1
|
Singh S, Shah H, Dalal A, Shukla A, Bhavani GS, Girisha KM. Two sisters with RSPRY1-related spondyloepimetaphyseal dysplasia. Am J Med Genet A 2024:e63601. [PMID: 38562122 DOI: 10.1002/ajmg.a.63601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/07/2024] [Accepted: 03/09/2024] [Indexed: 04/04/2024]
Abstract
Biallelic variants in RSPRY1 have been found to result in spondyloepimetaphyseal dysplasia. Two siblings presenting with short stature, facial dysmorphism, progressive vertebral defects, small epiphysis, cupping and fraying of metaphyses, brachydactyly, and short metatarsals harbored a homozygous missense variant c.1652G>A;p.(Cys551Tyr) in the RSPRY1 gene. The phenotype in our patients resembles spondyloepimetaphyseal dysplasia, Faden-Alkuraya type. Thus, our study provides further evidence to support the association of RSPRY1 variants with spondyloepimetaphyseal dysplasia. We observed joint dislocation as a novel clinical feature of this condition.
Collapse
Affiliation(s)
- Swati Singh
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Hitesh Shah
- Department of Pediatric Orthopedics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting & Diagnostics, Hyderabad, India
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Gandham SriLakshmi Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
- Department of Genetics, College of Medicine and Health Sciences, Sultan Qaboos University Muscat, Oman
| |
Collapse
|
2
|
Lavillaureix A, Rollier P, Kim A, Panasenkava V, De Tayrac M, Carré W, Guyodo H, Faoucher M, Poirel E, Akloul L, Quelin C, Whalen S, Bos J, Broekema M, van Hagen JM, Grand K, Allen-Sharpley M, Magness E, McLean S, Kayserili H, Altunoglu U, En Qi Chong A, Xue S, Jeanne M, Almontashiri N, Habhab W, Vanlerberghe C, Faivre L, Viora Dupont E, Philippe C, Safraou H, Laffargue F, Mittendorf L, Abou Jamra R, Patil SJ, Dalal A, Sarma AS, Keren B, Reversade B, Dubourg C, Odent S, Dupé V. DISP1 deficiency: monoallelic and biallelic variants cause a spectrum of midline craniofacial malformations. Genet Med 2024:101126. [PMID: 38529886 DOI: 10.1016/j.gim.2024.101126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 03/21/2024] [Accepted: 03/21/2024] [Indexed: 03/27/2024] Open
Abstract
PURPOSE DISP1 encodes a transmembrane protein that regulates the secretion of the morphogen, Sonic hedgehog (SHH), a deficiency of which is a major cause of holoprosencephaly (HPE). This disorder covers a spectrum of brain and midline craniofacial malformations. The objective of the present study was to better delineate the clinical phenotypes associated with DISP1 variants. METHODS This study was based on the identification of at least one pathogenic variant of the DISP1 gene in individuals for whom detailed clinical data were available. RESULTS A total of 23 DISP1 variants were identified in heterozygous, compound heterozygous or homozygous states in 25 individuals with midline craniofacial defects. Most cases were minor forms of HPE, with craniofacial features such as orofacial cleft, solitary median maxillary central incisor (SMMCI), and congenital nasal pyriform aperture stenosis (CNPAS). These individuals had either monoallelic loss-of-function variants or biallelic missense variants in DISP1. In individuals with severe HPE, the DISP1 variants were commonly found associated with a variant in another HPE-linked gene (i.e. oligogenic inheritance). CONCLUSION The genetic findings we have acquired demonstrate a significant involvement of DISP1 variants in the phenotypic spectrum of midline defects. This underlines its importance as a crucial element in the efficient secretion of SHH. We also demonstrated that the very rare SMMCI-CNPAS combination is part of the DISP1-related phenotype. The present study highlights the clinical risks to be flagged up during genetic counseling after the discovery of a pathogenic DISP1 variant.
Collapse
Affiliation(s)
- Alinoë Lavillaureix
- Génétique clinique, Centre de Référence Maladies Rares CLAD-Ouest, ERN-ITHACA, FHU GenOMedS, CHU de Rennes, Rennes, France; Univ Rennes, CNRS, INSERM, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, ERL U1305, Rennes, France
| | - Paul Rollier
- Génétique clinique, Centre de Référence Maladies Rares CLAD-Ouest, ERN-ITHACA, FHU GenOMedS, CHU de Rennes, Rennes, France; Univ Rennes, CNRS, INSERM, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, ERL U1305, Rennes, France
| | - Artem Kim
- Univ Rennes, CNRS, INSERM, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, ERL U1305, Rennes, France; Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California
| | - Veranika Panasenkava
- Univ Rennes, CNRS, INSERM, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, ERL U1305, Rennes, France
| | - Marie De Tayrac
- Univ Rennes, CNRS, INSERM, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, ERL U1305, Rennes, France; Génétique Moléculaire et Génomique, FHU GenOMedS, CHU de Rennes, Rennes, France
| | - Wilfrid Carré
- Univ Rennes, CNRS, INSERM, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, ERL U1305, Rennes, France; Génétique Moléculaire et Génomique, FHU GenOMedS, CHU de Rennes, Rennes, France
| | - Hélène Guyodo
- Univ Rennes, CNRS, INSERM, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, ERL U1305, Rennes, France
| | - Marie Faoucher
- Univ Rennes, CNRS, INSERM, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, ERL U1305, Rennes, France; Génétique Moléculaire et Génomique, FHU GenOMedS, CHU de Rennes, Rennes, France
| | - Elisabeth Poirel
- Génétique clinique, Centre de Référence Maladies Rares CLAD-Ouest, ERN-ITHACA, FHU GenOMedS, CHU de Rennes, Rennes, France
| | - Linda Akloul
- Génétique clinique, Centre de Référence Maladies Rares CLAD-Ouest, ERN-ITHACA, FHU GenOMedS, CHU de Rennes, Rennes, France
| | - Chloe Quelin
- Génétique clinique, Centre de Référence Maladies Rares CLAD-Ouest, ERN-ITHACA, FHU GenOMedS, CHU de Rennes, Rennes, France
| | - Sandra Whalen
- APHP, Sorbonne Université, Département de Génétique, Centre de Référence Maladies Rares des anomalies du développement et syndromes malformatifs, Hôpital Trousseau & Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | - Jessica Bos
- Department of Human Genetics, section Clinical Genetic, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Marjoleine Broekema
- Department of Human Genetics, section Clinical Genetic, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Johanna M van Hagen
- Department of Human Genetics, section Clinical Genetic, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Katheryn Grand
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | | | - Emily Magness
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Scott McLean
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Division of Clinical Genetics, Christus Children's, San Antonio, TX, USA
| | - Hülya Kayserili
- Department of Medical Genetics, Koç University School of Medicine, Istanbul, Turkey
| | - Umut Altunoglu
- Department of Medical Genetics, Koç University School of Medicine, Istanbul, Turkey
| | - Angie En Qi Chong
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Shifeng Xue
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Mederic Jeanne
- Service de génétique, FHU GenOMedS, CHRU de Tours, Tours, France; UMR1253, iBrain, Inserm, University of Tours, Tours, France
| | - Naif Almontashiri
- Center for Genetics and Inherited Diseases (CGID), Taibah University, Madinah, Saudi Arabia
| | - Wisam Habhab
- Department of Genetic Medicine, Faculty of Medicine, Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Laurence Faivre
- Centre de référence Anomalies du Développement et Syndromes Malformatifs, FHU TRANSLAD, Centre hospitalier Universitaire, Dijon, France; Genetics of Developmental Disorders, INSERM UMR1231, Université de Bourgogne, Dijon, France
| | - Eleonore Viora Dupont
- Centre de référence Déficiences intellectuelles de causes rares, FHU TRANSLAD, Centre hospitalier Universitaire, Dijon, France; Genetics of Developmental Disorders, INSERM UMR1231, Université de Bourgogne, Dijon, France
| | - Christophe Philippe
- Genetics of Developmental Disorders, INSERM UMR1231, Université de Bourgogne, Dijon, France; Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon, Dijon, France
| | - Hana Safraou
- Genetics of Developmental Disorders, INSERM UMR1231, Université de Bourgogne, Dijon, France; Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon, Dijon, France
| | - Fanny Laffargue
- CHU Clermont Ferrand, Service de génétique clinique, Clermont Ferrand - France
| | - Luisa Mittendorf
- Department for children and adolescents; University Hospital Leipzig, Leipzig, Germany
| | | | | | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, 500039, India
| | - Asodu Sandeep Sarma
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, 500039, India
| | - Boris Keren
- APHP, Sorbonne Université, Département de génétique médicale, GH Pitié Salpêtrière, 75013 Paris, France
| | - Bruno Reversade
- Laboratory of Human Genetics & Therapeutics, Genome Institute of Singapore (GIS), A*STAR, Department of Physiology, Cardiovascular Disease, Translational research programme, Yong Loo Lin School of Medicine, National. University of Singapore, Singapore. Department of Medical Genetics,Koç University School of Medicine, Istanbul, Turkey. Laboratory of Human Genetics & Therapeutics Smart-Health Initiative, BESE, KAUST, Thuwal, Kingdom of Saudi Arabia
| | - Christèle Dubourg
- Univ Rennes, CNRS, INSERM, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, ERL U1305, Rennes, France; Génétique Moléculaire et Génomique, FHU GenOMedS, CHU de Rennes, Rennes, France
| | - Sylvie Odent
- Génétique clinique, Centre de Référence Maladies Rares CLAD-Ouest, ERN-ITHACA, FHU GenOMedS, CHU de Rennes, Rennes, France; Univ Rennes, CNRS, INSERM, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, ERL U1305, Rennes, France
| | - Valérie Dupé
- Univ Rennes, CNRS, INSERM, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, ERL U1305, Rennes, France.
| |
Collapse
|
3
|
Mathews I, Wagh S, Baby A, Chandrashekar L, Dalal A. Basan syndrome in a family from South India: a novel SMARCAD1 variant. Clin Exp Dermatol 2024; 49:437-440. [PMID: 37966719 DOI: 10.1093/ced/llad393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 10/29/2023] [Accepted: 11/08/2023] [Indexed: 11/16/2023]
Abstract
Basan syndrome is a rare ectodermal dysplasia characterized by a triad of adermatoglyphia, reticulate pigmentation and nail dystrophy, in addition to transient neonatal findings of acral blistering and facial milia. The genetic basis was recently established to be heterozygous mutations affecting the skin-specific isoform of SMARCAD1. It is now considered part of the spectrum of disorders resulting from haploinsufficiency of this isoform, which includes both Huriez syndrome and autosomal dominant adermatoglyphia. Here, we describe a family with Basan syndrome from South India with a novel SMARCAD1 variant (c.378+1delGTAA) affecting the known mutational hotspot in exon 1.
Collapse
Affiliation(s)
- Irene Mathews
- Department of Dermatology, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
- Department of Dermatology, AIIMS, Patna, India
| | - Shivangi Wagh
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India
| | - Aimin Baby
- Department of Dermatology, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
| | - Laxmisha Chandrashekar
- Department of Dermatology, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
| | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India
| |
Collapse
|
4
|
Nair LS, Nurul Jain JM, Dalal A, Ranganath P. Etiologic Spectrum of Pediatric-Onset Leukodystrophies and Genetic Leukoencephalopathies: The Five-Year Experience of a Tertiary Care Center in Southern India. Pediatr Neurol 2024; 152:130-152. [PMID: 38277958 DOI: 10.1016/j.pediatrneurol.2023.12.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 07/28/2023] [Accepted: 12/29/2023] [Indexed: 01/28/2024]
Abstract
BACKGROUND White matter (WM) disorders with a genetic etiology are classified as leukodystrophies (LDs) and genetic leukoencephalopathies (GLEs). There are very few studies pertaining to the etiologic spectrum of these disorders in the Asian Indian population. METHODS This study was conducted over a period of five years from January 2016 to December 2020, in the medical genetics department of a tertiary care hospital in southern India. A total of 107 patients up to age 18 years, with a diagnosis of a genetic WM disorder confirmed by molecular genetic testing and/or metabolic testing, were included in the study and categorized into LD or GLE group as per the classification suggested by the Global Leukodystrophy Initiative consortium in 2015. RESULTS Forty-one patients were diagnosed to have LDs, and 66 patients had GLEs. The two most common LDs were metachromatic LD (16 patients) and X-linked adrenoleukodystrophy (seven patients). In the GLE group, lysosomal storage disorders were the most common (40 patients) followed by mitochondrial disorders (nine patients), with other metabolic disorders and miscellaneous conditions making up the rest. The clinical presentations, neuroimaging findings, and mutation spectrum of the patients in our cohort are discussed. CONCLUSIONS This is one of the largest cohorts of genetic WM disorders reported till date from the Asian Indian population. The etiologies and clinical presentations identified in our study cohort are similar to those found in other Indian studies as well as in studies based on other populations from different parts of the world.
Collapse
Affiliation(s)
- Lekshmi S Nair
- Senior Resident, Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, Telangana, India
| | - Jamal Mohammed Nurul Jain
- Technical Officer, Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India
| | - Ashwin Dalal
- Head, Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India
| | - Prajnya Ranganath
- Additional Professor and Head, Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, Telangana, India; Adjunct Scientist, Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India.
| |
Collapse
|
5
|
Sithambaram S, Jacob P, Neethukrishna K, Bhavani GS, Dalal A, Shah H, Girisha KM. PRKACA-related, atrial defects-polydactyly-multiple congenital malformation syndrome in an Indian patient. Am J Med Genet A 2024:e63566. [PMID: 38357848 DOI: 10.1002/ajmg.a.63566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/16/2024] [Accepted: 01/27/2024] [Indexed: 02/16/2024]
Abstract
PRKACA-related, atrial defects-polydactyly-multiple congenital malformation syndrome is a recently described skeletal ciliopathy, which is caused by disease-causing variants in PRKACA. The primary phenotypic description includes atrial septal defects, and limb anomalies including polydactyly and short limbs. To date, only four molecularly proven patients have been reported in the literature with a recurrent variant, c.409G>A p.Gly137Arg in PRKACA. In this study, we report the fifth affected individual with the same variant and review the clinical features and radiographic findings of this rare syndrome.
Collapse
Affiliation(s)
| | - Prince Jacob
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Kausthubham Neethukrishna
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Gandham SriLakshmi Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting & Diagnostics, Hyderabad, India
| | - Hitesh Shah
- Department of Pediatric Orthopaedics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
- Department of Genetics, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| |
Collapse
|
6
|
Gonawala L, Wijekoon N, Attanayake D, Ratnayake P, Sirisena D, Gunasekara H, Dissanayake A, Keshavaraj A, Mohan C, Steinbusch HWM, Hoffman EP, Dalal A, de Silva KRD. Diagnostic outcome of pro bono neurogenetic diagnostic service in Sri Lanka: A wealth creation. Eur J Hum Genet 2024:10.1038/s41431-023-01525-3. [PMID: 38253783 DOI: 10.1038/s41431-023-01525-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 11/29/2023] [Accepted: 12/14/2023] [Indexed: 01/24/2024] Open
Abstract
The inherited disease community in Sri Lanka has been widely neglected. This article aimed to present accumulated knowledge in establishing a pro bono cost-effective national, island-wide, free-of-charge molecular diagnostic service, suggesting a model for other developing countries. The project provided 637 molecular diagnostic tests and reports free of charge to a nation with limited resources. We pioneered the implementation of mobile clinics and home visits, where the research team acted as barefoot doctors with the concept of the doctor and the researcher at the patient's doorstep. Establishing pro bono, cost-effective molecular diagnostics is feasible in developing countries with limited resources and state funding through the effort of dedicated postgraduate students. This service could provide an accurate molecular diagnosis of Duchenne muscular dystrophy, Huntington's disease, Spinocerebellar ataxia, and Spinal muscular atrophy, a diagnostic yield of 54% (343/637), of which 43% (147/343) of the patients identified as amenable for available gene therapies. Initiated human resource development by double doctoral degree opportunities with international collaborations. Established a neurobiobank and a national registry in Sri Lanka, a rich and unique repository, wealth creation for translational collaborative research and sharing of information in neurological diseases, as well as a lodestar for aspiring initiatives from other developing countries.
Collapse
Affiliation(s)
- Lakmal Gonawala
- Centre for Innovations in Biotechnology and Neuroscience, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, 10250, Sri Lanka
- Department of Cellular and Translational Neuroscience, School for Mental Health and Neuroscience, Faculty of Health, Medicine & Life Sciences, Maastricht University, 6200, Maastricht, The Netherlands
| | - Nalaka Wijekoon
- Centre for Innovations in Biotechnology and Neuroscience, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, 10250, Sri Lanka
- Department of Cellular and Translational Neuroscience, School for Mental Health and Neuroscience, Faculty of Health, Medicine & Life Sciences, Maastricht University, 6200, Maastricht, The Netherlands
| | - Darshika Attanayake
- Centre for Innovations in Biotechnology and Neuroscience, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, 10250, Sri Lanka
| | | | | | | | | | | | - Chandra Mohan
- Department of Bioengineering, University of Houston, Houston, TX, USA
| | - Harry W M Steinbusch
- Department of Cellular and Translational Neuroscience, School for Mental Health and Neuroscience, Faculty of Health, Medicine & Life Sciences, Maastricht University, 6200, Maastricht, The Netherlands
| | - Eric P Hoffman
- School of Pharmacy and Pharmaceutical Sciences, Binghamton University, New York, USA
| | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India
| | - K Ranil D de Silva
- Centre for Innovations in Biotechnology and Neuroscience, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, 10250, Sri Lanka.
- Department of Cellular and Translational Neuroscience, School for Mental Health and Neuroscience, Faculty of Health, Medicine & Life Sciences, Maastricht University, 6200, Maastricht, The Netherlands.
- Institute for Combinatorial Advanced Research and Education (KDU-CARE), General Sir John Kotelawala Defence University, Ratmalana, Sri Lanka.
| |
Collapse
|
7
|
Wijekoon N, Gonawala L, Ratnayake P, Liyanage R, Amaratunga D, Hathout Y, Steinbusch HWM, Dalal A, Hoffman EP, de Silva KRD. Title-molecular diagnostics of dystrophinopathies in Sri Lanka towards phenotype predictions: an insight from a South Asian resource limited setting. Eur J Med Res 2024; 29:37. [PMID: 38195599 PMCID: PMC10775540 DOI: 10.1186/s40001-023-01600-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 12/15/2023] [Indexed: 01/11/2024] Open
Abstract
BACKGROUND The phenotype of Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD) patients is determined by the type of DMD gene variation, its location, effect on reading frame, and its size. The primary objective of this investigation was to determine the frequency and distribution of DMD gene variants (deletions/duplications) in Sri Lanka through the utilization of a combined approach involving multiplex polymerase chain reaction (mPCR) followed by Multiplex Ligation Dependent Probe Amplification (MLPA) and compare to the international literature. The current consensus is that MLPA is a labor efficient yet expensive technique for identifying deletions and duplications in the DMD gene. METHODOLOGY Genetic analysis was performed in a cohort of 236 clinically suspected pediatric and adult myopathy patients in Sri Lanka, using mPCR and MLPA. A comparative analysis was conducted between our findings and literature data. RESULTS In the entire patient cohort (n = 236), mPCR solely was able to identify deletions in the DMD gene in 131/236 patients (DMD-120, BMD-11). In the same cohort, MLPA confirmed deletions in 149/236 patients [DMD-138, BMD -11]. These findings suggest that mPCR has a detection rate of 95% (131/138) among all patients who received a diagnosis. The distal and proximal deletion hotspots for DMD were exons 45-55 and 6-15. Exon 45-60 identified as a novel in-frame variation hotspot. Exon 45-59 was a hotspot for BMD deletions. Comparisons with the international literature show significant variations observed in deletion and duplication frequencies in DMD gene across different populations. CONCLUSION DMD gene deletions and duplications are concentrated in exons 45-55 and 2-20 respectively, which match global variation hotspots. Disparities in deletion and duplication frequencies were observed when comparing our data to other Asian and Western populations. Identified a 95% deletion detection rate for mPCR, making it a viable initial molecular diagnostic approach for low-resource countries where MLPA could be used to evaluate negative mPCR cases and cases with ambiguous mutation borders. Our findings may have important implications in the early identification of DMD with limited resources in Sri Lanka and to develop tailored molecular diagnostic algorithms that are regional and population specific and easily implemented in resource limited settings.
Collapse
Affiliation(s)
- Nalaka Wijekoon
- Interdisciplinary Center for Innovation in Biotechnology and Neuroscience, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, 10250, Sri Lanka
- Department of Cellular and Translational Neuroscience, School for Mental Health and Neuroscience, Faculty of Health, Medicine & Life Sciences, Maastricht University, 6200, Maastricht, The Netherlands
| | - Lakmal Gonawala
- Interdisciplinary Center for Innovation in Biotechnology and Neuroscience, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, 10250, Sri Lanka
- Department of Cellular and Translational Neuroscience, School for Mental Health and Neuroscience, Faculty of Health, Medicine & Life Sciences, Maastricht University, 6200, Maastricht, The Netherlands
| | | | - Roshan Liyanage
- Interdisciplinary Center for Innovation in Biotechnology and Neuroscience, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, 10250, Sri Lanka
| | | | - Yetrib Hathout
- School of Pharmacy and Pharmaceutical Sciences, Binghamton University, Binghamton, NY, 13902, USA
| | - Harry W M Steinbusch
- Department of Cellular and Translational Neuroscience, School for Mental Health and Neuroscience, Faculty of Health, Medicine & Life Sciences, Maastricht University, 6200, Maastricht, The Netherlands
| | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, 500039, India
| | - Eric P Hoffman
- School of Pharmacy and Pharmaceutical Sciences, Binghamton University, Binghamton, NY, 13902, USA
| | - K Ranil D de Silva
- Interdisciplinary Center for Innovation in Biotechnology and Neuroscience, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, 10250, Sri Lanka.
- Department of Cellular and Translational Neuroscience, School for Mental Health and Neuroscience, Faculty of Health, Medicine & Life Sciences, Maastricht University, 6200, Maastricht, The Netherlands.
- Institute for Combinatorial Advanced Research and Education (KDU-CARE), General Sir John Kotelawala Defence University, Ratmalana, 10390, Sri Lanka.
| |
Collapse
|
8
|
Kar A, P S, Dalal A. Rare genetic diseases in India: Steps toward a nationwide mission program. J Biosci 2024; 49:34. [PMID: 38383979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Rare genetic diseases are rare by themselves with prevalence of 1 in 25,000, but collectively they are a significant cause of morbidity and mortality. Till date, collectively there are more than 9,000 rare diseases documented, which impose a devastating impact on patients, their families, and the healthcare system, including enormous societal burden. Obtaining a conclusive diagnosis for a patient with a rare genetic disease can be long and gruelling. For some patients it takes months or years to receive a definite diagnosis, and around 50% of the patients remain undiagnosed even with expert clinical and advanced high-end laboratory investigations. Owing to the large population and practice of consanguinity the Indian population is a pool of indigenous variants and unreported phenotypes or diseases. A mission program on pediatric rare diseases is an unparalleled initiative to study unique clinical conditions via the use of latest state-of-art technologies and with the combination of a mulit-omics approach. Our initiative will not only provide diagnosis to patients with rare disease but also build a platform for translational research for rare disease screening, management, and treatment.
Collapse
Affiliation(s)
- Anjana Kar
- Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | | | | |
Collapse
|
9
|
Wilson LA, Macken WL, Perry LD, Record CJ, Schon KR, Frezatti RSS, Raga S, Naidu K, Köken ÖY, Polat I, Kapapa MM, Dominik N, Efthymiou S, Morsy H, Nel M, Fassad MR, Gao F, Patel K, Schoonen M, Bisschoff M, Vorster A, Jonvik H, Human R, Lubbe E, Nonyane M, Vengalil S, Nashi S, Srivastava K, Lemmers RJLF, Reyaz A, Mishra R, Töpf A, Trainor CI, Steyn EC, Mahungu AC, van der Vliet PJ, Ceylan AC, Hiz AS, Çavdarlı B, Semerci Gündüz CN, Ceylan GG, Nagappa M, Tallapaka KB, Govindaraj P, van der Maarel SM, Narayanappa G, Nandeesh BN, Wa Somwe S, Bearden DR, Kvalsund MP, Ramdharry GM, Oktay Y, Yiş U, Topaloğlu H, Sarkozy A, Bugiardini E, Henning F, Wilmshurst JM, Heckmann JM, McFarland R, Taylor RW, Smuts I, van der Westhuizen FH, Sobreira CFDR, Tomaselli PJ, Marques W, Bhatia R, Dalal A, Srivastava MVP, Yareeda S, Nalini A, Vishnu VY, Thangaraj K, Straub V, Horvath R, Chinnery PF, Pitceathly RDS, Muntoni F, Houlden H, Vandrovcova J, Reilly MM, Hanna MG. Neuromuscular disease genetics in under-represented populations: increasing data diversity. Brain 2023; 146:5098-5109. [PMID: 37516995 PMCID: PMC10690022 DOI: 10.1093/brain/awad254] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 07/04/2023] [Indexed: 08/01/2023] Open
Abstract
Neuromuscular diseases (NMDs) affect ∼15 million people globally. In high income settings DNA-based diagnosis has transformed care pathways and led to gene-specific therapies. However, most affected families are in low-to-middle income countries (LMICs) with limited access to DNA-based diagnosis. Most (86%) published genetic data is derived from European ancestry. This marked genetic data inequality hampers understanding of genetic diversity and hinders accurate genetic diagnosis in all income settings. We developed a cloud-based transcontinental partnership to build diverse, deeply-phenotyped and genetically characterized cohorts to improve genetic architecture knowledge, and potentially advance diagnosis and clinical management. We connected 18 centres in Brazil, India, South Africa, Turkey, Zambia, Netherlands and the UK. We co-developed a cloud-based data solution and trained 17 international neurology fellows in clinical genomic data interpretation. Single gene and whole exome data were analysed via a bespoke bioinformatics pipeline and reviewed alongside clinical and phenotypic data in global webinars to inform genetic outcome decisions. We recruited 6001 participants in the first 43 months. Initial genetic analyses 'solved' or 'possibly solved' ∼56% probands overall. In-depth genetic data review of the four commonest clinical categories (limb girdle muscular dystrophy, inherited peripheral neuropathies, congenital myopathy/muscular dystrophies and Duchenne/Becker muscular dystrophy) delivered a ∼59% 'solved' and ∼13% 'possibly solved' outcome. Almost 29% of disease causing variants were novel, increasing diverse pathogenic variant knowledge. Unsolved participants represent a new discovery cohort. The dataset provides a large resource from under-represented populations for genetic and translational research. In conclusion, we established a remote transcontinental partnership to assess genetic architecture of NMDs across diverse populations. It supported DNA-based diagnosis, potentially enabling genetic counselling, care pathways and eligibility for gene-specific trials. Similar virtual partnerships could be adopted by other areas of global genomic neurological practice to reduce genetic data inequality and benefit patients globally.
Collapse
Affiliation(s)
- Lindsay A Wilson
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK
| | - William L Macken
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK
| | - Luke D Perry
- Institute of Child Health and Centre for Neuromuscular Diseases, Neurosciences Unit, The Dubowitz Neuromuscular Centre, University College London, UCL Great Ormond Street, Great Ormond Street Hospital, London WC1N 3JH, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Christopher J Record
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK
| | - Katherine R Schon
- Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Rodrigo S S Frezatti
- Department of Neurosciences, School of Medicine of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Sharika Raga
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Division of Paediatric Neurology, Department of Paediatrics and Child Health, Red Cross War Memorial Children’s Hospital, Cape Town, South Africa
| | - Kireshnee Naidu
- Neurology Research Group, Division of Neurology, Department of Medicine, University of Cape Town, Cape Town, South Africa
- Division of Neurology, Department of Medicine, Stellenbosch University, Cape Town, South Africa
| | - Özlem Yayıcı Köken
- Faculty of Medicine, Department of Pediatric Neurology, Akdeniz University, Antalya, Turkey
| | - Ipek Polat
- Faculty of Medicine, Pediatric Neurology Department, Dokuz Eylül University, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
| | - Musambo M Kapapa
- Department of Physiotherapy, University of Zambia School of Health Sciences & University Teaching Hospital Neurology Research Office, Lusaka, Zambia
| | - Natalia Dominik
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK
| | - Stephanie Efthymiou
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK
| | - Heba Morsy
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK
| | - Melissa Nel
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Neurology Research Group, Division of Neurology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Mahmoud R Fassad
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Fei Gao
- Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Krutik Patel
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Maryke Schoonen
- Focus Area for Human Metabolomics, North-West University, Potchefstroom, South Africa
| | - Michelle Bisschoff
- Focus Area for Human Metabolomics, North-West University, Potchefstroom, South Africa
| | - Armand Vorster
- Focus Area for Human Metabolomics, North-West University, Potchefstroom, South Africa
| | - Hallgeir Jonvik
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK
| | - Ronel Human
- Department of Paediatrics, Steve Biko Academic Hospital, University of Pretoria, Pretoria, South Africa
| | - Elsa Lubbe
- Department of Paediatrics, Steve Biko Academic Hospital, University of Pretoria, Pretoria, South Africa
| | - Malebo Nonyane
- Department of Paediatrics, Steve Biko Academic Hospital, University of Pretoria, Pretoria, South Africa
| | - Seena Vengalil
- Department of Neurology, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, India
| | - Saraswati Nashi
- Department of Neurology, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, India
| | - Kosha Srivastava
- Department of Neurology, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, India
| | - Richard J L F Lemmers
- Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Alisha Reyaz
- Department of Neurology, All India Institute of Medical Sciences (AIIMS), Delhi, India
| | - Rinkle Mishra
- Department of Neurology, All India Institute of Medical Sciences (AIIMS), Delhi, India
| | - Ana Töpf
- John Walton Muscular Dystrophy Research Centre, Newcastle University Translational and Clinical Research Institute and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Christina I Trainor
- John Walton Muscular Dystrophy Research Centre, Newcastle University Translational and Clinical Research Institute and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Elizabeth C Steyn
- Neurology Research Group, Division of Neurology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Amokelani C Mahungu
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Neurology Research Group, Division of Neurology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Patrick J van der Vliet
- Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Ahmet Cevdet Ceylan
- Department of Medical Genetics, Ankara Bilkent City Hospital, Ankara, Turkey
- Faculty of Medicine, Department of Medical Genetics, Ankara Yıldırım Beyazıt University, Ankara, Turkey
| | - A Semra Hiz
- Faculty of Medicine, Pediatric Neurology Department, Dokuz Eylül University, Izmir, Turkey
- Izmir Biomedicine and Genome Center (IBG), Izmir, Turkey
| | - Büşranur Çavdarlı
- Department of Medical Genetics, Ankara Bilkent City Hospital, Ankara, Turkey
| | - C Nur Semerci Gündüz
- Department of Medical Genetics, Ankara Bilkent City Hospital, Ankara, Turkey
- Faculty of Medicine, Department of Medical Genetics, Ankara Yıldırım Beyazıt University, Ankara, Turkey
| | - Gülay Güleç Ceylan
- Department of Medical Genetics, Ankara Bilkent City Hospital, Ankara, Turkey
- Faculty of Medicine, Department of Medical Genetics, Ankara Yıldırım Beyazıt University, Ankara, Turkey
| | - Madhu Nagappa
- Department of Neurology, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, India
| | - Karthik B Tallapaka
- CSIR—Centre for Cellular and Molecular Biology (CCMB), Hyderabad, Telangana, India
| | - Periyasamy Govindaraj
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India
| | | | - Gayathri Narayanappa
- Department of Neuropathology, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, India
| | - Bevinahalli N Nandeesh
- Department of Neuropathology, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, India
| | - Somwe Wa Somwe
- Department of Clinical Sciences, School of Medicine and Health Sciences, University of Lusaka, Lusaka, Zambia
| | - David R Bearden
- University of Zambia Department of Educational Psychology, Lusaka, Zambia
- Department of Neurology, School of Medicine and Dentistry, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Michelle P Kvalsund
- Department of Neurology, School of Medicine and Dentistry, University of Rochester Medical Center, Rochester, NY 14642, USA
- Department of Internal Medicine, University of Zambia School of Medicine, Lusaka, Zambia
| | - Gita M Ramdharry
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK
| | - Yavuz Oktay
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
- Izmir Biomedicine and Genome Center (IBG), Izmir, Turkey
| | - Uluç Yiş
- Faculty of Medicine, Pediatric Neurology Department, Dokuz Eylül University, Izmir, Turkey
| | | | - Anna Sarkozy
- NIHR Great Ormond Street Hospital Biomedical Research Centre, UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Enrico Bugiardini
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK
| | - Franclo Henning
- Division of Neurology, Department of Medicine, Stellenbosch University, Cape Town, South Africa
| | - Jo M Wilmshurst
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Division of Paediatric Neurology, Department of Paediatrics and Child Health, Red Cross War Memorial Children’s Hospital, Cape Town, South Africa
| | - Jeannine M Heckmann
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Neurology Research Group, Division of Neurology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Robert McFarland
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne NE1 4LP, UK
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne NE1 4LP, UK
| | - Izelle Smuts
- Department of Paediatrics, Steve Biko Academic Hospital, University of Pretoria, Pretoria, South Africa
| | | | | | - Pedro J Tomaselli
- Department of Neurosciences, School of Medicine of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Wilson Marques
- Department of Neurosciences, School of Medicine of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Rohit Bhatia
- Department of Neurology, All India Institute of Medical Sciences (AIIMS), Delhi, India
| | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India
| | - M V Padma Srivastava
- Department of Neurology, All India Institute of Medical Sciences (AIIMS), Delhi, India
| | - Sireesha Yareeda
- Department of Neurology, Nizam’s Institute of Medical Sciences (NIMS), Hyderabad, Telangana, India
| | - Atchayaram Nalini
- Department of Neurology, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, India
| | - Venugopalan Y Vishnu
- Department of Neurology, All India Institute of Medical Sciences (AIIMS), Delhi, India
| | - Kumarasamy Thangaraj
- CSIR—Centre for Cellular and Molecular Biology (CCMB), Hyderabad, Telangana, India
| | - Volker Straub
- John Walton Muscular Dystrophy Research Centre, Newcastle University Translational and Clinical Research Institute and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Rita Horvath
- Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Patrick F Chinnery
- Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Robert D S Pitceathly
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK
| | - Francesco Muntoni
- Institute of Child Health and Centre for Neuromuscular Diseases, Neurosciences Unit, The Dubowitz Neuromuscular Centre, University College London, UCL Great Ormond Street, Great Ormond Street Hospital, London WC1N 3JH, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK
| | - Jana Vandrovcova
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK
| | - Mary M Reilly
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK
| | - Michael G Hanna
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK
| |
Collapse
|
10
|
Jacob P, Bhavani GS, Udupa P, Wang Z, Hariharan SV, Delampady K, Dalal A, Kamath N, Ikegawa S, Shenoy RD, Handattu K, Shah H, Girisha KM. Exome Sequencing in Monogenic Forms of Rickets. Indian J Pediatr 2023; 90:1182-1190. [PMID: 36692815 PMCID: PMC10627992 DOI: 10.1007/s12098-022-04393-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 09/27/2022] [Indexed: 01/25/2023]
Abstract
OBJECTIVE To understand the phenotypic and genotypic spectrum of genetic forms of rickets in 10 families. METHODS Detailed clinical, radiographic, and biochemical evaluation of 10 families with phenotypes suggestive of a genetic cause of rickets was performed. Molecular testing using exome sequencing aided in the diagnosis of six different forms of known genetic causes. RESULTS Eleven disease-causing variants including five previously reported variants (CYP27B1:c.1319_1325dup, p.(Phe443Profs*24), VDR:c.1171C>T, p.(Arg391Cys), PHEX: c.1586_1586+1del, PHEX: c.1482+5G>C, PHEX: c.58C>T, p.(Arg20*)) and six novel variants (CYP27B1:c.974C>T, p.(Thr325Met), CYP27B1: c.1376G>A, p.(Arg459His), CYP2R1: c.595C>T, p.(Arg199*), CYP2R1:c.1330G>C, p.(Gly444Arg),SLC34A3:c.1336-11_1336-1del, SLC2A2: c.589G>C, p.(Val197Leu)) in the genes known to cause monogenic rickets were identified. CONCLUSION The authors hereby report a case series of individuals from India with a molecular diagnosis of rickets and provide the literature review which would help in enhancing the clinical and molecular profile for rapid and differential diagnosis of rickets.
Collapse
Affiliation(s)
- Prince Jacob
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Gandham SriLakshmi Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Prajna Udupa
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Zheng Wang
- Laboratory for Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Sankar V Hariharan
- Department of Pediatrics, Genetics Clinic, SAT Hospital, Government Medical College, Thiruvananthapuram, Kerala, India
| | - Kishan Delampady
- Department of Endocrinology, AJ Hospital & Research Center, Mangalore, Karnataka, India
| | - Ashwin Dalal
- Diagnostics Division, Center for DNA Fingerprinting & Diagnostics, Hyderabad, Telangana, India
| | - Nutan Kamath
- Department of Pediatrics, Kasturba Medical College, Mangalore, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Shiro Ikegawa
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
- Laboratory for Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Rathika D Shenoy
- Department of Pediatrics, K S Hegde Medical Academy, Nitte University, Mangalore, Karnataka, India
| | - Koushik Handattu
- Department of Pediatrics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Hitesh Shah
- Department of Pediatric Orthopedics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India.
| |
Collapse
|
11
|
Jacob P, Lindelöf H, Rustad CF, Sutton VR, Moosa S, Udupa P, Hammarsjö A, Bhavani GS, Batkovskyte D, Tveten K, Dalal A, Horemuzova E, Nordgren A, Tham E, Shah H, Merckoll E, Orellana L, Nishimura G, Girisha KM, Grigelioniene G. Clinical, genetic and structural delineation of RPL13-related spondyloepimetaphyseal dysplasia suggest extra-ribosomal functions of eL13. NPJ Genom Med 2023; 8:39. [PMID: 37993442 PMCID: PMC10665555 DOI: 10.1038/s41525-023-00380-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 10/10/2023] [Indexed: 11/24/2023] Open
Abstract
Spondyloepimetaphyseal dysplasia with severe short stature, RPL13-related (SEMD-RPL13), MIM#618728), is a rare autosomal dominant disorder characterized by short stature and skeletal changes such as mild spondylar and epimetaphyseal dysplasia affecting primarily the lower limbs. The genetic cause was first reported in 2019 by Le Caignec et al., and six disease-causing variants in the gene coding for a ribosomal protein, RPL13 (NM_000977.3) have been identified to date. This study presents clinical and radiographic data from 12 affected individuals aged 2-64 years from seven unrelated families, showing highly variable manifestations. The affected individuals showed a range from mild to severe short stature, retaining the same radiographic pattern of spondylar- and epi-metaphyseal dysplasia, but with varying severity of the hip and knee deformities. Two new missense variants, c.548 G>A, p.(Arg183His) and c.569 G>T, p.(Arg190Leu), and a previously known splice variant c.477+1G>A were identified, confirming mutational clustering in a highly specific RNA binding motif. Structural analysis and interpretation of the variants' impact on the protein suggests that disruption of extra-ribosomal functions of the protein through binding of mRNA may play a role in the skeletal phenotype of SEMD-RPL13. In addition, we present gonadal and somatic mosaicism for the condition.
Collapse
Affiliation(s)
- Prince Jacob
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Hillevi Lindelöf
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Cecilie F Rustad
- Department of Medial Genetics, Oslo University Hospital, Oslo, Norway
| | - Vernon Reid Sutton
- Department of Molecular & Human Genetics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA
| | - Shahida Moosa
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University and Medical Genetics, Tygerberg Hospital, Cape Town, South Africa
| | - Prajna Udupa
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Anna Hammarsjö
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Gandham SriLakshmi Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Dominyka Batkovskyte
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Kristian Tveten
- Department of Medical Genetics, Telemark Hospital Trust, Skien, Norway
| | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting & Diagnostics, Hyderabad, India
| | - Eva Horemuzova
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
- Institute of Biomedicine, Department of Laboratory Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Emma Tham
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Hitesh Shah
- Department of Pediatric Orthopedics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Else Merckoll
- Department of Radiology, Oslo University Hospital, Oslo, Norway
| | - Laura Orellana
- Protein Dynamics and Mutation lab, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Gen Nishimura
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Radiology, Musashino-Yowakai Hospital, Tokyo, Japan
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India.
| | - Giedre Grigelioniene
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.
| |
Collapse
|
12
|
Pasumarthi D, Ranganath P, Mandal K, Dhanya LN, Dalal A, Aggarwal S. Identification of three novel mutations in SLCO2A1 in Asian-Indians with Pachydermoperiostosis. Indian J Med Res 2023; 158:319-323. [PMID: 37861627 PMCID: PMC10720970 DOI: 10.4103/ijmr.ijmr_3353_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Indexed: 10/21/2023] Open
Affiliation(s)
- Divya Pasumarthi
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500 082, Telangana, India
| | - Priya Ranganath
- Department of Medical Genetics, Nizam’s Institute of Medical Sciences, Hyderabad 500 082, Telangana, India
| | - Kausik Mandal
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow 226 014, Uttar Pradesh, India
| | - Lakshmi N Dhanya
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow 226 014, Uttar Pradesh, India
| | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500 082, Telangana, India
| | - Shagun Aggarwal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500 082, Telangana, India
- Department of Medical Genetics, Nizam’s Institute of Medical Sciences, Hyderabad 500 082, Telangana, India
| |
Collapse
|
13
|
Wijekoon N, Gonawala L, Ratnayake P, Amaratunga D, Hathout Y, Mohan C, Steinbusch HWM, Dalal A, Hoffman EP, de Silva KRD. Duchenne Muscular Dystrophy from Brain to Muscle: The Role of Brain Dystrophin Isoforms in Motor Functions. J Clin Med 2023; 12:5637. [PMID: 37685704 PMCID: PMC10488491 DOI: 10.3390/jcm12175637] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/26/2023] [Accepted: 08/27/2023] [Indexed: 09/10/2023] Open
Abstract
Brain function and its effect on motor performance in Duchenne muscular dystrophy (DMD) is an emerging concept. The present study explored how cumulative dystrophin isoform loss, age, and a corticosteroid treatment affect DMD motor outcomes. A total of 133 genetically confirmed DMD patients from Sri Lanka were divided into two groups based on whether their shorter dystrophin isoforms (Dp140, Dp116, and Dp71) were affected: Group 1, containing patients with Dp140, Dp116, and Dp71 affected (n = 98), and Group 2, containing unaffected patients (n = 35). A subset of 52 patients (Group 1, n = 38; Group 2, n = 14) was followed for up to three follow-ups performed in an average of 28-month intervals. The effect of the cumulative loss of shorter dystrophin isoforms on the natural history of DMD was analyzed. A total of 74/133 (56%) patients encountered developmental delays, with 66/74 (89%) being in Group 1 and 8/74 (11%) being in Group 2 (p < 0.001). Motor developmental delays were predominant. The hip and knee muscular strength, according to the Medical Research Council (MRC) scale and the North Star Ambulatory Assessment (NSAA) activities, "standing on one leg R", "standing on one leg L", and "walk", declined rapidly in Group 1 (p < 0.001 In the follow-up analysis, Group 1 patients became wheelchair-bound at a younger age than those of Group 2 (p = 0.004). DMD motor dysfunction is linked to DMD mutations that affect shorter dystrophin isoforms. When stratifying individuals for clinical trials, considering the DMD mutation site and its impact on a shorter dystrophin isoform is crucial.
Collapse
Affiliation(s)
- Nalaka Wijekoon
- Interdisciplinary Center for Innovation in Biotechnology and Neuroscience, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda 10250, Sri Lanka; (N.W.); (L.G.)
- Department of Cellular and Translational Neuroscience, School for Mental Health and Neuroscience, Faculty of Health, Medicine & Life Sciences, Maastricht University, 6200 Maastricht, The Netherlands;
| | - Lakmal Gonawala
- Interdisciplinary Center for Innovation in Biotechnology and Neuroscience, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda 10250, Sri Lanka; (N.W.); (L.G.)
- Department of Cellular and Translational Neuroscience, School for Mental Health and Neuroscience, Faculty of Health, Medicine & Life Sciences, Maastricht University, 6200 Maastricht, The Netherlands;
| | | | | | - Yetrib Hathout
- School of Pharmacy and Pharmaceutical Sciences, Binghamton University, Binghamton, NY 13902, USA; (Y.H.); (E.P.H.)
| | - Chandra Mohan
- Department of Bioengineering, University of Houston, Houston, TX 77204, USA;
| | - Harry W. M. Steinbusch
- Department of Cellular and Translational Neuroscience, School for Mental Health and Neuroscience, Faculty of Health, Medicine & Life Sciences, Maastricht University, 6200 Maastricht, The Netherlands;
| | - Ashwin Dalal
- Diagnostics Division, Center for DNA Fingerprinting and Diagnostics, Hyderabad 500039, India;
| | - Eric P. Hoffman
- School of Pharmacy and Pharmaceutical Sciences, Binghamton University, Binghamton, NY 13902, USA; (Y.H.); (E.P.H.)
| | - K. Ranil D. de Silva
- Interdisciplinary Center for Innovation in Biotechnology and Neuroscience, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda 10250, Sri Lanka; (N.W.); (L.G.)
- Department of Cellular and Translational Neuroscience, School for Mental Health and Neuroscience, Faculty of Health, Medicine & Life Sciences, Maastricht University, 6200 Maastricht, The Netherlands;
- Institute for Combinatorial Advanced Research and Education (KDU-CARE), General Sir John Kotelawala Defence University, Ratmalana 10390, Sri Lanka
| |
Collapse
|
14
|
Wijekoon N, Gonawala L, Ratnayake P, Dissanayaka P, Gunarathne I, Amaratunga D, Liyanage R, Senanayaka S, Wijesekara S, Gunasekara HH, Vanarsa K, Castillo J, Hathout Y, Dalal A, Steinbusch HW, Hoffman E, Mohan C, de Silva KRD. Integrated genomic, proteomic and cognitive assessment in Duchenne Muscular Dystrophy suggest astrocyte centric pathology. Heliyon 2023; 9:e18530. [PMID: 37593636 PMCID: PMC10432191 DOI: 10.1016/j.heliyon.2023.e18530] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 07/15/2023] [Accepted: 07/20/2023] [Indexed: 08/19/2023] Open
Abstract
Introduction Documented Duchenne Muscular Dystrophy (DMD) biomarkers are confined to Caucasians and are poor indicators of cognitive difficulties and neuropsychological alterations. Materials and methods This study correlates serum protein signatures with cognitive performance in DMD patients of South Asian origin. Study included 25 DMD patients aged 6-16 years. Cognitive profiles were assessed by Wechsler Intelligence Scale for Children. Serum proteome profiling of 1317 proteins was performed in eight DMD patients and eight age-matched healthy volunteers. Results Among the several novel observations we report, better cognitive performance in DMD was associated with increased serum levels of MMP9 and FN1 but decreased Siglec-3, C4b, and C3b. Worse cognitive performance was associated with increased serum levels of LDH-H1 and PDGF-BB but reduced GDF-11, MMP12, TPSB2, and G1B. Secondly, better cognitive performance in Processing Speed (PSI) and Perceptual Reasoning (PRI) domains was associated with intact Dp116, Dp140, and Dp71 dystrophin isoforms while better performance in Verbal Comprehension (VCI) and Working Memory (WMI) domains was associated with intact Dp116 and Dp140 isoforms. Finally, functional pathways shared with Alzheimer's Disease (AD) point towards an astrocyte-centric model for DMD. Conclusion Astrocytic dysfunction leading to synaptic dysfunction reported previously in AD may be a common pathogenic mechanism underlying both AD and DMD, linking protein alterations to cognitive impairment. This new insight may pave the path towards novel therapeutic approaches targeting reactive astrocytes.
Collapse
Affiliation(s)
- Nalaka Wijekoon
- Interdisciplinary Center for Innovation in Biotechnology and Neuroscience, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, 10250, Sri Lanka
- Department of Cellular and Translational Neuroscience, School for Mental Health and Neuroscience, Faculty of Health, Medicine & Life Sciences, Maastricht University, Maastricht, The Netherlands
| | - Lakmal Gonawala
- Interdisciplinary Center for Innovation in Biotechnology and Neuroscience, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, 10250, Sri Lanka
- Department of Cellular and Translational Neuroscience, School for Mental Health and Neuroscience, Faculty of Health, Medicine & Life Sciences, Maastricht University, Maastricht, The Netherlands
| | | | - Pulasthi Dissanayaka
- Interdisciplinary Center for Innovation in Biotechnology and Neuroscience, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, 10250, Sri Lanka
| | - Isuru Gunarathne
- Interdisciplinary Center for Innovation in Biotechnology and Neuroscience, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, 10250, Sri Lanka
| | | | - Roshan Liyanage
- Interdisciplinary Center for Innovation in Biotechnology and Neuroscience, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, 10250, Sri Lanka
| | | | - Saraji Wijesekara
- Department of Pediatrics, University of Sri Jayewardenepura, 10250, Sri Lanka
- Colombo South Teaching Hospital, 10350, Sri Lanka
| | | | - Kamala Vanarsa
- Department of Bioengineering, University of Houston, Houston, 77204, USA
| | - Jessica Castillo
- Department of Bioengineering, University of Houston, Houston, 77204, USA
| | - Yetrib Hathout
- School of Pharmacy and Pharmaceutical Sciences, Binghamton University, New York, USA
| | - Ashwin Dalal
- Diagnostics Division, Center for DNA Fingerprinting and Diagnostics, India
| | - Harry W.M. Steinbusch
- Department of Cellular and Translational Neuroscience, School for Mental Health and Neuroscience, Faculty of Health, Medicine & Life Sciences, Maastricht University, Maastricht, The Netherlands
| | - Eric Hoffman
- School of Pharmacy and Pharmaceutical Sciences, Binghamton University, New York, USA
| | - Chandra Mohan
- Department of Bioengineering, University of Houston, Houston, 77204, USA
| | - K. Ranil D. de Silva
- Interdisciplinary Center for Innovation in Biotechnology and Neuroscience, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, 10250, Sri Lanka
- Department of Cellular and Translational Neuroscience, School for Mental Health and Neuroscience, Faculty of Health, Medicine & Life Sciences, Maastricht University, Maastricht, The Netherlands
- Institute for Combinatorial Advanced Research and Education (KDU-CARE), General Sir John Kotelawala Defence University, Ratmalana, 10390, Sri Lanka
| |
Collapse
|
15
|
Vengurlekar D, Walker C, Mahajan R, Dalal A, Chavan V, Galindo MA, Iyer A, Mansoor H, Silsarma A, Isaakidis P, Spencer H. Linezolid resistance in patients with drug-resistant TB. Int J Tuberc Lung Dis 2023; 27:567-569. [PMID: 37353865 DOI: 10.5588/ijtld.22.0632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2023] Open
Affiliation(s)
- D Vengurlekar
- Médecins Sans Frontières (MSF) Operational Centre Brussels, Mumbai, India
| | - C Walker
- MSF Operational Centre Brussels, Southern Africa Medical Unit, Cape Town, South Africa, MSF Luxembourg Operational Research Unit (LuxOR), Luxembourg, Luxembourg
| | - R Mahajan
- MSF Operational Centre Barcelona-Athens, New Delhi, India
| | - A Dalal
- Jupiter Hospital, Mumbai, India
| | - V Chavan
- Médecins Sans Frontières (MSF) Operational Centre Brussels, Mumbai, India
| | - M A Galindo
- Médecins Sans Frontières (MSF) Operational Centre Brussels, Mumbai, India
| | - A Iyer
- Médecins Sans Frontières (MSF) Operational Centre Brussels, Mumbai, India
| | - H Mansoor
- Médecins Sans Frontières (MSF) Operational Centre Brussels, Mumbai, India
| | - A Silsarma
- Médecins Sans Frontières (MSF) Operational Centre Brussels, Mumbai, India
| | - P Isaakidis
- MSF Operational Centre Brussels, Southern Africa Medical Unit, Cape Town, South Africa, Clinical and Molecular Epidemiology Unit, Department of Hygiene and Epidemiology, University of Ioannina School of Medicine, Ioannina, Greece
| | - H Spencer
- MSF Operational Centre Brussels, Southern Africa Medical Unit, Cape Town, South Africa
| |
Collapse
|
16
|
Sarma AS, Siddardha B, T PL, Ranganath P, Dalal A. A novel homozygous synonymous splicing variant in SELENOI gene causes spastic paraplegia 81. J Gene Med 2023; 25:e3501. [PMID: 36942482 DOI: 10.1002/jgm.3501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 02/28/2023] [Accepted: 03/17/2023] [Indexed: 03/23/2023] Open
Abstract
BACKGROUND Hereditary spastic paraplegia 81 is a recently identified, rare autosomal recessive disease, caused by biallelic pathogenic variants in the SELENOI gene, with only two families reported to date. The features documented in the two previous affected families include sensorineural deafness, blindness, cleft palate, delayed motor development, regression of motor skills, impaired intellectual development, poor speech and language acquisition, spasticity, hyperreflexia, white matter abnormalities and cerebral and cerebellar atrophy. METHODS In the present study, we performed exome sequencing analysis in a single family with two affected siblings to identify the genetic cause of complicated hereditary spastic paraplegia. The results were further confirmed by Sanger sequencing, cDNA analysis and 3D protein modelling. RESULTS Exome sequencing identified a homozygous, synonymous variant in the SELENOI gene (NM_033505.4:c.126G>A:p.(Lys42Lys)) in both of the siblings. Sanger sequencing confirmed the heterozygous status in both parents consistent with the autosomal recessive inheritance. This variant has been found to disrupt normal splicing and lead to skipping of exon 2, causing in-frame deletion of SELENOI N-terminal 23 amino acids [NM_033505.4:c.57_126del:p.(Tyr20_Lys42del)] and further leading to structural changes in the protein. CONCLUSIONS We report a novel homozygous synonymous variant in the SELENOI gene causing abnormal splicing in two patients affected with hereditary spastic paraplegia 81. This report further expands the phenotypic and genotypic spectrum of hereditary spastic paraplegia 81.
Collapse
Affiliation(s)
- Asodu Sandeep Sarma
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India
- Graduate Studies, Regional Centre for Biotechnology, Faridabad, Haryana, India
| | - Bathula Siddardha
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India
| | - Pragna Lakshmi T
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India
| | - Prajnya Ranganath
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, Telangana, India
| | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India
| |
Collapse
|
17
|
Vanaja MC, Jain JMN, Dalal A, Ranganath P. Long-range PCR amplification-based targeted enrichment & next generation sequencing: A cost-effective testing strategy for lysosomal storage disorders. Indian J Med Res 2023; 157:577-590. [PMID: 37530313 PMCID: PMC10466493 DOI: 10.4103/ijmr.ijmr_2707_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Indexed: 07/08/2023] Open
Abstract
Background & objectives Lysosomal storage disorders (LSDs) are genetic metabolic disorders which result from deficiency of lysosomal enzymes or defects in other lysosomal components. Molecular genetic testing of LSDs is required for diagnostic confirmation when lysosomal enzyme assays are not available or not feasible to perform, and for the identification of the disease causing genetic variants. The aim of this study was to develop a cost-effective, readily customizable and scalable molecular genetic testing strategy for LSDs. Methods A testing method was designed based on the in-house creation of selective amplicons through long range PCR amplification for targeted capture and enrichment of different LSD genes of interest, followed by next generation sequencing of pooled samples. Results In the first phase of the study, standardization and validation of the study protocol were done using 28 samples of affected probands and/or carrier parents (group A) with previously identified variants in seven genes, and in the second phase of the study, 30 samples of enzymatically confirmed or biopsy-proven patients with LSDs and/or their carrier parents who had not undergone any prior mutation analysis (group B) were tested and the sequence variants identified in them through the study method were validated by targeted Sanger sequencing. Interpretation & conclusions This testing approach was found to be reliable, easily customizable and cost-effective for the molecular genetic evaluation of LSDs. The same strategy may be applicable, especially in resource poor settings, for developing cost-effective multigene panel tests for other conditions with genetic heterogeneity.
Collapse
Affiliation(s)
- Maria Celestina Vanaja
- Diagnostics Division, Centre for DNA Fingerprinting & Diagnostics, Hyderabad, Telangana, India
| | | | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting & Diagnostics, Hyderabad, Telangana, India
| | - Prajnya Ranganath
- Diagnostics Division, Centre for DNA Fingerprinting & Diagnostics, Hyderabad, Telangana, India
- Department of Medical Genetics, Nizam’s Institute of Medical Sciences, Hyderabad, Telangana, India
| |
Collapse
|
18
|
Priestley JRC, Deshwar AR, Murthy H, D'Agostino MD, Dupuis L, Gangaram B, Gray C, Jobling R, Pannia E, Platzer K, Prescott K, Redman M, Rippert AL, Rosenfeld JA, Scott DA, Wang YW, Schmederer Z, Dalal A, Sarma AS, Skraban C, Dowling JJ, Mendoza-Londono R, Slavotinek A, Bhoj EJ. Monoallelic Loss of Function BMP2 Variants Result in BMP2-Related Skeletal Dysplasia Spectrum. Genet Med 2023:100863. [PMID: 37125634 DOI: 10.1016/j.gim.2023.100863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 04/17/2023] [Accepted: 04/18/2023] [Indexed: 05/02/2023] Open
Abstract
PURPOSE Bone morphogenic proteins (BMPs) regulate gene expression related to many critical developmental processes, including osteogenesis for which they are named. BMP2 is widely expressed in cells of mesenchymal origin, including bone, cartilage, skeletal and cardiac muscle, and adipose tissue. It also participates in neurodevelopment by inducing differentiation of neural stem cells. In humans, BMP2 variants result in a multiple congenital anomaly syndrome through a haploinsufficiency mechanism. We sought to expand the phenotypic spectrum and highlight phenotypes of patients harboring monoallelic missense variants in BMP2. METHODS We employed retrospective chart review to examine phenotypes from an international cohort of 18 individuals and compared these to published cases. Patient-derived missense variants were modeled in zebrafish to examine their effect on the ability of bmp2b to promote embryonic ventralization. RESULTS The presented cases recapitulated existing descriptions of BMP2-related disorder including craniofacial, cardiac, and skeletal anomalies and exhibit a wide phenotypic spectrum. We also identified patients with neural tube defects, structural brain anomalies, and endocrinopathies. Missense variants modeled in zebrafish resulted in loss of protein function. CONCLUSIONS We use this expansion of reported phenotypes to suggest multidisciplinary medical monitoring and management of patients with BMP2-related skeletal dysplasia spectrum.
Collapse
Affiliation(s)
- Jessica R C Priestley
- Division of Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Ashish R Deshwar
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children and the University of Toronto, Toronto, Ontario, Canada; Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Harsha Murthy
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Maria Daniela D'Agostino
- Division of Medical Genetics, Departments of Specialized Medicine and Human Genetics, McGill University Health Center, Montreal, Quebec, Canada
| | - Lucie Dupuis
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children and the University of Toronto, Toronto, Ontario, Canada
| | - Balram Gangaram
- Division of Medical Genetics, University of California San Francisco, San Francisco, California, USA
| | - Christopher Gray
- Division of Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Rebekah Jobling
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children and the University of Toronto, Toronto, Ontario, Canada; Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Emanuela Pannia
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Katrina Prescott
- Clinical Genetics, The Leeds Teaching Hospital NHS Trust, Leeds, West Yorkshire, UK
| | - Melody Redman
- Clinical Genetics, The Leeds Teaching Hospital NHS Trust, Leeds, West Yorkshire, UK
| | - Alyssa L Rippert
- Division of Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA; Baylor Genetics Laboratories, Houston, Texas, USA
| | - Daryl A Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA; Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas, USA
| | - Yi Wen Wang
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children and the University of Toronto, Toronto, Ontario, Canada; Division of Medical Genetics, Departments of Specialized Medicine and Human Genetics, McGill University Health Center, Montreal, Quebec, Canada
| | - Zelia Schmederer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany; Medizinisch Genetisches Zentrum, Munich, Germany
| | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Asodu Sandeep Sarma
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Cara Skraban
- Division of Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - James J Dowling
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada; Division of Neurology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Roberto Mendoza-Londono
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children and the University of Toronto, Toronto, Ontario, Canada
| | - Anne Slavotinek
- Division of Medical Genetics, University of California San Francisco, San Francisco, California, USA; Division of Human Genetics, Department of Pediatrics, Cincinnati Children's Hospital, Cincinnati, Ohio, USA
| | - Elizabeth J Bhoj
- Division of Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
| |
Collapse
|
19
|
Sarma AS, Peter Mathew R, Dalal A, Bhat V, Patil SJ. Familial monoallelic CYP26B1 truncating variant causes a syndromic craniosynostosis due to haploinsufficiency ? Eur J Med Genet 2023; 66:104772. [PMID: 37100236 DOI: 10.1016/j.ejmg.2023.104772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 04/17/2023] [Accepted: 04/22/2023] [Indexed: 04/28/2023]
Abstract
Autosomal recessive CYP26B1 disorder is characterised by syndromic craniosynostosis of variable severity, and survival ranging from prenatal lethality to survival into adulthood. Here we report on two related individuals of Asian-Indian origin with syndromic craniosynostosis characterised by craniosynostosis, and dysplastic radial heads, caused by monoallelic CYP26B1 likely pathogenic variant NM_019885.4:c.86C > A:p. (Ser29Ter). We propose the possibility of autosomal dominant phenotype of CYP26B1 variant.
Collapse
Affiliation(s)
- Asodu Sandeep Sarma
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, 500039, India; Graduate Studies, Regional Centre for Biotechnology, Faridabad, Haryana, India
| | - Rohan Peter Mathew
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, 500039, India; Graduate Studies, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, 500039, India
| | - Venkatraman Bhat
- Department of Radiology, Mazumdar Shaw Medical Centre, Narayana Hrudayalaya Hospitals, Bangalore, India
| | - Siddaramappa Jagdish Patil
- Division of Medical Genetics, Mazumdar Shaw Medical Centre, Narayana Hrudayalaya Hospitals, Bangalore, India.
| |
Collapse
|
20
|
Bhattacherjee A, Desa E, Lone KA, Jaiswal A, Tyagi S, Dalal A. Genotype first approach & familial segregation analysis help in the elucidation of disease-causing variant for fucosidosis. Indian J Med Res 2023; 157:363-366. [PMID: 37282399 PMCID: PMC10438398 DOI: 10.4103/ijmr.ijmr_3568_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Indexed: 06/08/2023] Open
Affiliation(s)
- Amrita Bhattacherjee
- Diagnostics Division, Centre for DNA Fingerprinting & Diagnostics, Hyderabad 500 039, India
| | - Elyska Desa
- Department of Pediatrics, Hospicio Hospital, Margao 403 601, Goa, India
| | - Kaisar Ahmad Lone
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting & Diagnostics, Hyderabad 500 039, India
| | - Arjita Jaiswal
- Diagnostics Division, Centre for DNA Fingerprinting & Diagnostics, Hyderabad 500 039, India
| | - Shweta Tyagi
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting & Diagnostics, Hyderabad 500 039, India
| | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting & Diagnostics, Hyderabad 500 039, India
| |
Collapse
|
21
|
Udupa P, Ghosh DK, Kausthubham N, Shah H, Bartakke S, Dalal A, Girisha KM, Bhavani GS. Genome sequencing identifies a large non-coding region deletion of SNX10 causing autosomal recessive osteopetrosis. J Hum Genet 2023; 68:287-290. [PMID: 36526684 PMCID: PMC10040338 DOI: 10.1038/s10038-022-01104-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/23/2022]
Abstract
Autosomal recessive osteopetrosis (ARO) is a rare genetic disorder caused by impaired osteoclast activity. In this study, we describe a 4-year-old boy with increased bone density due to osteopetrosis, autosomal recessive 8. Using genome sequencing, we identified a large deletion in the 5'-untranslated region (UTR) of SNX10 (sorting nexin 10), where the regulatory region of this gene is located. This large deletion resulted in the absence of the SNX10 transcript and led to abnormal osteoclast activity. SNX10 is one of the nine genes known to cause ARO, shown to interact with V-ATPase (vacuolar type H( + )-ATPase), as it plays an important role in bone resorption. Our study highlights the importance of regulatory regions in the 5'-UTR of SNX10 for its expression while also demonstrating the importance of genome sequencing for detecting large deletion of the regulatory region of SNX10.
Collapse
Affiliation(s)
- Prajna Udupa
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Debasish Kumar Ghosh
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Neethukrishna Kausthubham
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Hitesh Shah
- Department of Pediatric Orthopedics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Sandip Bartakke
- Department of Clinical Hematology, Aditya Birla Memorial Hospital, Pune, India
| | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Gandham SriLakshmi Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India.
| |
Collapse
|
22
|
Ranganath P, Dalal A. Does Every Child With Autism Need Investigations for Inborn Errors of Metabolism? Indian Pediatr 2023; 60:177-178. [PMID: 36916356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Affiliation(s)
- Prajnya Ranganath
- Department of Medical Genetics, Nizam's Institute of Medical Sciences (NIMS), Hyderabad, Telangana and Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana
| | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana.
| |
Collapse
|
23
|
Ranganath P, Dalal A. Does Every Child With Autism Need Investigations for Inborn Errors of Metabolism? Indian Pediatr 2023. [DOI: 10.1007/s13312-023-2828-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
|
24
|
Ranganath P, Vs V, Rungsung I, Dalal A, Aggarwal S. Next Generation Sequencing in a Case of Early Onset Hydrops: Closing the Loop on the Diagnostic Odyssey! Fetal Pediatr Pathol 2023; 42:103-109. [PMID: 35380090 DOI: 10.1080/15513815.2022.2058660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Non-immune fetal hydrops (NIFH) is an etiologically heterogeneous condition. Cardiac anomalies are one of the common causes of NIFH. Cardiac anomalies can be isolated, multifactorial malformations or have a genetic basis. PLD1 variants have been associated with developmental defects involving the right heart. We present a NIFH with a PLD1 associated right heart malformation. We describe a spontaneously aborted 14 weeks old NIFH fetus with a rudimentary right ventricle, pulmonary valve atresia and pulmonary artery stenosis found at fetopsy. After a normal microarray, whole exome sequencing revealed a homozygous missense variant c.2023 C > T (p. Arg675Trp) in the PLD1 gene. Conclusion: Detailed fetopsy and genetic evaluation in this NIFH allowed an etiological explanation, further corroborated the association of PLD1 gene variants and developmental right heart defects, and that this defect can be associated with NIHF.
Collapse
Affiliation(s)
- Priya Ranganath
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, Telangana, India
| | - Vineeth Vs
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India
| | - Ikromi Rungsung
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India
| | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India
| | - Shagun Aggarwal
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, Telangana, India
| |
Collapse
|
25
|
Wijekoon N, Gonawala L, Ratnayake P, Sirisena D, Gunasekara H, Dissanayake A, Senanayake S, Keshavaraj A, Hathout Y, Steinbusch HW, Mohan C, Dalal A, Hoffman E, D de Silva K. Gene therapy for selected neuromuscular and trinucleotide repeat disorders - An insight to subsume South Asia for multicenter clinical trials. IBRO Neurosci Rep 2023; 14:146-153. [PMID: 36819775 PMCID: PMC9931913 DOI: 10.1016/j.ibneur.2023.01.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 01/27/2023] [Indexed: 01/31/2023] Open
Abstract
Background In this article, the authors discuss how they utilized the genetic mutation data in Sri Lankan Duchenne muscular dystrophy (DMD), Spinal muscular atrophy (SMA), Spinocerebellar ataxia (SCA) and Huntington's disease (HD) patients and compare the available literature from South Asian countries to identifying potential candidates for available gene therapy for DMD, SMA, SCA and HD patients. Methods Rare disease patients (n = 623) with the characteristic clinical findings suspected of HD, SCA, SMA and Muscular Dystrophy were genetically confirmed using Multiplex Ligation Dependent Probe Amplification (MLPA), and single plex PCR. A survey was conducted in the "Wiley database on Gene Therapy Trials Worldwide" to identify DMD, SMA, SCA, and HD gene therapy clinical trials performed worldwide up to April 2021. In order to identify candidates for gene therapy in other neighboring countries we compared our findings with available literature from India and Pakistan which has utilized the same molecular diagnostic protocol to our study. Results From the overall cohort of 623 rare disease patients with the characteristic clinical findings suspected of HD, SCA, SMA and Muscular Dystrophy, n = 343 (55%) [Muscular Dystrophy- 65%; (DMD-139, Becker Muscular Dystrophy -BMD-11), SCA type 1-3-53% (SCA1-61,SCA2- 23, SCA3- 39), HD- 52% (45) and SMA- 34% (22)] patients were positive for molecular diagnostics by MLPA and single plex PCR. A total of 147 patients in Sri Lanka amenable to available gene therapy; [DMD-83, SMA-15 and HD-49] were identified. A comparison of Sri Lankan finding with available literature from India and Pakistan identified a total of 1257 patients [DMD-1076, SMA- 57, and HD-124] from these three South Asian Countries as amenable for existing gene therapy trials. DMD, SMA, and HD gene therapy clinical trials (113 studies) performed worldwide up to April 2021 were concentrated mostly (99%) in High Income Countries (HIC) and Upper Middle-Income Countries (UMIC). However, studies on the potential use of anti-sense oligonucleotides (ASO) for treatment of SCAs have yet to reach clinical trials. Conclusion Most genetic therapies for neurodegenerative and neuromuscular disorders have been evaluated for efficacy primarily in Western populations. No multicenter gene therapy clinical trial sites for DMD, SMA and HD in the South Asian region, leading to lack of knowledge on the safety and efficacy of such personalized therapies in other populations, including South Asians. By fostering collaboration between researchers, clinicians, patient advocacy groups, government and industry in gene therapy initiatives for the inherited-diseases community in the developing world would link the Global North and Global South and breathe life into the motto "Together we can make a difference".
Collapse
Key Words
- BMD, Becker muscular dystrophy
- Bio Bank
- DMD, Duchenne muscular dystrophy
- Developing Countries
- Duchenne Muscular Dystrophy
- EMA, European Medical Agency
- EMQN, European Molecular Quality Genetics Network
- FDA, U. S. Food and Drug Administration
- HD, Huntington’s disease
- HIC, High Income Countries
- Huntington’s Disease
- Indian Sub-continent
- MLPA, Multiplex Ligation Dependent Probe Amplification
- Neurogenetic Disorders
- SCA, Spinocerebellar ataxia
- SMA, Spinal muscular atrophy
- Spinal Muscular Atrophy
- Spinocerebellar Ataxia
- UMIC, Upper Middle Income Countries
- WTO, World Trade Organization
Collapse
Affiliation(s)
- Nalaka Wijekoon
- Interdisciplinary Centre for Innovations in Biotechnology and Neuroscience, University of Sri Jayewardenepura, Nugegoda, Sri Lanka,School for Mental Health and Neuroscience, Faculty of Health, Medicine & Life Sciences, Maastricht University, Maastricht, the Netherlands,EURON - European Graduate School of Neuroscience, the Netherlands
| | - Lakmal Gonawala
- Interdisciplinary Centre for Innovations in Biotechnology and Neuroscience, University of Sri Jayewardenepura, Nugegoda, Sri Lanka,School for Mental Health and Neuroscience, Faculty of Health, Medicine & Life Sciences, Maastricht University, Maastricht, the Netherlands,EURON - European Graduate School of Neuroscience, the Netherlands
| | | | | | | | | | | | | | - Yetrib Hathout
- Pharmaceutical Sciences Department, School of Pharmacy and Pharmaceutical Sciences, Binghamton University, New York, USA
| | - Harry W.M. Steinbusch
- School for Mental Health and Neuroscience, Faculty of Health, Medicine & Life Sciences, Maastricht University, Maastricht, the Netherlands,EURON - European Graduate School of Neuroscience, the Netherlands,Dept. of Brain & Cognitive Sciences, Daegu Gyeungbuk Institute of Science and Technology (DGIST), Daegu, Republic of Korea
| | - Chandra Mohan
- Department of Bioengineering, University of Houston, Houston, TX, USA
| | - Ashwin Dalal
- Diagnostics Division, Center for DNA Fingerprinting and Diagnostics, India
| | - Eric Hoffman
- Pharmaceutical Sciences Department, School of Pharmacy and Pharmaceutical Sciences, Binghamton University, New York, USA
| | - K.Ranil D de Silva
- Interdisciplinary Centre for Innovations in Biotechnology and Neuroscience, University of Sri Jayewardenepura, Nugegoda, Sri Lanka,EURON - European Graduate School of Neuroscience, the Netherlands,Institute for Combinatorial Advanced Research and Education (KDU-CARE), General Sir John Kotelawala Defence University, Ratmalana, Sri Lanka,Corresponding author at: Institute for Combinatorial Advanced Research and Education (KDU-CARE), General Sir John Kotelawala Defence University, Ratmalana, Sri Lanka.
| |
Collapse
|
26
|
Chieng CY, Dalal A, Ilankovan V. Occupational exposure and risk of oral and oropharyngeal squamous cell carcinoma: systematic review and 25-year retrospective cohort study of patients. Br J Oral Maxillofac Surg 2023; 61:39-48. [PMID: 36443129 DOI: 10.1016/j.bjoms.2022.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/23/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022]
Abstract
Social habits such as smoking and drinking alcohol are well-known causative agents for oral and oropharyngeal squamous cell carcinoma (OSCC/OPSCC). Human papillomavirus (HPV) is a known causative agent for OPSCC. However, we often encounter patients with no identifiable risk factors. There is growing evidence of the role of occupational carcinogens in the pathogenesis of oral cancer. The aim of this study therefore was to identify any occupational carcinogens linked to oral cancer. We carried out a systematic review of the literature using PubMed, EMBASE, and Medline, along with a retrospective review of patients treated in a regional unit over 25 years. Occupations were classified based on the UK Standard of Classification 2020. Data analysis was completed using the chi-squared test. A total of 17 papers met the inclusion criteria for review. In our retrospective study a total of 874 patients were identified of whom 31% were blue-collar workers, 32.8% were white-collar workers, 20.2% were unemployed/housewives, and 16% workers in other occupations. The majority of blue-collar workers were in the construction industry and had maximum exposure to hydrocarbons and exhaust fumes. The aetiology of oral and oropharyngeal SCC is multifactorial and there is no consensus on the role of occupational carcinogens. We showcase our patient cohort and discuss the occupational exposures that appear to make them susceptible to OSCC and OPSCC. Further multicentre studies are required to enable us to understand fully the pathogenesis of oral cancer and help us to inform relevant organisations, the aim being to reduce the incidence of occupation-related cancer.
Collapse
Affiliation(s)
- C Y Chieng
- Oral & Maxillofacial Surgery Department, University Hospital Dorset NHS Foundation Trust, United Kingdom.
| | - A Dalal
- Oral & Maxillofacial Surgery Department, University Hospital Dorset NHS Foundation Trust, United Kingdom
| | - V Ilankovan
- Oral & Maxillofacial Surgery Department, University Hospital Dorset NHS Foundation Trust, United Kingdom
| |
Collapse
|
27
|
Saini N, Das Bhowmik A, Yareeda S, Venkatapuram V, Jabeen SA, Tallapaka K, Dalal A, Aggarwal S. Muscle spasms as presenting feature of Nivelon-Nivelon-Mabile syndrome. Am J Med Genet A 2023; 191:238-248. [PMID: 36271814 DOI: 10.1002/ajmg.a.63000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 07/05/2022] [Accepted: 08/01/2022] [Indexed: 12/14/2022]
Abstract
Hedgehog acyltransferase gene (HHAT)-associated Nivelon-Nivelon-Mabile syndrome (NNMS) is a rare genetic disorder of multiple system involvement with microcephaly, central nervous system malformations, skeletal dysplasia, and 46,XY sex reversal. Other variable and inconsistent features reported in this disorder are muscle spasms, facial dysmorphism, prenatal onset growth restriction, microphthalmia, and holoprosencephaly. This is the sixth postnatal reported patient with biallelic variants in HHAT gene, who presented with microcephaly, short stature, muscle hypertrophy, muscle spasms, and facial dysmorphism. The most prominent and presenting finding in this patient were muscle hypertrophy and muscle spasms which had a clinical response to phenytoin and acetazolamide treatment. Our report emphasizes the phenotypic variability of NNMS and further reiterates muscle spasms as an important clinical manifestation of this extremely rare condition.
Collapse
Affiliation(s)
- Neelam Saini
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, India
| | - Aneek Das Bhowmik
- Diagnostics Services (NGS), AIC - Centre for Cellular & Molecular Biology (AIC-CCMB), CCMB Annexe II, Hyderabad, India
| | - Sireesha Yareeda
- Department of Neurology, Nizam's Institute of Medical Sciences, Hyderabad, India
| | | | - Shaik Afshan Jabeen
- Department of Neurology, Nizam's Institute of Medical Sciences, Hyderabad, India
| | - Karthik Tallapaka
- Diagnostics Services (NGS), AIC - Centre for Cellular & Molecular Biology (AIC-CCMB), CCMB Annexe II, Hyderabad, India
| | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting & Diagnostics, Hyderabad, India
| | - Shagun Aggarwal
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, India.,Diagnostics Division, Centre for DNA Fingerprinting & Diagnostics, Hyderabad, India
| |
Collapse
|
28
|
Dutta UR, Bhattacherjee A, Bahal A, Posanapally LP, Lone KA, Bathula S, Dalal A. Cytogenomic Characterization of a Novel de novo Balanced Reciprocal Translocation t(1;12) by Genome Sequencing Leading to Fusion Gene Formation of EYA3/EFCAB4b. Mol Syndromol 2022; 13:370-380. [PMID: 36588754 PMCID: PMC9801327 DOI: 10.1159/000522011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 01/17/2022] [Indexed: 01/04/2023] Open
Abstract
Introduction The accurate detection of breakpoint regions of disease-associated chromosomal rearrangements helps understand the molecular mechanisms and identify the risks involved with disrupted genes. Methods In this study, a girl with growth retardation is characterized using positional cloning and genome sequencing. The techniques include fluorescence in situ hybridization (FISH) with paint (WCP) and bacterial-artificial chromosomes (BAC) probes, PCR, real-time PCR, and short and long-read sequencing. Results The translocation was identified by GTG banding and confirmed by WCP FISH. Microarray ruled out the involvement of other copy number variations except for 6 homozygous regions which are not disease-causing variants. Fine mapping with FISH showed split signals with BAC clone RP11-312A3. Genome sequencing of short-read with an average 30× depth and long-read sequencing technology with a 3.8× coverage identified both breakpoints, confirmed by Sanger sequencing, that showed microhomology. The breakpoint at 1p and 12p regions disrupted EYA3 and EFCAB4B genes. Expression analysis of EYA3 showed a 7-fold increase, suggesting the formation of a fusion gene with EFCAB4B. EYA3 is involved in skeleton development, and EFCAB4B plays a role in calcium metabolism, which may be relevant for the patient's phenotype. Conclusion The systematic application of genome techniques to translocations and their advantages is discussed.
Collapse
Affiliation(s)
- Usha R. Dutta
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India,*Usha R Dutta,
| | - Amrita Bhattacherjee
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Ashish Bahal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Laxmi P. Posanapally
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | | | - Siddardha Bathula
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| |
Collapse
|
29
|
Saini N, Vijayasree V, Nandury EC, Dalal A, Aggarwal S. Prenatal phenotype of FBXL4-associated encephalomyopathic mitochondrial DNA depletion syndrome-13. Prenat Diagn 2022; 42:1682-1685. [PMID: 36411461 DOI: 10.1002/pd.6272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 11/23/2022]
Abstract
FBXL4 -associated encephalomyopathic mitochondrial DNA depletion syndrome-13 (MTDPS13) is a rare genetic disorder characterized by early neonatal onset of encephalopathy, seizures, lactic acidosis, hypotonia, dysmorphism, and severe global developmental delay. Prenatal phenotype of molecularly confirmed MTDPS13 has not been well studied. This is the case report of a non-consanguineously conceived fetus ascertained first at 20 weeks of gestation with multiple soft markers. Follow-up fetal ultrasonogram at 26 weeks revealed periventricular cysts, periventricular echogenicity, ventriculomegaly, thin corpus callosum, mega cisterna magna, and large cavum. Fetal MRI confirmed these findings. Postnatally, the baby had clinical and biochemical findings indicative of a mitochondriopathy and died on neonatal day 3. Whole exome sequencing on stored amniotic fluid DNA confirmed the diagnosis of encephalomyopathic mitochondrial DNA depletion syndrome-13 (MTDPS13). This report presents the prenatal phenotype of this rare mitochondriopathy, which has been recognized primarily in postnatal patients. The brain imaging findings in the reported fetus indicate that MTDPS13 is associated with progressive neurological involvement and brain tissue destructive changes starting as early as the second trimester of pregnancy. The case also raises concerns regarding the association of so-called soft markers, which were the only initial finding in this case, with severe monogenic diseases.
Collapse
Affiliation(s)
- Neelam Saini
- Department of Medical Genetics, Nizam's Institute of Medical Sciences Hyderabad, Hyderabad, India
| | - Venkatapuram Vijayasree
- Department of Medical Genetics, Nizam's Institute of Medical Sciences Hyderabad, Hyderabad, India
| | | | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Shagun Aggarwal
- Department of Medical Genetics, Nizam's Institute of Medical Sciences Hyderabad, Hyderabad, India.,Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| |
Collapse
|
30
|
Saini N, Venkatapuram VS, Vineeth VS, Kulkarni A, Tandon A, Koppolu G, Patil SJ, Dalal A, Aggarwal S. Fetal phenotypes of Mendelian disorders: A descriptive study from India. Prenat Diagn 2022; 42:911-926. [PMID: 35587316 DOI: 10.1002/pd.6172] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/12/2022] [Accepted: 05/14/2022] [Indexed: 11/12/2022]
Abstract
OBJECTIVE Exome sequencing(ES) based diagnosis of Mendelian diseases in the fetus is limited by paucity of phenotypic information. This study reports the comprehensive phenotypes of some fetuses with Mendelian disorders. METHODS Next generation technology based sequencing of all coding regions of the genome(Exome sequencing) or targeted gene sequencing using Sanger or next generation platforms was performed in a cohort of deeply phenotyped, cytogenetically normal fetuses with morphological defects. Prenatal ultrasonographic phenotypes and Postmortem details including dysmorphology, histopathology, radiography were ascertained. Novel candidate genes, novel/ unusual findings and unusual genotypes in cases with confirmed Mendelian disorders are described. RESULTS Of the 102 fetuses sequenced, 45 (44%) achieved definitive diagnosis of a Mendelian disorder with 50 pathogenic/likely pathogenic variants. The majority (87%) were autosomal recessive, 69% families were consanguineous and 54% variants were novel. Dysmorphic syndromes, skeletal dysplasias and metabolic disorders were the commonest disease categories, ciliopathies and dystroglycanopathies commonest molecular categories. We describe the first fetal description of six monogenic diseases, and nine cases with novel histological findings. Nineteen cases had novel/ unusual findings. CONCLUSION This cohort demonstrates how deep fetal phenotypes of some Mendelian disorders can show novel/unusual findings which have important implications for prenatal diagnosis of these conditions. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Neelam Saini
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, India
| | | | | | | | - Ashwani Tandon
- Department of Pathology, All India Institute of Medical Sciences, Bhopal, India
| | | | - Siddaramappa Jagdish Patil
- Division of Medical Genetics, Mazumdar Shaw Medical Center, Narayana Hrudayalaya Hospitals, Bangalore, India
| | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting & Diagnostics, Hyderabad, India
| | - Shagun Aggarwal
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, India.,Diagnostics Division, Centre for DNA Fingerprinting & Diagnostics, Hyderabad, India
| |
Collapse
|
31
|
Balakrishnan S, Aggarwal S, Muthulakshmi M, Meena AK, Borgohain R, Mridula KR, Yareeda S, Ranganath P, Dalal A. Clinical and Molecular Spectrum of Degenerative Cerebellar Ataxia: A Single Centre Study. Neurol India 2022; 70:934-942. [PMID: 35864621 DOI: 10.4103/0028-3886.349660] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
BACKGROUND Cerebellar ataxia is a disabling neurological symptom with extreme clinical and etiological heterogeneity. OBJECTIVE To study the clinical and molecular characteristics in patients with degenerative cerebellar ataxia. MATERIALS AND METHODS In this study, 150 South-Indian patients with degenerative cerebellar ataxia underwent a phenotype guided, sequential tiered testing. Phenotypic features studied included cerebellar symptoms, pyramidal and extrapyramidal features, and ophthalmic and systemic findings. Tier one included conventional tests such as short PCR/fragment analysis for spinocerebellar ataxia (SCA) subtypes 1, 2, 3, 6, 7, 8, 12, 17, and 36 and TP-PCR for Friedreich ataxia (FA). Tier two testing comprised next-generation sequencing (NGS)-based strategies reserved for select undiagnosed cases. RESULTS The clinical features were highly overlapping and had limited specificity, except in autosomal recessive ataxias and SCA 34. The overall diagnostic yield of our study was 49.3%. SCA 1, 2, and 3 were noted in 13 (12.6%), 12 (11.6%) and 14 (13.5%), respectively, out of the 103 tested, and FA was noted in 17/55 (30.9%) patients. SCA subtypes 6, 7, 8, 12, 17, and 36 were absent in the cohort studied. Targeted Sanger sequencing and NGS revealed some rare diagnoses in 17 among the 18 patients tested. Whole exome sequencing uncovered a novel genotype-phenotype association in a sibling-pair with ataxia, dysmorphism, and retinopathy. CONCLUSION SCA 1, 2, 3 and FRDA were the most common causes of ataxia. SCA 6, 7, 8, 12, 17, and 36 were absent in the cohort studied. NGS testing revealed several rare forms of ataxia. Clinical features based testing is cost-effective, achieves good genotype-phenotype correlation, and prioritizes variants for further studies.
Collapse
Affiliation(s)
- Surya Balakrishnan
- Department of Medical Genetics, Nizam's institute of Medical Sciences, Hyderabad, Telangana, India
| | - Shagun Aggarwal
- Department of Medical Genetics, Nizam's institute of Medical Sciences, Hyderabad, Telangana, India
| | | | | | - Rupam Borgohain
- Department of Neurology, Nizam's institute of Medical Sciences, Hyderabad, Telangana, India
| | | | - Sireesha Yareeda
- Department of Neurology, Nizam's institute of Medical Sciences, Hyderabad, Telangana, India
| | - Prajnya Ranganath
- Department of Medical Genetics, Nizam's institute of Medical Sciences, Hyderabad, Telangana, India
| | - Ashwin Dalal
- Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India
| |
Collapse
|
32
|
Nerakh G, Vineeth VS, Tallapaka K, Nair L, Dalal A, Aggarwal S. Microcephalic primordial dwarfism with predominant Meier-Gorlin phenotype, ichthyosis, and multiple joint deformities-Further expansion of DONSON Cell Cycle-opathy phenotypic spectrum. Am J Med Genet A 2022; 188:2139-2146. [PMID: 35298084 DOI: 10.1002/ajmg.a.62725] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 01/18/2022] [Accepted: 02/26/2022] [Indexed: 11/10/2022]
Abstract
We report a patient with microcephalic primordial dwarfism with predominant Meier-Gorlin syndrome phenotype with ichthyosis and disabling multiple joint deformities in addition to classic features of the syndrome. The patient was a 10.5-year-old girl referred in view of short stature, joint deformities, and facial dysmorphism. There was history of intrauterine growth restriction and collodion like skin abnormality at birth. She had normal developmental milestones and intellect. On clinical evaluation, anthropometry was suggestive of proportionate short stature and microcephaly. There was abnormal posture due to spine and peripheral joint deformities, along with ichthyosis, facial, and digital dysmorphism. Skeletal radiographs showed radial subluxation, acetabular dysplasia and hip dislocation, bilateral knee joint dislocation, absent patellae, slender long bones with delayed bone age, and subluxation of small joints of hands and feet. Work up for metabolic bone disease and peripheral blood karyotype was normal. Whole exome sequencing revealed a pathogenic homozygous variant c.C1297T (p.Pro433Ser) in the exon 8 of DONSON gene. This report further expands the genotypic-phenotypic spectrum of the group of disorders known as Cell Cycle-opathies.
Collapse
Affiliation(s)
- Gayatri Nerakh
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, Telangana, India.,Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India
| | - Venugopal S Vineeth
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India
| | - Karthik Tallapaka
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, Telangana, India.,Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India
| | - Lekshmi Nair
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, Telangana, India.,Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India
| | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India
| | - Shagun Aggarwal
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, Telangana, India.,Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India
| |
Collapse
|
33
|
Puri RD, Dalal A, Moirangthem A. Indian Undiagnosed Diseases Program (I-UDP) - The Unmet Need. Indian Pediatr 2022; 59:198-200. [PMID: 35105821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Genomics is an integral part of many pediatric diseases spanning all sub-specialities. While many genetic disorders are diagnosed with the currently available genomic tests, there still are many patients who do not receive a definitive diagnosis. The Indian Undiagnosed Diseases Program is a multicenter effort to address these challenges and unmet needs of rare disease patients where current available genetic tests have failed to make a diagnosis. It embodies the principles of collaborative effort across multispecialty disciplines, and uses detailed phenotype. Diagnostic methods are tailored to patient specifics and the large genomic data is interrogated with precise, in-house bioinformatics pipelines using patient-specific phenotype to build the diagnostic algorithm. The inception of this research initiative in India is a step towards creating awareness and appreciation of the needs for our undiagnosed cohorts to enable appropriate management in this era of precision medicine.
Collapse
Affiliation(s)
- Ratna Dua Puri
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi. Correspondence to: Dr Ratna Dua Puri, Professor, Ganga Ram Institute of Postgraduate Medical Education and Research, Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi 110 060.
| | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana
| | - Amita Moirangthem
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh
| |
Collapse
|
34
|
Puri RD, Dalal A, Moirangthem A. Indian Undiagnosed Diseases Program (I-UDP) — The Unmet Need. Indian Pediatr 2022. [DOI: 10.1007/s13312-022-2464-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
35
|
Narayanan DL, Majethia P, Shrikiran A, Siddiqui S, Dalal A, Shukla A. Further evidence of affected females with a heterozygous variant in FGF13 causing X-linked developmental and epileptic encephalopathy 90. Eur J Med Genet 2022; 65:104403. [PMID: 34871784 PMCID: PMC8918359 DOI: 10.1016/j.ejmg.2021.104403] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 10/18/2021] [Accepted: 11/28/2021] [Indexed: 01/03/2023]
Abstract
Developmental and epileptic encephalopathies (DEE) are a genetically heterogeneous group of disorders characterised by early onset epilepsy, epileptiform activity on electroencephalogram and associated developmental delay or neuroregression. With the advent of high throughput sequencing, novel gene-disease associations have been described for DEEs. Voltage activated sodium channels (Nav) regulate neuronal excitability. Fibroblast growth factor homologous factors (FHFs) are proteins, which bind to the C terminal cytoplasmic tails of alpha subunits of Nav channels and influence their function and surface expression. Gain of function hemizygous or heterozygous variants in FGF13 (also known as FHF2) were recently identified as the cause for X-linked developmental and epileptic encephalopathy 90 (DEE90; MIM# 301058) in seven individuals from five families, which included one female. We report an additional female, providing further evidence for a novel de novo heterozygous missense variant in FGF13, NM_004114.5: c.14T > G p.(Ile5Ser) causing X-linked DEE90. In addition, we review the genotype and phenotype of affected individuals with DEE90.
Collapse
Affiliation(s)
- Dhanya Lakshmi Narayanan
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Purvi Majethia
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Aroor Shrikiran
- Department of Pediatrics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Shahyan Siddiqui
- Department of Neuroimaging and Interventional Radiology, STAR Institute of Neurosciences, STAR Hospitals, Hyderabad, India
| | - Ashwin Dalal
- Diagnostics Division, Center for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India.
| |
Collapse
|
36
|
Ramchandani JP, Gupta A, Goh M, Dalal A. Kikuchi-Fujimoto disease: a rare cause of histiocytic necrotising lymphadenitis in young ethnic women. Ann R Coll Surg Engl 2021; 104:e79-e80. [PMID: 34812682 DOI: 10.1308/rcsann.2021.0116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Kikuchi-Fujimoto is a rare but self-limiting disease usually affecting young ethnic females. The main clinical presentation is fever and cervical lymphadenopathy. Here we describe the cases of two patients with cervical lymphadenopathy, fever and fatigue. In addition, patients can present with neutropenia; hence, early diagnosis is crucial to exclude a malignant cause.
Collapse
Affiliation(s)
| | - A Gupta
- King's College London Medical School, UK
| | - M Goh
- OMFS Department, Poole Hospital, UK
| | - A Dalal
- OMFS Department, Poole Hospital, UK
| |
Collapse
|
37
|
Dhar MS, Marwal R, Vs R, Ponnusamy K, Jolly B, Bhoyar RC, Sardana V, Naushin S, Rophina M, Mellan TA, Mishra S, Whittaker C, Fatihi S, Datta M, Singh P, Sharma U, Ujjainiya R, Bhatheja N, Divakar MK, Singh MK, Imran M, Senthivel V, Maurya R, Jha N, Mehta P, A V, Sharma P, Vr A, Chaudhary U, Soni N, Thukral L, Flaxman S, Bhatt S, Pandey R, Dash D, Faruq M, Lall H, Gogia H, Madan P, Kulkarni S, Chauhan H, Sengupta S, Kabra S, Gupta RK, Singh SK, Agrawal A, Rakshit P, Nandicoori V, Tallapaka KB, Sowpati DT, Thangaraj K, Bashyam MD, Dalal A, Sivasubbu S, Scaria V, Parida A, Raghav SK, Prasad P, Sarin A, Mayor S, Ramakrishnan U, Palakodeti D, Seshasayee ASN, Bhat M, Shouche Y, Pillai A, Dikid T, Das S, Maitra A, Chinnaswamy S, Biswas NK, Desai AS, Pattabiraman C, Manjunatha MV, Mani RS, Arunachal Udupi G, Abraham P, Atul PV, Cherian SS. Genomic characterization and epidemiology of an emerging SARS-CoV-2 variant in Delhi, India. Science 2021; 374:995-999. [PMID: 34648303 DOI: 10.1101/2021.06.02.21258076] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Delhi, the national capital of India, experienced multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreaks in 2020 and reached population seropositivity of >50% by 2021. During April 2021, the city became overwhelmed by COVID-19 cases and fatalities, as a new variant, B.1.617.2 (Delta), replaced B.1.1.7 (Alpha). A Bayesian model explains the growth advantage of Delta through a combination of increased transmissibility and reduced sensitivity to immune responses generated against earlier variants (median estimates: 1.5-fold greater transmissibility and 20% reduction in sensitivity). Seropositivity of an employee and family cohort increased from 42% to 87.5% between March and July 2021, with 27% reinfections, as judged by increased antibody concentration after a previous decline. The likely high transmissibility and partial evasion of immunity by the Delta variant contributed to an overwhelming surge in Delhi.
Collapse
Affiliation(s)
| | - Robin Marwal
- National Centre for Disease Control, Delhi, India
| | | | | | - Bani Jolly
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Rahul C Bhoyar
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Viren Sardana
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Salwa Naushin
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Mercy Rophina
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Thomas A Mellan
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Swapnil Mishra
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Charles Whittaker
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Saman Fatihi
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Meena Datta
- National Centre for Disease Control, Delhi, India
| | | | - Uma Sharma
- National Centre for Disease Control, Delhi, India
| | - Rajat Ujjainiya
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Nitin Bhatheja
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Mohit Kumar Divakar
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | | | - Mohamed Imran
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Vigneshwar Senthivel
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Ranjeet Maurya
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Neha Jha
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Priyanka Mehta
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Vivekanand A
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Pooja Sharma
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Arvinden Vr
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | | | - Namita Soni
- National Centre for Disease Control, Delhi, India
| | - Lipi Thukral
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Seth Flaxman
- Department of Mathematics, Imperial College London, London, UK
| | - Samir Bhatt
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Rajesh Pandey
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Debasis Dash
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Mohammed Faruq
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Hemlata Lall
- National Centre for Disease Control, Delhi, India
| | - Hema Gogia
- National Centre for Disease Control, Delhi, India
| | - Preeti Madan
- National Centre for Disease Control, Delhi, India
| | | | | | - Shantanu Sengupta
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | | | - Ravindra K Gupta
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge, Cambridge, UK
- Africa Health Research Institute, KwaZulu-Natal, South Africa
| | | | - Anurag Agrawal
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
38
|
Mukherjee S, Roy M, Ghosh S, Guha G, Prasad Saha S, Dalal A. Rare mutation in ELOVL4 gene in SCA34 and cognitive affection: Expounding the role of cerebellum. Clin Neurol Neurosurg 2021; 210:106983. [PMID: 34700276 DOI: 10.1016/j.clineuro.2021.106983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 10/04/2021] [Accepted: 10/05/2021] [Indexed: 11/19/2022]
Affiliation(s)
- Soumava Mukherjee
- Department of Neuromedicine, Nil Ratan Sircar Medical College and Hospital, 138 A.J.C Bose Road, Kolkata, West Bengal 700014, India.
| | - Manoj Roy
- Department of Neuromedicine, Nil Ratan Sircar Medical College and Hospital, 138 A.J.C Bose Road, Kolkata, West Bengal 700014, India.
| | - Sinjan Ghosh
- Department of Neuromedicine, Nil Ratan Sircar Medical College and Hospital, 138 A.J.C Bose Road, Kolkata, West Bengal 700014, India.
| | - Gautam Guha
- Department of Neuromedicine, Nil Ratan Sircar Medical College and Hospital, 138 A.J.C Bose Road, Kolkata, West Bengal 700014, India.
| | - Shankar Prasad Saha
- Department of Neuromedicine, Nil Ratan Sircar Medical College and Hospital, 138 A.J.C Bose Road, Kolkata, West Bengal 700014, India.
| | - Ashwin Dalal
- Department of Diagnostics, Centre for DNA Fingerprinting and Diagnostics, Inner Ring Road, Uppal, Hyderabad, Telangana 500039, India.
| |
Collapse
|
39
|
Ranganath P, Ranganath P, Vineeth VS, Dalal A, Patil SJ. Report of an Asian-Indian patient with Okur-Chung Syndrome and comparison of the clinical phenotype in different ethnic groups. Clin Dysmorphol 2021; 30:209-212. [PMID: 34417372 DOI: 10.1097/mcd.0000000000000383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Priya Ranganath
- Department of Medical genetics, Nizam's Institute of Medical Sciences
| | - Prajnya Ranganath
- Department of Medical genetics, Nizam's Institute of Medical Sciences
| | - V S Vineeth
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana
| | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana
| | - Siddaramappa J Patil
- Division of Medical Genetics, Mazumdar Shaw Medical Centre, Narayana Hrudayalaya Hospitals, Bangalore, Karnataka, India
| |
Collapse
|
40
|
Jakhar D, Das A, Kaul S, Kaur I, Madke B, Dalal A. Prevalence and characteristics of dermatological manifestations in COVID-19 positive dermatologists: Report from a web-based survey in India. J Eur Acad Dermatol Venereol 2021; 35:e832-e833. [PMID: 34297886 PMCID: PMC8447020 DOI: 10.1111/jdv.17532] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/07/2021] [Accepted: 07/06/2021] [Indexed: 01/08/2023]
Affiliation(s)
- D Jakhar
- Dermosphere clinic, New Delhi, India
| | - A Das
- Department of Dermatology, KPC Medical College & Hospital, Kolkata, India
| | - S Kaul
- Department of Internal Medicine, John H Stroger Hospital of Cook county, Chicago, USA
| | - I Kaur
- Department of Dermatology, North Delhi Municipal Corporation Medical College & Hindu Rao Hospital, New Delhi, India
| | - B Madke
- Department of Dermatology, Venereology and Leprology, Jawaharlal Nehru Medical College, Datta Meghe Institute of Medical Sciences, Sawangi Meghe, Wardha, Maharashtra, India
| | - A Dalal
- Department of Dermatology, Saheed Hasan Khan Mewati Government Medical College and Hospital, Nuh, India
| |
Collapse
|
41
|
Sait H, Srivastava P, Gupta N, Kabra M, Kapoor S, Ranganath P, Rungsung I, Mandal K, Saxena D, Dalal A, Roy A, Pabbati J, Phadke SR. Phenotypic and genotypic spectrum of CTSK variants in a cohort of twenty-five Indian patients with pycnodysostosis. Eur J Med Genet 2021; 64:104235. [PMID: 33945887 DOI: 10.1016/j.ejmg.2021.104235] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 03/28/2021] [Accepted: 04/26/2021] [Indexed: 11/24/2022]
Abstract
BACKGROUND Pycnodysostosis is an autosomal recessive skeletal dysplasia with easily recognizable clinical features and marked molecular heterogeneity. In this study, we explored the clinical and molecular spectrum of 25 Indian patients with pycnodysostosis from 20 families. METHODS Clinical information was collected on a predesigned clinical proforma. Sanger method was employed to sequence all the exons and exon/intron boundaries of the CTSK gene. Novel variants were systematically assessed by prediction softwares and protein modelling. The pathogenicity of variant was established based on ACMG-AMP criteria. An attempt was also made to establish a genotype-phenotype correlation and devise a diagnostic scoring system based on clinical and radiological findings. RESULTS Consanguinity and positive family history were present in 65% (13/20) and 45% (9/20) of the families respectively. Short stature and fractures were the predominant presenting complaints and was evident in 96% (24/25) and 32% (8/25) of affected individuals respectively. Gestalt facial phenotype and acro-osteolysis were present in 76% (19/25) and 82.6% (19/23) of the individuals respectively. Hepatosplenomegaly was present in 15% (3/20) of the individuals with one of them having severe anaemia. Causative sequence variations were identified in all of them. A total of 19 variants were identified from 20 families amongst which 10 were novel. Homozygous variants were identified in 90% (18/20) families. Amongst the novel variants, there was a considerable proportion (40%) of frameshift variants (4/10). No significant genotype-phenotype correlation was noted. Scoring based on clinical and radiological findings led to the proposal that a minimum of 2 scores in each category is required in addition to high bone density to diagnose pycnodysostosis with certainty. CONCLUSION This study delineated the genotypic and phenotypic characterisation of Indian patients with pycnodysostosis with identification of 10 novel variants. We also attempted to develop a clinically useful diagnostic scoring system which requires further validation.
Collapse
Affiliation(s)
- Haseena Sait
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Priyanka Srivastava
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Neerja Gupta
- Division of Genetics, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Madhulika Kabra
- Division of Genetics, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Seema Kapoor
- Division of Genetics & Metabolism, Department of Pediatrics, LokNayak Hospital and Maulana Azad Medical College, New Delhi, India
| | - Prajnya Ranganath
- Department of Medical Genetics,Nizam's Institute of Medical Sciences, Hyderabad, India
| | - Ikrormi Rungsung
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Kausik Mandal
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Deepti Saxena
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Ajitesh Roy
- Department of Endocrinology, Vivekananda Institute of Medical Sciences, Ramakrishna Mission Seva Pratishthan, Kolkata, India
| | - Jayalakshmi Pabbati
- Department of Pediatrics, Gandhi Medical College and Hospital, Secunderabad, India
| | - Shubha R Phadke
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India.
| |
Collapse
|
42
|
Brennan PA, Dalal A, Knighton J, Jones R, Oeppen RS. Pilot study to evaluate safety culture perception in the operating theatres of an acute NHS Trust using the National Air Traffic Services (NATS) App. Br J Oral Maxillofac Surg 2021; 59:1085-1089. [PMID: 34281735 DOI: 10.1016/j.bjoms.2021.04.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 04/15/2021] [Indexed: 11/19/2022]
Abstract
An area critical to safety in an organisation is the perceived and actual culture. National Air Traffic Services (NATS) work closely with large safety-critical industries including various aviation companies to enable them to identify strengths and vulnerabilities with the aim of improving safe practice. NATS have developed a simple free downloadable self-assessment App that individuals can use to assess their own culture perception in their organisation. The App has 16 questions arranged in four domains but to our knowledge it has not been used to date in healthcare. As part of the initiatives to improve staff culture, we evaluated operating theatre colleagues' safety perception in our large acute NHS Trust in a pilot study using the NATS safety App. Staff downloaded the App to their smart device before completing it. Responses were sent anonymously through the App and collated by NATS. A total of 146 colleagues downloaded and completed the questionnaire. One hundred and seventeen staff (80%) felt encouraged to report safety concerns, but 86% (n=126) confirmed a lack of available support from healthcare managers. Only 43% of respondents (n=63) would find it easy to challenge colleagues if they observed unsafe behaviour. This pilot study has identified positive indicators of an evolving NHS safety culture, and some concerns about speaking up, support, and challenging colleagues without fear. These issues are known to occur across healthcare. Further work is needed in the NHS to provide a supportive environment to improve patient safety, and lower hierarchy in surgical teams.
Collapse
Affiliation(s)
- P A Brennan
- Maxillofacial Unit, Queen Alexandra Hospital, Portsmouth PO6 3LY, UK.
| | - A Dalal
- Poole Hospital, Longfleet Road, Poole BH15 2JB, UK
| | - J Knighton
- Queen Alexandra Hospital, Portsmouth PO6 3LY, UK
| | - R Jones
- Queen Alexandra Hospital, Portsmouth PO6 3LY, UK
| | - R S Oeppen
- Southampton University Hospitals Trust, Tremona Road, Southampton SO16 6YD, UK
| |
Collapse
|
43
|
Kausthubham N, Shukla A, Gupta N, Bhavani GS, Kulshrestha S, Das Bhowmik A, Moirangthem A, Bijarnia-Mahay S, Kabra M, Puri RD, Mandal K, Verma IC, Bielas SL, Phadke SR, Dalal A, Girisha KM. A data set of variants derived from 1455 clinical and research exomes is efficient in variant prioritization for early-onset monogenic disorders in Indians. Hum Mutat 2021; 42:e15-e61. [PMID: 33502066 PMCID: PMC10052794 DOI: 10.1002/humu.24172] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 01/05/2021] [Accepted: 01/24/2021] [Indexed: 12/16/2022]
Abstract
Given the genomic uniqueness, a local data set is most desired for Indians, who are underrepresented in existing public databases. We hypothesize patients with rare monogenic disorders and their family members can provide a reliable source of common variants in the population. Exome sequencing (ES) data from families with rare Mendelian disorders was aggregated from five centers in India. The dataset was refined by excluding related individuals and removing the disease-causing variants (refined cohort). The efficiency of these data sets was assessed in a new set of 50 exomes against gnomAD and GenomeAsia. Our original cohort comprised 1455 individuals from 1203 families. The refined cohort had 836 unrelated individuals that retained 1,251,064 variants with 181,125 population-specific and 489,618 common variants. The allele frequencies from our cohort helped to define 97,609 rare variants in gnomAD and 44,520 rare variants in GenomeAsia as common variants in our population. Our variant dataset provided an additional 1.7% and 0.1% efficiency for prioritizing heterozygous and homozygous variants respectively for rare monogenic disorders. We observed additional 19 genes/human knockouts. We list carrier frequency for 142 recessive disorders. This is a large and useful resource of exonic variants for Indians. Despite limitations, datasets from patients are efficient tools for variant prioritization in a resource-limited setting.
Collapse
Affiliation(s)
- Neethukrishna Kausthubham
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Neerja Gupta
- Division of Genetics, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Gandham S Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Samarth Kulshrestha
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Aneek Das Bhowmik
- Division of Diagnostics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India.,ASPIRE (Diagnostics Facility), CSIR-Centre for Cellular & Molecular Biology, CCMB Annexe II, Hyderabad, India
| | - Amita Moirangthem
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Sunita Bijarnia-Mahay
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Madhulika Kabra
- Division of Genetics, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Ratna D Puri
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Kausik Mandal
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Ishwar C Verma
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Stephanie L Bielas
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Shubha R Phadke
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Ashwin Dalal
- Division of Diagnostics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| |
Collapse
|
44
|
Gupta A, Sabarinathan R, Bala P, Donipadi V, Vashisht D, Katika MR, Kandakatla M, Mitra D, Dalal A, Bashyam MD. A comprehensive profile of genomic variations in the SARS-CoV-2 isolates from the state of Telangana, India. J Gen Virol 2021; 102:001562. [PMID: 33587028 PMCID: PMC8515869 DOI: 10.1099/jgv.0.001562] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 01/15/2021] [Indexed: 12/29/2022] Open
Abstract
The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing COVID-19 has rapidly turned into a pandemic, infecting millions and causing 1 157 509 (as of 27 October 2020) deaths across the globe. In addition to studying the mode of transmission and evasion of host immune system, analysing the viral mutational landscape constitutes an area under active research. The latter is expected to impart knowledge on the emergence of different clades, subclades, viral protein functions and protein-protein and protein-RNA interactions during replication/transcription cycle of virus and response to host immune checkpoints. In this study, we have attempted to bring forth the viral genomic variants defining the major clade(s) as identified from samples collected from the state of Telangana, India. We further report a comprehensive draft of all genomic variations (including unique mutations) present in SARS-CoV-2 strain in the state of Telangana. Our results reveal the presence of two mutually exclusive subgroups defined by specific variants within the dominant clade present in the population. This work attempts to bridge the critical gap regarding the genomic landscape and associate mutations in SARS-CoV-2 from a highly infected southern region of India, which was lacking to date.
Collapse
Affiliation(s)
- Asmita Gupta
- Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | | | - Pratyusha Bala
- Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Vinay Donipadi
- Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Divya Vashisht
- Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | | | | | - Debashis Mitra
- Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
- Present address: National Centre for Cell Science, Pune, India
| | - Ashwin Dalal
- Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | | |
Collapse
|
45
|
Knapp KM, Fellows B, Aggarwal S, Dalal A, Bicknell LS. A synonymous variant in a non-canonical exon of CDC45 disrupts splicing in two affected sibs with Meier-Gorlin syndrome with craniosynostosis. Eur J Med Genet 2021; 64:104182. [PMID: 33639314 DOI: 10.1016/j.ejmg.2021.104182] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 12/10/2020] [Accepted: 01/23/2021] [Indexed: 11/30/2022]
Abstract
Disruption of the initiation of DNA replication is significantly associated with Meier-Gorlin syndrome (MGORS), an autosomal recessive condition of reduced growth, microtia and patellar a/hypoplasia. Biallelic mutations in CDC45, a member of the pre-initiation complex in DNA replication, cause a spectrum of phenotypes ranging from MGORS with craniosynostosis, through to isolated short stature and craniosynostosis. Here we report two affected sibs with MGORS and craniosynostosis, with biallelic variants in CDC45 identified by 10X Chromium whole genome sequencing. One variant is a frameshift mutation, predicted to be pathogenic, and is inherited in trans with a synonymous variant in a non-canonical exon (exon 7) of CDC45. An in vitro splicing assay showed that while the canonical CDC45 exon 6-exon 8 transcript (with skipping of exon 7; numbering as per NM001178010.2) remained as the predominant transcript, the variant allele induced the use of novel splice acceptor sites in intron 6, all of which produced transcripts harbouring premature stop codons. This perturbation of canonical splicing provides evidence that this synonymous variant is indeed a deleterious alteration in this family. This report adds to the initial patient cohort in which several synonymous variants were also described, further highlighting the contribution of this variant type in CDC45. It also reiterates the true potential pathogenicity of synonymous variants, which is a mutation type that is commonly ignored in variant prioritization strategies.
Collapse
Affiliation(s)
- Karen M Knapp
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Bridget Fellows
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Shagun Aggarwal
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, India
| | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India; Department of Medical Genetics, Kasturba Medical College, Manipal, Karnataka, India
| | - Louise S Bicknell
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand.
| |
Collapse
|
46
|
Nampoothiri S, Yesodharan D, Bhattacherjee A, Ahamed H, Puri RD, Gupta N, Kabra M, Ranganath P, Bhat M, Phadke S, Radha Rama Devi A, Jagadeesh S, Danda S, Sylaja PN, Mandal K, Bijarnia‐Mahay S, Makkar R, Verma IC, Dalal A, Ramaswami U. Fabry disease in India: A multicenter study of the clinical and mutation spectrum in 54 patients. JIMD Rep 2020; 56:82-94. [PMID: 33204599 PMCID: PMC7653245 DOI: 10.1002/jmd2.12156] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 07/14/2020] [Accepted: 07/20/2020] [Indexed: 11/18/2022] Open
Abstract
Fabry disease (FD) is a treatable X linked lysosomal storage disorder with a wide phenotypic spectrum. There is a scarcity of published data on the burden of FD in India. This study evaluates the clinical and molecular spectrum of Indian patients with FD. In this multicentric study involving 10 tertiary referral centers in India, we analyzed the clinical course and genotype of 54 patients from 37 families. Family screening identified 19 new patients (35%) from 12 index cases. Then, 33 GLA gene variants were identified in 49/54 (90.7%) which included 11 novel and 22 known pathogenic variants. Of the 54 patients in our cohort, 40 patients had "classical" and 10 patients had a "nonclassical" presentation. The symptoms and signs included kidney dysfunction in 38/54 (70.3%), neuropathic pain in 34/54 (62.9%), left ventricular hypertrophy in 22/49 (44.8%) and stroke in 5/54 (9.2%). Female heterozygotes were 10/54 (18.5%) of whom 2 were index cases. There was a significant delay in reaching the diagnosis of 11.7 years. Enzyme replacement therapy was initiated in 28/54 (51.8%) patients with significant improvement of neuropathic pain and gastrointestinal symptoms. This study highlights the clinical presentation and mutational spectrum of FD in India and suggests that family screening and screening of high-risk groups (hypertrophic cardiomyopathy, idiopathic chronic renal failure and cryptogenic stroke) could be the most cost-effective strategies for early identification of FD.
Collapse
Affiliation(s)
- Sheela Nampoothiri
- Department of Pediatric GeneticsAmrita Institute of Medical Sciences and Research CentreCochinKeralaIndia
| | - Dhanya Yesodharan
- Department of Pediatric GeneticsAmrita Institute of Medical Sciences and Research CentreCochinKeralaIndia
| | - Amrita Bhattacherjee
- Diagnostics DivisionCentre for DNA Fingerprinting and Diagnostics (CDFD)HyderabadIndia
| | - Hisham Ahamed
- Department of CardiologyAmrita Institute of Medical Sciences and Research CentreCochinKeralaIndia
| | - Ratna Dua Puri
- Institute of Genetics and GenomicsSir Ganga Ram HospitalNew DelhiIndia
| | - Neerja Gupta
- Division of Genetics, Department of PediatricsAll India Institute of Medical SciencesNew DelhiIndia
| | - Madhulika Kabra
- Division of Genetics, Department of PediatricsAll India Institute of Medical SciencesNew DelhiIndia
| | - Prajnya Ranganath
- Department of Medical GeneticsNizam's Institute of Medical SciencesHyderabadIndia
| | - Meenakshi Bhat
- Department of Clinical GeneticsCentre for Human GeneticsBangaloreIndia
| | - Shubha Phadke
- Department of Medical GeneticsSanjay Gandhi Postgraduate Institute of Medical SciencesLucknowIndia
| | | | - Sujatha Jagadeesh
- Department of Clinical Genetics and Genetic CounselingMediscan SystemsChennaiIndia
| | - Sumita Danda
- Department of Clinical GeneticsChristian Medical College and HospitalVelloreIndia
| | - Padmavathy Narayana Sylaja
- Comprehensive Stroke Care Program, Sree Chitra Tirunal Institute for Medical Sciences and Technology (SCTIMST)TrivandrumKeralaIndia
| | - Kausik Mandal
- Department of Medical GeneticsSanjay Gandhi Postgraduate Institute of Medical SciencesLucknowIndia
| | | | | | | | - Ashwin Dalal
- Diagnostics DivisionCentre for DNA Fingerprinting and Diagnostics (CDFD)HyderabadIndia
| | - Uma Ramaswami
- Lysosomal Disorders Unit, Institute of Immunity and TransplantationRoyal Free London NHS Foundation TrustLondonUK
| |
Collapse
|
47
|
Komaravalli PL, Rani S V, Dalal A, Jahan P. Association analysis of FMR1 genetic variants and primary ovarian insufficiency in South Indian women with a novel approach of CGG repeats classification. Eur J Med Genet 2020; 63:104081. [PMID: 33039683 DOI: 10.1016/j.ejmg.2020.104081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 07/27/2020] [Accepted: 10/04/2020] [Indexed: 10/23/2022]
Abstract
Around 20-28% of FMR1gene CGG premutation (PM) carriers are at augmented risk towards an infertility related disorder, Fragile X-associated primary ovarian insufficiency (FXPOI). Except the effect of CGG repeats, reports are not available on the mechanism through which the cis-acting variations, namely, SNPs involved in POI susceptibility. Addressing the hypothesis that the FMR1 gene polymorphisms [CGG repeats, rs25731(T > A) and rs4949(A > G)] might increase their individual and combined impact in disease predisposition, we tested the genetic variants in 200 south Indian DNA samples consists of 100 patients and 100 healthy volunteers. We used gene scan method to score the CGG repeat length, and ARMS and RFLP methods to genotype the SNPs. Only 0.5% of each Gray zone and PM alleles were found among patient group, however, no disease association was noticed with repeat length. The rs25731 showed protection [OR:0.32; (0.13-0.76), p = 0.006] and rs4949 reported a 2.5-fold risk towards the disease predisposition [OR:2.46; (1.06-5.74), p = 0.031] but, both found insignificant after Bonferroni correction was done under different Genetic Models. Novel classification of genotype combinations, 'Normal&Variant Homozygote' [OR:2.89,(1.12-7.9), p < 0.05] and 'Allele2-T-G' haplotype block (6%vs.1%, p = 0.08) were noticed to be at marginal risk for POI. We demonstrated a susceptible role of the combined effect of variant allele-G and Allele-2 (repeat allele outside the normal range) for FXPOI. To support our findings of its first kind, further studies with large samples are warranted in understanding the role of FMR1 genetic variants in FXPOI etio-pathophysiology, the outcome might help in providing better reproductive treatment options for females, who are at risk for FXPOI.
Collapse
Affiliation(s)
| | - Vasantha Rani S
- Human and Medical Genetics Laboratory, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana state, 500039, India
| | - Ashwin Dalal
- Human and Medical Genetics Laboratory, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana state, 500039, India
| | - Parveen Jahan
- School of Sciences, Moulana Azad National Urdu University, Hyderabad, Telangana state, 500032, India.
| |
Collapse
|
48
|
Girisha KM, Pande S, Dalal A, Phadke SR. Untapped opportunities for rare disease gene discovery in India. Am J Med Genet A 2020; 182:3056-3059. [PMID: 32914504 DOI: 10.1002/ajmg.a.61866] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 08/22/2020] [Indexed: 11/08/2022]
Affiliation(s)
- Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Shruti Pande
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Ashwin Dalal
- Diagnostics Division, Center for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Shubha R Phadke
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| |
Collapse
|
49
|
Dutta UR, Suttur MS, Venugopal VS, Posanapally LP, Gopalasetty S, Talwar S, Anand S, Billapati S, Jesudasan RA, Dalal A. Cytogenetic and molecular study of 370 infertile men in South India highlighting the importance of copy number variations by multiplex ligation-dependent probe amplification. Andrologia 2020; 52:e13761. [PMID: 32790203 DOI: 10.1111/and.13761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 06/05/2020] [Accepted: 06/23/2020] [Indexed: 02/01/2023] Open
Abstract
Male infertility is a common and severe problem affecting 7% of population. The main objective of this study is to identify the chromosomal abnormalities, Y microdeletions in infertile men and also to access the frequency of abnormal sperm count. Based on the sperm count and viability, the infertile men were grouped as Azoospermia, Asthenospermia, Oligospermia and the remaining as Idiopathic infertility. A total of 370 infertile men and 60 normal control men were recruited. Chromosomal abnormalities were identified in 3 men (3/370). The prevalence of Y microdeletions in the infertile group is 8/370 in the Azoospermia factor (AZF) region with four AZFc deletion/duplication, two AZFa deletion, one AZF b & AZFc deletion and one case of total AZF a, AZFb & AZFc deletion. However, only five cases of Y microdeletions were identified by Multiplex PCR but an additional three cases by MLPA (Multiplex ligation-dependent probe amplification). Fluorescence in situ hybridisation also confirmed the deletions. Here, we performed MLPA post-multiplex PCR, and our study revealed good yield of the Y microdeletion identification. The partial duplications which are difficult to be identified can now be easily identified by MLPA, and hence, we recommend MLPA as the choice of investigation compared to multiplex PCR for infertile men.
Collapse
Affiliation(s)
- Usha R Dutta
- Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | | | | | | | | | | | - Suhana Anand
- DOS in Zoology, University of Mysore, Mysore, India
| | | | | | - Ashwin Dalal
- Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| |
Collapse
|
50
|
Shetty K, Sarma AS, Devan M, Dalal A, Dash GK, Jannabhatla A, Patil SJ. Recurrent ADCY5 Mutation in Mosaic Form with Nocturnal Paroxysmal Dyskinesias and Video Electroencephalography Documentation of Dramatic Response to Caffeine Treatment. J Mov Disord 2020; 13:238-240. [PMID: 32713175 PMCID: PMC7502297 DOI: 10.14802/jmd.20014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 05/26/2020] [Indexed: 12/27/2022] Open
Affiliation(s)
- Kuldeep Shetty
- Department of Neurology, Mazumdar Shaw Medical Center, Narayana Hrudayalaya Hospital, Bangalore, India
| | - Asodu Sandeep Sarma
- Diagnostic Division, Center for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Meera Devan
- Diagnostic Division, Center for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Ashwin Dalal
- Diagnostic Division, Center for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Gopal Krishna Dash
- Department of Neurology, Mazumdar Shaw Medical Center, Narayana Hrudayalaya Hospital, Bangalore, India
| | - Apuroopa Jannabhatla
- Department of Neurology, Mazumdar Shaw Medical Center, Narayana Hrudayalaya Hospital, Bangalore, India
| | | |
Collapse
|