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Sivasubbu S, Scaria V. Genomics of rare genetic diseases-experiences from India. Hum Genomics 2019; 14:52. [PMID: 31554517 PMCID: PMC6760067 DOI: 10.1186/s40246-019-0215-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 06/26/2019] [Indexed: 12/15/2022] Open
Abstract
Home to a culturally heterogeneous population, India is also a melting pot of genetic diversity. The population architecture characterized by multiple endogamous groups with specific marriage patterns, including the widely prevalent practice of consanguinity, not only makes the Indian population distinct from rest of the world but also provides a unique advantage and niche to understand genetic diseases. Centuries of genetic isolation of population groups have amplified the founder effects, contributing to high prevalence of recessive alleles, which translates into genetic diseases, including rare genetic diseases in India.Rare genetic diseases are becoming a public health concern in India because a large population size of close to a billion people would essentially translate to a huge disease burden for even the rarest of the rare diseases. Genomics-based approaches have been demonstrated to accelerate the diagnosis of rare genetic diseases and reduce the socio-economic burden. The Genomics for Understanding Rare Diseases: India Alliance Network (GUaRDIAN) stands for providing genomic solutions for rare diseases in India. The consortium aims to establish a unique collaborative framework in health care planning, implementation, and delivery in the specific area of rare genetic diseases. It is a nation-wide collaborative research initiative catering to rare diseases across multiple cohorts, with over 240 clinician/scientist collaborators across 70 major medical/research centers. Within the GUaRDIAN framework, clinicians refer rare disease patients, generate whole genome or exome datasets followed by computational analysis of the data for identifying the causal pathogenic variations. The outcomes of GUaRDIAN are being translated as community services through a suitable platform providing low-cost diagnostic assays in India. In addition to GUaRDIAN, several genomic investigations for diseased and healthy population are being undertaken in the country to solve the rare disease dilemma.In summary, rare diseases contribute to a significant disease burden in India. Genomics-based solutions can enable accelerated diagnosis and management of rare diseases. We discuss how a collaborative research initiative such as GUaRDIAN can provide a nation-wide framework to cater to the rare disease community of India.
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Affiliation(s)
| | - Sridhar Sivasubbu
- CSIR Institute of Genomics and Integrative Biology, Delhi, 110025, India.
| | - Vinod Scaria
- CSIR Institute of Genomics and Integrative Biology, Delhi, 110025, India.
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Yenamandra VK, Shamsudheen KV, Madhumita RC, Rijith J, Ankit V, Scaria V, Sridhar S, Kabra M, Sharma VK, Sethuraman G. Autosomal recessive epidermolysis bullosa simplex: report of three cases from India. Clin Exp Dermatol 2018; 42:800-803. [PMID: 28925504 DOI: 10.1111/ced.13182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2016] [Indexed: 11/28/2022]
Affiliation(s)
- V K Yenamandra
- Departments of Dermatology and Venereology, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - K V Shamsudheen
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India.,Academy of Scientific and Innovative Research, CSIR, New Delhi, India
| | - R C Madhumita
- Departments of Pediatrics, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - J Rijith
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - V Ankit
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - V Scaria
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India.,Academy of Scientific and Innovative Research, CSIR, New Delhi, India
| | - S Sridhar
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India.,Academy of Scientific and Innovative Research, CSIR, New Delhi, India
| | - M Kabra
- Departments of Pediatrics, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - V K Sharma
- Departments of Dermatology and Venereology, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - G Sethuraman
- Departments of Dermatology and Venereology, All India Institute of Medical Sciences, New Delhi, 110029, India
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Yenamandra VK, Vellarikkal SK, Kumar M, Chowdhury MR, Jayarajan R, Verma A, Scaria V, Sivasubbu S, Ray SB, Dinda AK, Kabra M, Kaur P, Sharma VK, Sethuraman G. Application of whole exome sequencing in elucidating the phenotype and genotype spectrum of junctional epidermolysis bullosa: A preliminary experience of a tertiary care centre in India. J Dermatol Sci 2017; 86:30-36. [PMID: 28087116 DOI: 10.1016/j.jdermsci.2016.12.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 12/20/2016] [Accepted: 12/28/2016] [Indexed: 10/20/2022]
Abstract
BACKGROUND Junctional epidermolysis bullosa (JEB) is a diverse group of genodermatoses associated with extreme skin fragility. Despite several well-characterized genetic studies, molecular diagnosis of this heterogeneous group is still challenging. Recent advances in the field of genomics have seen the successful implementation of whole exome sequencing (WES) as a fast and efficient diagnostic strategy in several genodermatoses. OBJECTIVE In view of the scarcity and need of molecular studies for JEB in India, we sought to explore the potential of WES in understanding the mutational spectrum of this rare, in certain subtypes lethal, sub-group of EB. METHODS WES was performed using genomic DNA from each case of EB, followed by massively parallel sequencing. Resulting reads were mapped to the human reference genome hg19. Sanger sequencing subsequently confirmed the potentially pathogenic mutations. RESULTS Overall, four unrelated families (6 patients) of JEB with a highly variable clinical presentation including a rare case of LOC syndrome were studied. WES revealed 4 variations in 3 genes (LAMA3, LAMB3 and COL17A1) that are implicated in JEB. None of the variations were recurrent. In addition we proposed the probable molecular consequence of a missense mutation on the structure-function relationship of lamininβ3 protein through computational modeling studies. CONCLUSIONS Being the first report documenting the phenotype-genotype correlations of JEB patients from India, our preliminary experience with WES is clearly encouraging and serves as a nidus for future large-scale molecular studies to actively identify and understand JEB patients in Indian population.
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Affiliation(s)
- Vamsi K Yenamandra
- Departments of Dermatology & Venereology, All India Institute of Medical Sciences, New Delhi, India
| | - Shamsudheen K Vellarikkal
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, India; Academy of Scientific and Innovative Research, CSIR, India
| | - Manoj Kumar
- Departments of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Madhumita R Chowdhury
- Departments of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Rijith Jayarajan
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, India
| | - Ankit Verma
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, India
| | - Vinod Scaria
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, India; Academy of Scientific and Innovative Research, CSIR, India
| | - Sridhar Sivasubbu
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, India; Academy of Scientific and Innovative Research, CSIR, India
| | - Subrata B Ray
- Departments of Anatomy, All India Institute of Medical Sciences, New Delhi, India
| | - Amit K Dinda
- Departments of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Madhulika Kabra
- Departments of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Punit Kaur
- Departments of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Vinod K Sharma
- Departments of Dermatology & Venereology, All India Institute of Medical Sciences, New Delhi, India
| | - Gomathy Sethuraman
- Departments of Dermatology & Venereology, All India Institute of Medical Sciences, New Delhi, India.
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Sandhya P, Vellarikkal SK, Nair A, Ravi R, Mathew J, Jayarajan R, Kumar A, Verma A, Sivadas A, Danda D, Sivasubbu S, Scaria V. Egyptian tale from India: application of whole-exome sequencing in diagnosis of atypical familial Mediterranean fever. Int J Rheum Dis 2017; 20:1770-1775. [DOI: 10.1111/1756-185x.13042] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Pulukool Sandhya
- Department of Rheumatology; Christian Medical College and Hospital; Vellore India
| | - Shamsudheen Karuthedath Vellarikkal
- Genomics and Molecular Medicine; CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB); Delhi India
- Academy of Scientific and Innovative Research (AcSIR); Delhi India
| | - Aswin Nair
- Department of Rheumatology; Christian Medical College and Hospital; Vellore India
| | - Rowmika Ravi
- Genomics and Molecular Medicine; CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB); Delhi India
| | - John Mathew
- Department of Rheumatology; Christian Medical College and Hospital; Vellore India
| | - Rijith Jayarajan
- Genomics and Molecular Medicine; CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB); Delhi India
| | - Anoop Kumar
- Genomics and Molecular Medicine; CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB); Delhi India
| | - Ankit Verma
- Genomics and Molecular Medicine; CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB); Delhi India
| | - Ambily Sivadas
- Academy of Scientific and Innovative Research (AcSIR); Delhi India
- GN Ramachandran Knowledge Center for Genome Informatics; CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB); Delhi India
| | - Debashish Danda
- Department of Rheumatology; Christian Medical College and Hospital; Vellore India
| | - Sridhar Sivasubbu
- Genomics and Molecular Medicine; CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB); Delhi India
- Academy of Scientific and Innovative Research (AcSIR); Delhi India
| | - Vinod Scaria
- Academy of Scientific and Innovative Research (AcSIR); Delhi India
- GN Ramachandran Knowledge Center for Genome Informatics; CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB); Delhi India
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Karuthedath Vellarikkal S, Jayarajan R, Verma A, Nair S, Ravi R, Senthivel V, Sivasubbu S, Scaria V. Case Report: Whole exome sequencing reveals a novel frameshift deletion mutation p.G2254fs in COL7A1 associated with autosomal recessive dystrophic epidermolysis bullosa. F1000Res 2016; 5:900. [PMID: 27408687 PMCID: PMC4926754 DOI: 10.12688/f1000research.8380.2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/29/2016] [Indexed: 11/20/2022] Open
Abstract
Dystrophic epidermolysis bullosa simplex (DEB) is a phenotypically diverse inherited skin fragility disorder. It is majorly manifested by appearance of epidermal bullae upon friction caused either by physical or environmental trauma. The phenotypic manifestations also include appearance of milia, scarring all over the body and nail dystrophy. DEB can be inherited in a recessive or dominant form and the recessive form of DEB (RDEB) is more severe. In the present study, we identify a novel p.G2254fs mutation in COL7A1 gene causing a sporadic case of RDEB by whole exome sequencing (WES). Apart from adding a novel frameshift Collagen VII mutation to the repertoire of known mutations reported in the disease, to the best of our knowledge, this is the first report of a genetically characterized case of DEB from India.
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Affiliation(s)
- Shamsudheen Karuthedath Vellarikkal
- Genomics and Molecular Medicine Unit, CSIR Institute of Genomics and Integrative Biology, Delhi, India; Academy of Scientific and Innovative Research, CSIR-IGIB South Campus, Delhi, India
| | - Rijith Jayarajan
- Genomics and Molecular Medicine Unit, CSIR Institute of Genomics and Integrative Biology, Delhi, India
| | - Ankit Verma
- Genomics and Molecular Medicine Unit, CSIR Institute of Genomics and Integrative Biology, Delhi, India
| | - Sreelata Nair
- Department of Fetal Medicine, Lifeline Super Specialty Hospital, Kerala, India
| | - Rowmika Ravi
- Genomics and Molecular Medicine Unit, CSIR Institute of Genomics and Integrative Biology, Delhi, India
| | - Vigneshwar Senthivel
- Genomics and Molecular Medicine Unit, CSIR Institute of Genomics and Integrative Biology, Delhi, India
| | - Sridhar Sivasubbu
- Genomics and Molecular Medicine Unit, CSIR Institute of Genomics and Integrative Biology, Delhi, India; Academy of Scientific and Innovative Research, CSIR-IGIB South Campus, Delhi, India
| | - Vinod Scaria
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, Delhi, India; Academy of Scientific and Innovative Research, CSIR-IGIB South Campus, Delhi, India
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Gupta A, Sharma Y, Deo K, Vellarikkal S, Jayarajan R, Dixit V, Verma A, Scaria V, Sivasubbu S. Case Report: Whole exome sequencing helps in accurate molecular diagnosis in siblings with a rare co-occurrence of paternally inherited 22q12 duplication and autosomal recessive non-syndromic ichthyosis. F1000Res 2015; 4:446. [PMID: 26594337 PMCID: PMC4648218 DOI: 10.12688/f1000research.6779.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/29/2015] [Indexed: 12/30/2022] Open
Abstract
Lamellar ichthyosis (LI), considered an autosomal recessive monogenic genodermatosis, has an incidence of approximately 1 in 250,000. Usually associated with mutations in the transglutaminase gene (
TGM1), mutations in six other genes have, less frequently, been shown to be causative. Two siblings, born in a collodion membrane, presented with fish like scales all over the body. Karyotyping revealed duplication of the chromosome arm on 22q12+ in the father and two siblings. Whole exome sequencing revealed a homozygous p.Gly218Ser variation in
TGM1; a variation reported earlier in an isolated Finnish population in association with autosomal recessive non-syndromic ichthyosis. This concurrence of a potentially benign 22q12+ duplication and LI, both rare individually, is reported here likely for the first time.
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Affiliation(s)
- Aayush Gupta
- Department of Dermatology, Dr. D.Y. Patil Medical College, Pune, India
| | - Yugal Sharma
- Department of Dermatology, Dr. D.Y. Patil Medical College, Pune, India
| | - Kirti Deo
- Department of Dermatology, Dr. D.Y. Patil Medical College, Pune, India
| | - Shamsudheen Vellarikkal
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Delhi, India ; Academy of Scientific and Innovative Research, Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, Delhi, India
| | - Rijith Jayarajan
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Delhi, India
| | - Vishal Dixit
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Delhi, India
| | - Ankit Verma
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Delhi, India
| | - Vinod Scaria
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, Delhi, India ; Academy of Scientific and Innovative Research, Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, Delhi, India
| | - Sridhar Sivasubbu
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Delhi, India ; Academy of Scientific and Innovative Research, Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, Delhi, India
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