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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.
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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.
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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.
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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
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Narayanan DL, Matta D, Gupta N, Kabra M, Ranganath P, Aggarwal S, Phadke SR, Datar C, Gowrishankar K, Kamate M, Jain JMN, Dalal A. Spectrum of ARSA variations in Asian Indian patients with Arylsulfatase A deficient metachromatic leukodystrophy. J Hum Genet 2019; 64:323-331. [PMID: 30674982 DOI: 10.1038/s10038-019-0560-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 12/26/2018] [Accepted: 12/28/2018] [Indexed: 01/08/2023]
Abstract
Metachromatic leukodystrophy due to Arylsulfatase A enzyme deficiency is an autosomal recessive disorder caused by biallelic variations in ARSA gene. Till date 186 variations have been reported in ARSA gene worldwide, but the variation spectrum in India is not known. The aim of this study was to identify the variation profile in Indian patients presenting with features of Arylsulfatase A deficient metachromatic leukodystrophy. We sequenced the ARSA gene in 51 unrelated families and identified 36 variants out of which 16 were novel. The variations included 23 missense, 3 nonsense, and 6 frameshift variants (3 single-base deletions and 3 single-base duplications), 1 indel, one 3 bp deletion, and 2 splice site variations. The pathogenicity of the novel variations was inferred with the help of mutation prediction softwares like MutationTaster, SIFT, Polyphen-2, PROVEAN, and HANSA. The effects of the identified sequence variants on the protein structure were studied using in silico methods. The most common variation was c.931 C > T(p.Arg311*), found in 11.4% (14 out of 122 alleles) of the tested individuals. To the best of our knowledge, this study is the first of its kind in India with respect to the size of the cohort and the molecular diagnostic method used and one of the largest cohorts of metachromatic leukodystrophy studied till date.
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Affiliation(s)
| | - Divya Matta
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Neerja Gupta
- Department of Pediatrics, Division of Genetics, All India Institute of Medical Sciences, New Delhi, India
| | - Madhulika Kabra
- Department of Pediatrics, Division of Genetics, All India Institute of Medical Sciences, New Delhi, India
| | - Prajnya Ranganath
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, India
| | - Shagun Aggarwal
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, India
| | - Shubha R Phadke
- Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India
| | - Chaitanya Datar
- Sahyadri Medical Genetics and Tissue Engineering Facility (SMGTEF), Pune, India
| | | | - Mahesh Kamate
- Division of Pediatric Neurology, Department of Pediatrics, KAHER's J N Medical College, Belagavi, India
| | | | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India.
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Ranganath P, Matta D, Bhavani GS, Wangnekar S, Jain JMN, Verma IC, Kabra M, Puri RD, Danda S, Gupta N, Girisha KM, Sankar VH, Patil SJ, Devi ARR, Bhat M, Gowrishankar K, Mandal K, Aggarwal S, Tamhankar PM, Tilak P, Phadke SR, Dalal A. Spectrum of mutations in the SMPD1
gene in Asian Indian patients with acid sphingomyelinase deficient Niemann-Pick disease. Am J Med Genet A 2017. [DOI: 10.1002/ajmg.a.38040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Ranganath P, Matta D, Bhavani GS, Wangnekar S, Jain JMN, Verma IC, Kabra M, Puri RD, Danda S, Gupta N, Girisha KM, Sankar VH, Patil SJ, Ramadevi AR, Bhat M, Gowrishankar K, Mandal K, Aggarwal S, Tamhankar PM, Tilak P, Phadke SR, Dalal A. Spectrum of SMPD1 mutations in Asian-Indian patients with acid sphingomyelinase (ASM)-deficient Niemann-Pick disease. Am J Med Genet A 2016; 170:2719-30. [PMID: 27338287 DOI: 10.1002/ajmg.a.37817] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [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: 03/30/2016] [Accepted: 06/13/2016] [Indexed: 01/02/2023]
Abstract
Acid sphingomyelinase (ASM)-deficient Niemann-Pick disease is an autosomal recessive lysosomal storage disorder caused by biallelic mutations in the SMPD1 gene. To date, around 185 mutations have been reported in patients with ASM-deficient NPD world-wide, but the mutation spectrum of this disease in India has not yet been reported. The aim of this study was to ascertain the mutation profile in Indian patients with ASM-deficient NPD. We sequenced SMPD1 in 60 unrelated families affected with ASM-deficient NPD. A total of 45 distinct pathogenic sequence variants were found, of which 14 were known and 31 were novel. The variants included 30 missense, 4 nonsense, and 9 frameshift (7 single base deletions and 2 single base insertions) mutations, 1 indel, and 1 intronic duplication. The pathogenicity of the novel mutations was inferred with the help of the mutation prediction software MutationTaster, SIFT, Polyphen-2, PROVEAN, and HANSA. The effects of the identified sequence variants on the protein structure were studied using the structure modeled with the help of the SWISS-MODEL workspace program. The p. (Arg542*) (c.1624C>T) mutation was the most commonly identified mutation, found in 22% (26 out of 120) of the alleles tested, but haplotype analysis for this mutation did not identify a founder effect for the Indian population. To the best of our knowledge, this is the largest study on mutation analysis of patients with ASM-deficient Niemann-Pick disease reported in literature and also the first study on the SMPD1 gene mutation spectrum in India. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Prajnya Ranganath
- Department of Medical Genetics, Nizam's Institute of Medical Genetics, Hyderabad, Telangana, India.,Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India
| | - Divya Matta
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India
| | | | - Savita Wangnekar
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India
| | | | - Ishwar C Verma
- Center of Medical Genetics, Sir GangaRam Hospital, New Delhi, India
| | - Madhulika Kabra
- Genetics Unit, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Ratna Dua Puri
- Center of Medical Genetics, Sir GangaRam Hospital, New Delhi, India
| | - Sumita Danda
- Department of Clinical Genetics, Christian Medical College and Hospital, Vellore, Tamil Nadu, India
| | - Neerja Gupta
- Genetics Unit, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, Karnataka, India
| | - Vaikom H Sankar
- Genetic Clinic, Department of Pediatrics, SAT Hospital, Government Medical College, Thiruvananthapuram, Kerala, India
| | - Siddaramappa J Patil
- Clinical Genetics Unit, Mazumdhar Shaw Medical Center, Bengaluru, Karnataka, India
| | | | | | - Kalpana Gowrishankar
- Department of Medical Genetics, CHILDS Trust Medical Research Foundation, Kanchi Kamakoti CHILDS Trust Hospital, Chennai, Tamil Nadu, India
| | - Kausik Mandal
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Shagun Aggarwal
- Department of Medical Genetics, Nizam's Institute of Medical Genetics, Hyderabad, Telangana, India.,Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India
| | - Parag Mohan Tamhankar
- Genetic Research Centre, National Institute for Research in Reproductive Health, Mumbai, Maharashtra, India
| | - Preetha Tilak
- Division of Human Genetics, St. John's Medical College, Bengaluru, Karnataka, India
| | - Shubha R Phadke
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India.
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