1
|
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
|
2
|
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
|
3
|
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
|
4
|
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
|
5
|
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]
|
6
|
John ST, Gayathri K, Ahmed S, Multtani KS, Menon PSN, Kumar RK, Sankar VH, Ranganath P, Gupta N, Nair M, Vijayakumar M, Unni JC. Consensus Statement of the Neurodevelopmental Pediatrics Chapter of Indian Academy of Pediatrics (IAP) on the Management of Children With Down Syndrome. Indian Pediatr 2023; 60:298-307. [PMID: 36814128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
JUSTIFICATION The diagnosis of Down syndrome (DS) is easily made clinically but the management is multi-disciplinary and life-long. There is no standard protocol available for its management in India. PROCESS A committee was formed under the Indian Academy of Pediatrics (IAP) chapter of Neuro developmental pediatrics consisting of 20 experts working in the related field. The various aspects of the condition were discussed and allotted to the concerned experts related for preparing the guidelines. The material received was collated to form a set of guidelines, which were reviewed by the committee, and a consensus statement made. The guidelines were then approved by the chapter, and by the IAP. OBJECTIVES To define the condition and to look into the various aspects of antenatal and postnatal diagnosis. To explain briefly about the involvement of the various systems that are involved and formulate recommendations for management. To recommend early and sustained interventional therapies to enable children with DS lead an independent life. RECOMMENDATIONS The stress on bio-psycho-social strategy for the management of children with DS is reiterated, and the need for a medical, social and rights model is recommended after each section. The age-wise recommendations are also highlighted in addition to the recommendations under each system.
Collapse
Affiliation(s)
- Shaji Thomas John
- Paediatrics and Neonatology, Baby Memorial Hospital, Calicut, Kerala, India. Correspondence to: Dr Shaji Thomas John, Chief of Paediatrics and Neonatology, Baby Memorial Hospital, Calicut, Kerala, India.
| | - Kizhanipurath Gayathri
- Down Syndrome Clinic, Department of Pediatrics, Baby Memorial Hospital, Calicut, Kerala, India
| | - Shabina Ahmed
- Chairperson, IAP Chapter of Neurodevelopmental Pediatrics, Assam, India
| | | | | | | | - Vaikom Hariharan Sankar
- Department of Paediatrics, SAT Hospital, Government Medical College, Thiruvananthapuram, Kerala, India
| | - Prajnya Ranganath
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, Telengana, India
| | - Neerja Gupta
- Division of Genetics, Department of Pediatrics, AIIMS, New Delhi, India
| | - Mohandas Nair
- Department of Pediatrics, Government Medical College, Idukki, Kerala, India
| | - Madhava Vijayakumar
- Department of Pediatrics, Government Medical College, Manjeri, Kerala, India
| | - Jeeson C Unni
- Department of Child and Adolescent Health, Aster Medcity, Kochi, Kerala, India
| |
Collapse
|
7
|
Pranav Chand R, Vinit W, Vaidya V, Iyer AS, Shelke M, Aggarwal S, Magar S, Danda S, Moirangthem A, Phadke SR, Goyal M, Ranganath P, Mistri M, Shah P, Shah N, Kotecha UH. Proband only exome sequencing in 403 Indian children with neurodevelopmental disorders: Diagnostic yield, utility and challenges in a resource-limited setting. Eur J Med Genet 2023; 66:104730. [PMID: 36801247 DOI: 10.1016/j.ejmg.2023.104730] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 02/02/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023]
Abstract
Whole exome sequencing is recommended as the first tier test for neurodevelopmental disorders (NDDs) with trio being an ideal option for the detection of de novo variants. Cost constraints have led to adoption of sequential testing i.e. proband-only whole exome followed by targeted testing of parents. The reported diagnostic yield for proband exome approach ranges between 31 and 53%. Typically, these study designs have aptly incorporated targeted parental segregation before concluding a genetic diagnosis to be confirmed. The reported estimates however do not accurately reflect the yield of proband only standalone whole -exome, a question commonly posed to the referring clinician in self pay medical systems like India. To assess the utility of standalone proband exome (without follow up targeted parental testing), we retrospectively evaluated 403 cases of neurodevelopmental disorders referred for proband-only whole exome sequencing at Neuberg Centre for Genomic Medicine (NCGM), Ahmedabad during the period of January 2019 and December 2021. A diagnosis was considered confirmed only upon the detection of Pathogenic/Likely Pathogenic variants in concordance with patient's phenotype as well as established inheritance pattern. Targeted parental/familial segregation analysis was recommended as a follow up test where applicable. The diagnostic yield of the proband-only standalone whole exome was 31.5%. Only 20 families submitted samples for follow up targeted testing, and a genetic diagnosis was confirmed in twelve cases increasing the yield to 34.5%. To understand factors leading to poor uptake of sequential parental testing, we focused on cases where an ultra-rare variant was detected in hitherto described de novo dominant neurodevelopmental disorder. A total of 40 novel variants in genes associated with de novo autosomal dominant disorders could not be reclassified as parental segregation was denied. Semi-structured telephonic interviews were conducted upon informed consent to comprehend reasons for denial. Major factors influencing decision making included lack of definitive cure in the detected disorders; especially when couples not planning further conception and financial constraints to fund further targeted testing. Our study thus depicts the utility and challenges of proband-only exome approach and highlights the need for larger studies to understand factors influencing decision making in sequential testing.
Collapse
Affiliation(s)
| | - Wankhede Vinit
- Kids Neuro Clinic and Child Rehabilitation Center, Nagpur, Maharashtra, India
| | - Varsha Vaidya
- Kpond Children Super Specialty Hospital, Aurangabad, Maharashtra, India
| | | | - Madhavi Shelke
- Integrated Centre for Child Neurodevelopment, Aurangabad, Maharashtra, India
| | | | - Suvarna Magar
- MGM Medical College and Hospitals, Aurangabad, India
| | - Sumita Danda
- Christian Medical College and Hospital, Vellore, India
| | - Amita Moirangthem
- Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | | | | | | | - Mehul Mistri
- Neuberg Centre for Genomic Medicine, Ahmedabad, 380059, Gujarat, India
| | - Parth Shah
- Neuberg Centre for Genomic Medicine, Ahmedabad, 380059, Gujarat, India
| | - Nidhi Shah
- Neuberg Centre for Genomic Medicine, Ahmedabad, 380059, Gujarat, India
| | | |
Collapse
|
8
|
Gayatri N, Ranganath P. Genetic Evaluation of the Parents Following Demise of the Index Case: Report of a Family with Fucosidosis. J Obstet Gynaecol India 2022; 72:369-371. [PMID: 35923507 PMCID: PMC9339439 DOI: 10.1007/s13224-020-01421-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 12/29/2020] [Indexed: 11/29/2022] Open
Abstract
It is common in obstetric practice to encounter couples who seek prenatal genetic counseling and testing in view of history of known or suspected genetic disorders in the previous offspring or in other family members. Recent advances in genetic testing techniques, especially the availability of the next-generation sequencing (NGS) technology, have greatly facilitated genetic evaluation of the proband and/or the consultand couple and enabled provision of accurate genetic counseling and prenatal genetic testing in such clinical scenarios. However, even in this era of NGS, comprehensive clinical history taking and detailed phenotype characterization through clinical examination and thorough perusal of available medical records, are very important and essential for accurate diagnosis, as reiterated by this report of a 30-year-old third gravida, who was referred for prenatal genetic counseling and testing, in view of history of death of the first offspring due to a suspected neurogenetic disorder. Retrospective clinical diagnosis for the deceased index child with the help of available medical records and reports, followed by relevant NGS-based clinical exome sequencing of the couple, helped to arrive at a definitive diagnosis of fucosidosis, based on which accurate prenatal genetic testing could be done.
Collapse
|
9
|
Takigami A, Thondapu V, Ranganath P, Zhang E, Parakh A, Goiffon R, Baliyan V, Foldyna B, Lu M, Tower-Rader A, Meyersohn N, Hedgire S, Ghoshhajra B. 432 Feasibility And Clinical Outcomes Of Integrating CT-derived Fractional Flow Reserve (FFRCT) Into Clinical Practice: Insights From A Large Academic Medical Center. J Cardiovasc Comput Tomogr 2022. [DOI: 10.1016/j.jcct.2022.06.037] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|
10
|
Nerakh G, Shah A, Seshan V, Ranganath P. Phenotypic Overlap of 22q11.2 Microduplication and Noonan Syndrome in a Fetus with Increased NT, Facial Dysmorphism, and Narrow Pulmonary Trunk. J Fetal Med 2022. [DOI: 10.1007/s40556-022-00343-9] [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: 10/17/2022]
|
11
|
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
|
12
|
Abstract
Muscular dystrophies are a clinically and genetically heterogeneous group of disorders involving the skeletal muscles. They have a progressive clinical course and are characterized by muscle fiber degeneration. Congenital muscular dystrophies (CMD) include dystroglycanopathies, merosin-deficient CMD, collagen VI-deficient CMD, SELENON-related rigid spine muscular dystrophy, and LMNA-related CMD. Childhood and adult-onset muscular dystrophies include dystrophinopathies, limb-girdle muscular dystrophies, Emery-Dreifuss muscular dystrophy, facioscapulohumeral muscular dystrophy, and myotonic dystrophy. Traditionally, muscle biopsy and histopathology along with special pathology techniques such as immunohistochemistry or immunoblotting were used for the diagnosis of muscular dystrophies. However, recent advances in molecular genetic testing, especially the next-generation sequencing technology, have revolutionized the diagnosis of muscular dystrophies. Identification of the underlying genetic basis helps in appropriate management and prognostication of the affected individual and genetic counseling of the family. In addition, identification of the exact disease-causing mutations is necessary for accurate prenatal genetic testing and carrier testing, to prevent recurrence in the family. Mutation identification is also essential for initiating mutation-specific therapies (which have been developed recently, especially for Duchenne muscular dystrophy) and for enrolment of patients into ongoing therapeutic clinical trials. The 'genetic testing first' approach has now become the norm in most centers. Nonetheless, muscle biopsy-based testing still has an important role to play, especially for cases where genetic testing is negative or inconclusive for the etiology.
Collapse
Affiliation(s)
- Deepti Narasimhaiah
- Department of Pathology, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala, India
| | - Megha S Uppin
- Department of Pathology, Nizam's Institute of Medical Sciences, Punjagutta, Hyderabad, Telangana, India
| | - Prajnya Ranganath
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Punjagutta, Hyderabad, Telangana, India
| |
Collapse
|
13
|
Baisya R, Ranganath P, Rajasekhar L. PEPD-Related Prolidase Deficiency Presenting as Hyper-immunoglobulin E Syndrome. J Clin Immunol 2022; 42:892-897. [PMID: 35296989 DOI: 10.1007/s10875-022-01249-x] [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: 12/02/2021] [Accepted: 03/09/2022] [Indexed: 11/26/2022]
Affiliation(s)
- Ritasman Baisya
- Department of Clinical Immunology and Rheumatology, Nizam's Institute of Medical Sciences, Hyderabad, 500082, Telangana, India
| | - Prajnya Ranganath
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, 500082, Telangana, India.
| | - Liza Rajasekhar
- Department of Clinical Immunology and Rheumatology, Nizam's Institute of Medical Sciences, Hyderabad, 500082, Telangana, India
| |
Collapse
|
14
|
Ranganath P, Perala S, Rasheed N. eP465: Role of next-generation sequencing in the evaluation of families with non-immune fetal hydrops. Genet Med 2022. [DOI: 10.1016/j.gim.2022.01.498] [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: 11/24/2022] Open
|
15
|
Chaudhary AK, Gholse A, Nagarajaram HA, Dalal AB, Gupta N, Dutta AK, Danda S, Gupta R, Sankar HV, Bhavani GS, Girisha KM, Phadke SR, Ranganath P, Bashyam MD. Ectodysplasin pathogenic variants affecting the furin-cleavage site and unusual clinical features define X-linked hypohidrotic ectodermal dysplasia in India. Am J Med Genet A 2021; 188:788-805. [PMID: 34863015 DOI: 10.1002/ajmg.a.62579] [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: 07/21/2021] [Revised: 09/20/2021] [Accepted: 11/02/2021] [Indexed: 11/09/2022]
Abstract
Hypohidrotic ectodermal dysplasia (HED) is a rare genetic disorder caused by mutational inactivation of a developmental pathway responsible for generation of tissues of ectodermal origin. The X-linked form accounts for the majority of HED cases and is caused by Ectodysplasin (EDA) pathogenic variants. We performed a combined analysis of 29 X-linked hypohidrotic ectodermal dysplasia (XLHED) families (including 12 from our previous studies). In addition to the classical triad of symptoms including loss (or reduction) of ectodermal structures, such as hair, teeth, and sweat glands, we detected additional HED-related clinical features including facial dysmorphism and hyperpigmentation in several patients. Interestingly, global developmental delay was identified as an unusual clinical symptom in many patients. More importantly, we identified 22 causal pathogenic variants that included 15 missense, four small in-dels, and one nonsense, splice site, and large deletion each. Interestingly, we detected 12 unique (India-specific) pathogenic variants. Of the 29 XLHED families analyzed, 11 (38%) harbored pathogenic variant localized to the furin cleavage site. A comparison with HGMD revealed significant differences in the frequency of missense pathogenic variants; involvement of specific exons and/or protein domains and transition/transversion ratios. A significantly higher proportion of missense pathogenic variants (33%) localized to the EDA furin cleavage when compared to HGMD (7%), of which p.R155C, p.R156C, and p.R156H were detected in three families each. Therefore, the first comprehensive analysis of XLHED from India has revealed several unique features including unusual clinical symptoms and high frequency of furin cleavage site pathogenic variants.
Collapse
Affiliation(s)
- Ajay Kumar Chaudhary
- Laboratory of Molecular Oncology, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Aishwarya Gholse
- Laboratory of Computational Biology, Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Hampapathalu Adimurthy Nagarajaram
- Laboratory of Computational Biology, Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Ashwin Bhikaji Dalal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Neerja Gupta
- Division of Genetics, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Atanu Kumar Dutta
- Department of Clinical Genetics, Christian Medical College and Hospital, Vellore, India
| | - Sumita Danda
- Department of Clinical Genetics, Christian Medical College and Hospital, Vellore, India
| | - Rekha Gupta
- Department of Medical Genetics, Mahatma Gandhi Medical College and Hospital, Jaipur, India
| | - Hariharan V Sankar
- Department of Pediatrics, SAT Hospital, Medical College, Trivandrum, India
| | - Gandham SriLakshmi Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Shubha Rao Phadke
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Prajnya Ranganath
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India.,Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, India
| | - Murali Dharan Bashyam
- Laboratory of Molecular Oncology, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| |
Collapse
|
16
|
Balakrishnan S, Ranganath P. Report of an unusual association of hydrosyringomyelia with Gabriele-de Vries syndrome in an Asian-Indian patient. Clin Dysmorphol 2021; 30:204-206. [PMID: 34456245 DOI: 10.1097/mcd.0000000000000385] [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: 11/26/2022]
Affiliation(s)
- Surya Balakrishnan
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, Telangana, India
| | | |
Collapse
|
17
|
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
|
18
|
Affiliation(s)
- A T Kharat
- Department of Radio diagnosis., Dr Padm D.Y. Patil Medical College., (Deemed University), Pimpri 18, India
| | - A Singh
- Department of Radio diagnosis., Dr Padm D.Y. Patil Medical College., (Deemed University), Pimpri 18, India
| | - P Ranganath
- Department of Radio diagnosis., Dr Padm D.Y. Patil Medical College., (Deemed University), Pimpri 18, India
| | - V M Kulkarni
- Department of Radio diagnosis., Dr Padm D.Y. Patil Medical College., (Deemed University), Pimpri 18, India
| |
Collapse
|
19
|
Buch J, Ranganath P. Approach to inherited hypertrichosis: A brief review. Indian J Dermatol Venereol Leprol 2021; 88:11-21. [PMID: 34379956 DOI: 10.25259/ijdvl_629_20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 05/01/2020] [Accepted: 12/01/2020] [Indexed: 11/04/2022]
Abstract
Hypertrichosis refers to the growth of hair, of an excessive amount and thickness, on any part of the body. It must be distinguished from hirsutism which is characterized by excess growth of hair in androgen-dependent areas on the upper lip, chin, chest, linea alba, thigh and axilla. Hypertrichosis may be localized or generalized, and congenital or acquired. Excess hair growth has a psychological impact on the child as well as the parents due to the cosmetic disfigurement it produces. Current treatment options are limited and not wholly satisfactory. Treatment should be customized according to the area, nature and amount of hair growth, age of the patient and personal preferences. In addition, when hypertrichosis occurs as a component of a syndrome, multidisciplinary management is required to address the associated systemic features. A detailed review of inherited generalized hypertrichosis is presented here with emphasis on clinical clues to identifying complex syndromes with multisystem involvement.
Collapse
Affiliation(s)
- Jeta Buch
- Dermaclinix - The Complete Skin and Hair Solution Centre, New Delhi, India
| | - Prajnya Ranganath
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, Telangana, India
| |
Collapse
|
20
|
Deshpande D, Gupta SK, Sarma AS, Ranganath P, Jain S JMN, Sheth J, Mistri M, Gupta N, Kabra M, Phadke SR, Girisha KM, Dua Puri R, Aggarwal S, Datar C, Mandal K, Tilak P, Muranjan M, Bijarnia-Mahay S, Rama Devi A R, Tayade NB, Ranjan A, Dalal AB. Functional characterization of novel variants in SMPD1 in Indian patients with acid sphingomyelinase deficiency. Hum Mutat 2021; 42:1336-1350. [PMID: 34273913 DOI: 10.1002/humu.24263] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 02/08/2021] [Revised: 06/29/2021] [Accepted: 07/15/2021] [Indexed: 02/03/2023]
Abstract
Pathogenic variations in SMPD1 lead to acid sphingomyelinase deficiency (ASMD), that is, Niemann-Pick disease (NPD) type A and B (NPA, NPB), which is a recessive lysosomal storage disease. The knowledge of variant spectrum in Indian patients is crucial for early and accurate NPD diagnosis and genetic counseling of families. In this study, we recruited 40 unrelated pediatric patients manifesting symptoms of ASMD and subnormal ASM enzyme activity. Variations in SMPD1 were studied using Sanger sequencing for all exons, followed by interpretation of variants based on American College of Medical Genetics and Genomics & Association for Molecular Pathology (ACMG/AMP) criteria. We identified 18 previously unreported variants and 21 known variants, including missense, nonsense, deletions, duplications, and splice site variations with disease-causing potential. Eight missense variants were functionally characterized using in silico molecular dynamic simulation and in vitro transient transfection in HEK293T cells, followed by ASM enzyme assay, immunoblot, and immunofluorescence studies. All the variants showed reduced ASM activity in transfected cells confirming their disease-causing potential. The study provides data for efficient prenatal diagnosis and genetic counseling of families with NPD type A and B.
Collapse
Affiliation(s)
- Dipti Deshpande
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India.,Graduate Studies, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Shailesh Kumar Gupta
- Laboratory of Computational and Functional Genomics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India
| | - Asodu Sandeep Sarma
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India
| | - Prajnya Ranganath
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India.,Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, Telangana, India
| | - Jamal Md Nurul Jain S
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India
| | - Jayesh Sheth
- Institute of Human Genetics, FRIGE House, Ahmedabad, Gujarat, India
| | - Mehul Mistri
- Institute of Human Genetics, FRIGE House, Ahmedabad, Gujarat, India
| | - Neerja Gupta
- Division of Genetics, Department of Pediatrics, AIIMS, New Delhi, India
| | - Madhulika Kabra
- Division of Genetics, Department of Pediatrics, AIIMS, New Delhi, India
| | - Shubha R Phadke
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Ratna Dua Puri
- Institute of Medical Genetics & Genomics, Sir Ganga Ram hospital, New Delhi, India
| | - Shagun Aggarwal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India.,Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, Telangana, India
| | - Chaitanya Datar
- Bharati Hospital and Research Center, Pune, Maharashtra, India
| | - Kausik Mandal
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Preetha Tilak
- Division of Human Genetics, St. John's National Academy of Health, Science, Bangalore, Karnataka, India
| | - Mamta Muranjan
- Genetic Clinic, Department of Pediatrics, Seth GS Medical College & KEM Hospital, Mumbai, India
| | | | | | - Naresh B Tayade
- Life Care Hospital, Amravati, India.,Dr. Panjabarao Deshmukh Medical College Amravati, India
| | - Akash Ranjan
- Laboratory of Computational and Functional Genomics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India
| | - Ashwin B Dalal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India.,Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka, India
| |
Collapse
|
21
|
Thondapu V, Ranganath P, Zhang E, Takigami A, Kohanski M, McGowan J, Harris G, Tower-Rader A, Meyersohn N, Lu M, Hoffmann U, Hedgire S, Ghoshhajra B. Integration Of Fractional Flow Reserve Derived From Coronary Ct Angiography (FFRCT) Into Clinical Practice: Initial Experience From A Tertiary Care Center. J Cardiovasc Comput Tomogr 2021. [DOI: 10.1016/j.jcct.2021.06.212] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
22
|
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
|
23
|
Ranganath P, Patil M. Eye of the Tiger: Looking Beyond Neurodegeneration with Brain Iron Accumulation Disorders. J Pediatr Genet 2021; 12:163-166. [PMID: 37090832 PMCID: PMC10118706 DOI: 10.1055/s-0041-1723959] [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: 08/06/2020] [Accepted: 12/24/2020] [Indexed: 10/22/2022]
Abstract
AbstractThe “eye-of-the-tiger” sign in brain magnetic resonance imaging (MRI) is typically associated with neurodegeneration with brain iron accumulation disorders, especially pantothenate kinase-associated neurodegeneration. However, very similar neuroimaging findings may be seen in other neurodegenerative disorders involving the basal ganglia. We report here a patient with fucosidosis who had MRI brain findings closely resembling the “eye-of-the-tiger” sign.
Collapse
Affiliation(s)
- Prajnya Ranganath
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, Telangana, India
| | - Mallikarjun Patil
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, Telangana, India
| |
Collapse
|
24
|
Nerakh G, Ranganath P, Murugan S. Next-Generation Sequencing in a Cohort of Asian Indian Patients with the Duchenne Muscular Dystrophy Phenotype: Diagnostic Yield and Mutation Spectrum. J Pediatr Genet 2021; 10:23-28. [PMID: 33552634 DOI: 10.1055/s-0040-1713850] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 04/17/2020] [Accepted: 05/22/2020] [Indexed: 01/01/2023]
Abstract
Multiplex ligation-dependent probe amplification (MLPA) detects exonic deletions and duplications in the DMD gene in around 65 to 70% of patients with the Duchenne muscular dystrophy (DMD) phenotype. This study looks at the diagnostic yield of next-generation sequencing (NGS) and the mutation spectrum in an Asian Indian cohort of MLPA-negative cases with the DMD phenotype. NGS-based sequencing of DMD gene was done in 28 MLPA-negative cases (25 male probands with the DMD phenotype and 3 obligate carrier mothers of deceased affected male patients) and disease-causing variants were identified in 19 (67.9%) of these cases. Further molecular testing in four of the remaining nine cases revealed gene variants associated with limb girdle muscular dystrophies. Thus, NGS-based multigene panel testing for muscular dystrophy-associated genes or clinical exome sequencing rather than targeted DMD gene sequencing appears to be a more cost-effective testing modality with better diagnostic yield, for MLPA-negative patients with the DMD phenotype.
Collapse
Affiliation(s)
- Gayatri Nerakh
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, Telangana, India
| | - Prajnya Ranganath
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, Telangana, India
| | | |
Collapse
|
25
|
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
|
26
|
Pasumarthi D, Gupta N, Sheth J, Jain SJMN, Rungsung I, Kabra M, Ranganath P, Aggarwal S, Phadke SR, Girisha KM, Shukla A, Datar C, Verma IC, Puri RD, Bhavsar R, Mistry M, Sankar VH, Gowrishankar K, Agrawal D, Nair M, Danda S, Soni JP, Dalal A. Identification and characterization of 30 novel pathogenic variations in 69 unrelated Indian patients with Mucolipidosis Type II and Type III. J Hum Genet 2020; 65:971-984. [PMID: 32651481 DOI: 10.1038/s10038-020-0797-8] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 05/13/2020] [Accepted: 06/05/2020] [Indexed: 11/09/2022]
Abstract
Mucolipidosis (ML) (OMIM 607840 & 607838) is a rare autosomal recessive inherited disorder that occurs due to the deficiency of golgi enzyme uridine diphosphate (UDP)- N-acetylglucosamine-1-phosphotransferase (GlcNAc-phosphotransferase) responsible for tagging mannose-6-phosphate for proper trafficking of lysosomal enzymes to lysosomes. Variants in GlcNAc-phosphotransferase (GNPTAB (α, β subunits) and GNPTG (γ subunits) are known to result in impaired targeting of lysosomal enzymes leading to Mucolipidosis (ML) Type II or Type III. We analyzed 69 Indian families of MLII/III for clinical features and molecular spectrum and performed in silico analysis for novel variants. We identified 38 pathogenic variants in GNPTAB and 5 pathogenic variants in GNPTG genes including missense, frame shift, deletion, duplication and splice site variations. A total of 26 novel variants were identified in GNPTAB and 4 in GNPTG gene. In silico studies using mutation prediction software like SIFT, Polyphen2 and protein structure analysis further confirmed the pathogenic nature of the novel sequence variants detected in our study. Except for a common variant c.3503_3504delTC in early onset MLII, we could not establish any other significant genotype and phenotype correlation. This is one of the largest studies reported till date on Mucolipidosis II/III in order to identify mutation spectrum and any recurrent mutations specific to the Indian ethnic population. The mutational spectrum information in Indian patients will be useful in better genetic counselling, carrier detection and prenatal diagnosis for patients with ML II/III.
Collapse
Affiliation(s)
- Divya Pasumarthi
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India
| | - Neerja Gupta
- Division of Genetics, Department of Pediatrics, AIIMS, New Delhi, India
| | - Jayesh Sheth
- Institute of Human Genetics, FRIGE House, Ahmedabad, GJ, India
| | - S Jamal Md Nurul Jain
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India
| | - Ikrormi Rungsung
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India
| | - Madhulika Kabra
- Division of Genetics, Department of Pediatrics, AIIMS, New Delhi, India
| | - Prajnya Ranganath
- 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
| | - Shubha R Phadke
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, UP, India
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, KA, India
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, KA, India
| | - Chaitanya Datar
- Bharati Hospital and Research Center, Bharati Hospital and Research Center, Pune, MH, India
| | - Ishwar C Verma
- Center of Medical Genetics, Sir Ganga Ram hospital, New Delhi, India
| | - Ratna Dua Puri
- Center of Medical Genetics, Sir Ganga Ram hospital, New Delhi, India
| | - Riddhi Bhavsar
- Institute of Human Genetics, FRIGE House, Ahmedabad, GJ, India
| | - Mehul Mistry
- Institute of Human Genetics, FRIGE House, Ahmedabad, GJ, India
| | - V H Sankar
- Genetics Clinic, Department of Pediatrics, SAT Hospital, Government Medical College, Trivandrum, KL, India
| | | | - Divya Agrawal
- Center of Medical Genetics, Sir Ganga Ram hospital, New Delhi, India
| | - Mohandas Nair
- Additional Professor in Pediatrics, Government Medical College, Calicut, Kerala, India
| | - Sumita Danda
- ChristianMedical College and Hospital, Vellore, TN, India
| | | | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India.
| |
Collapse
|
27
|
Ranganath P, Perala S, Nair L, Pamu PK, Shankar A, Murugan S, Dalal A. A newly recognized multiple malformation syndrome with caudal regression associated with a biallelic c.402G>A variant in TBX4. Eur J Hum Genet 2020; 28:669-673. [PMID: 31965066 DOI: 10.1038/s41431-020-0572-5] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 11/26/2019] [Accepted: 12/17/2019] [Indexed: 11/09/2022] Open
Abstract
The T-box4 (TBX4) gene (OMIM *601719) belongs to the T-box family of transcription regulators that share a conserved homology domain and are expressed at specific sites during various stages of embryonic development. Tbx4 has been found to be a crucial transcriptional regulator in embryonic hindlimb development in animal models. Monoallelic variants in the TBX4 gene are reported to be associated with skeletal defects of the pelvis and lower limbs. We report here a fetus with a novel multiple malformation syndrome associated with sacrococcygeal agenesis, bilateral lower limb aplasia, hypoplastic left heart, bilateral lung hypoplasia, hydroureteronephrosis, and nonimmune fetal hydrops, found to have a homozygous nonsense variant in the TBX4 gene. We propose that biallelic variants in the TBX4 gene are associated with a severe syndromic phenotype of sacrococcygeal agenesis and lower limb reduction defects.
Collapse
Affiliation(s)
- Prajnya Ranganath
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, Telangana, India. .,Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India.
| | - Sreeja Perala
- 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
| | - Pramod Kumar Pamu
- Department of Pathology, Nizam's Institute of Medical Sciences, Hyderabad, Telangana, India
| | | | | | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India
| |
Collapse
|
28
|
Narayanan DL, Ranganath P, Aggarwal S, Dalal A, Phadke SR, Mandal K. Computer-aided Facial Analysis in Diagnosing Dysmorphic Syndromes in Indian Children. Indian Pediatr 2019. [DOI: 10.1007/s13312-019-1682-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
29
|
Narayanan DL, Ranganath P, Aggarwal S, Dalal A, Phadke SR, Mandal K. Computer-aided Facial Analysis in Diagnosing Dysmorphic Syndromes in Indian Children. Indian Pediatr 2019; 56:1017-1019. [PMID: 31884430] [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: 06/10/2023]
Abstract
OBJECTIVE To assess the utility of computer-aided facial analysis in identifying dysmorphic syndromes in Indian children. METHODS Fifty-one patients with a definite molecular or cytogenetic diagnosis and recognizable facial dysmorphism were enrolled in the study and their facial photographs were uploaded in the Face2Gene software. The results provided by the software were compared with the molecular diagnosis. RESULTS Of the 51 patients, the software predicted the correct diagnosis in 37 patients (72.5%); predicted as the first in the top ten suggestions in 26 (70.2%). In 14 patients, the software did not suggest a correct diagnosis. CONCLUSIONS Computer-aided facial analysis is a method that can aid in diagnosis of genetic syndromes in Indian children. As more clinicians start to use this software, its accuracy is expected to improve.
Collapse
Affiliation(s)
- Dhanya Lakshmi Narayanan
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, Andhra Pradesh, India. Correspondence to: Dr Dhanya Lakshmi Narayanan, Assistant Professor, Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad , Andhra Pradesh, India.
| | - Prajnya Ranganath
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, Andhra Pradesh, India
| | - Shagun Aggarwal
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, Andhra Pradesh, India
| | - Ashwin Dalal
- Diagnostics, Centre and DNA Fingerprinting and Diagnosis, Hyderabad, Andhra Pradesh, India
| | - Shubha R Phadke
- Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Kaushik Mandal
- Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| |
Collapse
|
30
|
Bhattacherjee A, Ranganath P, Pasumarthi D, Dalal AB. Identification and in-silico analysis of a novel disease-causing variant in the GUSB gene for Mucopolysaccharidosis VII presenting as non-immune fetal hydrops. Gene Reports 2019. [DOI: 10.1016/j.genrep.2019.100437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
31
|
Tallapaka K, Ranganath P, Ramachandran A, Uppin MS, Perala S, Aggarwal S, Lakshmi D, Meena AK, Dalal AB. Molecular and Histopathological Characterization of Patients Presenting with the Duchenne Muscular Dystrophy Phenotype in a Tertiary Care Center in Southern India. Indian Pediatr 2019; 56:556-559. [PMID: 31333208] [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: 06/10/2023]
Abstract
OBJECTIVE To study the histopathological characteristics and mutation spectrum of patients presenting with the Duchenne muscular dystrophy (DMD) phenotype. METHODS This was a descriptive study conducted over a period of 8 years. Multiplex ligation-dependent probe amplification (MLPA) was done in patients presenting with the DMD phenotype. If MLPA was negative, patients were offered muscle biopsy for histopathological studies and/or next generation sequencing (NGS) based multigene panel testing for muscular dystrophies. RESULTS Of the 510 patients included, mutation in the DMD gene was detected by MLPA in 372 (72.9%), of whom 342 (67.1%) had exonic deletions and 30 (5.9%) had exonic duplications. Exons 45-55 were most commonly involved in large deletions and exons 1-10 were the commonest exons involved in duplications. In the MLPA-negative cohort, 27 proceeded for muscle biopsy. NGS was done in 14 patients, 10 of whom had pathogenic mutations in the DMD gene, 3 were non dystrophinopathies and no pathogenic variant could be identified in one patient. CONCLUSIONS For patients presenting with the DMD phenotype, MLPA of the DMD gene has a high diagnostic rate of about 73%, and non-dystrophinopathies may constitute a small but significant proportion.
Collapse
Affiliation(s)
- Karthik Tallapaka
- Department of Medical Genetics, Nizam's Institute of Medical Sciences and Diagnostics division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India
| | - Prajnya Ranganath
- Department of Medical Genetics, Nizam's Institute of Medical Sciences and Diagnostics division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India. Correspondence to: Dr Prajnya Ranganath, Associate Professor and Head, Department of Medical Genetics, Nizam's Institute of Medical Sciences, Panjagutta, Hyderabad, Telangana 500 082, India.
| | - Angalena Ramachandran
- Diagnostics division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India
| | - Megha S Uppin
- Department of Pathology, Nizam's Institute of Medical Sciences, Hyderabad, Telangana, India
| | - Sreeja Perala
- Department of Medical Genetics, Nizam's Institute of Medical Sciences and Diagnostics division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India
| | - Shagun Aggarwal
- Department of Medical Genetics, Nizam's Institute of Medical Sciences and Diagnostics division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India
| | - Dhanya Lakshmi
- Department of Medical Genetics, Nizam's Institute of Medical Sciences and Diagnostics division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India
| | - A K Meena
- Department of Neurology, Nizam's Institute of Medical Sciences, Hyderabad, Telangana, India
| | - Ashwin B Dalal
- Diagnostics division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India
| |
Collapse
|
32
|
Sheth J, Bhavsar R, Mistri M, Pancholi D, Bavdekar A, Dalal A, Ranganath P, Girisha KM, Shukla A, Phadke S, Puri R, Panigrahi I, Kaur A, Muranjan M, Goyal M, Ramadevi R, Shah R, Nampoothiri S, Danda S, Datar C, Kapoor S, Bhatwadekar S, Sheth F. Gaucher disease: single gene molecular characterization of one-hundred Indian patients reveals novel variants and the most prevalent mutation. BMC Med Genet 2019; 20:31. [PMID: 30764785 PMCID: PMC6376752 DOI: 10.1186/s12881-019-0759-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 01/22/2019] [Indexed: 12/20/2022]
Abstract
Background Gaucher disease is a rare pan-ethnic, lysosomal storage disorder resulting due to beta-Glucosidase (GBA1) gene defect. This leads to the glucocerebrosidase enzyme deficiency and an increased accumulation of undegraded glycolipid glucocerebroside inside the cells’ lysosomes. To date, nearly 460 mutations have been described in the GBA1 gene. With the aim to determine mutations spectrum and molecular pathology of Gaucher disease in India, the present study investigated one hundred unrelated patients (age range: 1 day to 31 years) having splenomegaly, with or without hepatomegaly, cytopenia and bone abnormality in some of the patients. Methods The biochemical investigation for the plasma chitotriosidase enzyme activity and β-Glucosidase enzyme activity confirmed the Gaucher disease. The mutations were identified by screening the patients’ whole GBA gene coding region using bidirectional Sanger sequencing. Results The biochemical analysis revealed a significant reduction in the β-Glucosidase activity in all patients. Sanger sequencing established 71 patients with homozygous mutation and 22 patients with compound heterozygous mutation in GBA1 gene. Lack of identification of mutations in three patients suggests the possibility of either large deletion/duplication or deep intronic variations in the GBA1 gene. In four cases, where the proband died due to confirmed Gaucher disease, the parents were found to be a carrier. Overall, the study identified 33 mutations in 100 patients that also covers four missense mutations (p.Ser136Leu, p.Leu279Val, p.Gly383Asp, p.Gly399Arg) not previously reported in Gaucher disease patients. The mutation p.Leu483Pro was identified as the most commonly occurring Gaucher disease mutation in the study (62% patients). The second common mutations identified were p.Arg535Cys (7% patients) and RecNcil (7% patients). Another complex mutation Complex C was identified in a compound heterozygous status (3% patients). The homology modeling of the novel mutations suggested the destabilization of the GBA protein structure due to conformational changes. Conclusions The study reports four novel and 29 known mutations identified in the GBA1 gene in one-hundred Gaucher patients. The given study establishes p.Leu483Pro as the most prevalent mutation in the Indian patients with type 1 Gaucher disease that provide new insight into the molecular basis of Gaucher Disease in India. Electronic supplementary material The online version of this article (10.1186/s12881-019-0759-1) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Jayesh Sheth
- FRIGE's Institute of Human Genetics, FRIGE House, Jodhpur Gam Road, Satellite, Ahmedabad, Gujarat, 380015, India.
| | - Riddhi Bhavsar
- FRIGE's Institute of Human Genetics, FRIGE House, Jodhpur Gam Road, Satellite, Ahmedabad, Gujarat, 380015, India
| | - Mehul Mistri
- FRIGE's Institute of Human Genetics, FRIGE House, Jodhpur Gam Road, Satellite, Ahmedabad, Gujarat, 380015, India
| | - Dhairya Pancholi
- FRIGE's Institute of Human Genetics, FRIGE House, Jodhpur Gam Road, Satellite, Ahmedabad, Gujarat, 380015, India
| | | | - Ashwin Dalal
- Centre for DNA Fingerprinting and Diagnostics, Hyderabad, 500039, India
| | - Prajnya Ranganath
- Centre for DNA Fingerprinting and Diagnostics, Hyderabad, 500039, India
| | - Katta M Girisha
- Kasturba Medical College, Tiger Cir Rd, Madhav Nagar, Manipal, 576104, Karnataka, India
| | - Anju Shukla
- Kasturba Medical College, Tiger Cir Rd, Madhav Nagar, Manipal, 576104, Karnataka, India
| | - Shubha Phadke
- Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, 226014, India
| | - Ratna Puri
- Sir Ganga Ram Hospital, New Delhi, 110060, India
| | - Inusha Panigrahi
- The Postgraduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Anupriya Kaur
- The Postgraduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | | | - Manisha Goyal
- J.K. Lone Mother and Child Hospital, Jaipur, 302004, India
| | | | - Raju Shah
- Ankur Institute of Child Health, Ahmedabad, 380009, India
| | - Sheela Nampoothiri
- Amrita Institute of Medical Sciences & Research Centre, Cochin, 682041, India
| | - Sumita Danda
- Christian Medical College & Hospital, Vellore, 632004, India
| | - Chaitanya Datar
- Sahyadri Medical Genetics & Tissue Engineering Facility, Pune, 411038, India
| | - Seema Kapoor
- Maulana Azad medical College and Associated Loknayak Hospital, New Delhi, 110002, India
| | | | - Frenny Sheth
- FRIGE's Institute of Human Genetics, FRIGE House, Jodhpur Gam Road, Satellite, Ahmedabad, Gujarat, 380015, India
| |
Collapse
|
33
|
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.
Collapse
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.
| |
Collapse
|
34
|
Abstract
Prenatal testing is the best strategy for reducing the burden of genetic disorders and congenital disabilities that cause significant postnatal functional impairment. Universal prenatal screening is advisable for common genetic disorders and congenital anomalies such as Down syndrome, beta-thalassaemia and neural tube defects. Several prenatal-screening tests are now available for Down syndrome, but knowledge about the appropriate timing of the test and the need for pre- and post-test counselling may not be updated among the primary care physicians. There is also a considerable degree of confusion regarding the prenatal screening test to be chosen in each case, due to the availability of a number of new and advanced screening techniques. At present, there is no nation-wide consensus regarding the nature and timing of these prenatal-screening protocols. Due to the absence of any definite guidelines and the additional lacunae in the awareness regarding the appropriate prenatal screening in the country, the optimum benefits of these screening protocols are not reaching the population. This review focuses on the various prenatal screening and diagnostic tests that are available for common genetic conditions and congenital disabilities and attempts to outline the most cost-effective and gestational age-appropriate strategies for prenatal screening for the Indian healthcare set-up. The recommendations suggested would serve as a source guide for formulating prenatal-screening guidelines for reducing the incidence of common genetic disorders and congenital disabilities in India.
Collapse
Affiliation(s)
- Shubha R Phadke
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Ratna D Puri
- Institute of Medical Genetics & Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Prajnya Ranganath
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, India
| |
Collapse
|
35
|
Dutta UR, Bahal A, Vineeth V, Sarvade V, Ranganath P, Dalal A. A novel mosaic complex supernumerary marker chromosome in a girl with seizures: systematic characterization of the complex marker. Gene Reports 2017. [DOI: 10.1016/j.genrep.2017.07.002] [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: 01/22/2023]
|
36
|
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]
|
37
|
Uttarilli A, Pasumarthi D, Ranganath P, Dalal AB. Functional characterization of arylsulfatase B mutations in Indian patients with Maroteaux-Lamy syndrome (mucopolysaccharidosis type VI). Gene 2017; 599:19-27. [DOI: 10.1016/j.gene.2016.11.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 11/02/2016] [Accepted: 11/04/2016] [Indexed: 11/27/2022]
|
38
|
Uttarilli A, Ranganath P, Jain SJMN, Prasad CK, Sinha A, Verma IC, Phadke SR, Puri RD, Danda S, Muranjan MN, Jevalikar G, Nagarajaram HA, Dalal AB. Novel mutations of the arylsulphatase B (ARSB) gene in Indian patients with mucopolysaccharidosis type VI. Indian J Med Res 2016; 142:414-25. [PMID: 26609033 PMCID: PMC4683826 DOI: 10.4103/0971-5916.169201] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Background & objectives: Mucopolysaccharidosis type VI (MPS VI) is a rare, autosomal recessive lysosomal storage disorder caused by deficient enzymatic activity of N-acetyl galactosamine-4-sulphatase resulting from mutations in the arylsulphatase B (ARSB) gene. The ARSB gene is located on chromosome 5q11-q13 and is composed of eight exons. More than hundred ARSB mutations have been reported so far, but the mutation spectrum of MPS VI in India is still unknown. Hence, the aim of the present study was to identify the mutational spectrum in patients with MPS VI in India and to study the genotype-phenotype association and functional outcomes of these mutations. Methods: Molecular characterization of the ARSB gene by Sanger sequencing was done for 15 patients (aged 15 months to 11 yr) who were enzymatically confirmed to have MPS VI. Age of onset, clinical progression and enzyme activity levels in each patient were studied to look for genotype-phenotype association. Haplotype analysis performed for unrelated patients with the recurring mutation W450C, was suggestive of a founder effect. Sequence and structural analyses of the ARSB protein using standard software were carried out to determine the impact of detected mutations on the function of the ARSB protein. Results: A total of 12 mutations were identified, of which nine were novel mutations namely, p.D53N, p.L98R, p.Y103SfsX9, p.W353X, p.H393R, p.F166fsX18, p.I220fsX5, p.W450L, and p.W450C, and three were known mutations (p.D54N, p.A237D and p.S320R). The nine novel sequence variants were confirmed not to be polymorphic variants by performing sequencing in 50 unaffected individuals from the same ethnic population. Interpretation & conclusions: Nine novel mutations were identified in MPS VI cases from India in the present study. The study also provides some insights into the genotype-phenotype association in MPS VI.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Ashwin B Dalal
- Diagnostics Division, Centre for DNA Fingerprinting & Diagnostics, Hyderabad, India
| |
Collapse
|
39
|
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.
Collapse
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.
| |
Collapse
|
40
|
Uttarilli A, Ranganath P, Matta D, Md Nurul Jain J, Prasad K, Babu AS, Girisha KM, Verma IC, Phadke SR, Mandal K, Puri RD, Aggarwal S, Danda S, Sankar VH, Kapoor S, Bhat M, Gowrishankar K, Hasan AQ, Nair M, Nampoothiri S, Dalal A. Identification and characterization of 20 novel pathogenic variants in 60 unrelated Indian patients with mucopolysaccharidoses type I and type II. Clin Genet 2016; 90:496-508. [PMID: 27146977 DOI: 10.1111/cge.12795] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [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: 01/11/2016] [Revised: 04/23/2016] [Accepted: 05/01/2016] [Indexed: 11/30/2022]
Abstract
Mucopolysaccharidoses (MPS), a subgroup of lysosomal storage disorders, are caused due to deficiency of specific lysosomal enzyme involved in catabolism of glycosaminoglycans. To date more than 200 pathogenic variants in the alpha-l-iduronidase (IDUA) for MPS I and ∼500 pathogenic variants in the iduronate-2-sulphatase (IDS) for MPS II have been reported worldwide. The mutation spectrum of MPS type I and MPS type II disorders in Indian population is not characterized yet. In this study, we carried out clinical, biochemical, molecular and in silico analyses to establish the mutation spectrum of MPS I and MPS II in the Indian population. We conducted molecular analysis for 60 MPS-affected patients [MPS I (n = 30) (Hurler syndrome = 17, Hurler-Scheie syndrome = 13), and MPS II (n = 30) (severe = 18, attenuated = 12)] and identified a total of 44 [MPS I (n = 22) and MPS II (n = 22)] different pathogenic variants comprising missense, nonsense, frameshift, gross deletions and splice site variants. A total of 20 [MPS I (n = 14), and MPS II (n = 6)] novel pathogenic sequence variants were identified in our patient cohort. We found that 32% of pathogenic variants detected in IDUA were recurrent and 25% in MPS II. This is the first study revealing the mutation spectrum of MPS I and MPS II patients in the Indian population.
Collapse
Affiliation(s)
- A Uttarilli
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India.,Graduate Studies, Manipal University, Manipal, India
| | - P Ranganath
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India.,Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, India
| | - D Matta
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - J Md Nurul Jain
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - K Prasad
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - A S Babu
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - K M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, India
| | - I C Verma
- Center of Medical Genetics, Sir Ganga Ram Hospital, New Delhi, India
| | - S R Phadke
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - K Mandal
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - R D Puri
- Center of Medical Genetics, Sir Ganga Ram Hospital, New Delhi, India
| | - S Aggarwal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India.,Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, India
| | - S Danda
- Department of Clinical Genetics, Christian Medical College and Hospital, Vellore, India
| | - V H Sankar
- Genetics Clinic, Department of Pediatrics, SAT Hospital, Government Medical College, Trivandrum, India
| | - S Kapoor
- Department of Pediatrics, Maulana Azad Medical College, New Delhi, India
| | - M Bhat
- Centre for Human Genetics, Bengaluru, India
| | | | - A Q Hasan
- Department of Genetics, Kamineni Hospital, Hyderabad, India
| | - M Nair
- Additional Professor in Pediatrics, Government Medical College, Manjeri, India
| | - S Nampoothiri
- Department of Pediatric Genetics, Amrita Institute of Medical Sciences, Kochi, India
| | - A Dalal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| |
Collapse
|
41
|
Chaudhary AK, Mohapatra R, Nagarajaram HA, Ranganath P, Dalal A, Dutta A, Danda S, Girisha KM, Bashyam MD. The novel EDAR p.L397H missense mutation causes autosomal dominant hypohidrotic ectodermal dysplasia. J Eur Acad Dermatol Venereol 2016; 31:e17-e20. [PMID: 27168349 DOI: 10.1111/jdv.13587] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
| | - R Mohapatra
- Laboratory of Computational biology, Hyderabad, India
| | | | - P Ranganath
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India.,Nizam's Institute of Medical Sciences, Hyderabad, India
| | - A Dalal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - A Dutta
- Christian Medical College, Vellore, India
| | - S Danda
- Christian Medical College, Vellore, India
| | - K M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, India
| | - M D Bashyam
- Laboratory of Molecular Oncology, Hyderabad, India
| |
Collapse
|
42
|
Bhavani GS, Shah H, Shukla A, Gupta N, Gowrishankar K, Rao AP, Kabra M, Agarwal M, Ranganath P, Ekbote AV, Phadke SR, Kamath A, Dalal A, Girisha KM. Clinical and mutation profile of multicentric osteolysis nodulosis and arthropathy. Am J Med Genet A 2015; 170A:410-417. [DOI: 10.1002/ajmg.a.37447] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 10/15/2015] [Indexed: 01/17/2023]
Affiliation(s)
| | - Hitesh Shah
- Department of Orthopedics, Pediatric Orthopedics services, Kasturba Medical College; Manipal University; Manipal India
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College; Manipal University; Manipal India
| | - Neerja Gupta
- Division of Genetics, Department of Pediatrics; All India Institute of Medical Sciences; New Delhi India
| | - Kalpana Gowrishankar
- Department of Medical Genetics; Kanchi Kamakoti Childs Trust Hospital; Chennai Tamilnadu India
| | | | - Madhulika Kabra
- Division of Genetics, Department of Pediatrics; All India Institute of Medical Sciences; New Delhi India
| | - Meenal Agarwal
- Department of Medical Genetics; Sanjay Gandhi Postgraduate Institute of Medical Sciences; Lucknow India
| | - Prajnya Ranganath
- Department of Medical Genetics; Nizam's Institute of Medical Sciences; Hyderabad India
- Division of Diagnostics; Centre for DNA Fingerprinting and Diagnostics; Hyderabad India
| | - Alka V. Ekbote
- Department of Clinical Genetics; Christian Medical College and Hospital; Vellore India
| | - Shubha R. Phadke
- Department of Medical Genetics; Sanjay Gandhi Postgraduate Institute of Medical Sciences; Lucknow India
| | - Asha Kamath
- Department of Community Medicine; Kasturba Medical College, Manipal University; Manipal Karnataka India
| | - Ashwin Dalal
- Division of Diagnostics; Centre for DNA Fingerprinting and Diagnostics; Hyderabad India
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College; Manipal University; Manipal India
| |
Collapse
|
43
|
Abstract
MicroRNA-155 (miR-155) is a multifunctional molecule involved in both normal and malignant hematopoiesis. It has been found to be involved in the pathogenesis of many different hematological malignancies with either an oncogenic or a tumor-repressor effect, depending on the nature of the cell and the type of malignancy. In particular, it has been strongly implicated in the causation of diffuse large B-cell lymphomas. This review focuses on the molecular interactions of miR-155, its oncogenic mechanisms, and its potential as an effective therapeutic target for the associated malignancies.
Collapse
Affiliation(s)
- Prajnya Ranganath
- 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
|
44
|
Bidchol AM, Dalal A, Trivedi R, Shukla A, Nampoothiri S, Sankar VH, Danda S, Gupta N, Kabra M, Hebbar SA, Bhat RY, Matta D, Ekbote AV, Puri RD, Phadke SR, Gowrishankar K, Aggarwal S, Ranganath P, Sharda S, Kamate M, Datar CA, Bhat K, Kamath N, Shah H, Krishna S, Gopinath PM, Verma IC, Nagarajaram HA, Satyamoorthy K, Girisha KM. Recurrent and novel GLB1 mutations in India. Gene 2015; 567:173-81. [PMID: 25936995 DOI: 10.1016/j.gene.2015.04.078] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [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: 03/23/2015] [Revised: 04/27/2015] [Accepted: 04/28/2015] [Indexed: 02/08/2023]
Abstract
GM1 gangliosidosis is a lysosomal storage disorder caused by mutations in the GLB1 gene, leading to the deficiency of the enzyme β-d-galactosidase. In this study, we report molecular findings in 50 Asian Indian families with GM1 gangliosidosis. We sequenced all the exons and flanking intronic sequences of GLB1 gene. We identified 33 different mutations (20 novel and 13 previously reported). The novel mutations include 12 missense (p.M1?, p.E129Q, p.G134R, p.L236P, p.G262E, p.L297F, p.Y331C, p.G414V, p.K493N, p.L514P, p.P597L, p.T600I), four splicing (c.246-2A>G, c.397-2A>G, c.552+1G>T, c.956-2A>G), three indels (p.R22Qfs*8, p.L24Cfs*47, p.I489Qfs*4) and one nonsense mutation (p.Q452*). Most common mutations identified in this study were c.75+2InsT (14%) and p.L337P (10%). Known mutations accounted for 67% of allele frequency in our cohort of patients, suggesting that these mutations in GLB1 are recurrent across different populations. Twenty three mutations were localized in the TIM barrel domain, β-domain 1 and β-domain 2. In silico sequence and structure analysis of GLB1 reveal that all the novel mutations affect the function and structure of the protein. We hereby report on the largest series of patients with GM1 gangliosidosis and the first from India.
Collapse
Affiliation(s)
- Abdul Mueed Bidchol
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, Karnataka, India
| | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India
| | - Rakesh Trivedi
- Laboratory of Computational Biology & Bioinformatics Facility, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India; Graduate Studies, Manipal University, Manipal, Karnataka, India
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, Karnataka, India
| | - Sheela Nampoothiri
- Department of Pediatric Genetics, Amrita Institute of Medical Sciences and Research Center, Kochi, AIMS Ponekkara, Kerala, India
| | - V H Sankar
- Genetic Clinic, Department of Pediatrics, SAT Hospital, Government Medical College, Thiruvananthapuram, Kerala, 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
| | - Madhulika Kabra
- Genetics Unit, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Shrikiran A Hebbar
- Department of Pediatrics, Kasturba Medical College, Manipal University, Manipal, Karnataka, India
| | - Ramesh Y Bhat
- Department of Pediatrics, Kasturba Medical College, Manipal University, Manipal, Karnataka, India
| | - Divya Matta
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India
| | - Alka V Ekbote
- Department of Clinical Genetics, Christian Medical College and Hospital, Vellore, Tamil Nadu, India
| | - Ratna Dua Puri
- Center of Medical Genetics, Sir Ganga Ram Hospital, New Delhi, India
| | - Shubha R Phadke
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Kalpana Gowrishankar
- Department of Medical Genetics, Childs Trust Medical Research Foundation, Kanchi Kamakoti Childs Trust Hospital, Chennai, Tamil Nadu, India
| | - Shagun Aggarwal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India; Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, Telangana, India
| | - Prajnya Ranganath
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India; Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, Telangana, India
| | - Sheetal Sharda
- Post Graduate Institute of Medical Education and Research, Chandigarh, Punjab, India
| | - Mahesh Kamate
- Pediatric Neurology, KLE University's J N Medical College, Belgaum, Karnataka, India
| | - Chaitanya A Datar
- Rare Genetic Disorder Clinic, Sahyadri Hospital, Pune, Maharashtra, India
| | - Kamalakshi Bhat
- Department of Pediatrics, Kasturba Medical College, Mangalore, Manipal University, Karnataka, India
| | - Nutan Kamath
- Department of Pediatrics, Kasturba Medical College, Mangalore, Manipal University, Karnataka, India
| | - Hitesh Shah
- Pediatric Orthopedics Services, Department of Orthopedics, Kasturba Medical College, Manipal, Manipal University, Karnataka, India
| | - Shuba Krishna
- Strand Life Sciences Pvt Ltd, Bengaluru, Karnataka, India
| | - Puthiya Mundyat Gopinath
- Division of Biotechnology, School of Life Sciences, Manipal University, Manipal, Karnataka, India
| | - Ishwar C Verma
- Center of Medical Genetics, Sir Ganga Ram Hospital, New Delhi, India
| | - H A Nagarajaram
- Laboratory of Computational Biology & Bioinformatics Facility, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India
| | - Kapaettu Satyamoorthy
- Division of Biotechnology, School of Life Sciences, Manipal University, Manipal, Karnataka, India
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, Karnataka, India.
| |
Collapse
|
45
|
Lakkireddy M, Chilakamarri V, Ranganath P, Arora AJ, Vanaja MC. Clinical and Genetic Analysis of Fibrodysplasia Ossificans Progressiva: A Case Report and Literature Review. J Clin Diagn Res 2015; 9:RD01-3. [PMID: 26436010 DOI: 10.7860/jcdr/2015/15160.6393] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [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: 06/09/2015] [Accepted: 07/10/2015] [Indexed: 11/24/2022]
Abstract
Fibrodysplasia ossificans progressiva (FOP) is a rare genetic disorder characterized by congenital malformation of the great toes and disabling heterotopic ossification in specific anatomic locations with a world wide prevalence of 1 in 2 million population. Nearly 90% of patients with FOP are misdiagnosed and mismanaged. We present a case of a four-year-old boy brought by his parents with the complaints of stiffness of right shoulder, neck and multiple swellings over the upper back noted over the past 4 months. On examination bilateral symmetrical hallux valgus with microdactyly of great toes and multiple bony hard swellings on both the scapulae were noted. Skeletal survey revealed all the classical features of FOP. Mutation of the ACVR1gene on genetic analysis confirmed the diagnosis of FOP. Invasive surgical procedures including biopsy and manipulations for stiff joints were avoided as they strikingly end up in rapid progression of FOP. Congenital hallux valgus with short great toe in a child should be considered as an early diagnostic tool for FOP even before the onset of mass lesions. Genetic analysis for mutation of ACVR1gene is confirmatory. Prevention of injury, medical management of acute painful flare-ups and rehabilitation are the mainstay of treatment.
Collapse
Affiliation(s)
- Maheshwar Lakkireddy
- Assistant Professor, Department of Orthopaedics, Nizam's Institute of Medical Sciences , Hyderabad, India
| | | | - Prajnya Ranganath
- Assistant Professor, Department of Medical Genetics, Nizam's Institute of Medical Sciences , Hyderabad, India
| | | | - Maria Celestina Vanaja
- Research Associate, Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics , Hyderabad, India
| |
Collapse
|
46
|
Bhavani GS, Shah H, Dalal AB, Shukla A, Danda S, Aggarwal S, Phadke SR, Gupta N, Kabra M, Gowrishankar K, Gupta A, Bhat M, Puri RD, Bijarnia-Mahay S, Nampoothiri S, Mohanasundaram KM, Rajeswari S, Kulkarni AM, Kulkarni ML, Ranganath P, Ramadevi AR, Hariharan SV, Girisha KM. Novel and recurrent mutations in WISP3 and an atypical phenotype. Am J Med Genet A 2015; 167A:2481-4. [PMID: 25988854 DOI: 10.1002/ajmg.a.37164] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 05/03/2015] [Indexed: 12/22/2022]
Affiliation(s)
| | - Hitesh Shah
- Department of Orthopedics, Pediatric Orthopedics Services, Kasturba Medical College, Manipal University, Manipal, India
| | - Ashwin B Dalal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, India
| | - Sumita Danda
- Department of Clinical Genetics, Christian Medical College and Hospital, Vellore, India
| | - Shagun Aggarwal
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, India
| | - Shubha R Phadke
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Neerja Gupta
- Department of Pediatrics, Division of Genetics, All India Institute of Medical Science, New Delhi, India
| | - Madhulika Kabra
- Department of Pediatrics, Division of Genetics, All India Institute of Medical Science, New Delhi, India
| | - Kalpana Gowrishankar
- Department of Medical Genetics, Kanchi Kamakoti Childs Trust Hospital, Chennai, Tamil Nadu, India
| | - Anju Gupta
- Department of Pediatrics, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | | | - Ratna D Puri
- Centre of Medical Genetics, Sir Ganga Ram Hospital, New Delhi, India
| | | | - Sheela Nampoothiri
- Department of Pediatric Genetics, Amrita Institute of Medical Sciences and Research Centre, Ponekkara, Cochin, Kerala, India
| | | | - S Rajeswari
- Department of Rheumatology, Madras Medical College, Chennai, India
| | - Akhil M Kulkarni
- Department of Radiodiagnosis, SS Institute of Medical Sciences and Research Centre, Davangere, India
| | - Muralidhar L Kulkarni
- Department of Pediatrics, Jagadguru Jayadeva Murugarajendra Medical College, Davangere, India
| | - Prajnya Ranganath
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India.,Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, India
| | - A Radha Ramadevi
- Department of Clinical Genetics, Genetics Unit, Rainbow Children Hospital, Hyderabad, India
| | - Sankar V Hariharan
- Department of Pediatrics, Sree Avittom Thirunal Hospital, Government Medical College, Trivandrum, India
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, India
| |
Collapse
|
47
|
Bidchol AM, Dalal A, Shah H, S S, Nampoothiri S, Kabra M, Gupta N, Danda S, Gowrishankar K, Phadke SR, Kapoor S, Kamate M, Verma IC, Puri RD, Sankar VH, Devi ARR, Patil SJ, Ranganath P, Jain SJMN, Agarwal M, Singh A, Mishra P, Tamhankar PM, Gopinath PM, Nagarajaram HA, Satyamoorthy K, Girisha KM. GALNS mutations in Indian patients with mucopolysaccharidosis IVA. Am J Med Genet A 2014; 164A:2793-801. [PMID: 25252036 DOI: 10.1002/ajmg.a.36735] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [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: 10/26/2013] [Accepted: 06/27/2014] [Indexed: 01/20/2023]
Abstract
Mucopolysaccharidosis IV A (Morquio syndrome A, MPS IVA) is a lysosomal storage disease caused by the deficiency of N-acetylgalactosamine-6-sulfatase (GALNS). The mutation spectrum in this condition is yet to be determined in Indians. We aimed to analyze the mutations in the GALNS gene in Asian Indians with MPS IVA. All the exons and the adjacent intronic regions of the gene were amplified and sequenced in sixty-eight unrelated Indian families. We identified 136 mutant alleles comprising of 40 different mutations. We report twenty-two novel mutations that comprise of seventeen missense (p.Asn32Thr, p.Leu36Arg, p.Pro52Leu, p.Pro77Ser, p.Cys79Arg, p.His142Pro, p.Tyr191Asp, p.Asn204Thr, p.Gly188Ser, p.Phe216Ser, p.Trp230Cys, p.Ala291Ser, p.Gly317Arg, p.His329Pro, p.Arg386Ser, p.Glu450Gly, p.Cys501Ser), three splice-site variants (c.120+1G>C, c.1003-3C>G, c.1139+1G>A), one nonsense mutation (p.Gln414*) and one frameshift mutation (p.Pro420Leufs*440). Eighteen mutations have been reported earlier. Among these p.Ser287Leu (8.82%), p.Phe216Ser (7.35%), p.Asn32Thr (6.61%) and p.Ala291Ser (5.88%) were the most frequent mutations in Indian patients but were rare in the mutational profiles reported in other populations. These results indicate that the Indian patients may have a distinct mutation spectrum compared to those of other populations. Mutant alleles in exon 1, 7 and 8 accounted for 44.8% of the mutations, and sequencing of these exons initially may be a cost-effective approach in Asian Indian patients. This is the largest study on molecular analysis of patients with MPS IVA reported in the literature, and the first report from India.
Collapse
Affiliation(s)
- Abdul Mueed Bidchol
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, Karnataka, India
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Nandagopalan RS, Phadke SR, Dalal AB, Ranganath P. Novel mutations in PRG4 gene in two Indian families with camptodactyly-arthropathy-coxa vara-pericarditis (CACP) syndrome. Indian J Med Res 2014; 140:221-6. [PMID: 25297354 PMCID: PMC4216495] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND & OBJECTIVES Camptodactyly--arthropathy-coxa vara-pericarditis (CACP) syndrome is an autosomal recessive disorder caused by mutations in the PRG4 (proteoglycan 4) gene. Hallmarks of the syndrome include congenital or early-onset camptodactyly and arthropathy with synovial hyperplasia, progressive coxa vara deformity and non-inflammatory pericardial effusions. Till date only around 25 pathogenic mutations have been reported in this gene and none have been reported from India. We report here the mutations in the PRG4 gene in three patients of CACP from two unrelated families from India. METHODS Molecular genetic studies were done for the three patients with the CACP syndrome, from two unrelated Indian families, through sequence analysis of all coding exons and the exon-intron boundaries of the PRG4 gene. RESULTS Two novel frame-shift deletion mutations leading to premature protein termination were found. One patient was identified to be homozygous for a 2 base pair deletion in exon 6 (c.2645_2646delGA) and the two affected siblings from the other family were found to be homozygous for a 4 base pair deletion in exon 6 (c.2883_2886delAAGA). CONCLUSIONS This is perhaps the first report of PRG4 mutations from India. Further mutation studies in Indian CACP cases will help to determine the mutation spectrum of the PRG4 gene in the Indian population and also help to further elucidate the molecular pathology and the genotype-phenotype correlation of this rare disease.
Collapse
Affiliation(s)
| | - Shubha R. Phadke
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Ashwin B. Dalal
- Diagnostics Division, Centre for DNA Fingerprinting & Diagnostics, Hyderabad, India
| | - Prajnya Ranganath
- Diagnostics Division, Centre for DNA Fingerprinting & Diagnostics, Hyderabad, India,Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, India,Reprint requests: Dr Prajnya Ranganath, Assistant Professor & Head, Department of Medical Genetics Nizam's Institute of Medical Sciences, Hyderabad 500 082, India e-mail:
| |
Collapse
|
49
|
Chittem L, Bhattacharjee S, Ranganath P. Craniosynostosis in a child with I-cell disease: The need for genetic analysis before contemplating surgery in craniosynostosis. J Pediatr Neurosci 2014; 9:33-5. [PMID: 24891900 PMCID: PMC4040029 DOI: 10.4103/1817-1745.131480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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] [Indexed: 11/12/2022] Open
Abstract
We are reporting a rare case of I-cell disease presenting with craniosynostosis. An 11-month-old child presented with abnormal head shape, developmental delay and bent bones. We planned for corrective surgery for craniosynostosis, but on genetic analysis I-cell disease was confirmed. After explaining the prognosis of I-cell disease, parents denied surgery. This case report emphasizes the fact that syndromic evaluation of craniosynostosis is very much essential before proceeding for corrective surgery.
Collapse
Affiliation(s)
- Lakshmanarao Chittem
- Department of Neurosurgery, Nizam's Institute of Medical Sciences, Panjagutta, Hyderabad, Andhra Pradesh, India
| | - Suchanda Bhattacharjee
- Department of Neurosurgery, Nizam's Institute of Medical Sciences, Panjagutta, Hyderabad, Andhra Pradesh, India
| | - Prajnya Ranganath
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Panjagutta, Hyderabad, Andhra Pradesh, India
| |
Collapse
|
50
|
Dutta UR, Vempally S, Ranganath P, Dalal A. A novel combined 15q11.2 duplication and a bisatellited supernumerary marker derived from chromosome 22: molecular characterization of the marker. Gene 2014; 539:162-7. [PMID: 24508374 DOI: 10.1016/j.gene.2014.02.002] [Citation(s) in RCA: 3] [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: 07/29/2013] [Revised: 12/16/2013] [Accepted: 02/04/2014] [Indexed: 10/25/2022]
Abstract
Supernumerary marker chromosomes (SMC) are heterogeneous group of chromosomes which are reported in variable phenotypes. Approximately 70% originate from acrocentric chromosomes. Here we report a couple with recurrent miscarriages and a SMC originating from an acrocentric chromosome. The cytogenetic analysis of the husband revealed a karyotype of 47,XY+marker whereas the wife had a normal karyotype. Analysis of SMC with C-banding showed the presence of a big centromere in the center and silver staining showed prominent satellites on both sides of the marker. Apparently, microarray analysis revealed a 2.1 Mb duplication of 15q11.2 region but molecular cytogenetic analysis by fluorescence in situ hybridization (FISH) with whole chromosome paint (WCP) 15 showed that the SMC is not of chromosome 15 origin. Subsequently, FISH with centromere 22 identified the SMC to originate from chromosome 22 which was also confirmed by WCP 22. Additional dual FISH with centromere 22 and Acro-p-arm probes confirmed the centromere 22 and satellites on the SMC. Further fine mapping of the marker with Bacterial Artificial Chromosome (BAC) clones; two on chromosome 22 and four on chromosome 15 determined the marker to possess only centromere 22 sequences and that the duplication 15 exists directly on chromosome 15. In our study, we had identified and characterized a SMC showing inversion duplication 22(p11.1) combined with a direct tandem duplication of 15q11.2. The possible genotype-phenotype in relation with the two rearrangements is discussed.
Collapse
Affiliation(s)
- Usha R Dutta
- Diagnostics Division, Center for DNA Fingerprinting and Diagnostics, Tuljaguda Complex, 4-1-714, Hyderabad 500 001, Andhra-Pradesh, India.
| | - Subhash Vempally
- Diagnostics Division, Center for DNA Fingerprinting and Diagnostics, Tuljaguda Complex, 4-1-714, Hyderabad 500 001, Andhra-Pradesh, India
| | - Prajnya Ranganath
- Diagnostics Division, Center for DNA Fingerprinting and Diagnostics, Tuljaguda Complex, 4-1-714, Hyderabad 500 001, Andhra-Pradesh, India
| | - Ashwin Dalal
- Diagnostics Division, Center for DNA Fingerprinting and Diagnostics, Tuljaguda Complex, 4-1-714, Hyderabad 500 001, Andhra-Pradesh, India
| |
Collapse
|