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Sharma P, Sonakar AK, Tyagi N, Suroliya V, Kumar M, Kutum R, Asokchandran V, Ambawat S, Shamim U, Anand A, Ahmad I, Shakya S, Uppili B, Mathur A, Parveen S, Jain S, Singh J, Seth M, Zahra S, Joshi A, Goel D, Sahni S, Kamai A, Wadhwa S, Murali A, Saifi S, Chowdhury D, Pandey S, Anand KS, Narasimhan RL, Laskar S, Kushwaha S, Kumar M, Shaji CV, Srivastava MVP, Srivastava AK, Faruq M. Genetics of Ataxias in Indian Population: A Collative Insight from a Common Genetic Screening Tool. ADVANCED GENETICS (HOBOKEN, N.J.) 2022; 3:2100078. [PMID: 36618024 PMCID: PMC9744545 DOI: 10.1002/ggn2.202100078] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Indexed: 01/11/2023]
Abstract
Cerebellar ataxias (CAs) represent a group of autosomal dominant and recessive neurodegenerative disorders affecting cerebellum with or without spinal cord. Overall, CAs have preponderance for tandem nucleotide repeat expansions as an etiological factor (10 TREs explain nearly 30-40% of ataxia cohort globally). The experience of 10 years of common genetic ataxia subtypes for ≈5600 patients' referrals (Pan-India) received at a single center is shared herein. Frequencies (in %, n) of SCA types and FRDA in the sample cohort are observed as follows: SCA12 (8.6%, 490); SCA2 (8.5%, 482); SCA1 (4.8%, 272); SCA3 (2%, 113); SCA7 (0.5%, 28); SCA6 (0.1%, 05); SCA17 (0.1%, 05), and FRDA (2.2%, 127). A significant amount of variability in TRE lengths at each locus is observed, we noted presence of biallelic expansion, co-occurrence of SCA-subtypes, and the presence of premutable normal alleles. The frequency of mutated GAA-FRDA allele in healthy controls is 1/158 (0.63%), thus an expected FRDA prevalence of 1:100 000 persons. The data of this study are relevant not only for clinical decision making but also for guidance in direction of genetic investigations, transancestral comparison of genotypes, and lastly provide insight for policy decision for the consideration of SCAs under rare disease category.
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Affiliation(s)
- Pooja Sharma
- Genomics and Molecular MedicineCSIR‐Institute of Genomics and Integrative Biology (CSIR‐IGIB)Mall RoadDelhi110007India,Academy for Scientific and Innovative ResearchGhaziabadUttar Pradesh201002India
| | | | - Nishu Tyagi
- Genomics and Molecular MedicineCSIR‐Institute of Genomics and Integrative Biology (CSIR‐IGIB)Mall RoadDelhi110007India,Academy for Scientific and Innovative ResearchGhaziabadUttar Pradesh201002India
| | - Varun Suroliya
- Neurology DepartmentNeuroscience CentreNew Delhi110029India
| | - Manish Kumar
- Genomics and Molecular MedicineCSIR‐Institute of Genomics and Integrative Biology (CSIR‐IGIB)Mall RoadDelhi110007India,Academy for Scientific and Innovative ResearchGhaziabadUttar Pradesh201002India
| | - Rintu Kutum
- Genomics and Molecular MedicineCSIR‐Institute of Genomics and Integrative Biology (CSIR‐IGIB)Mall RoadDelhi110007India
| | - Vivekananda Asokchandran
- Genomics and Molecular MedicineCSIR‐Institute of Genomics and Integrative Biology (CSIR‐IGIB)Mall RoadDelhi110007India,Academy for Scientific and Innovative ResearchGhaziabadUttar Pradesh201002India
| | - Sakshi Ambawat
- Genomics and Molecular MedicineCSIR‐Institute of Genomics and Integrative Biology (CSIR‐IGIB)Mall RoadDelhi110007India
| | - Uzma Shamim
- Genomics and Molecular MedicineCSIR‐Institute of Genomics and Integrative Biology (CSIR‐IGIB)Mall RoadDelhi110007India
| | - Avni Anand
- Genomics and Molecular MedicineCSIR‐Institute of Genomics and Integrative Biology (CSIR‐IGIB)Mall RoadDelhi110007India
| | - Ishtaq Ahmad
- Neurology DepartmentNeuroscience CentreNew Delhi110029India
| | - Sunil Shakya
- Neurology DepartmentNeuroscience CentreNew Delhi110029India
| | - Bharathram Uppili
- Genomics and Molecular MedicineCSIR‐Institute of Genomics and Integrative Biology (CSIR‐IGIB)Mall RoadDelhi110007India,Academy for Scientific and Innovative ResearchGhaziabadUttar Pradesh201002India
| | - Aradhana Mathur
- Genomics and Molecular MedicineCSIR‐Institute of Genomics and Integrative Biology (CSIR‐IGIB)Mall RoadDelhi110007India
| | - Shaista Parveen
- Genomics and Molecular MedicineCSIR‐Institute of Genomics and Integrative Biology (CSIR‐IGIB)Mall RoadDelhi110007India
| | - Shweta Jain
- Genomics and Molecular MedicineCSIR‐Institute of Genomics and Integrative Biology (CSIR‐IGIB)Mall RoadDelhi110007India
| | - Jyotsna Singh
- Genomics and Molecular MedicineCSIR‐Institute of Genomics and Integrative Biology (CSIR‐IGIB)Mall RoadDelhi110007India,Neurology DepartmentNeuroscience CentreNew Delhi110029India
| | - Malika Seth
- Genomics and Molecular MedicineCSIR‐Institute of Genomics and Integrative Biology (CSIR‐IGIB)Mall RoadDelhi110007India
| | - Sana Zahra
- Genomics and Molecular MedicineCSIR‐Institute of Genomics and Integrative Biology (CSIR‐IGIB)Mall RoadDelhi110007India,Academy for Scientific and Innovative ResearchGhaziabadUttar Pradesh201002India
| | - Aditi Joshi
- Genomics and Molecular MedicineCSIR‐Institute of Genomics and Integrative Biology (CSIR‐IGIB)Mall RoadDelhi110007India
| | - Divya Goel
- Genomics and Molecular MedicineCSIR‐Institute of Genomics and Integrative Biology (CSIR‐IGIB)Mall RoadDelhi110007India
| | - Shweta Sahni
- Genomics and Molecular MedicineCSIR‐Institute of Genomics and Integrative Biology (CSIR‐IGIB)Mall RoadDelhi110007India
| | - Asangla Kamai
- Genomics and Molecular MedicineCSIR‐Institute of Genomics and Integrative Biology (CSIR‐IGIB)Mall RoadDelhi110007India,Academy for Scientific and Innovative ResearchGhaziabadUttar Pradesh201002India
| | - Saruchi Wadhwa
- Genomics and Molecular MedicineCSIR‐Institute of Genomics and Integrative Biology (CSIR‐IGIB)Mall RoadDelhi110007India,Academy for Scientific and Innovative ResearchGhaziabadUttar Pradesh201002India
| | - Aparna Murali
- Genomics and Molecular MedicineCSIR‐Institute of Genomics and Integrative Biology (CSIR‐IGIB)Mall RoadDelhi110007India
| | - Sheeba Saifi
- Genomics and Molecular MedicineCSIR‐Institute of Genomics and Integrative Biology (CSIR‐IGIB)Mall RoadDelhi110007India
| | | | - Sanjay Pandey
- Department of NeurologyGB Pant HospitalDelhi110002India
| | - Kuljeet Singh Anand
- Department of NeurologyPost Graduate Institute of Medical Education and ResearchDr. Ram Manohar Lohia HospitalNew Delhi110001India
| | | | | | - Suman Kushwaha
- Department of NeurologyInstitute of Human Behaviour and Allied SciencesDelhi110095India
| | | | | | | | | | - Mohammed Faruq
- Genomics and Molecular MedicineCSIR‐Institute of Genomics and Integrative Biology (CSIR‐IGIB)Mall RoadDelhi110007India,Academy for Scientific and Innovative ResearchGhaziabadUttar Pradesh201002India
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Chintalaphani SR, Pineda SS, Deveson IW, Kumar KR. An update on the neurological short tandem repeat expansion disorders and the emergence of long-read sequencing diagnostics. Acta Neuropathol Commun 2021; 9:98. [PMID: 34034831 PMCID: PMC8145836 DOI: 10.1186/s40478-021-01201-x] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/17/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Short tandem repeat (STR) expansion disorders are an important cause of human neurological disease. They have an established role in more than 40 different phenotypes including the myotonic dystrophies, Fragile X syndrome, Huntington's disease, the hereditary cerebellar ataxias, amyotrophic lateral sclerosis and frontotemporal dementia. MAIN BODY STR expansions are difficult to detect and may explain unsolved diseases, as highlighted by recent findings including: the discovery of a biallelic intronic 'AAGGG' repeat in RFC1 as the cause of cerebellar ataxia, neuropathy, and vestibular areflexia syndrome (CANVAS); and the finding of 'CGG' repeat expansions in NOTCH2NLC as the cause of neuronal intranuclear inclusion disease and a range of clinical phenotypes. However, established laboratory techniques for diagnosis of repeat expansions (repeat-primed PCR and Southern blot) are cumbersome, low-throughput and poorly suited to parallel analysis of multiple gene regions. While next generation sequencing (NGS) has been increasingly used, established short-read NGS platforms (e.g., Illumina) are unable to genotype large and/or complex repeat expansions. Long-read sequencing platforms recently developed by Oxford Nanopore Technology and Pacific Biosciences promise to overcome these limitations to deliver enhanced diagnosis of repeat expansion disorders in a rapid and cost-effective fashion. CONCLUSION We anticipate that long-read sequencing will rapidly transform the detection of short tandem repeat expansion disorders for both clinical diagnosis and gene discovery.
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Affiliation(s)
- Sanjog R. Chintalaphani
- School of Medicine, University of New South Wales, Sydney, 2052 Australia
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW 2010 Australia
| | - Sandy S. Pineda
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW 2010 Australia
- Brain and Mind Centre, University of Sydney, Camperdown, NSW 2050 Australia
| | - Ira W. Deveson
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW 2010 Australia
- Faculty of Medicine, St Vincent’s Clinical School, University of New South Wales, Sydney, NSW 2010 Australia
| | - Kishore R. Kumar
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW 2010 Australia
- Molecular Medicine Laboratory and Neurology Department, Central Clinical School, Concord Repatriation General Hospital, University of Sydney, Concord, NSW 2137 Australia
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Tantray JA, Reddy KP, Jamil K, Lone WG, Yerra SK. Genetic and Epigenetic Factors of E3/E3 Genotypes of APO-E Gene as a Strong Predictor for the Diagnosis of Coronary Artery Disease Patients of South India. CURR PROTEOMICS 2020. [DOI: 10.2174/1570164616666190724095158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
The role of Apolipoprotein-E (APO-E) in lipid metabolism and cholesterol
transport is a key component of lipid metabolism which plays a role in diseases like hypercholesterolemia,
diabetes, and cardiovascular disease. The aim of this study was to determine the genotypes, allelic
frequencies, gene expression and methylation related to apolipoprotein E polymorphism in Coronary Artery
Disease (CAD) patients and compare with non-CAD healthy subjects of South Indian population.
Methods:
The APO-E alleles and genotypes were determined by PCR-RFLP. Gene expression profiles
for E3/E3 genotypes were determined using RT-PCR and methylation status was determined using
Methyl Specific PCR assay in one hundred patients and an equal number of controls.
Results:
Four APO-E genotypes (E4/E4, E3/E3, E3/E4, and E2/E3) were identified with different allele
frequency. Among these, E3/E3 genotype and E3 allele were found to be significantly higher in
cases than controls. The present study showed that the mRNA expression of APO-E was up-regulated
in CAD patients with E3/E3 genotype in comparison with controls. Methylation status indicated a significant
association of E3/E3 genotypes with the disease.
Conclusion:
Different populations studied worldwide showed inherent variable frequencies of the
APO-E alleles and genotypes, with the most frequent allele being E3. In this study, the APO-E genotypes
E2/E3/E4 showed variable response to CAD, further, there was a significant association of E3/E3
genotypes to CAD risk; this genotype can be suggested for the diagnosis of CAD.
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Affiliation(s)
| | | | - Kaiser Jamil
- Department of Genetics, Bhagwan Mahavir Medical Research Centre, 10-1-1, Mahavir Marg, Hyderabad-500004, Telangana, India
| | - Waseem Gul Lone
- Department of Pathology and Microbiology, University of Nebraska Medical Centre, Omaha, Nebraska, United States
| | - Shiva Kumar Yerra
- Department of Cardiology, Mahavir Hospital and Research Centre Hyderabad (Telangana), India
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Abstract
The spinocerebellar ataxias (SCAs) are a genetically heterogeneous group of autosomal dominantly inherited progressive disorders, the clinical hallmark of which is loss of balance and coordination accompanied by slurred speech; onset is most often in adult life. Genetically, SCAs are grouped as repeat expansion SCAs, such as SCA3/Machado-Joseph disease (MJD), and rare SCAs that are caused by non-repeat mutations, such as SCA5. Most SCA mutations cause prominent damage to cerebellar Purkinje neurons with consecutive cerebellar atrophy, although Purkinje neurons are only mildly affected in some SCAs. Furthermore, other parts of the nervous system, such as the spinal cord, basal ganglia and pontine nuclei in the brainstem, can be involved. As there is currently no treatment to slow or halt SCAs (many SCAs lead to premature death), the clinical care of patients with SCA focuses on managing the symptoms through physiotherapy, occupational therapy and speech therapy. Intense research has greatly expanded our understanding of the pathobiology of many SCAs, revealing that they occur via interrelated mechanisms (including proteotoxicity, RNA toxicity and ion channel dysfunction), and has led to the identification of new targets for treatment development. However, the development of effective therapies is hampered by the heterogeneity of the SCAs; specific therapeutic approaches may be required for each disease.
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Srivastava A, Kumar D, Faruq M, Gundluru V. Spinocerebellar ataxia type 12: An update. ANNALS OF MOVEMENT DISORDERS 2019. [DOI: 10.4103/aomd.aomd_5_19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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