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Duraisamy AJ, Liu R, Sureshkumar S, Rose R, Jagannathan L, da Silva C, Coovadia A, Ramachander V, Chandrasekar S, Raja I, Sajnani M, Selvaraj SM, Narang B, Darvishi K, Bhayal AC, Katikala L, Guo F, Chen-Deutsch X, Balciuniene J, Ma Z, Nallamilli BRR, Bean L, Collins C, Hegde M. Focused Exome Sequencing Gives a High Diagnostic Yield in the Indian Subcontinent. J Mol Diagn 2024; 26:510-519. [PMID: 38582400 DOI: 10.1016/j.jmoldx.2024.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 09/11/2023] [Accepted: 03/01/2024] [Indexed: 04/08/2024] Open
Abstract
The genetically isolated yet heterogeneous and highly consanguineous Indian population has shown a higher prevalence of rare genetic disorders. However, there is a significant socioeconomic burden for genetic testing to be accessible to the general population. In the current study, we analyzed next-generation sequencing data generated through focused exome sequencing from individuals with different phenotypic manifestations referred for genetic testing to achieve a molecular diagnosis. Pathogenic or likely pathogenic variants are reported in 280 of 833 cases with a diagnostic yield of 33.6%. Homozygous sequence and copy number variants were found as positive diagnostic findings in 131 cases (15.7%) because of the high consanguinity in the Indian population. No relevant findings related to reported phenotype were identified in 6.2% of the cases. Patients referred for testing due to metabolic disorder and neuromuscular disorder had higher diagnostic yields. Carrier testing of asymptomatic individuals with a family history of the disease, through focused exome sequencing, achieved positive diagnosis in 54 of 118 cases tested. Copy number variants were also found in trans with single-nucleotide variants and mitochondrial variants in a few of the cases. The diagnostic yield and the findings from this study signify that a focused exome test is a good lower-cost alternative for whole-exome and whole-genome sequencing and as a first-tier approach to genetic testing.
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Affiliation(s)
| | - Ruby Liu
- Revvity Omics, Pittsburgh, Pennsylvania
| | | | - Rajiv Rose
- PerkinElmer Genomics, Revvity Omics, Chennai, India
| | | | | | | | | | | | - Indu Raja
- PerkinElmer Genomics, Revvity Omics, Chennai, India
| | | | | | | | | | | | | | - Fen Guo
- Revvity Omics, Pittsburgh, Pennsylvania
| | | | | | | | | | - Lora Bean
- Revvity Omics, Pittsburgh, Pennsylvania
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2
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Zhao W, Smith J, Wang Y, Chintalapati M, Ammous F, Yu M, Moorjani P, Ganna A, Gross A, Dey S, Benerjee J, Chatterjee P, Dey A, Lee J, Kardia S. Polygenic Risk Scores for Alzheimer's Disease and General Cognitive Function Are Associated With Measures of Cognition in Older South Asians. J Gerontol A Biol Sci Med Sci 2023; 78:743-752. [PMID: 36782352 PMCID: PMC10172981 DOI: 10.1093/gerona/glad057] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Indexed: 02/15/2023] Open
Abstract
Genome-wide association studies (GWAS) conducted in European ancestry (EA) have identified hundreds of single-nucleotide polymorphisms (SNPs) associated with general cognitive function and/or Alzheimer's disease (AD). The association between these SNPs and cognitive function has not been fully evaluated in populations with complex genetic substructure such as South Asians. This study investigated whether SNPs identified in EA GWAS, either individually or as polygenic risk scores (PRSs), were associated with general cognitive function and 5 broad cognitive domains in 932 South Asians from the Diagnostic Assessment of Dementia for the Longitudinal Aging Study in India (LASI-DAD). We found that SNPs identified from AD GWAS were more strongly associated with cognitive function in LASI-DAD than those from a GWAS of general cognitive function. PRSs for general cognitive function and AD explained up to 1.1% of the variability in LASI-DAD cognitive domain scores. Our study represents an important stepping stone toward better characterization of the genetic architecture of cognitive aging in the Indian/South Asian population and highlights the need for further research that may lead to the identification of new variants unique to this population.
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Affiliation(s)
- Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, Michigan, USA
| | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, Michigan, USA
| | - Yi Zhe Wang
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Manjusha Chintalapati
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA
- Center for Computational Biology, University of California, Berkeley, Berkeley, California, USA
| | - Farah Ammous
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Miao Yu
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Priya Moorjani
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA
- Center for Computational Biology, University of California, Berkeley, Berkeley, California, USA
| | - Andrea Ganna
- Institute for Molecular Medicine Finland, Helsinki, Finland
| | - Alden Gross
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Sharmistha Dey
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Joyita Benerjee
- Department of Geriatric Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Prasun Chatterjee
- Department of Geriatric Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Aparajit B Dey
- Department of Geriatric Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Jinkook Lee
- Department of Economics, University of Southern California, Los Angeles, California, USA
| | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
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3
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Manjunath V, Thenral SG, Lakshmi BR, Nalini A, Bassi A, Karthikeyan KP, Piyusha K, Menon R, Malhotra A, Praveena LS, Anjanappa RM, Murugan SMS, Polavarapu K, Bardhan M, Preethish-Kumar V, Vengalil S, Nashi S, Sanga S, Acharya M, Raju R, Pai VR, Ramprasad VL, Gupta R. Large Region of Homozygous (ROH) Identified in Indian Patients with Autosomal Recessive Limb-Girdle Muscular Dystrophy with p.Thr182Pro Variant in SGCB Gene. Hum Mutat 2023. [DOI: 10.1155/2023/4362273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
The sarcoglycanopathies are autosomal recessive limb-girdle muscular dystrophies (LGMDs) caused by the mutations in genes encoding the α, β, γ, and δ proteins which stabilizes the sarcolemma of muscle cells. The clinical phenotype is characterized by progressive proximal muscle weakness with childhood onset. Muscle biopsy findings are diagnostic in confirming dystrophic changes and deficiency of one or more sarcoglycan proteins. In this study, we summarized 1,046 LGMD patients for which a precise diagnosis was identified using targeted sequencing. The most frequent phenotypes identified in the patients are LGMDR1 (19.7%), LGMDR4 (19.0%), LGMDR2 (17.5%), and MMD1 (14.5%). Among the reported genes, each of CAPN3, SGCB, and DYSF variants was reported in more than 10% of our study cohort. The most common variant SGCB p.Thr182Pro was identified in 146 (12.5%) of the LGMD patients, and in 97.9% of these patients, the variant was found to be homozygous. To understand the genetic structure of the patients carrying SGCB p.Thr182Pro, we genotyped 68 LGMD patients using a whole genome microarray. Analysis of the array data identified a large ~1 Mb region of homozygosity (ROH) (chr4:51817441-528499552) suggestive of a shared genomic region overlapping the recurrent missense variant and shared across all 68 patients. Haplotype analysis identified 133 marker haplotypes that were present in ~85.3% of the probands as a double allele and absent in all random controls. We also identified 5 markers (rs1910739, rs6852236, rs13122418, rs13353646, and rs6554360) which were present in a significantly higher proportion in the patients compared to random control set (
) and the population database. Of note, admixture analysis was suggestive of greater proportion of West Eurasian/European ancestry as compared to random controls. Haplotype analysis and frequency in the population database indicate a probable event of founder effect. Further systematic study is needed to identify the communities and regions where the SGCB p.Thr182Pro variant is observed in higher proportions. After identifying these communities and//or region, a screening program is needed to identify carriers and provide them counselling.
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Mishra R, Kulshreshtha S, Mandal K, Khurana A, Diego‐Álvarez D, Pradas L, Saxena R, Phadke S, Moirangthem A, Masih S, Sud S, Verma IC, Dua Puri R.
COASY
related pontocerebellar hypoplasia type 12: A common Indian mutation with expansion of the phenotypic spectrum. Am J Med Genet A 2022; 188:2339-2350. [DOI: 10.1002/ajmg.a.62768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 03/19/2022] [Accepted: 03/26/2022] [Indexed: 11/12/2022]
Affiliation(s)
- Ranjana Mishra
- Institute of Medical Genetics and Genomics, Sir Gangaram Hospital New Delhi India
| | - Samarth Kulshreshtha
- Institute of Medical Genetics and Genomics, Sir Gangaram Hospital New Delhi India
| | - Kausik Mandal
- Sanjay Gandhi Post‐Graduate Institute Lucknow Uttar Pradesh India
| | | | | | | | - Renu Saxena
- Institute of Medical Genetics and Genomics, Sir Gangaram Hospital New Delhi India
| | - Shubha Phadke
- Sanjay Gandhi Post‐Graduate Institute Lucknow Uttar Pradesh India
| | | | - Suzena Masih
- Sanjay Gandhi Post‐Graduate Institute Lucknow Uttar Pradesh India
| | - Seema Sud
- Department of CT Scan and MRI Sir Gangaram Hospital New Delhi India
| | - Ishwar Chander Verma
- Institute of Medical Genetics and Genomics, Sir Gangaram Hospital New Delhi India
| | - Ratna Dua Puri
- Institute of Medical Genetics and Genomics, Sir Gangaram Hospital New Delhi India
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Kaur P, do Rosario MC, Hebbar M, Sharma S, Kausthubham N, Nair K, A S, Bhat Y R, Lewis LES, Nampoothiri S, Patil SJ, Suresh N, Bijarnia Mahay S, Dua Puri R, Pai S, Kaur A, Kc R, Kamath N, Bajaj S, Kumble A, Shetty R, Shenoy R, Kamate M, Shah H, Muranjan MN, Bl Y, Avabratha KS, Subramaniam G, Kadavigere R, Bielas S, Girisha KM, Shukla A. Clinical and genetic spectrum of 104 Indian families with central nervous system white matter abnormalities. Clin Genet 2021; 100:542-550. [PMID: 34302356 PMCID: PMC8918360 DOI: 10.1111/cge.14037] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 07/19/2021] [Accepted: 07/20/2021] [Indexed: 12/15/2022]
Abstract
Genetic disorders with predominant central nervous system white matter abnormalities (CNS WMAs), also called leukodystrophies, are heterogeneous entities. We ascertained 117 individuals with CNS WMAs from 104 unrelated families. Targeted genetic testing was carried out in 16 families and 13 of them received a diagnosis. Chromosomal microarray (CMA) was performed for three families and one received a diagnosis. Mendeliome sequencing was used for testing 11 families and all received a diagnosis. Whole exome sequencing (WES) was performed in 80 families and was diagnostic in 52 (65%). Singleton WES was diagnostic for 50/75 (66.67%) families. Overall, genetic diagnoses were obtained in 77 families (74.03%). Twenty-two of 47 distinct disorders observed in this cohort have not been reported in Indian individuals previously. Notably, disorders of nuclear mitochondrial pathology were most frequent (9 disorders in 20 families). Thirty-seven of 75 (49.33%) disease-causing variants are novel. To sum up, the present cohort describes the phenotypic and genotypic spectrum of genetic disorders with CNS WMAs in our population. It demonstrates WES, especially singleton WES, as an efficient tool in the diagnosis of these heterogeneous entities. It also highlights possible founder events and recurrent disease-causing variants in our population and their implications on the testing strategy.
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Affiliation(s)
- Parneet Kaur
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Michelle C do Rosario
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Malavika Hebbar
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Suvasini Sharma
- Department of Paediatrics, Lady Hardinge Medical College and Associated Kalawati Saran Children's Hospital, New Delhi, India
| | - Neethukrishna Kausthubham
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Karthik Nair
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Shrikiran A
- Department of Paediatrics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Ramesh Bhat Y
- Department of Paediatrics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Leslie Edward S Lewis
- Department of Paediatrics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Sheela Nampoothiri
- Department of Paediatric Genetics, Amrita Institute of Medical Sciences and Research Centre, Kochi, India
| | | | - Narayanaswami Suresh
- Department of Paediatrics, Lady Hardinge Medical College and Associated Kalawati Saran Children's Hospital, New Delhi, India
| | - Sunita Bijarnia Mahay
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Ratna Dua Puri
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Shivanand Pai
- Department of Neurology, Kasturba Medical College, Mangalore, Manipal Academy of Higher Education, Manipal, India
| | - Anupriya Kaur
- Department of Paediatrics, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Rakshith Kc
- Department of Neurology, Kasturba Medical College, Mangalore, Manipal Academy of Higher Education, Manipal, India
| | - Nutan Kamath
- Department of Paediatrics, Kasturba Medical College, Mangalore, Manipal Academy of Higher Education, Manipal, India
| | - Shruti Bajaj
- Jaslok Hospital and Research Centre, Mumbai, India
| | - Ali Kumble
- Department of Paediatrics, Indiana Hospital and Heart Institute, Mangalore, India
| | | | - Rathika Shenoy
- Department of Paediatrics, K.S. Hegde Medical Academy, NITTE University, Mangalore, India
| | - Mahesh Kamate
- Department of Paediatrics, Jawaharlal Nehru Medical College, Belgaum, India
| | - Hitesh Shah
- Department of Orthopaedics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Mamta N Muranjan
- Department of Pediatrics, Genetics Division, Seth Gordhandas Sunderdas Medical College and King Edward VII Memorial Hospital, Mumbai, Maharashtra, India
| | - Yatheesha Bl
- Dheemahi Child Neurology and Development Center, Shimoga, India
| | | | | | - Rajagopal Kadavigere
- Department of Radiodiagnosis, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Stephanie Bielas
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
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6
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Homozygosity stretches around homozygous mutations in autosomal recessive disorders: patients from nonconsanguineous Indian families. J Genet 2021. [DOI: 10.1007/s12041-020-01250-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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7
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Singh K, Bijarnia-Mahay S, Ramprasad VL, Puri RD, Nair S, Sharda S, Saxena R, Kohli S, Kulshreshtha S, Ganguli I, Gujral K, Verma IC. NGS-based expanded carrier screening for genetic disorders in North Indian population reveals unexpected results - a pilot study. BMC MEDICAL GENETICS 2020; 21:216. [PMID: 33138774 PMCID: PMC7607710 DOI: 10.1186/s12881-020-01153-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 10/20/2020] [Indexed: 12/25/2022]
Abstract
Background To determine the carrier frequency and pathogenic variants of common genetic disorders in the north Indian population by using next generation sequencing (NGS). Methods After pre-test counselling, 200 unrelated individuals (including 88 couples) were screened for pathogenic variants in 88 genes by NGS technology. The variants were classified as per American College of Medical Genetics criteria. Pathogenic and likely pathogenic variants were subjected to thorough literature-based curation in addition to the regular filters. Variants of unknown significance were not reported. Individuals were counselled explaining the implications of the results, and cascade screening was advised when necessary. Results Of the 200 participants, 52 (26%) were found to be carrier of one or more disorders. Twelve individuals were identified to be carriers for congenital deafness, giving a carrier frequency of one in 17 for one of the four genes tested (SLC26A4, GJB2, TMPRSS3 and TMC1 in decreasing order). Nine individuals were observed to be carriers for cystic fibrosis, with a frequency of one in 22. Three individuals were detected to be carriers for Pompe disease (frequency one in 67). None of the 88 couples screened were found to be carriers for the same disorder. The pathogenic variants observed in many disorders (such as deafness, cystic fibrosis, Pompe disease, Canavan disease, primary hyperoxaluria, junctional epidermolysis bullosa, galactosemia, medium chain acyl CoA deficiency etc.) were different from those commonly observed in the West. Conclusion A higher carrier frequency for genetic deafness, cystic fibrosis and Pompe disease was unexpected, and contrary to the generally held view about their prevalence in Asian Indians. In spite of the small sample size, this study would suggest that population-based carrier screening panels for India would differ from those in the West, and need to be selected with due care. Testing should comprise the study of all the coding exons with its boundaries in the genes through NGS, as all the variants are not well characterized. Only study of entire coding regions in the genes will detect carriers with adequate efficiency, in order to reduce the burden of genetic disorders in India and other resource poor countries. Supplementary Information The online version contains supplementary material available at 10.1186/s12881-020-01153-4.
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Affiliation(s)
- Kanika Singh
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Sunita Bijarnia-Mahay
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India.
| | | | - Ratna Dua Puri
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Sandhya Nair
- Medgenome Laboratories Pvt Ltd., Bangalore, India
| | | | - Renu Saxena
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Sudha Kohli
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Samarth Kulshreshtha
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Indrani Ganguli
- Institute of Obstetrics and Gynaecology, Sir Ganga Ram Hospital, New Delhi, India
| | - Kanwal Gujral
- Institute of Obstetrics and Gynaecology, Sir Ganga Ram Hospital, New Delhi, India
| | - Ishwar C Verma
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India.
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Angural A, Spolia A, Mahajan A, Verma V, Sharma A, Kumar P, Dhar MK, Pandita KK, Rai E, Sharma S. Review: Understanding Rare Genetic Diseases in Low Resource Regions Like Jammu and Kashmir - India. Front Genet 2020; 11:415. [PMID: 32425985 PMCID: PMC7203485 DOI: 10.3389/fgene.2020.00415] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Accepted: 04/01/2020] [Indexed: 12/11/2022] Open
Abstract
Rare diseases (RDs) are the clinical conditions affecting a few percentage of individuals in a general population compared to other diseases. Limited clinical information and a lack of reliable epidemiological data make their timely diagnosis and therapeutic management difficult. Emerging Next-Generation DNA Sequencing technologies have enhanced our horizons on patho-physiological understanding of many of the RDs and ushered us into an era of diagnostic and therapeutic research related to this ignored health challenge. Unfortunately, relevant research is meager in developing countries which lack a reliable estimate of the exact burden of most of the RDs. India is to be considered as the "Pandora's Box of genetic disorders." Owing to its huge population heterogeneity and high inbreeding or endogamy rates, a higher burden of rare recessive genetic diseases is expected and supported by the literature findings that endogamy is highly detrimental to health as it enhances the degree of homozygosity of recessive alleles in the general population. The population of a low resource region Jammu and Kashmir (J&K) - India, is highly inbred. Some of its population groups variably practice consanguinity. In context with the region's typical geographical topography, highly inbred population structure and unique but heterogeneous gene pool, a huge burden of known and uncharacterized genetic disorders is expected. Unfortunately, many suspected cases of genetic disorders remain undiagnosed or misdiagnosed due to lack of appropriate clinical as well as diagnostic resources in the region, causing patients to face a huge psycho-socio-economic crisis and many a time suffer life-long with their ailment. In this review, the major challenges associated with RDs are highlighted in general and an account on the methods that can be adopted for conducting fruitful molecular genetic studies in genetically vulnerable and low resource regions is also provided, with an example of a region like J&K - India.
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Affiliation(s)
- Arshia Angural
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Akshi Spolia
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Ankit Mahajan
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Vijeshwar Verma
- Bioinformatics Infrastructure Facility, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Ankush Sharma
- Shri Mata Vaishno Devi Narayana Superspeciality Hospital, Katra, India
| | - Parvinder Kumar
- Institute of Human Genetics, University of Jammu, Jammu, India
| | | | - Kamal Kishore Pandita
- Shri Mata Vaishno Devi Narayana Superspeciality Hospital, Katra, India
- Independent Researcher, Health Clinic, Jammu, India
| | - Ekta Rai
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Swarkar Sharma
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
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9
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Genetic analysis of ATP7B in 102 south Indian families with Wilson disease. PLoS One 2019; 14:e0215779. [PMID: 31059521 PMCID: PMC6502322 DOI: 10.1371/journal.pone.0215779] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 04/08/2019] [Indexed: 01/02/2023] Open
Abstract
Wilson disease (WD) is an autosomal recessive disorder, characterized by excessive deposition of copper in various parts of the body, mainly in the liver and brain. It is caused by mutations in ATP7B. We report here the genetic analysis of 102 WD families from a south Indian population. Thirty-six different ATP7B mutations, including 13 novel ones [p.Ala58fs*19, p.Lys74fs*9, p.Gln281*, p.Pro350fs*12, p.Ser481*, p.Leu735Arg, p.Val752Gly, p.Asn812fs*2, p.Val845Ala, p.His889Pro, p.Ile1184fs*1, p.Val1307Glu and p.Ala1339Pro], were identified in 76/102 families. Interestingly, the mutation analysis of affected individuals in two families identified two different homozygous mutations in each family, and thus each affected individual from these families harbored two mutations in each ATP7B allele. Of 36 mutations, 28 were missense, thus making them the most prevalent mutations identified in the present study. Nonsense, insertion and deletion represented 3/36, 2/36 and 3/36 mutations, respectively. The haplotype analysis suggested founder effects for all the 14 recurrent mutations. Our study thus expands the mutational landscape of ATP7B with a total number of 758 mutations. The mutations identified during the present study will facilitate carrier and pre-symptomatic detection, and prenatal genetic diagnosis in affected families.
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10
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High-depth whole genome sequencing of an Ashkenazi Jewish reference panel: enhancing sensitivity, accuracy, and imputation. Hum Genet 2018; 137:343-355. [PMID: 29705978 DOI: 10.1007/s00439-018-1886-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Accepted: 04/21/2018] [Indexed: 12/31/2022]
Abstract
While increasingly large reference panels for genome-wide imputation have been recently made available, the degree to which imputation accuracy can be enhanced by population-specific reference panels remains an open question. Here, we sequenced at full-depth (≥ 30×), across two platforms (Illumina X Ten and Complete Genomics, Inc.), a moderately large (n = 738) cohort of samples drawn from the Ashkenazi Jewish population. We developed a series of quality control steps to optimize sensitivity, specificity, and comprehensiveness of variant calls in the reference panel, and then tested the accuracy of imputation against target cohorts drawn from the same population. Quality control (QC) thresholds for the Illumina X Ten platform were identified that permitted highly accurate calling of single nucleotide variants across 94% of the genome. QC procedures also identified numerous regions that are poorly mapped using current reference or alternate assemblies. After stringent QC, the population-specific reference panel produced more accurate and comprehensive imputation results relative to publicly available, large cosmopolitan reference panels, especially in the range of rare variants that may be most critical to further progress in mapping of complex phenotypes. The population-specific reference panel also permitted enhanced filtering of clinically irrelevant variants from personal genomes.
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11
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Battu R, Mallipatna A, Elackatt NJ, Schouten JSAG, Webers CAB. Challenges of managing retinal dystrophies: An experience from south India. Ophthalmic Genet 2017; 39:1-3. [PMID: 28704110 DOI: 10.1080/13816810.2017.1329446] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Rajani Battu
- a Department of Ophthalmology , Aster CMI Hospital , Bangalore , India.,b Centre for Eye Genetics and Research , Bangalore , India
| | - Ashwin Mallipatna
- c Department of Ophthalmology , Women's and Children's Hospital , Adelaide , Australia
| | - Niby Jacob Elackatt
- d Department of Genetic Counseling , Organization for Rare Diseases India , Bangalore , India
| | - Jan S A G Schouten
- e University Eye Clinic Maastricht, Maastricht University , Maastricht , the Netherlands
| | - Carroll A B Webers
- e University Eye Clinic Maastricht, Maastricht University , Maastricht , the Netherlands
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Harlalka GV, McEntagart ME, Gupta N, Skrzypiec AE, Mucha MW, Chioza BA, Simpson MA, Sreekantan-Nair A, Pereira A, Günther S, Jahic A, Modarres H, Moore-Barton H, Trembath RC, Kabra M, Baple EL, Thakur S, Patton MA, Beetz C, Pawlak R, Crosby AH. Novel Genetic, Clinical, and Pathomechanistic Insights into TFG-Associated Hereditary Spastic Paraplegia. Hum Mutat 2016; 37:1157-1161. [PMID: 27492651 DOI: 10.1002/humu.23060] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 07/30/2016] [Indexed: 11/05/2022]
Abstract
Hereditary spastic paraplegias (HSPs) are genetically and clinically heterogeneous axonopathies primarily affecting upper motor neurons and, in complex forms, additional neurons. Here, we report two families with distinct recessive mutations in TFG, previously suggested to cause HSP based on findings in a single small family with complex HSP. The first carried a homozygous c.317G>A (p.R106H) variant and presented with pure HSP. The second carried the same homozygous c.316C>T (p.R106C) variant previously reported and displayed a similarly complex phenotype including optic atrophy. Haplotyping and bisulfate sequencing revealed evidence for a c.316C>T founder allele, as well as for a c.316_317 mutation hotspot. Expression of mutant TFG proteins in cultured neurons revealed mitochondrial fragmentation, the extent of which correlated with clinical severity. Our findings confirm the causal nature of bi-allelic TFG mutations for HSP, broaden the clinical and mutational spectra, and suggest mitochondrial impairment to represent a pathomechanistic link to other neurodegenerative conditions.
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Affiliation(s)
- Gaurav V Harlalka
- University of Exeter Medical School, RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, UK
| | - Meriel E McEntagart
- Medical Genetics Unit, Floor 0, Jenner Wing, St. George's University of London, Cranmer Terrace, London, UK
| | - Neerja Gupta
- Division of Genetics, Department of Pediatrics, Old O.T. Block, All India Institute of Medical Sciences, New Delhi, India
| | - Anna E Skrzypiec
- Laboratory of Neuronal Plasticity and Behaviour, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Mariusz W Mucha
- Laboratory of Neuronal Plasticity and Behaviour, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Barry A Chioza
- University of Exeter Medical School, RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, UK
| | - Michael A Simpson
- Division of Genetics and Molecular Medicine, King's College London School of Medicine, Guy's Hospital, London, UK
| | - Ajith Sreekantan-Nair
- University of Exeter Medical School, RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, UK
| | - Anthony Pereira
- Department of Neurology, Atkinson Morley Wing, St. George's Hospital, Tooting, London, UK
| | - Sven Günther
- Department of Clinical Chemistry and Laboratory Medicine, Jena University Hospital, Jena, Germany
| | - Amir Jahic
- Department of Clinical Chemistry and Laboratory Medicine, Jena University Hospital, Jena, Germany
| | - Hamid Modarres
- Department of Neurology, Atkinson Morley Wing, St. George's Hospital, Tooting, London, UK
| | - Heather Moore-Barton
- Medical Genetics Unit, Floor 0, Jenner Wing, St. George's University of London, Cranmer Terrace, London, UK
| | - Richard C Trembath
- Division of Genetics and Molecular Medicine, King's College London School of Medicine, Guy's Hospital, London, UK
| | - Madhulika Kabra
- Division of Genetics, Department of Pediatrics, Old O.T. Block, All India Institute of Medical Sciences, New Delhi, India
| | - Emma L Baple
- University of Exeter Medical School, RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, UK
| | - Seema Thakur
- Department of Genetics and Fetal Medicine, Fortis La femme, S-549, New Delhi, India
| | - Michael A Patton
- Medical Genetics Unit, Floor 0, Jenner Wing, St. George's University of London, Cranmer Terrace, London, UK
| | - Christian Beetz
- Department of Clinical Chemistry and Laboratory Medicine, Jena University Hospital, Jena, Germany.
| | - Robert Pawlak
- Laboratory of Neuronal Plasticity and Behaviour, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Andrew H Crosby
- University of Exeter Medical School, RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, UK
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Chakrabarty S, Kabekkodu SP, Brand A, Satyamoorthy K. Perspectives on Translational Genomics and Public Health in India. Public Health Genomics 2015; 19:61-8. [PMID: 26683060 DOI: 10.1159/000442518] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 11/18/2015] [Indexed: 11/19/2022] Open
Abstract
It is now recognized worldwide that anticipation and prevention of diseases have significant advantages for the health and healthy ageing of the population. Early recognition of the disease in a vulnerable population such as in children aged <5 years and adults aged >60 years enhances our preparedness for any eventualities and future burden of the diseases to society. It is also recognized that current public health practices alone cannot bring about the desired outcome. When tackling public health-related issues, such problems must be recognized and state-of-the-art principles and innovations from genomic sciences, information technologies, and medical specialties must be encompassed and embraced. These will enhance strategies for preparedness and provide us with a better understanding of how to identify, manage, and control disease burdens. The ever expanding landscape of genomics research also includes experimental and computational approaches for effectively utilizing DNA sequence information. From these perspectives, the intricacies of Mendelian single gene disorders are the least challenging compared to intricacies of multi-dimensional host factors for infectious diseases or complex disorders such as cancer. The concepts of public health in India are on firm footing; however, integration of contemporary advances to implement public health principles into practice has neither been attempted nor impacted on disease burden or our preparedness to prevent eventualities. At the same time, translational genomics is gradually paving the way for personalized medicine. Principles of personalized medicine remain to be fully understood and practiced despite the pharmacogenomics-based future of drug development, and treatment has not been as exciting as the advances in genomics we are witnessing today. The relevance, importance, and translational impediments of these advances will be discussed.
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Verma IC, Puri RD. Global burden of genetic disease and the role of genetic screening. Semin Fetal Neonatal Med 2015; 20:354-63. [PMID: 26251359 DOI: 10.1016/j.siny.2015.07.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
It is estimated that 5.3% of newborns will suffer from a genetic disorder, when followed up until the age of 25 years. In developing, as compared to western countries, hemoglobinopathies and glucose-6-phosphate dehydrogenase deficiency have a higher incidence due to severe falciparum malaria in the distant past, and autosomal recessive disorders have a higher frequency due to greater proportion of consanguineous marriages. Chromosomal disorders have a combined frequency of 1 in 153 births, therefore screening for chromosomal disorders is essential, using biochemical markers, ultrasonography, and recently by non-invasive prenatal diagnosis based on cell-free fetal DNA in maternal plasma. Preconceptional counseling should be encouraged. For genetic disorders screening should be carried out, ideally after marriage, but before pregnancy. The disorders to be screened depend upon ethnicity. Metabolic disorders have a high incidence in developing countries due to greater rate of consanguineous marriages. Newborn screening is recommended to reduce the burden of these disorders, as many metabolic disorders can be treated. Hearing and critical congenital heart disease should both be screened in the newborn period.
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Affiliation(s)
- I C Verma
- Center of Medical Genetics, Sir Ganga Ram Hospital, New Delhi, India.
| | - R D Puri
- Center of Medical Genetics, Sir Ganga Ram Hospital, New Delhi, India
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Identification of mutations, genotype–phenotype correlation and prenatal diagnosis of maple syrup urine disease in Indian patients. Eur J Med Genet 2015; 58:471-8. [DOI: 10.1016/j.ejmg.2015.08.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 08/03/2015] [Accepted: 08/03/2015] [Indexed: 01/01/2023]
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Aggarwal S, Phadke SR. Medical genetics and genomic medicine in India: current status and opportunities ahead. Mol Genet Genomic Med 2015; 3:160-71. [PMID: 26029702 PMCID: PMC4444157 DOI: 10.1002/mgg3.150] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Shagun Aggarwal
- Department of Medical Genetics, Nizam's Institute of Medical Sciences Hyderabad, India ; Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics Hyderabad, India
| | - Shubha R Phadke
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences Lucknow, India
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