1
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Jain A, Bhoyar RC, Pandhare K, Mishra A, Sharma D, Imran M, Senthivel V, Divakar MK, Rophina M, Jolly B, Batra A, Sharma S, Siwach S, Jadhao AG, Palande NV, Jha GN, Ashrafi N, Mishra PK, A K V, Jain S, Dash D, Kumar NS, Vanlallawma A, Sarma RJ, Chhakchhuak L, Kalyanaraman S, Mahadevan R, Kandasamy S, B M P, Rajagopal RE, Ramya J E, Devi P N, Bajaj A, Gupta V, Mathew S, Goswami S, Mangla M, Prakash S, Joshi K, Meyakumla, S S, Gajjar D, Soraisham R, Yadav R, Devi YS, Gupta A, Mukerji M, Ramalingam S, B K B, Scaria V, Sivasubbu S. Genetic epidemiology of autoinflammatory disease variants in Indian population from 1029 whole genomes. J Genet Eng Biotechnol 2021; 19:183. [PMID: 34905135 PMCID: PMC8671593 DOI: 10.1186/s43141-021-00268-2] [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] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 10/13/2021] [Indexed: 11/16/2022]
Abstract
Background Autoinflammatory disorders are the group of inherited inflammatory disorders caused due to the genetic defect in the genes that regulates innate immune systems. These have been clinically characterized based on the duration and occurrence of unprovoked fever, skin rash, and patient’s ancestry. There are several autoinflammatory disorders that are found to be prevalent in a specific population and whose disease genetic epidemiology within the population has been well understood. However, India has a limited number of genetic studies reported for autoinflammatory disorders till date. The whole genome sequencing and analysis of 1029 Indian individuals performed under the IndiGen project persuaded us to perform the genetic epidemiology of the autoinflammatory disorders in India. Results We have systematically annotated the genetic variants of 56 genes implicated in autoinflammatory disorder. These genetic variants were reclassified into five categories (i.e., pathogenic, likely pathogenic, benign, likely benign, and variant of uncertain significance (VUS)) according to the American College of Medical Genetics and Association of Molecular pathology (ACMG-AMP) guidelines. Our analysis revealed 20 pathogenic and likely pathogenic variants with significant differences in the allele frequency compared with the global population. We also found six causal founder variants in the IndiGen dataset belonging to different ancestry. We have performed haplotype prediction analysis for founder mutations haplotype that reveals the admixture of the South Asian population with other populations. The cumulative carrier frequency of the autoinflammatory disorder in India was found to be 3.5% which is much higher than reported. Conclusion With such frequency in the Indian population, there is a great need for awareness among clinicians as well as the general public regarding the autoinflammatory disorder. To the best of our knowledge, this is the first and most comprehensive population scale genetic epidemiological study being reported from India. Supplementary Information The online version contains supplementary material available at 10.1186/s43141-021-00268-2.
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Affiliation(s)
- Abhinav Jain
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Rahul C Bhoyar
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India
| | - Kavita Pandhare
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India
| | - Anushree Mishra
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India
| | - Disha Sharma
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India
| | - Mohamed Imran
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Vigneshwar Senthivel
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Mohit Kumar Divakar
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Mercy Rophina
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Bani Jolly
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Arushi Batra
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Sumit Sharma
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India
| | - Sanjay Siwach
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India
| | - Arun G Jadhao
- Department of Zoology, RTM Nagpur University, Nagpur, Maharashtra, 440033, India
| | - Nikhil V Palande
- Department of Zoology, Shri Mathuradas Mohota College of Science, Nagpur, Maharashtra, 440009, India
| | - Ganga Nath Jha
- Department of Anthropology, Vinoba Bhave University, Hazaribag, Jharkhand, 825301, India
| | - Nishat Ashrafi
- Department of Anthropology, Vinoba Bhave University, Hazaribag, Jharkhand, 825301, India
| | - Prashant Kumar Mishra
- Department of Biotechnology, Vinoba Bhave University, Hazaribag, Jharkhand, 825301, India
| | - Vidhya A K
- Department of Biochemistry, Dr. Kongu Science and Art College, Erode, Tamil Nadu, 638107, India
| | - Suman Jain
- Thalassemia and Sickle Cell Society, Hyderabad, Telangana, 500052, India
| | - Debasis Dash
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | | | - Andrew Vanlallawma
- Department of Biotechnology, Mizoram University, Aizawl, Mizoram, 796004, India
| | - Ranjan Jyoti Sarma
- Department of Biotechnology, Mizoram University, Aizawl, Mizoram, 796004, India
| | | | | | - Radha Mahadevan
- TVMC, Tirunelveli Medical College, Tirunelveli, Tamil Nadu, 627011, India
| | - Sunitha Kandasamy
- TVMC, Tirunelveli Medical College, Tirunelveli, Tamil Nadu, 627011, India
| | - Pabitha B M
- TVMC, Tirunelveli Medical College, Tirunelveli, Tamil Nadu, 627011, India
| | | | - Ezhil Ramya J
- TVMC, Tirunelveli Medical College, Tirunelveli, Tamil Nadu, 627011, India
| | - Nirmala Devi P
- TVMC, Tirunelveli Medical College, Tirunelveli, Tamil Nadu, 627011, India
| | - Anjali Bajaj
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Vishu Gupta
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Samatha Mathew
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Sangam Goswami
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Mohit Mangla
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Savinitha Prakash
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India
| | - Kandarp Joshi
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India
| | - Meyakumla
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India
| | - Sreedevi S
- Department of Microbiology, St.Pious X Degree & PG College for Women, Hyderabad, Telangana, 500076, India
| | - Devarshi Gajjar
- Department of Microbiology, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, 390002, India
| | - Ronibala Soraisham
- Department of Dermatology, Venereology and Leprology, Regional Institute of Medical Sciences, Imphal, Manipur, 795004, India
| | - Rohit Yadav
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Yumnam Silla Devi
- CSIR- North East Institute of Science and Technology, Jorhat, Assam, 785006, India
| | - Aayush Gupta
- Department of Dermatology, Dr. D.Y. Patil Medical College, Pune, Maharashtra, 411018, India
| | - Mitali Mukerji
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Sivaprakash Ramalingam
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Binukumar B K
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Vinod Scaria
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India.
| | - Sridhar Sivasubbu
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India.
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2
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Rophina M, Pandhare K, Jadhao S, Nagaraj SH, Scaria V. BGvar: A comprehensive resource for blood group immunogenetics. Transfus Med 2021; 32:229-236. [PMID: 34897852 DOI: 10.1111/tme.12844] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/11/2021] [Accepted: 12/01/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND Blood groups form the basis of effective and safe blood transfusion. There are about 43 well-recognised human blood group systems presently known. Blood groups are molecularly determined by the presence of specific antigens on the red blood cells and are genetically determined and inherited following Mendelian principles. The lack of a comprehensive, relevant, manually compiled and genome-ready dataset of red cell antigens limited the widespread application of genomic technologies to characterise and interpret the blood group complement of an individual from genomic datasets. MATERIALS AND METHODS A range of public datasets was used to systematically annotate the variation compendium for its functionality and allele frequencies across global populations. Details on phenotype or relevant clinical importance were collated from reported literature evidence. RESULTS We have compiled the Blood Group Associated Genomic Variant Resource (BGvar), a manually curated online resource comprising all known human blood group related allelic variants including a total of 1700 International Society of Blood Transfusion approved alleles and 1706 alleles predicted and curated from literature reports. This repository includes 1682 single nucleotide variations (SNVs), 310 Insertions, Deletions (InDels) and Duplications (Copy Number Variations) and about 1360 combination mutations corresponding to 43 human blood group systems and 2 transcription factors. This compendium also encompasses gene fusion and rearrangement events occurring in human blood group genes. CONCLUSION To the best of our knowledge, BGvar is a comprehensive and a user-friendly resource with most relevant collation of blood group alleles in humans. BGvar is accessible online at URL: http://clingen.igib.res.in/bgvar/.
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Affiliation(s)
- Mercy Rophina
- Genome Informatics and Big Data, CSIR Institute of Genomics and Integrative Biology, Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Kavita Pandhare
- Genome Informatics and Big Data, CSIR Institute of Genomics and Integrative Biology, Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Sudhir Jadhao
- Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia.,Translational Research Institute, Brisbane, Australia
| | - Shivashankar H Nagaraj
- Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia.,Translational Research Institute, Brisbane, Australia
| | - Vinod Scaria
- Genome Informatics and Big Data, CSIR Institute of Genomics and Integrative Biology, Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
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3
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Rophina M, Pandhare K, Shamnath A, Imran M, Jolly B, Scaria V. ESC: a comprehensive resource for SARS-CoV-2 immune escape variants. Nucleic Acids Res 2021; 50:D771-D776. [PMID: 34643704 PMCID: PMC8728294 DOI: 10.1093/nar/gkab895] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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] [Received: 08/15/2021] [Revised: 09/14/2021] [Accepted: 10/10/2021] [Indexed: 11/13/2022] Open
Abstract
Ever since the breakout of COVID-19 disease, ceaseless genomic research to inspect the epidemiology and evolution of the pathogen has been undertaken globally. Large scale viral genome sequencing and analysis have uncovered the functional impact of numerous genetic variants in disease pathogenesis and transmission. Emerging evidence of mutations in spike protein domains escaping antibody neutralization is reported. We have built a database with precise collation of manually curated variants in SARS-CoV-2 from literature with potential escape mechanisms from a range of neutralizing antibodies. This comprehensive repository encompasses a total of 5258 variants accounting for 2068 unique variants tested against 230 antibodies, patient convalescent plasma and vaccine breakthrough events. This resource enables the user to gain access to an extensive annotation of SARS-CoV-2 escape variants which would contribute to exploring and understanding the underlying mechanisms of immune response against the pathogen. The resource is available at http://clingen.igib.res.in/esc/.
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Affiliation(s)
- Mercy Rophina
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Kavita Pandhare
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Afra Shamnath
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, New Delhi, India
| | - Mohamed Imran
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Bani Jolly
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Vinod Scaria
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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4
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Mittal G, R I A, Vatsyayan A, Pandhare K, Scaria V. MUSTARD-a comprehensive resource of mutation-specific therapies in cancer. Database (Oxford) 2021; 2021:6328507. [PMID: 34309639 PMCID: PMC8312254 DOI: 10.1093/database/baab042] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 06/22/2021] [Accepted: 06/28/2021] [Indexed: 12/09/2022]
Abstract
The steady increase in global cancer burden has fuelled the development of several modes of treatment for the disease. In the presence of an actionable mutation, targeted therapies offer a method to selectively attack cancer cells, increasing overall efficacy and reducing harmful side effects. However, different drug molecules are in different stages of development, with new molecules obtaining approvals from regulatory agencies each year. To augment clinical impact, it is important that this information reaches clinicians, patients and researchers swiftly and in a structured, well-annotated manner. To this end, we have developed Mutation-Specific Therapies Resource and Database in Cancer (MUSTARD), a database that is designed to be a centralized resource with diverse information such as cancer subtype, associated mutations, therapy offered and its effect observed, along with links to external resources for a more comprehensive annotation. In its current version, MUSTARD comprises over 2105 unique entries, including associations between 418 unique drug therapies, 189 cancer subtypes and 167 genes curated and annotated from over 862 different publications. To the best of our knowledge, it is the only resource that offers comprehensive information on mutation-specific, gene fusions and overexpressed gene-targeted therapies for cancer. Database URL: http://clingen.igib.res.in/mustard/
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Affiliation(s)
- Gauri Mittal
- Indraprastha Institute of Information Technology, Okhla Industrial Estate, Phase III, Delhi 110020, India
| | - Anu R I
- Department of Clinical Biochemistry, MVR Cancer Center and Research Institute, CP 13/516 B, C, Vellalasseri NIT(Via), Poolacode, Kozhikode 673601, India.,Cancer Biology and Therapeutics: High-Impact Cancer Research Post Graduate Program, Harvard Medical School, 4 Blackfan Circle, Boston, MA 02115, USA
| | - Aastha Vatsyayan
- Department of Genome Informatics, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Sector 19, Kamla Nehru Nagar, Ghaziabad, UP 201002, India
| | - Kavita Pandhare
- Department of Genome Informatics, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India
| | - Vinod Scaria
- Department of Genome Informatics, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Sector 19, Kamla Nehru Nagar, Ghaziabad, UP 201002, India
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5
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Sahana S, Sivadas A, Mangla M, Jain A, Bhoyar RC, Pandhare K, Mishra A, Sharma D, Imran M, Senthivel V, Divakar MK, Rophina M, Jolly B, Batra A, Sharma S, Siwach S, Jadhao AG, Palande NV, Jha GN, Ashrafi N, Mishra PK, Vidhya AK, Jain S, Dash D, Kumar NS, Vanlallawma A, Sarma RJ, Chhakchhuak L, Kalyanaraman S, Mahadevan R, Kandasamy S, Devi P, Rajagopal RE, Ramya JE, Devi PN, Bajaj A, Gupta V, Mathew S, Goswami S, Prakash S, Joshi K, Kumla M, Sreedevi S, Gajjar D, Soraisham R, Yadav R, Devi YS, Gupta A, Mukerji M, Ramalingam S, Binukumar BK, Sivasubbu S, Scaria V. Pharmacogenomic landscape of COVID-19 therapies from Indian population genomes. Pharmacogenomics 2021; 22:603-618. [PMID: 34142560 PMCID: PMC8216321 DOI: 10.2217/pgs-2021-0028] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Aim: Numerous drugs are being widely prescribed for COVID-19 treatment without any direct evidence for the drug safety/efficacy in patients across diverse ethnic populations. Materials & methods: We analyzed whole genomes of 1029 Indian individuals (IndiGen) to understand the extent of drug–gene (pharmacogenetic), drug–drug and drug–drug–gene interactions associated with COVID-19 therapy in the Indian population. Results: We identified 30 clinically significant pharmacogenetic variants and 73 predicted deleterious pharmacogenetic variants. COVID-19-associated pharmacogenes were substantially overlapped with those of metabolic disorder therapeutics. CYP3A4, ABCB1 and ALB are the most shared pharmacogenes. Fifteen COVID-19 therapeutics were predicted as likely drug–drug interaction candidates when used with four CYP inhibitor drugs. Conclusion: Our findings provide actionable insights for future validation studies and improved clinical decisions for COVID-19 therapy in Indians.
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Affiliation(s)
- S Sahana
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Ambily Sivadas
- Division of Nutrition, St. John's Research Institute, St. John's National Academy of Health Sciences, Bangalore, India
| | - Mohit Mangla
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Abhinav Jain
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Rahul C Bhoyar
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Kavita Pandhare
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Anushree Mishra
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Disha Sharma
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Mohamed Imran
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Vigneshwar Senthivel
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Mohit Kumar Divakar
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Mercy Rophina
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Bani Jolly
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Arushi Batra
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Sumit Sharma
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Sanjay Siwach
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Arun G Jadhao
- Department of Zoology, RTM Nagpur University, Nagpur, Maharashtra, 440033, India
| | - Nikhil V Palande
- Department of Zoology, Shri Mathuradas Mohota College of Science, Nagpur, Maharashtra, 440009, India
| | - Ganga Nath Jha
- Department of Anthropology, Vinoba Bhave University, Hazaribag, Jharkhand, 825301, India
| | - Nishat Ashrafi
- Department of Anthropology, Vinoba Bhave University, Hazaribag, Jharkhand, 825301, India
| | - Prashant Kumar Mishra
- Department of Biotechnology, Vinoba Bhave University, Hazaribag, Jharkhand, 825301, India
| | - A K Vidhya
- Department of Biochemistry, Dr. Kongu Science & Art College, Erode, Tamil Nadu, 638107, India
| | - Suman Jain
- Thalassemia & Sickle cell Society, Hyderabad, Telangana, 500052, India
| | - Debasis Dash
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | | | - Andrew Vanlallawma
- Department of Biotechnology, Mizoram University, Aizawl, Mizoram, 796004, India
| | - Ranjan Jyoti Sarma
- Department of Biotechnology, Mizoram University, Aizawl, Mizoram, 796004, India
| | | | | | - Radha Mahadevan
- TVMC, Tirunelveli Medical College, Tirunelveli, Tamil Nadu, 627011, India
| | - Sunitha Kandasamy
- TVMC, Tirunelveli Medical College, Tirunelveli, Tamil Nadu, 627011, India
| | - Pabitha Devi
- TVMC, Tirunelveli Medical College, Tirunelveli, Tamil Nadu, 627011, India
| | | | - J Ezhil Ramya
- TVMC, Tirunelveli Medical College, Tirunelveli, Tamil Nadu, 627011, India
| | - P Nirmala Devi
- TVMC, Tirunelveli Medical College, Tirunelveli, Tamil Nadu, 627011, India
| | - Anjali Bajaj
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Vishu Gupta
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Samatha Mathew
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Sangam Goswami
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Savinitha Prakash
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Kandarp Joshi
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Meya Kumla
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - S Sreedevi
- Department of Microbiology, St. Pious X Degree & PG College for Women, Hyderabad, Telangana, 500076, India
| | - Devarshi Gajjar
- Department of Microbiology, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, 390002, India
| | - Ronibala Soraisham
- Department of Dermatology, Venereology & Leprology, Regional Institute of Medical Sciences, Imphal, Manipur, 795004, India
| | - Rohit Yadav
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Yumnam Silla Devi
- CSIR- North East Institute of Science & Technology, Jorhat, Assam, 785006, India
| | - Aayush Gupta
- Department of Dermatology, Dr. D.Y. Patil Medical College, Pune, Maharashtra, 411018, India
| | - Mitali Mukerji
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Sivaprakash Ramalingam
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - B K Binukumar
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Sridhar Sivasubbu
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Vinod Scaria
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
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6
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Bhoyar RC, Jain A, Sehgal P, Divakar MK, Sharma D, Imran M, Jolly B, Ranjan G, Rophina M, Sharma S, Siwach S, Pandhare K, Sahoo S, Sahoo M, Nayak A, Mohanty JN, Das J, Bhandari S, Mathur SK, Kumar A, Sahlot R, Rojarani P, Lakshmi JV, Surekha A, Sekhar PC, Mahajan S, Masih S, Singh P, Kumar V, Jose B, Mahajan V, Gupta V, Gupta R, Arumugam P, Singh A, Nandy A, P. V. R, Jha RM, Kumari A, Gandotra S, Rao V, Faruq M, Kumar S, Reshma G. B, Varma G. N, Roy SS, Sengupta A, Chattopadhyay S, Singhal K, Pradhan S, Jha D, Naushin S, Wadhwa S, Tyagi N, Poojary M, Scaria V, Sivasubbu S. High throughput detection and genetic epidemiology of SARS-CoV-2 using COVIDSeq next-generation sequencing. PLoS One 2021; 16:e0247115. [PMID: 33596239 PMCID: PMC7888613 DOI: 10.1371/journal.pone.0247115] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 02/01/2021] [Indexed: 01/10/2023] Open
Abstract
The rapid emergence of coronavirus disease 2019 (COVID-19) as a global pandemic affecting millions of individuals globally has necessitated sensitive and high-throughput approaches for the diagnosis, surveillance, and determining the genetic epidemiology of SARS-CoV-2. In the present study, we used the COVIDSeq protocol, which involves multiplex-PCR, barcoding, and sequencing of samples for high-throughput detection and deciphering the genetic epidemiology of SARS-CoV-2. We used the approach on 752 clinical samples in duplicates, amounting to a total of 1536 samples which could be sequenced on a single S4 sequencing flow cell on NovaSeq 6000. Our analysis suggests a high concordance between technical duplicates and a high concordance of detection of SARS-CoV-2 between the COVIDSeq as well as RT-PCR approaches. An in-depth analysis revealed a total of six samples in which COVIDSeq detected SARS-CoV-2 in high confidence which were negative in RT-PCR. Additionally, the assay could detect SARS-CoV-2 in 21 samples and 16 samples which were classified inconclusive and pan-sarbeco positive respectively suggesting that COVIDSeq could be used as a confirmatory test. The sequencing approach also enabled insights into the evolution and genetic epidemiology of the SARS-CoV-2 samples. The samples were classified into a total of 3 clades. This study reports two lineages B.1.112 and B.1.99 for the first time in India. This study also revealed 1,143 unique single nucleotide variants and added a total of 73 novel variants identified for the first time. To the best of our knowledge, this is the first report of the COVIDSeq approach for detection and genetic epidemiology of SARS-CoV-2. Our analysis suggests that COVIDSeq could be a potential high sensitivity assay for the detection of SARS-CoV-2, with an additional advantage of enabling the genetic epidemiology of SARS-CoV-2.
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Affiliation(s)
- Rahul C. Bhoyar
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Abhinav Jain
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
| | - Paras Sehgal
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
| | - Mohit Kumar Divakar
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
| | - Disha Sharma
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Mohamed Imran
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
| | - Bani Jolly
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
| | - Gyan Ranjan
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
| | - Mercy Rophina
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
| | - Sumit Sharma
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Sanjay Siwach
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Kavita Pandhare
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Swayamprabha Sahoo
- Institute of Medical Sciences and SUM Hospital, Siksha “O” Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India
| | - Maheswata Sahoo
- Institute of Medical Sciences and SUM Hospital, Siksha “O” Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India
| | - Ananya Nayak
- Institute of Medical Sciences and SUM Hospital, Siksha “O” Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India
| | - Jatindra Nath Mohanty
- Institute of Medical Sciences and SUM Hospital, Siksha “O” Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India
| | - Jayashankar Das
- Institute of Medical Sciences and SUM Hospital, Siksha “O” Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India
| | | | | | - Anshul Kumar
- Sawai Man Singh Medical College, Jaipur, Rajasthan, India
| | - Rahul Sahlot
- Sawai Man Singh Medical College, Jaipur, Rajasthan, India
| | | | | | | | | | - Shelly Mahajan
- Center for Advanced Research in Imaging, Neuroscience & Genomics, New Delhi, Delhi, India
| | - Shet Masih
- Center for Advanced Research in Imaging, Neuroscience & Genomics, New Delhi, Delhi, India
| | - Pawan Singh
- Center for Advanced Research in Imaging, Neuroscience & Genomics, New Delhi, Delhi, India
| | - Vipin Kumar
- Center for Advanced Research in Imaging, Neuroscience & Genomics, New Delhi, Delhi, India
| | - Blessy Jose
- Center for Advanced Research in Imaging, Neuroscience & Genomics, New Delhi, Delhi, India
| | - Vidur Mahajan
- Center for Advanced Research in Imaging, Neuroscience & Genomics, New Delhi, Delhi, India
| | - Vivek Gupta
- Government Institute of Medical Sciences, NOIDA, Uttar Pradesh, India
| | - Rakesh Gupta
- Government Institute of Medical Sciences, NOIDA, Uttar Pradesh, India
| | - Prabhakar Arumugam
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
| | - Anjali Singh
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
| | - Ananya Nandy
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
| | - Ragavendran P. V.
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
| | - Rakesh Mohan Jha
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
| | - Anupama Kumari
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
| | - Sheetal Gandotra
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
| | - Vivek Rao
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
| | - Mohammed Faruq
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
| | - Sanjeev Kumar
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
| | - Betsy Reshma G.
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
| | - Narendra Varma G.
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Shuvra Shekhar Roy
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
| | - Antara Sengupta
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
| | - Sabyasachi Chattopadhyay
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
| | - Khushboo Singhal
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
| | - Shalini Pradhan
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Diksha Jha
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
| | - Salwa Naushin
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
| | - Saruchi Wadhwa
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
| | - Nishu Tyagi
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
| | - Mukta Poojary
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
| | - Vinod Scaria
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
| | - Sridhar Sivasubbu
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
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7
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Vatsyayan A, Sharma P, Gupta S, Sandhu S, Venu SL, Sharma V, Badaoui B, Azedine K, Youssef S, Rajab A, Fayez A, Madinur S, Ranawat A, Pandhare K, Ramachandran S, Sivasubbu S, Scaria V. DALIA- a comprehensive resource of Disease Alleles in Arab population. PLoS One 2021; 16:e0244567. [PMID: 33439861 PMCID: PMC7806169 DOI: 10.1371/journal.pone.0244567] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 12/11/2020] [Indexed: 11/18/2022] Open
Abstract
The Arab population encompasses over 420 million people characterized by genetic admixture and a consequent rich genetic diversity. A number of genetic diseases have been reported for the first time from the population. Additionally a high prevalence of some genetic diseases including autosomal recessive disorders such as hemoglobinopathies and familial mediterranean fever have been found in the population and across the region. There is a paucity of databases cataloguing genetic variants of clinical relevance from the population. The availability of such a catalog could have implications in precise diagnosis, genetic epidemiology and prevention of disease. To fill in the gap, we have compiled DALIA, a comprehensive compendium of genetic variants reported in literature and implicated in genetic diseases reported from the Arab population. The database aims to act as an effective resource for population-scale and sub-population specific variant analyses, enabling a ready reference aiding clinical interpretation of genetic variants, genetic epidemiology, as well as facilitating rapid screening and a quick reference for evaluating evidence on genetic diseases.
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Affiliation(s)
- Aastha Vatsyayan
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Amity University, Noida, India
| | - Parul Sharma
- Indraprastha Institute of Information Technology Delhi (IIIT-D), Delhi, India
| | - Shrey Gupta
- Indraprastha Institute of Information Technology Delhi (IIIT-D), Delhi, India
| | | | | | | | | | | | | | - Anna Rajab
- National Genetic Center, Ministry of Health, Muscat, Oman
| | - Alaaeldin Fayez
- Human Genetics and Genome Research Division, Center of Excellence for Human Genetics, National Research Center, Cairo, Egypt
| | | | - Anop Ranawat
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Kavita Pandhare
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Srinivasan Ramachandran
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Sridhar Sivasubbu
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Vinod Scaria
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- * E-mail:
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8
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Jain A, Bhoyar RC, Pandhare K, Mishra A, Sharma D, Imran M, Senthivel V, Divakar MK, Rophina M, Jolly B, Batra A, Sharma S, Siwach S, Jadhao AG, Palande N, Jha GN, Ashrafi N, Mishra PK, A. K. V, Jain S, Dash D, Kumar NS, Vanlallawma A, Sarma R, Chhakchhuak L, Kalyanaraman S, Mahadevan R, Kandasamy S, B. M. P, Rajagopal RE, J. ER, P. ND, Bajaj A, Gupta V, Mathew S, Goswami S, Mangla M, Prakash S, Joshi K, S. S, Gajjar D, Soraisham R, Yadav R, Devi YS, Gupta A, Mukerji M, Ramalingam S, B. K. B, Scaria V, Sivasubbu S. IndiGenomes: a comprehensive resource of genetic variants from over 1000 Indian genomes. Nucleic Acids Res 2021; 49:D1225-D1232. [PMID: 33095885 PMCID: PMC7778947 DOI: 10.1093/nar/gkaa923] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/01/2020] [Accepted: 10/22/2020] [Indexed: 12/15/2022] Open
Abstract
With the advent of next-generation sequencing, large-scale initiatives for mining whole genomes and exomes have been employed to better understand global or population-level genetic architecture. India encompasses more than 17% of the world population with extensive genetic diversity, but is under-represented in the global sequencing datasets. This gave us the impetus to perform and analyze the whole genome sequencing of 1029 healthy Indian individuals under the pilot phase of the 'IndiGen' program. We generated a compendium of 55,898,122 single allelic genetic variants from geographically distinct Indian genomes and calculated the allele frequency, allele count, allele number, along with the number of heterozygous or homozygous individuals. In the present study, these variants were systematically annotated using publicly available population databases and can be accessed through a browsable online database named as 'IndiGenomes' http://clingen.igib.res.in/indigen/. The IndiGenomes database will help clinicians and researchers in exploring the genetic component underlying medical conditions. Till date, this is the most comprehensive genetic variant resource for the Indian population and is made freely available for academic utility. The resource has also been accessed extensively by the worldwide community since it's launch.
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Affiliation(s)
- Abhinav Jain
- CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Rahul C Bhoyar
- CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Kavita Pandhare
- CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Anushree Mishra
- CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Disha Sharma
- CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Mohamed Imran
- CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Vigneshwar Senthivel
- CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Mohit Kumar Divakar
- CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Mercy Rophina
- CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Bani Jolly
- CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Arushi Batra
- CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Sumit Sharma
- CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Sanjay Siwach
- CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Arun G Jadhao
- Department of Zoology, RTM Nagpur University, Nagpur, Maharashtra 440033, India
| | - Nikhil V Palande
- Department of Zoology, Shri Mathuradas Mohota College of Science, Nagpur, Maharashtra 440009, India
| | - Ganga Nath Jha
- Department of Anthropology, Vinoba Bhave University, Hazaribag, Jharkhand 825301, India
| | - Nishat Ashrafi
- Department of Anthropology, Vinoba Bhave University, Hazaribag, Jharkhand 825301, India
| | - Prashant Kumar Mishra
- Department of Biotechnology, Vinoba Bhave University, Hazaribag, Jharkhand 825301, India
| | - Vidhya A. K.
- Department of Biochemistry, Dr. Kongu Science and Art College, Erode, Tamil Nadu 638107, India
| | - Suman Jain
- Thalassemia and Sickle cell Society, Hyderabad, Telangana 500052, India
| | - Debasis Dash
- CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | | | - Andrew Vanlallawma
- Department of Biotechnology, Mizoram University, Aizawl, Mizoram 796004, India
| | - Ranjan Jyoti Sarma
- Department of Biotechnology, Mizoram University, Aizawl, Mizoram 796004, India
| | | | | | - Radha Mahadevan
- TVMC, Tirunelveli Medical College, Tirunelveli, Tamil Nadu 627011, India
| | - Sunitha Kandasamy
- TVMC, Tirunelveli Medical College, Tirunelveli, Tamil Nadu 627011, India
| | - Pabitha B. M.
- TVMC, Tirunelveli Medical College, Tirunelveli, Tamil Nadu 627011, India
| | | | - Ezhil Ramya J.
- TVMC, Tirunelveli Medical College, Tirunelveli, Tamil Nadu 627011, India
| | - Nirmala Devi P.
- TVMC, Tirunelveli Medical College, Tirunelveli, Tamil Nadu 627011, India
| | - Anjali Bajaj
- CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Vishu Gupta
- CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Samatha Mathew
- CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Sangam Goswami
- CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Mohit Mangla
- CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Savinitha Prakash
- CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Kandarp Joshi
- CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Sreedevi S.
- Department of Microbiology, St.Pious X Degree & PG College for Women, Hyderabad, Telangana 500076, India
| | - Devarshi Gajjar
- Department of Microbiology, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat 390002, India
| | - Ronibala Soraisham
- Department of Dermatology, Venereology and Leprology, Regional Institute of Medical Sciences, Imphal, Manipur 795004, India
| | - Rohit Yadav
- CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Yumnam Silla Devi
- CSIR- North East Institute of Science and Technology, Jorhat, Assam 785006, India
| | - Aayush Gupta
- Department of Dermatology, Dr. D.Y. Patil Medical College, Pune, Maharashtra 411018, India
| | - Mitali Mukerji
- CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Sivaprakash Ramalingam
- CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Binukumar B. K.
- CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Vinod Scaria
- CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Sridhar Sivasubbu
- CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
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9
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Mhaske A, Dileep K, Kumar M, Poojary M, Pandhare K, Zhang KY, Scaria V, Binukumar B. ATP7A Clinical Genetics Resource - A comprehensive clinically annotated database and resource for genetic variants in ATP7A gene. Comput Struct Biotechnol J 2020; 18:2347-2356. [PMID: 32994893 PMCID: PMC7501406 DOI: 10.1016/j.csbj.2020.08.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 08/25/2020] [Accepted: 08/26/2020] [Indexed: 12/21/2022] Open
Abstract
ATP7A is a critical copper transporter involved in Menkes Disease, Occipital horn Syndrome and X-linked distal spinal muscular atrophy type 3 which are X linked genetic disorders. These are rare diseases and their genetic epidemiology of the diseases is unknown. A number of genetic variants in the genes have been reported in published literature as well as databases, however, understanding the pathogenicity of variants and genetic epidemiology requires the data to be compiled in a unified format. To this end, we systematically compiled genetic variants from published literature and datasets. Each of the variants were systematically evaluated for evidences with respect to their pathogenicity and classified as per the American College of Medical Genetics and the Association of Molecular Pathologists (ACMG-AMP) guidelines into Pathogenic, Likely Pathogenic, Benign, Likely Benign and Variants of Uncertain Significance. Additional integrative analysis of population genomic datasets provides insights into the genetic epidemiology of the disease through estimation of carrier frequencies in global populations. To deliver a mechanistic explanation for the pathogenicity of selected variants, we also performed molecular modeling studies. Our modeling studies concluded that the small structural distortions observed in the local structures of the protein may lead to the destabilization of the global structure. To the best of our knowledge, ATP7A Clinical Genetics Resource is one of the most comprehensive compendium of variants in the gene providing clinically relevant annotations in gene.
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Affiliation(s)
- Aditi Mhaske
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110 025, India
| | - K.V. Dileep
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Mukesh Kumar
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110 025, India
- Academy of Scientific and Innovative Research, CSIR-IGIB South Campus, Mathura Road, Delhi, India
| | - Mukta Poojary
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110 025, India
- Academy of Scientific and Innovative Research, CSIR-IGIB South Campus, Mathura Road, Delhi, India
| | - Kavita Pandhare
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110 025, India
- Academy of Scientific and Innovative Research, CSIR-IGIB South Campus, Mathura Road, Delhi, India
| | - Kam Y.J. Zhang
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Vinod Scaria
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110 025, India
- Academy of Scientific and Innovative Research, CSIR-IGIB South Campus, Mathura Road, Delhi, India
- Corresponding author at: CSIR-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, Sukhdev Vihar, New Delhi 110025, India.
| | - B.K. Binukumar
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110 025, India
- Academy of Scientific and Innovative Research, CSIR-IGIB South Campus, Mathura Road, Delhi, India
- Corresponding author at: CSIR-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, Sukhdev Vihar, New Delhi 110025, India.
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Kumar M, Gaharwar U, Paul S, Poojary M, Pandhare K, Scaria V, Bk B. WilsonGen a comprehensive clinically annotated genomic variant resource for Wilson's Disease. Sci Rep 2020; 10:9037. [PMID: 32493955 PMCID: PMC7270127 DOI: 10.1038/s41598-020-66099-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [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] [Received: 03/07/2020] [Accepted: 05/14/2020] [Indexed: 12/20/2022] Open
Abstract
Wilson disease (WD) is one of the most prevalent genetic diseases with an estimated global carrier frequency of 1 in 90 and a prevalence of 1 in 30,000. The disease owes its genesis to Kinnier Wilson who described the disease, and is caused by accumulation of Copper (Cu) in various organs including the liver, central nervous system, cornea, kidney, joints and cardiac muscle which contribute to the characteristic clinical features of WD. A number of studies have reported genetic variants in the ATP7B gene from diverse ethnic and geographical origins. The recent advent of next-generation sequencing approaches has also enabled the discovery of a large number of novel variants in the gene associated with the disease. Previous attempts have been made to compile the knowledgebase and spectrum of genetic variants from across the multitude of publications, but have been limited by the utility due to the significant differences in approaches used to qualify pathogenicity of variants in each of the publications. The recent formulation of guidelines and algorithms for assessment of the pathogenicity of variants jointly put forward by the American College of Medical Genetics and the Association of Molecular Pathologists (ACMG &) has provided a framework for evidence based and systematic assessment of pathogenicity of variants. In this paper, we describe a comprehensive resource of genetic variants in ATP7B gene manually curated from literature and data resources and systematically annotated using the ACMG & AMP guidelines for assessing pathogenicity. The resource therefore serves as a central point for clinicians and geneticists working on WD and to the best of our knowledge is the most comprehensive and only clinically annotated resource for WD. The resource is available at URL http://clingen.igib.res.in/WilsonGen/. We compiled a total of 3662 genetic variants from publications and databases associated with WD. Of these variants compiled, a total of 1458 were found to be unique entries. This is the largest WD database comprising 656 pathogenic/likely pathogenic variants reported classified according to ACMG & AMP guidelines. We also mapped all the pathogenic variants corresponding to ATP7B protein from literature and other databases. In addition, geographical origin and distribution of ATP7B pathogenic variants reported are also mapped in the database.
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Affiliation(s)
- Mukesh Kumar
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi, 110 025, India.,Academy of Scientific and Innovative Research, CSIR-IGIB South Campus, Mathura Road, Delhi, India
| | - Utkarsh Gaharwar
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi, 110 025, India
| | - Sangita Paul
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi, 110 025, India.,Academy of Scientific and Innovative Research, CSIR-IGIB South Campus, Mathura Road, Delhi, India
| | - Mukta Poojary
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi, 110 025, India.,Academy of Scientific and Innovative Research, CSIR-IGIB South Campus, Mathura Road, Delhi, India
| | - Kavita Pandhare
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi, 110 025, India
| | - Vinod Scaria
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi, 110 025, India. .,Academy of Scientific and Innovative Research, CSIR-IGIB South Campus, Mathura Road, Delhi, India.
| | - Binukumar Bk
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi, 110 025, India. .,Academy of Scientific and Innovative Research, CSIR-IGIB South Campus, Mathura Road, Delhi, India.
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