, including pediatric presentation and patient phenotypes associated with an increased risk of a priori probability of a monogenic disorder, the inclusion of at least one family member in addition to the proband, and a CES prescription performed by an expert in the field of rare genetic disorders. CONCLUSIONS Based on a large dataset of consecutive patients with various Mendelian phenotypes referred for CES as a first-tier genetic test, we report a diagnostic yield of ~ 40% and several independent predictors of CES utility that might improve CES diagnostic efficiency.
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Affiliation(s)
- Tom Alix
- grid.410527.50000 0004 1765 1301Division of Biochemistry, Molecular Biology, and Nutrition, Department of Molecular Medicine, University Hospital of Nancy, 54000 Nancy, France
| | - Céline Chéry
- grid.410527.50000 0004 1765 1301Division of Biochemistry, Molecular Biology, and Nutrition, Department of Molecular Medicine, University Hospital of Nancy, 54000 Nancy, France ,grid.29172.3f0000 0001 2194 6418INSERM UMR_S 1256, Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, University of Lorraine, 9 Avenue de la Forêt de Haye, 54000 Nancy, France ,grid.410527.50000 0004 1765 1301Reference Center for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, 54000 Nancy, France
| | - Thomas Josse
- grid.410527.50000 0004 1765 1301Division of Biochemistry, Molecular Biology, and Nutrition, Department of Molecular Medicine, University Hospital of Nancy, 54000 Nancy, France
| | - Jean-Pierre Bronowicki
- grid.29172.3f0000 0001 2194 6418INSERM UMR_S 1256, Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, University of Lorraine, 9 Avenue de la Forêt de Haye, 54000 Nancy, France ,grid.410527.50000 0004 1765 1301Department of Gastroenterology and Liver Diseases, University Hospital of Nancy, 54000 Nancy, France
| | - François Feillet
- grid.29172.3f0000 0001 2194 6418INSERM UMR_S 1256, Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, University of Lorraine, 9 Avenue de la Forêt de Haye, 54000 Nancy, France ,grid.410527.50000 0004 1765 1301Reference Center for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, 54000 Nancy, France ,grid.410527.50000 0004 1765 1301Department of Pediatrics, University Hospital of Nancy, 54000 Nancy, France
| | - Rosa-Maria Guéant-Rodriguez
- grid.410527.50000 0004 1765 1301Division of Biochemistry, Molecular Biology, and Nutrition, Department of Molecular Medicine, University Hospital of Nancy, 54000 Nancy, France ,grid.29172.3f0000 0001 2194 6418INSERM UMR_S 1256, Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, University of Lorraine, 9 Avenue de la Forêt de Haye, 54000 Nancy, France ,grid.410527.50000 0004 1765 1301Reference Center for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, 54000 Nancy, France
| | - Farès Namour
- grid.410527.50000 0004 1765 1301Division of Biochemistry, Molecular Biology, and Nutrition, Department of Molecular Medicine, University Hospital of Nancy, 54000 Nancy, France ,grid.29172.3f0000 0001 2194 6418INSERM UMR_S 1256, Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, University of Lorraine, 9 Avenue de la Forêt de Haye, 54000 Nancy, France ,grid.410527.50000 0004 1765 1301Reference Center for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, 54000 Nancy, France
| | - Jean-Louis Guéant
- Division of Biochemistry, Molecular Biology, and Nutrition, Department of Molecular Medicine, University Hospital of Nancy, 54000, Nancy, France. .,INSERM UMR_S 1256, Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, University of Lorraine, 9 Avenue de la Forêt de Haye, 54000, Nancy, France. .,Reference Center for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, 54000, Nancy, France.
| | - Abderrahim Oussalah
- Division of Biochemistry, Molecular Biology, and Nutrition, Department of Molecular Medicine, University Hospital of Nancy, 54000, Nancy, France. .,INSERM UMR_S 1256, Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, University of Lorraine, 9 Avenue de la Forêt de Haye, 54000, Nancy, France. .,Reference Center for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, 54000, Nancy, France.
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12
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Jia A, Lei Y, Liu DP, Pan L, Guan HZ, Yang B. A Retrospective Analysis of Clinically Focused Exome Sequencing Results of 372 Infants with Suspected Monogenic Disorders in China. Pharmgenomics Pers Med 2023; 16:81-97. [PMID: 36755623 PMCID: PMC9901461 DOI: 10.2147/pgpm.s387767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 01/12/2023] [Indexed: 02/04/2023] Open
Abstract
Objective The context was designed to optimize the diagnostic utility of clinically focused exome sequencing (CFES) and shorten the diagnostic odyssey among pediatric patients suspected of monogenic disorders (MDs). Methods Here, we retrospectively analyzed the clinical notes of 372 patients from different areas in the Jiangxi province that were referred for a diagnostic CFES and analysis from June 2018 to March 2022 with symptoms suggestive of MDs. In our study, preliminary tests using the proband-only clinical exome sequencing as a cost-effective first-tier diagnostic test for pediatric patients with unidentified MDs, supplemented by family segregation studies for targeted variants when indicated. Results Probands with confirmed diagnostic (CD) or likely diagnostic (LD) genetic influences accounted for 12% of all cases, whereas those with an uncertain diagnosis accounted for 48%. We also found that systemic primary carnitine deficiency (CDSP) (SLC22A5 gene) and phenylketonuria (PAH gene) were relatively more prevalent, and these patients with CDSP had the most frequent c.1400C > G variant (p.S467C) and c.51C > G variant (p. F17L) in this study. In addition, statistical analysis revealed that the estimates of diagnostic yields varied across certain phenotypic features of patients, and patients with specific phenotypic traits tended to benefit more from CFES. Conclusion The CFES may be a first-line genetic test for diagnosing young children with suspected genetic conditions, as it validates the identification of molecular genetics alterations and facilitates comprehensive medical management. Moreover, we found that infants exhibiting metabolism/homeostasis abnormalities, craniofacial /otolaryngology/ ophthalmologic abnormalities, and/or the integument were significantly more likely to receive a genetic diagnosis via CFES than infants without such features. However, due to the current study's low diagnostic yield and inherent limitations, high-quality clinical studies with larger sample sizes are still needed to provide more likely results and confirm our findings.
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Affiliation(s)
- An Jia
- Medical School, Huanghe Science and Technology College, Zhengzhou, People’s Republic of China
| | - Yi Lei
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, People’s Republic of China
| | - Dan-Ping Liu
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, People’s Republic of China
| | - Lu Pan
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, People’s Republic of China
| | - Hui-Zhen Guan
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, People’s Republic of China
| | - Bicheng Yang
- Medical School, Huanghe Science and Technology College, Zhengzhou, People’s Republic of China,Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, People’s Republic of China,Correspondence: Bicheng Yang, Jiangxi Provincial Key Laboratory of Birth Defect for Prevention and Control, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, 330006, People’s Republic of China, Tel +86 15350402147, Email
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13
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Daum H, Harel T, Millo T, Eilat A, Fahham D, Gershon-Naamat S, Basal A, Rosenbluh C, Yanai N, Porat S, Kabiri D, Yagel S, Valsky DV, Elpeleg O, Meiner V, Mor-Shaked H. Exome sequencing for structurally normal fetuses-yields and ethical issues. Eur J Hum Genet 2023; 31:164-168. [PMID: 36071243 PMCID: PMC9905544 DOI: 10.1038/s41431-022-01169-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 06/01/2022] [Accepted: 07/26/2022] [Indexed: 11/08/2022] Open
Abstract
The yield of chromosomal microarray analysis (CMA) is well established in structurally normal fetuses (0.4-1.4%). We aimed to determine the incremental yield of exome sequencing (ES) in this population. From February 2017 to April 2022, 1,526 fetuses were subjected to ES; 482 of them were structurally normal (31.6%). Only pathogenic and likely pathogenic (P/LP) variants, per the American College of Medical Genetics and Genomics (ACMG) classification, were reported. Additionally, ACMG secondary findings relevant to childhood were reported. Four fetuses (4/482; 0.8%) had P/LP variants indicating a moderate to severe disease in ATP7B, NR2E3, SPRED1 and FGFR3, causing Wilson disease, Enhanced S-cone syndrome, Legius and Muenke syndromes, respectively. Two fetuses had secondary findings, in RET and DSP. Our data suggest that offering only CMA for structurally normal fetuses may provide false reassurance. Prenatal ES mandates restrictive analysis and careful management combined with pre and post-test genetic counseling.
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Affiliation(s)
- Hagit Daum
- Department of Genetics, Hadassah Medical Organization, Jerusalem, Israel.
- Department of Genetics, Hadassah Medical Organization and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Tamar Harel
- Department of Genetics, Hadassah Medical Organization, Jerusalem, Israel
- Department of Genetics, Hadassah Medical Organization and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Talya Millo
- Department of Genetics, Hadassah Medical Organization, Jerusalem, Israel
| | - Avital Eilat
- Department of Genetics, Hadassah Medical Organization, Jerusalem, Israel
- Department of Genetics, Hadassah Medical Organization and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Duha Fahham
- Department of Genetics, Hadassah Medical Organization, Jerusalem, Israel
- Department of Genetics, Hadassah Medical Organization and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | | | - Adily Basal
- Department of Genetics, Hadassah Medical Organization, Jerusalem, Israel
| | - Chaggai Rosenbluh
- Department of Genetics, Hadassah Medical Organization, Jerusalem, Israel
| | - Nili Yanai
- Department of Obstetrics and Gynecology, Hadassah Medical Organization and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Shay Porat
- Department of Obstetrics and Gynecology, Hadassah Medical Organization and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Doron Kabiri
- Department of Obstetrics and Gynecology, Hadassah Medical Organization and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Simcha Yagel
- Department of Obstetrics and Gynecology, Hadassah Medical Organization and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Dan V Valsky
- Department of Obstetrics and Gynecology, Hadassah Medical Organization and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Orly Elpeleg
- Department of Genetics, Hadassah Medical Organization, Jerusalem, Israel
- Department of Genetics, Hadassah Medical Organization and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Vardiella Meiner
- Department of Genetics, Hadassah Medical Organization, Jerusalem, Israel
- Department of Genetics, Hadassah Medical Organization and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Hagar Mor-Shaked
- Department of Genetics, Hadassah Medical Organization, Jerusalem, Israel.
- Department of Genetics, Hadassah Medical Organization and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.
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14
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Correia-Costa GR, dos Santos AM, de Leeuw N, Rigatto SZP, Belangero VMS, Steiner CE, Gil-da-Silva-Lopes VL, Vieira TP. Dual Molecular Diagnoses of Recessive Disorders in a Child from Consanguineous Parents: Case Report and Literature Review. Genes (Basel) 2022; 13:2377. [PMID: 36553645 PMCID: PMC9778442 DOI: 10.3390/genes13122377] [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: 11/25/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
The widespread use of whole exome sequencing (WES) resulted in the discovery of multilocus pathogenic variations (MPV), defined as two or more distinct or overlapping Mendelian disorders occurring in a patient, leading to a blended phenotype. In this study, we report on a child with autosomal recessive primary microcephaly-5 (MCPH5) and nephropathic cystinosis. The proband is the first child of consanguineous parents, presenting a complex phenotype including neurodevelopmental delay, microcephaly, growth restriction, significant delay of bone maturation, lissencephaly, and abnormality of neuronal migration, photophobia, and renal tubular acidosis. WES revealed two pathogenic and homozygous variants: a c.4174C>T variant in the ASPM gene and a c.382C>T variant in the CTNS gene, explaining the complex phenotype. The literature review showed that most of the patients harboring two variants in recessive disease genes are born to consanguineous parents. To the best of our knowledge, the patient herein described is the first one harboring pathogenic variants in both the ASPM and CTNS genes. These findings highlight the importance of searching for MPV in patients with complex phenotypes investigated by genome-wide testing methods, especially for those patients born to consanguineous parents.
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Affiliation(s)
- Gabriela Roldão Correia-Costa
- Department of Translational Medicine—Medical Genetics and Genomic Medicine, School of Medical Sciences, State University of Campinas, Campinas 13083-887, São Paulo, Brazil
| | - Ana Mondadori dos Santos
- Department of Translational Medicine—Medical Genetics and Genomic Medicine, School of Medical Sciences, State University of Campinas, Campinas 13083-887, São Paulo, Brazil
| | - Nicole de Leeuw
- Department of Human Genetics, Radboud University Medical Center, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Sumara Zuanazi Pinto Rigatto
- Department of Pediatrics, School of Medical Sciences, State University of Campinas, Campinas 13083-887, São Paulo, Brazil
| | - Vera Maria Santoro Belangero
- Department of Pediatrics, School of Medical Sciences, State University of Campinas, Campinas 13083-887, São Paulo, Brazil
| | - Carlos Eduardo Steiner
- Department of Translational Medicine—Medical Genetics and Genomic Medicine, School of Medical Sciences, State University of Campinas, Campinas 13083-887, São Paulo, Brazil
| | - Vera Lúcia Gil-da-Silva-Lopes
- Department of Translational Medicine—Medical Genetics and Genomic Medicine, School of Medical Sciences, State University of Campinas, Campinas 13083-887, São Paulo, Brazil
| | - Társis Paiva Vieira
- Department of Translational Medicine—Medical Genetics and Genomic Medicine, School of Medical Sciences, State University of Campinas, Campinas 13083-887, São Paulo, Brazil
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15
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Abulí A, Costa-Roger M, Codina-Solà M, Valenzuela I, Leno-Colorado J, Rovira-Moreno E, Cueto-González A, Fernández-Álvarez P, García-Arumí E, Cuscó I, Tizzano EF. Experience using singleton exome sequencing of probands as an approach to preconception carrier screening in consanguineous couples. J Med Genet 2022; 60:540-546. [PMID: 36600615 DOI: 10.1136/jmg-2022-108607] [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: 03/30/2022] [Accepted: 10/05/2022] [Indexed: 12/13/2022]
Abstract
BACKGROUND Consanguineous couples have an increased risk of severe diseases in offspring due to autosomal recessive disorders. Exome sequencing (ES) offers the possibility of extensive preconception carrier screening (PCS) in consanguineous couples who may be at risk of rare genetic disorders. METHODS We retrospectively analysed ES data from 65 probands affected with rare genetic disorders born from consanguineous couples. We explored diagnostic yield and carrier status for recessive disorders. RESULTS The overall diagnostic yield in a singleton approach was 53.8%, mostly recessive variants. In a hypothetical exome-based PCS, only 11.7% of these causative rare variants would have been missed in the filtering process. Carrier screening for recessive conditions allowed the identification of at least one additional pathogenic or likely pathogenic variant in 85.7% of the probands, being the majority with a gene carrier frequency <1 in 200. In addition, considering only clinically actionable conditions, we estimated that 12.3% of our close consanguineous couples may be at risk for an additional recessive disease. CONCLUSIONS Our results demonstrate that ES outperforms panel-based screening in a PCS context in consanguineous couples and could potentially increase their reproductive autonomy and facilitate informed decision-making.
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Affiliation(s)
- Anna Abulí
- Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron, Barcelona, Spain .,Medicine Genetics Group Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Mar Costa-Roger
- Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Medicine Genetics Group Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Marta Codina-Solà
- Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Medicine Genetics Group Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Irene Valenzuela
- Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Medicine Genetics Group Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Jordi Leno-Colorado
- Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Medicine Genetics Group Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Eulàlia Rovira-Moreno
- Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Medicine Genetics Group Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Anna Cueto-González
- Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Medicine Genetics Group Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Paula Fernández-Álvarez
- Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Medicine Genetics Group Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Elena García-Arumí
- Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Medicine Genetics Group Vall d'Hebron Research Institute (VHIR), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
| | - Ivon Cuscó
- Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Medicine Genetics Group Vall d'Hebron Research Institute (VHIR), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
| | - Eduardo F Tizzano
- Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Medicine Genetics Group Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
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16
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Hussain S, Nawaz S, Khan H, Acharya A, Schrauwen I, Ahmad W, Leal SM. A splice site variant in TCTN3 underlies an atypical form of orofaciodigital syndrome IV. Ann Hum Genet 2022; 86:291-296. [PMID: 36039988 PMCID: PMC9804382 DOI: 10.1111/ahg.12462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 09/20/2021] [Accepted: 02/14/2022] [Indexed: 01/05/2023]
Abstract
Orofaciodigital syndrome (OFD) is clinically heterogeneous and is characterized by abnormalities in the oral cavity, facial features, digits, and central nervous system. At least 18 subtypes of the condition have been described in the literature. OFD is caused by variants in several genes with overlapping phenotypes. We studied a consanguineous Pakistani family with two affected siblings with an atypical form of OFD type 4 (OFD4). In addition to the typical features of OFD4 that include limb defects and growth retardation, the siblings displayed rare features of scaphocephaly and seizures. Exome sequencing analysis revealed a novel homozygous splice site variant c.257-1G>A in TCTN3 that segregated with disease. This homozygous splice site variant in TCTN3 is most likely the underlying cause of the atypical form of OFD4 observed in this family. Our results contribute to the phenotypic spectrum of TCTN3 associated ciliopathies and will facilitate better clinical diagnosis.
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Affiliation(s)
- Shabir Hussain
- Department of Biochemistry, Faculty of Biological SciencesQuaid‐i‐Azam UniversityIslamabadPakistan
| | - Shoaib Nawaz
- Department of Biotechnology, Faculty of Biological SciencesQuaid‐i‐Azam UniversityIslamabadPakistan
| | - Hammal Khan
- Department of Biochemistry, Faculty of Biological SciencesQuaid‐i‐Azam UniversityIslamabadPakistan,Department of BiosciencesCOMSATS UniversityIslamabadPakistan
| | - Anushree Acharya
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of NeurologyColumbia University Medical CenterNew YorkNew YorkUSA
| | - Isabelle Schrauwen
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of NeurologyColumbia University Medical CenterNew YorkNew YorkUSA
| | - Wasim Ahmad
- Department of Biochemistry, Faculty of Biological SciencesQuaid‐i‐Azam UniversityIslamabadPakistan
| | - Suzanne M. Leal
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of NeurologyColumbia University Medical CenterNew YorkNew YorkUSA,Taub Institute for Alzheimer's Disease and the Aging BrainColumbia University Medical CenterNew YorkNew YorkUSA
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17
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Rafiullah R, Albalawi AM, Alaradi SR, Alluqmani M, Mushtaq M, Wali A, Basit S. An expansion of phenotype: novel homozygous variant in the MED17 identified in patients with progressive microcephaly and global developmental delay. J Neurogenet 2022; 36:108-114. [PMID: 36508181 DOI: 10.1080/01677063.2022.2149748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Global developmental delay (GDD) is a lifelong disability that affects 1-3% of the population around the globe. It is phenotypically variable and highly heterogeneous in terms of the underlying genetics. Patients with GDD are intellectually disabled (ID) manifesting cognitive impairment and deficient adaptive behavior. Here, we investigated a two-looped consanguineous family segregating severe ID, seizure, and progressive microcephaly. Magnetic resonance imaging (MRI) of the brain showed mild brain atrophy and myelination defect. Whole exome sequencing (WES) was performed on the DNA samples of two patients and a novel homozygous missense variant (Chr11:g0.93528085; NM_004268.5_c.871T > C; p. Trp291Gly) was identified in the MED17 gene. Sanger sequencing revealed that the identified variant is heterozygous in both parents and healthy siblings. This variant is conserved among different species, causes a non-conserved amino acid change, and is predicted deleterious by various in silico tools. The variant is not reported in population variant databases. MED17 (OMIM: 613668) encodes for the mediator of RNA polymerase II transcription complex subunit 17. Structure modeling of MED17 protein revealed that Trp291 is involved in different inter-helical interactions, providing structural stability. Replacement of Trp291Gly, a less hydrophobic amino acid loses the inter-helical interaction leading to a perturb variant of MED17 protein.
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Affiliation(s)
- Rafiullah Rafiullah
- Department of Biotechnology, Faculty of Life Sciences & Informatics, BUITEMS, Quetta, Pakistan
| | - Alia M Albalawi
- Center for Genetics and Inherited Diseases, Taibah University, Madinah, Saudi Arabia
| | - Sultan R Alaradi
- Department of Laboratory and Blood Bank, Alwajh General Hospital, Ministry of Health, Alwajh, Saudi Arabia
| | - Majed Alluqmani
- College of Medicine, Taibah University, Madinah, Saudi Arabia
| | - Muhammad Mushtaq
- Department of Biotechnology, Faculty of Life Sciences & Informatics, BUITEMS, Quetta, Pakistan
| | - Abdul Wali
- Department of Biotechnology, Faculty of Life Sciences & Informatics, BUITEMS, Quetta, Pakistan
| | - Sulman Basit
- Center for Genetics and Inherited Diseases, Taibah University, Madinah, Saudi Arabia.,Department of Biochemistry and Molecular Medicine, College of Medicine, Taibah University, Madinah, Saudi Arabia
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18
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Khan A, Tian S, Tariq M, Khan S, Safeer M, Ullah N, Akbar N, Javed I, Asif M, Ahmad I, Ullah S, Satti HS, Khan R, Naeem M, Ali M, Rendu J, Fauré J, Dieterich K, Latypova X, Baig SM, Malik NA, Zhang F, Khan TN, Liu C. NGS-driven molecular diagnosis of heterogeneous hereditary neurological disorders reveals novel and known variants in disease-causing genes. Mol Genet Genomics 2022; 297:1601-1613. [PMID: 36002593 DOI: 10.1007/s00438-022-01945-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 08/11/2022] [Indexed: 11/28/2022]
Abstract
Hereditary neurological disorders (HNDs) are a clinically and genetically heterogeneous group of disorders. These disorders arise from the impaired function of the central or peripheral nervous system due to aberrant electrical impulses. More than 600 various neurological disorders, exhibiting a wide spectrum of overlapping clinical presentations depending on the organ(s) involved, have been documented. Owing to this clinical heterogeneity, diagnosing these disorders has been a challenge for both clinicians and geneticists and a large number of patients are either misdiagnosed or remain entirely undiagnosed. Contribution of genetics to neurological disorders has been recognized since long; however, the complete picture of the underlying molecular bases are under-explored. The aim of this study was to accurately diagnose 11 unrelated Pakistani families with various HNDs deploying NGS as a first step approach. Using exome sequencing and gene panel sequencing, we successfully identified disease-causing genomic variants these families. We report four novel variants, one each in, ECEL1, NALCN, TBR1 and PIGP in four of the pedigrees. In the rest of the seven families, we found five previously reported pathogenic variants in POGZ, FA2H, PLA2G6 and CYP27A1. Of these, three families segregate a homozygous 18 bp in-frame deletion of FA2H, indicating a likely founder mutation segregating in Pakistani population. Genotyping for this mutation can help low-cost population wide screening in the corresponding regions of the country. Our findings not only expand the existing repertoire of mutational spectrum underlying neurological disorders but will also help in genetic testing of individuals with HNDs in other populations.
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Affiliation(s)
- Ayaz Khan
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan
| | - Shixiong Tian
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai, 200438, China
| | - Muhammad Tariq
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan
| | - Sheraz Khan
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan
| | - Muhammad Safeer
- Department of Biotechnology and Genetic Engineering, Hazara University, Mansehra, Pakistan
| | - Naimat Ullah
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan
| | - Nazia Akbar
- Department of Biotechnology and Genetic Engineering, Hazara University, Mansehra, Pakistan
| | - Iram Javed
- Department of Paediatric Neurology, Children Hospital and Institute of Child Health, Faisalabad, Pakistan
| | - Mahnoor Asif
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan
| | - Ilyas Ahmad
- Institute for Cardiogenetics, University of Lübeck, DZHK (German Research Centre for Cardiovascular Research), partner site Hamburg/Lübeck/Kiel, University Heart Center Lübeck, Lübeck, Germany
| | - Shahid Ullah
- Department of General Surgery, Hayatabad Medical Complex, Peshawar, 2500, Pakistan
| | - Humayoon Shafique Satti
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, 46000, Pakistan
| | - Raees Khan
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, 46000, Pakistan.,NUMS Institute of Advance Studies and Research, National University of Medical Sciences, Rawalpindi, 46000, Pakistan
| | - Muhammad Naeem
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, 46000, Pakistan
| | - Mahwish Ali
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, 46000, Pakistan.,NUMS Institute of Advance Studies and Research, National University of Medical Sciences, Rawalpindi, 46000, Pakistan
| | - John Rendu
- Inserm, U1216, CHU Grenoble Alpes, Grenoble Institute of Neurosciences, University of Grenoble Alpes, 38000, Grenoble, France
| | - Julien Fauré
- Inserm, U1216, CHU Grenoble Alpes, Grenoble Institute of Neurosciences, University of Grenoble Alpes, 38000, Grenoble, France
| | - Klaus Dieterich
- Inserm, U1209, CHU Grenoble Alpes, Institute of Advanced Biosciences, University of Grenoble Alpes, 38000, Grenoble, France
| | - Xenia Latypova
- Inserm, U1216, CHU Grenoble Alpes, Grenoble Institute of Neurosciences, University of Grenoble Alpes, 38000, Grenoble, France
| | - Shahid Mahmood Baig
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan.,Pakistan Science Foundation, Constitution Avenue, Islamabad, Pakistan
| | - Naveed Altaf Malik
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan
| | - Feng Zhang
- Obstetrics and Gynecology Hospital, Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Institute of Reproduction and Development, Fudan University, Shanghai, 200438, China
| | - Tahir Naeem Khan
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, 46000, Pakistan. .,NUMS Institute of Advance Studies and Research, National University of Medical Sciences, Rawalpindi, 46000, Pakistan. .,Advanced Center for Translational and Genetic Medicine, Stanley Manne Children's Research Institute, Lurie Children's Hospital, Departments of Pediatrics and Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, United States.
| | - Chunyu Liu
- Obstetrics and Gynecology Hospital, Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Institute of Reproduction and Development, Fudan University, Shanghai, 200438, China.
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19
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Mensch A, Cordts I, Scholle L, Joshi PR, Kleeberg K, Emmer A, Beck-Woedl S, Park J, Haack TB, Stoltenburg-Didinger G, Zierz S, Deschauer M. GFPT1-Associated Congenital Myasthenic Syndrome Mimicking a Glycogen Storage Disease – Diagnostic Pitfalls in Myopathology Solved by Next-Generation-Sequencing. J Neuromuscul Dis 2022; 9:533-541. [DOI: 10.3233/jnd-220822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
GFPT1-related congenital myasthenic syndrome (CMS) is characterized by progressive limb girdle weakness, and less prominent involvement of facial, bulbar, or respiratory muscles. While tubular aggregates in muscle biopsy are considered highly indicative in GFPT1-associated CMS, excessive glycogen storage has not been described. Here, we report on three affected siblings with limb-girdle myasthenia due to biallelic pathogenic variants in GFPT1: the previously reported missense variant c.41G > A (p.Arg14Gln) and the novel truncating variant c.1265_1268del (p.Phe422TrpfsTer26). Patients showed progressive proximal atrophic muscular weakness with respiratory involvement, and a lethal disease course in adulthood. In the diagnostic workup at that time, muscle biopsy suggested a glycogen storage disease. Initially, Pompe disease was suspected. However, enzymatic activity of acid alpha-glucosidase was normal, and gene panel analysis including 38 genes associated with limb-girdle weakness (GAA included) remained unevocative. Hence, a non-specified glycogen storage myopathy was diagnosed. A decade later, the diagnosis of GFPT1-related CMS was established by genome sequencing. Myopathological reexamination showed pronounced glycogen accumulations, that were exclusively found in denervated muscle fibers. Only single fibers showed very small tubular aggregates, identified in evaluation of serial sections. This family demonstrates how diagnostic pitfalls can be addressed by an integrative approach including broad genetic analysis and re-evaluation of clinical as well as myopathological findings.
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Affiliation(s)
- Alexander Mensch
- Department of Neurology, Martin Luther University Halle-Wittenberg and University Hospital Halle, Halle (Saale), Germany
| | - Isabell Cordts
- Department of Neurology, Klinikum rechts der Isar, Technical University Munich, Munich, Germany
| | - Leila Scholle
- Department of Neurology, Martin Luther University Halle-Wittenberg and University Hospital Halle, Halle (Saale), Germany
| | - Pushpa Raj Joshi
- Department of Neurology, Martin Luther University Halle-Wittenberg and University Hospital Halle, Halle (Saale), Germany
| | - Kathleen Kleeberg
- Department of Neurology, Martin Luther University Halle-Wittenberg and University Hospital Halle, Halle (Saale), Germany
| | - Alexander Emmer
- Department of Neurology, Martin Luther University Halle-Wittenberg and University Hospital Halle, Halle (Saale), Germany
| | - Stefanie Beck-Woedl
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Joohyun Park
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Tobias B. Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Gisela Stoltenburg-Didinger
- Department of Neurology, Martin Luther University Halle-Wittenberg and University Hospital Halle, Halle (Saale), Germany
| | - Stephan Zierz
- Department of Neurology, Martin Luther University Halle-Wittenberg and University Hospital Halle, Halle (Saale), Germany
| | - Marcus Deschauer
- Department of Neurology, Klinikum rechts der Isar, Technical University Munich, Munich, Germany
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20
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Pitfalls in Genetic Testing for Consanguineous Pediatric Populations. Case Rep Genet 2022; 2022:9393042. [PMID: 35663206 PMCID: PMC9159873 DOI: 10.1155/2022/9393042] [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] [Received: 02/01/2022] [Revised: 04/12/2022] [Accepted: 04/28/2022] [Indexed: 11/18/2022] Open
Abstract
We describe the diagnostic odyssey of an eight-year-old female born to consanguineous parents. Our patient presented with global developmental delay, regression, microcephaly, spastic diplegia, and leukodystrophy confirmed on brain magnetic resonance imaging (MRI). She was found on whole exome sequencing (WES) to have dual genetic diagnoses. The first was a homozygous pathogenic HERC2 gene partial deletion of exons 43–45 that causes HERC2-related disorder. The second was a homozygous pathogenic variant (c.836 C > T, p.A279 V) in the SUMF1 gene responsible for multiple sulfatase deficiency. This case highlights some of the challenges in diagnosing consanguineous pediatric populations where standard genetic and metabolic testing may not provide answers. Our case further supports the recent American College of Medical Genetics and Genomics (ACMG) recommendation of WES as a first or second-tier test for patients with developmental delay, particularly in a population where the chances of dual diagnosis is high.
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21
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Walsh M, West K, Taylor JA, Thompson BA, Hopkins A, Sexton A, Ragunathan A, Verma KP, Panetta J, Matotek E, Fahey MC, Christie M, Winship IM, Trainer AH, James PA. Real world outcomes and implementation pathways of exome sequencing in an adult genetic department. Genet Med 2022; 24:1536-1544. [PMID: 35416776 DOI: 10.1016/j.gim.2022.03.010] [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: 11/17/2021] [Revised: 03/14/2022] [Accepted: 03/15/2022] [Indexed: 10/18/2022] Open
Abstract
PURPOSE This study aimed to correlate the indications and diagnostic yield of exome sequencing (ES) in adult patients across various clinical settings. The secondary aim was to examine the clinical utility of ES in adult patients. METHODS Data on demographics, clinical indications, results, management changes, and cascade testing were collected for 250 consecutive patients who underwent ES through an adult genetics department between 2016 and 2021. Data were analyzed using descriptive and inferential statistics. Testing in which traditional gene panels were in standard use, such as in heritable cancers, was excluded. RESULTS The average age at testing was 43 years (range = 17-80 years). A molecular diagnosis was identified in 29% of patients. Older age at symptom onset did not pre-exclude a substantial diagnostic yield. Patients with syndromic intellectual disability and multiple system disorders had the highest yield. In >50% of patients with an exome diagnosis, the results changed management. Cascade testing occured in at least one family member for 30% of patients with a diagnosis. Diagnostic results had reproductive implications for 26% of patients and 31% of patients' relatives. CONCLUSION ES has a robust diagnostic yield and clear clinical utility in adult patients across a range of ages and phenotypes.
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Affiliation(s)
- Maie Walsh
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia; Department of Medicine at Royal Melbourne Hospital, Melbourne Medical School, The University of Melbourne, Parkville, Victoria, Australia.
| | - Kirsty West
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Jessica A Taylor
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Bryony A Thompson
- Department of Pathology, The Royal Melbourne Hospital, Parkville, Victoria, Australia; Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Parkville, Victoria, Australia
| | - Adelaide Hopkins
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Adrienne Sexton
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia; Department of Medicine at Royal Melbourne Hospital, Melbourne Medical School, The University of Melbourne, Parkville, Victoria, Australia
| | - Abiramy Ragunathan
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Kunal P Verma
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Julie Panetta
- Metabolic Diseases Unit (MDU), The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Ebony Matotek
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Michael C Fahey
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Michael Christie
- Department of Medicine at Royal Melbourne Hospital, Melbourne Medical School, The University of Melbourne, Parkville, Victoria, Australia; Department of Pathology, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Ingrid M Winship
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia; Department of Medicine at Royal Melbourne Hospital, Melbourne Medical School, The University of Melbourne, Parkville, Victoria, Australia
| | - Alison H Trainer
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia; Department of Medicine at Royal Melbourne Hospital, Melbourne Medical School, The University of Melbourne, Parkville, Victoria, Australia
| | - Paul A James
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia; Department of Medicine at Royal Melbourne Hospital, Melbourne Medical School, The University of Melbourne, Parkville, Victoria, Australia
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22
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Rajabi F, Bereshneh AH, Ramezanzadeh M, Garshasbi M. Novel compound heterozygous variants in XYLT1 gene caused Desbuquois dysplasia type 2 in an aborted fetus: a case report. BMC Pediatr 2022; 22:63. [PMID: 35081921 PMCID: PMC8790879 DOI: 10.1186/s12887-022-03132-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 01/15/2022] [Indexed: 11/16/2022] Open
Abstract
Background Desbuquois dysplasia type 2 (DBQD2) is an infrequent dysplasia with a wide range of symptoms, including facial deformities, growth retardation and short long bones. It is an autosomal recessive disorder caused by mutations in the XYLT1 gene that encodes xylosyltransferase-1. Case presentation We studied an aborted fetus from Iranian non-consanguineous parents who was therapeutically aborted at 19 weeks of gestation. Ultrasound examinations at 18 weeks of gestation revealed growth retardation in her long bones and some facial problems. Whole-exome sequencing was performed on the aborted fetus which revealed compound heterozygous XYLT1 mutations: c.742G>A; p.(Glu248Lys) and c.1537 C>A; p.(Leu513Met). Sanger sequencing and segregation analysis confirmed the compound heterozygosity of these variants in XYLT1. Conclusion The c.1537 C>A; p.(Leu513Met) variant has not been reported in any databases so far and therefore is novel. This is the third compound heterozygote report in XYLT1 and further supports the high heterogeneity of this disease. Supplementary Information The online version contains supplementary material available at 10.1186/s12887-022-03132-5.
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Affiliation(s)
- Fatemeh Rajabi
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Ali Hosseini Bereshneh
- Prenatal Diagnosis and Genetic Research Center, Dastgheib Hospital, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mahboubeh Ramezanzadeh
- Department of Genetics and Molecular Medicine, Faculty of Medicine, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Masoud Garshasbi
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.
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23
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Borgio JF. Heterogeneity in biomarkers, mitogenome and genetic disorders of the Arab population with special emphasis on large-scale whole-exome sequencing. Arch Med Sci 2021; 19:765-783. [PMID: 37313193 PMCID: PMC10259412 DOI: 10.5114/aoms/145370] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 12/27/2021] [Indexed: 09/20/2024] Open
Abstract
More than 25 million DNA variations have been discovered as novel including major alleles from the Arab population. Exome studies on the Saudi genome discovered > 3000 novel nucleotide variants associated with > 1200 rare genetic disorders. Reclassification of many pathogenic variants in the Human Gene Mutation Database and ClinVar Database as benign through the Arab database facilitates building a detailed and comprehensive map of the human morbid genome. Intellectual disability comes first with the combined and observed carrier frequency of 0.06779 among Saudi Arabians; retinal dystrophy is the next highest. Genome studies have discovered interesting novel candidate disease marker variations in many genes from consanguineous families. More than 7 pathogenic variants in the C12orf57 gene are prominently associated with the etiology of developmental delay/intellectual impairment in Arab ancestries. Advances in large-scale genome studies open a new outlook on Mendelian genes and disorders. In the past half-dozen years, candidate genes of intellectual disability, neurogenetic disorders, blood and bleeding disorders and rare genetic diseases have been well documented through genomic medicine studies in combination with advanced computational biology applications. The Arab mitogenome exposed hundreds of variations in the mtDNA genome and ancestral sharing with Africa, the Near East and East Asia and its association with obesity. These recent discoveries in disease markers and molecular genetics of the Arab population will have a positive impact towards supporting genetic counsellors on reaching consanguineous families to manage stress linked to genetics and precision medicine. This narrative review summarizes the advances in molecular medical genetics and recent discoveries on pathogenic variants. Despite the fact that these initiatives are targeting the genetics and genomics of disorders prevalent in Arab populations, a lack of complete cooperation across the projects needed to be revisited to uncover the Arab population's prominent disease markers. This shows that further study is needed in genomics to fully comprehend the molecular abnormalities and associated pathogenesis that cause inherited disorders in Arab ancestries.
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Affiliation(s)
- J Francis Borgio
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
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24
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Bennett RL, Malleda NR, Byers PH, Steiner RD, Barr KM. Genetic counseling and screening of consanguineous couples and their offspring practice resource: Focused Revision. J Genet Couns 2021; 30:1354-1357. [PMID: 34309119 DOI: 10.1002/jgc4.1477] [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: 12/11/2020] [Revised: 06/25/2021] [Accepted: 06/26/2021] [Indexed: 11/08/2022]
Abstract
There are no evidence-based guidelines to inform genetic counseling for consanguineous couples and their offspring. This focused revision builds on the expert opinions from the original publication of "Genetic Counseling and Screening of Consanguineous Couples and Their Offspring," based on a review of literature published since 2002.
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Affiliation(s)
- Robin L Bennett
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington, USA
| | | | - Peter H Byers
- Department of Laboratory Medicine and Pathology, Department of Medicine (Medical Genetics), University of Washington, Seattle, Washington, USA
| | - Robert D Steiner
- Marshfield Clinic Health System, Prevention Genetics, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Kimberly M Barr
- Department of Genetics, Kaiser Permanente Medical Center, San Francisco, California, USA
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25
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Bitarafan F, Khodaeian M, Amjadi Sardehaei E, Darvishi FZ, Almadani N, Nilipour Y, Garshasbi M. Identification of a novel MICU1 nonsense variant causes myopathy with extrapyramidal signs in an Iranian consanguineous family. Mol Cell Pediatr 2021; 8:6. [PMID: 33969448 PMCID: PMC8107061 DOI: 10.1186/s40348-021-00116-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 04/14/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Ca2+ as a universal second messenger regulates basic biological functions including cell cycle, cell proliferation, cell differentiation, and cell death. Lack of the protein mitochondrial calcium uptake1 (MICU1), which has been regarded as a gatekeeper of Ca ions, leads to the abnormal mitochondrial Ca2+ handling, excessive production of reactive oxygen species (ROS), and increased cell death. Mutations in MICU1 gene causes a very rare neuromuscular disease, myopathy with extrapyramidal signs (MPXPS), due to primary alterations in mitochondrial calcium signaling which demonstrates the key role of mitochondrial Ca2+ uptake. To date, 13 variants have been reported in MICU1 gene in 44 patients presented with the vast spectrum of symptoms. CASE PRESENTATION Here, we report a 44-year-old Iranian patient presented with learning disability, muscle weakness, easy fatigability, reduced tendon reflexes, ataxia, gait disturbance, elevated hepatic transaminases, elevated serum creatine kinase (CK), and elevated lactate dehydrogenase (LDH). We identified a novel nonsense variant c.385C>T; p.(R129*) in MICU1 gene by whole exome sequencing (WES) and segregation analysis. CONCLUSIONS Our finding along with previous studies provides more evidence on the clinical presentation of the disease caused by pathogenic mutations in MICU1. Finding more variants and expanding the spectrum of the disease increases the diagnostic rate of molecular testing in screening of this kind of diseases and in turn improves the quality of counseling for at risk couples and helps them to minimize the risks of having affected children.
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Affiliation(s)
- Fatemeh Bitarafan
- Department of Biology, Faculty of Biological Sciences, North Tehran Branch, Islamic Azad University, Tehran, Iran
| | | | | | | | - Navid Almadani
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - Yalda Nilipour
- Pediatric Pathology Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Masoud Garshasbi
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.
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26
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Vinkšel M, Writzl K, Maver A, Peterlin B. Improving diagnostics of rare genetic diseases with NGS approaches. J Community Genet 2021; 12:247-256. [PMID: 33452619 PMCID: PMC8141085 DOI: 10.1007/s12687-020-00500-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 12/08/2020] [Indexed: 01/08/2023] Open
Abstract
According to a rough estimate, one in fifteen people worldwide is affected by a rare disease. Rare diseases are therefore common in clinical practice; however, timely diagnosis of rare diseases is still challenging. Introduction of novel methods based on next-generation sequencing (NGS) technology offers a successful diagnosis of genetically heterogeneous disorders, even in case of unclear clinical diagnostic hypothesis. However, the application of novel technology differs among the centres and health systems significantly. Our goal is to discuss the impact of the implementation of NGS in the diagnosis of rare diseases and present advantages along with challenges of diagnostic approach. Systematic implementation of NGS in health systems can significantly improve the access of patients with rare diseases to diagnosis and reduce the dependence of national health systems for cross-border collaboration.
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Affiliation(s)
- Mateja Vinkšel
- Clinical Institute of Genomic Medicine, University medical Centre Ljubljana, Zaloška cesta 7, Ljubljana, Slovenia
| | - Karin Writzl
- Clinical Institute of Genomic Medicine, University medical Centre Ljubljana, Zaloška cesta 7, Ljubljana, Slovenia
| | - Aleš Maver
- Clinical Institute of Genomic Medicine, University medical Centre Ljubljana, Zaloška cesta 7, Ljubljana, Slovenia
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University medical Centre Ljubljana, Zaloška cesta 7, Ljubljana, Slovenia.
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27
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Elliott AM, Dragojlovic N, Campbell T, Adam S, Souich CD, Fryer M, Lehman A, Karnebeek CV, Lynd LD, Friedman JM. Utilization of telehealth in paediatric genome-wide sequencing: Health services implementation issues in the CAUSES Study. J Telemed Telecare 2021; 29:318-327. [PMID: 33470133 DOI: 10.1177/1357633x20982737] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
INTRODUCTION Genome-wide sequencing (exome or whole genome) is transforming the care and management of paediatric patients with a rare disease because of its diagnostic capabilities. Genome-wide sequencing is most effective when both parents and the child are sequenced as a trio. Genetic counselling is recommended for all families considering genome-wide sequencing. Although telehealth is well established in genetic counselling for hereditary cancer and prenatal genetics, its use with genome-wide sequencing has not been well studied. The CAUSES Clinic at BC Children's and Women's Hospitals was a translational paediatric trio-based genome-wide sequencing initiative. Pre-test genetic counselling via telehealth (at a clinical site near the family's residence) was offered to families who had been previously evaluated by a clinical geneticist. We report on the first 300 families seen in the CAUSES clinic and compare health services implementation issues of families seen via telehealth versus on-site. METHODS Demographics, cost to families (travel and time), time to first appointment, complete trio sample accrual and diagnostic rates were studied. RESULTS Of the 300 patients, 58 (19%) were seen via telehealth and 242 (81%) were seen on-site for pre-test counselling. The mean time to completion of accrual of trio samples in the telehealth group was 56.3 (standard deviation ±87.3) days versus 18.9 (standard deviation ±62.4) days in the onsite group (p < 2.2 × 10-16). The mean per-family estimated actual or potential travel/time cost savings were greater in the telehealth group (Can$987; standard deviation = Can$1151) than for those seen on-site (Can$305; standard deviation = Can$589) (p = 0.0004). CONCLUSIONS Telehealth allowed for access to genome-wide sequencing for families in remote communities and for them to avoid significant travel and time costs; however, there was a significant delay to accrual of the complete trio samples in the telehealth group, impacting on time of result reporting and delaying diagnoses for families for whom genome-wide sequencing was diagnostic.
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Affiliation(s)
- Alison M Elliott
- Department of Medical Genetics, University of British Columbia, Canada.,BC Children's Hospital Research Institute, Canada.,Women's Health Research Institute, Canada
| | - Nick Dragojlovic
- Collaboration for Outcomes Research and Evaluation (CORE), University of British Columbia, Canada
| | - Teresa Campbell
- Department of Medical Genetics, University of British Columbia, Canada
| | - Shelin Adam
- Department of Medical Genetics, University of British Columbia, Canada.,BC Children's Hospital Research Institute, Canada
| | - Christèle du Souich
- Department of Medical Genetics, University of British Columbia, Canada.,BC Children's Hospital Research Institute, Canada
| | - Michele Fryer
- Office of Virtual Health, Provincial Health Services Authority, Canada
| | - Anna Lehman
- Department of Medical Genetics, University of British Columbia, Canada.,BC Children's Hospital Research Institute, Canada
| | - Clara van Karnebeek
- BC Children's Hospital Research Institute, Canada.,Emma Children's Hospital, University of Amsterdam, The Netherlands
| | - Larry D Lynd
- Collaboration for Outcomes Research and Evaluation (CORE), University of British Columbia, Canada.,Centre for Health Evaluation and Outcomes Sciences, Providence Health Research Institute, Canada
| | - Jan M Friedman
- Department of Medical Genetics, University of British Columbia, Canada.,BC Children's Hospital Research Institute, Canada
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28
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Vatsyayan A, Sharma P, Gupta S, Sandhu S, Venu SL, Sharma V, Badaoui B, Azedine K, Youssef S, Rajab A, Fayez A, Madinur S, Ranawat A, Pandhare K, Ramachandran S, Sivasubbu S, Scaria V. DALIA- a comprehensive resource of Disease Alleles in Arab population. PLoS One 2021; 16:e0244567. [PMID: 33439861 PMCID: PMC7806169 DOI: 10.1371/journal.pone.0244567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 12/11/2020] [Indexed: 11/18/2022] Open
Abstract
The Arab population encompasses over 420 million people characterized by genetic admixture and a consequent rich genetic diversity. A number of genetic diseases have been reported for the first time from the population. Additionally a high prevalence of some genetic diseases including autosomal recessive disorders such as hemoglobinopathies and familial mediterranean fever have been found in the population and across the region. There is a paucity of databases cataloguing genetic variants of clinical relevance from the population. The availability of such a catalog could have implications in precise diagnosis, genetic epidemiology and prevention of disease. To fill in the gap, we have compiled DALIA, a comprehensive compendium of genetic variants reported in literature and implicated in genetic diseases reported from the Arab population. The database aims to act as an effective resource for population-scale and sub-population specific variant analyses, enabling a ready reference aiding clinical interpretation of genetic variants, genetic epidemiology, as well as facilitating rapid screening and a quick reference for evaluating evidence on genetic diseases.
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Affiliation(s)
- Aastha Vatsyayan
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Amity University, Noida, India
| | - Parul Sharma
- Indraprastha Institute of Information Technology Delhi (IIIT-D), Delhi, India
| | - Shrey Gupta
- Indraprastha Institute of Information Technology Delhi (IIIT-D), Delhi, India
| | | | | | | | | | | | | | - Anna Rajab
- National Genetic Center, Ministry of Health, Muscat, Oman
| | - Alaaeldin Fayez
- Human Genetics and Genome Research Division, Center of Excellence for Human Genetics, National Research Center, Cairo, Egypt
| | | | - Anop Ranawat
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Kavita Pandhare
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Srinivasan Ramachandran
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Sridhar Sivasubbu
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Vinod Scaria
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- * E-mail:
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29
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Genomic testing in 1019 individuals from 349 Pakistani families results in high diagnostic yield and clinical utility. NPJ Genom Med 2020; 5:44. [PMID: 33083013 PMCID: PMC7536406 DOI: 10.1038/s41525-020-00150-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 08/06/2020] [Indexed: 11/08/2022] Open
Abstract
We implemented a collaborative diagnostic program in Lahore (Pakistan) aiming to establish the genetic diagnosis, and to asses diagnostic yield and clinical impact in patients with suspected genetic diseases. Local physicians ascertained pediatric patients who had no previous access to genetic testing. More than 1586 genetic tests were performed in 1019 individuals (349 index cases, 670 relatives). Most frequently performed tests were exome/genome sequencing (ES/GS, 284/78 index cases) and specific gene panels (55 index cases). In 61.3% of the patients (n = 214) a genetic diagnosis was established based on pathogenic and likely pathogenic variants. Diagnostic yield was higher in consanguineous families (60.1 vs. 39.5%). In 27 patients, genetic diagnosis relied on additional biochemical testing, allowing rapid assessment of the functional effect of the variants. Remarkably, the genetic diagnosis had a direct impact on clinical management. Most relevant consequences were therapy related such as initiation of the appropriated treatment in a timely manner in 51.9% of the patients (n = 111). Finally, we report 12 candidate genes among 66 cases with no genetic diagnosis. Importantly, three of these genes were validated as 'diagnostic' genes given the strong evidence supporting causality derived from our data repository (CAP2-dilated cardiomyopathy, ITFG2-intellectual disability and USP53-liver cholestasis). The high diagnostic yield, clinical impact, and research findings demonstrate the utility of genomic testing, especially when used as first-line genetic test. For patients with suspected genetic diseases from resource-limited regions, ES can be considered as the test of choice to achieve genetic diagnosis.
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30
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Solomon BD, Slavotinek AM. Announcing a new manuscript category for the American Journal of Medical Genetics Part A: Dispatches from Biotech. Am J Med Genet A 2020; 182:2003-2004. [PMID: 32700360 DOI: 10.1002/ajmg.a.61766] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 06/22/2020] [Indexed: 01/05/2023]
Affiliation(s)
| | - Anne M Slavotinek
- Division of Medical Genetics, Department of Pediatrics, University of California, San Francisco, San Francisco, California, USA
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31
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Palombo F, Graziano C, Al Wardy N, Nouri N, Marconi C, Magini P, Severi G, La Morgia C, Cantalupo G, Cordelli DM, Gangarossa S, Al Kindi MN, Al Khabouri M, Salehi M, Giorgio E, Brusco A, Pisani F, Romeo G, Carelli V, Pippucci T, Seri M. Autozygosity-driven genetic diagnosis in consanguineous families from Italy and the Greater Middle East. Hum Genet 2020; 139:1429-1441. [PMID: 32488467 DOI: 10.1007/s00439-020-02187-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 05/25/2020] [Indexed: 12/12/2022]
Abstract
Autozygosity-driven exome analysis has been shown effective for identification of genes underlying recessive diseases especially in countries of the so-called Greater Middle East (GME), where high consanguinity unravels the phenotypic effects of recessive alleles and large family sizes facilitate homozygosity mapping. In Italy, as in most European countries, consanguinity is estimated low. Nonetheless, consanguineous Italian families are not uncommon in publications of genetic findings and are often key to new associations of genes with rare diseases. We collected 52 patients from 47 consanguineous families with suspected recessive diseases, 29 originated in GME countries and 18 of Italian descent. We performed autozygosity-driven exome analysis by detecting long runs of homozygosity (ROHs > 1.5 Mb) and by prioritizing candidate clinical variants within. We identified a pathogenic synonymous variant that had been previously missed in NARS2 and we increased an initial high diagnostic rate (47%) to 55% by matchmaking our candidate genes and including in the analysis shorter ROHs that may also happen to be autozygous. GME and Italian families contributed to diagnostic yield comparably. We found no significant difference either in the extension of the autozygous genome, or in the distribution of candidate clinical variants between GME and Italian families, while we showed that the average autozygous genome was larger and the mean number of candidate clinical variants was significantly higher (p = 0.003) in mutation-positive than in mutation-negative individuals, suggesting that these features influence the likelihood that the disease is autozygosity-related. We highlight the utility of autozygosity-driven genomic analysis also in countries and/or communities, where consanguinity is not widespread cultural tradition.
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Affiliation(s)
- Flavia Palombo
- Medical Genetics Sant'Orsola, Malpighi University Hospital of Bologna, Via Massarenti 9, 40138, Bologna, Italy.,IRCCS Istituto Delle Scienze Neurologiche Di Bologna, UOC Clinica Neurologica, Bologna, Italy
| | - Claudio Graziano
- Medical Genetics Sant'Orsola, Malpighi University Hospital of Bologna, Via Massarenti 9, 40138, Bologna, Italy
| | - Nadia Al Wardy
- Department of Biochemistry, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Nayereh Nouri
- Department of Genetics and Molecular Biology, Isfahan University of Medical Sciences, Isfahan, Iran.,Craniofacial and Cleft Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Caterina Marconi
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
| | - Pamela Magini
- Medical Genetics Sant'Orsola, Malpighi University Hospital of Bologna, Via Massarenti 9, 40138, Bologna, Italy
| | - Giulia Severi
- Medical Genetics Sant'Orsola, Malpighi University Hospital of Bologna, Via Massarenti 9, 40138, Bologna, Italy
| | - Chiara La Morgia
- IRCCS Istituto Delle Scienze Neurologiche Di Bologna, UOC Clinica Neurologica, Bologna, Italy.,Department of Biomedical and Neuromotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Gaetano Cantalupo
- Child Neuropsychiatry, Department of Surgical Sciences, Dentistry, Gynecology and Pediatrics, University of Verona, Verona, Italy.,UOC Neuropsichiatria Infantile, DAI Materno-Infantile, AOUI Verona, Verona, Italy
| | - Duccio Maria Cordelli
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy.,Neuropsychiatry Sant'Orsola-Malpighi University Hospital of Bologna, Bologna, Italy
| | | | - Mohammed Nasser Al Kindi
- Department of Biochemistry, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Mazin Al Khabouri
- Department of Biochemistry, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman.,Department of ENT, Al Nahdha Hospital, Ministry of Health, Muscat, Oman
| | - Mansoor Salehi
- Department of Genetics and Molecular Biology, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Elisa Giorgio
- Department of Medical Sciences, University of Torino, Turin, Italy
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, Turin, Italy
| | - Francesco Pisani
- Child Neuropsychiatry Unit, Department of Medicine & Surgery, University of Parma, Parma, Italy
| | - Giovanni Romeo
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
| | - Valerio Carelli
- IRCCS Istituto Delle Scienze Neurologiche Di Bologna, UOC Clinica Neurologica, Bologna, Italy.,Department of Biomedical and Neuromotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Tommaso Pippucci
- Medical Genetics Sant'Orsola, Malpighi University Hospital of Bologna, Via Massarenti 9, 40138, Bologna, Italy.
| | - Marco Seri
- Medical Genetics Sant'Orsola, Malpighi University Hospital of Bologna, Via Massarenti 9, 40138, Bologna, Italy.,Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
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32
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Wilton KM, Morales‐Rosado JA, Selcen D, Muthusamy K, Ewing S, Agre K, Nickels K, Klee EW, Ho M, Morava E. Developmental brain abnormalities and acute encephalopathy in a patient with myopathy with extrapyramidal signs secondary to pathogenic variants in MICU1. JIMD Rep 2020; 53:22-28. [PMID: 32395406 PMCID: PMC7203647 DOI: 10.1002/jmd2.12114] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Revised: 02/09/2020] [Accepted: 03/03/2020] [Indexed: 01/01/2023] Open
Abstract
Mitochondria play a variety of roles in the cell, far beyond their widely recognized role in ATP generation. One such role is the regulation and sequestration of calcium, which is done with the help of the mitochondrial calcium uniporter (MCU) and its regulators, MICU1 and MICU2. Genetic variations in MICU1 and MICU2 have been reported to cause myopathy, developmental disability and neurological symptoms typical of mitochondrial disorders. The symptoms of MICU1/2 deficiency have generally been attributed to calcium regulation in the metabolic and biochemical roles of mitochondria. Here, we report a female child with heterozygous MICU1 variants and multiple congenital brain malformations on MRI. Specifically, she shows anterior perisylvian polymicrogyria, dysmorphic basal ganglia, and cerebellar dysplasia in addition to white matter abnormalities. These novel findings suggest that MICU1 is necessary for proper neurodevelopment through a variety of potential mechanisms, including calcium-mediated regulation of the neuronal cytoskeleton, Miro1-MCU complex-mediated mitochondrial movement, or enhancing ATP production. This case provides new insight into the molecular pathogenesis of MCU dysfunction and may represent a novel diagnostic feature of calcium-based mitochondrial disease.
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Affiliation(s)
- Katelynn M. Wilton
- Medical Scientist Training Program, Mayo Clinic Alix College of MedicineMayo ClinicRochesterMinnesotaUSA
| | - Joel A. Morales‐Rosado
- Center for Individualized MedicineMayo ClinicRochesterMinnesotaUSA
- Department of Health Science Research, Division of Biomedical Statistics and InformaticsMayo ClinicRochesterMinnesotaUSA
| | - Duygu Selcen
- Department of NeurologyMayo ClinicRochesterMinnesotaUSA
| | | | - Sarah Ewing
- Department of Clinical GenomicsMayo ClinicRochesterMinnesotaUSA
| | - Katherine Agre
- Department of Clinical GenomicsMayo ClinicRochesterMinnesotaUSA
| | | | - Eric W. Klee
- Center for Individualized MedicineMayo ClinicRochesterMinnesotaUSA
- Department of Health Science Research, Division of Biomedical Statistics and InformaticsMayo ClinicRochesterMinnesotaUSA
- Department of Clinical GenomicsMayo ClinicRochesterMinnesotaUSA
| | - Mai‐Lan Ho
- Department of RadiologyNationwide Children's HospitalColumbusOhioUSA
| | - Eva Morava
- Center for Individualized MedicineMayo ClinicRochesterMinnesotaUSA
- Department of Clinical GenomicsMayo ClinicRochesterMinnesotaUSA
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33
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Eaton A, Hartley T, Kernohan K, Ito Y, Lamont R, Parboosingh J, Barrowman N, Innes AM, Boycott K. When to think outside the autozygome: Best practices for exome sequencing in "consanguineous" families. Clin Genet 2020; 97:835-843. [PMID: 32162313 DOI: 10.1111/cge.13736] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/15/2020] [Accepted: 03/09/2020] [Indexed: 12/14/2022]
Abstract
Exome sequencing (ES) is an effective diagnostic tool with a high yield in consanguineous families. However, how diagnostic yield and mode of inheritance relate to family structure has not been well delineated. We reviewed ES results from families enrolled in the Care4Rare Canada research consortium with various degrees of consanguinity. We contrasted the diagnostic yield in families with parents who are second cousins or closer ("close" consanguinity) vs those more distantly related or from isolated populations ("presumed" consanguinity). We further stratified by number of affected individuals (multiple affected ["multiplex"] vs single affected [simplex]). The overall yield in 116 families was 45.7% (n = 53) with no significant difference between subgroups. Homozygous variants accounted for 100% and 75% of diagnoses in close and presumed consanguineous multiplex families, respectively. In simplex presumed consanguineous families, a striking 46.2% of diagnoses were due to de novo variants, vs only 11.8% in simplex closely consanguineous families (88.2% homozygous). Our data underscores the high yield of ES in consanguineous families and highlights that while a singleton approach may frequently be reasonable and a responsible use of resources, trio sequencing should be strongly considered in simplex families in the absence of confirmed consanguinity given the proportion of de novo variants.
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Affiliation(s)
- Alison Eaton
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Taila Hartley
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Kristin Kernohan
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada.,Newborn Screening Ontario, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Yoko Ito
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Ryan Lamont
- Alberta Children's Hospital Research Institute, Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Jillian Parboosingh
- Alberta Children's Hospital Research Institute, Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Nick Barrowman
- Clinical Research Unit, Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | -
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - A Micheil Innes
- Alberta Children's Hospital Research Institute, Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Kym Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
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34
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New Horizons for Molecular Genetics Diagnostic and Research in Autism Spectrum Disorder. ADVANCES IN NEUROBIOLOGY 2020; 24:43-81. [PMID: 32006356 DOI: 10.1007/978-3-030-30402-7_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Autism spectrum disorder (ASD) is a highly heritable, heterogeneous, and complex pervasive neurodevelopmental disorder (PND) characterized by distinctive abnormalities of human cognitive functions, social interaction, and speech development.Nowadays, several genetic changes including chromosome abnormalities, genetic variations, transcriptional epigenetics, and noncoding RNA have been identified in ASD. However, the association between these genetic modifications and ASDs has not been confirmed yet.The aim of this review is to summarize the key findings in ASD from genetic viewpoint that have been identified from the last few decades of genetic and molecular research.
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35
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Al-Dewik N, Mohd H, Al-Mureikhi M, Ali R, Al-Mesaifri F, Mahmoud L, Shahbeck N, El-Akouri K, Almulla M, Al Sulaiman R, Musa S, Al-Marri AAN, Richard G, Juusola J, Solomon BD, Alkuraya FS, Ben-Omran T. Clinical exome sequencing in 509 Middle Eastern families with suspected Mendelian diseases: The Qatari experience. Am J Med Genet A 2019; 179:927-935. [PMID: 30919572 PMCID: PMC6916397 DOI: 10.1002/ajmg.a.61126] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 01/22/2019] [Accepted: 02/25/2019] [Indexed: 12/24/2022]
Abstract
BACKGROUND Clinical exome sequencing (CES) is rapidly becoming the diagnostic test of choice in patients with suspected Mendelian diseases especially those that are heterogeneous in etiology and clinical presentation. Reporting large CES series can inform guidelines on best practices for test utilization, and improves accuracy of variant interpretation through clinically-oriented data sharing. METHODS This is a retrospective series of 509 probands from Qatar who underwent singleton or trio CES either as a reflex or naïve (first-tier) test from April 2014 to December 2016 for various clinical indications. RESULTS The CES diagnostic yield for the overall cohort was 48.3% (n = 246). Dual molecular diagnoses were observed in 2.1% of cases; nearly all of whom (91%) were consanguineous. We report compelling variants in 11 genes with no established Mendelian phenotypes. Unlike reflex-WES, naïve WES was associated with a significantly shorter diagnostic time (3 months vs. 18 months, p < 0.0001). CONCLUSION Middle Eastern patients tend to have a higher yield from CES than outbred populations, which has important implications in test choice especially early in the diagnostic process. The relatively high diagnostic rate is likely related to the predominance of recessive diagnoses (60%) since consanguinity and positive family history were strong predictors of a positive CES.
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Affiliation(s)
- Nader Al-Dewik
- Clinical and Metabolic Genetics, Department of Pediatrics, Hamad Medical Corporation, Doha, Qatar.,College of Health and Life Sciences, Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Howaida Mohd
- Clinical and Metabolic Genetics, Department of Pediatrics, Hamad Medical Corporation, Doha, Qatar
| | - Mariam Al-Mureikhi
- Clinical and Metabolic Genetics, Department of Pediatrics, Hamad Medical Corporation, Doha, Qatar
| | - Rehab Ali
- Clinical and Metabolic Genetics, Department of Pediatrics, Hamad Medical Corporation, Doha, Qatar
| | - Fatma Al-Mesaifri
- Clinical and Metabolic Genetics, Department of Pediatrics, Hamad Medical Corporation, Doha, Qatar
| | - Laila Mahmoud
- Clinical and Metabolic Genetics, Department of Pediatrics, Hamad Medical Corporation, Doha, Qatar
| | - Noora Shahbeck
- Clinical and Metabolic Genetics, Department of Pediatrics, Hamad Medical Corporation, Doha, Qatar
| | - Karen El-Akouri
- Clinical and Metabolic Genetics, Department of Pediatrics, Hamad Medical Corporation, Doha, Qatar
| | - Mariam Almulla
- Clinical and Metabolic Genetics, Department of Pediatrics, Hamad Medical Corporation, Doha, Qatar
| | - Reem Al Sulaiman
- Clinical and Metabolic Genetics, Department of Pediatrics, Hamad Medical Corporation, Doha, Qatar
| | - Sara Musa
- Clinical and Metabolic Genetics, Department of Pediatrics, Hamad Medical Corporation, Doha, Qatar
| | | | - Gabriele Richard
- Clinical Genomics Program, GeneDx, Inc., Gaithersburg, Maryland, USA
| | - Jane Juusola
- Clinical Genomics Program, GeneDx, Inc., Gaithersburg, Maryland, USA
| | | | - Fowzan S Alkuraya
- Department of Genetics, Research Center, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Tawfeg Ben-Omran
- Clinical and Metabolic Genetics, Department of Pediatrics, Hamad Medical Corporation, Doha, Qatar.,Department of pediatric, Weill Cornell Medical College, Doha, Qatar.,Division of Genetic & Genomics Medicine, Sidra Medicine, Doha, Qatar
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