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Institute of Genomics and Integrative Biology

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CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB) is a scientific research institute devoted primarily to biological research. It is a part of Council of Scientific and Industrial Research (CSIR), India.[1]

CSIR Institute of Genomics and Integrative Biology
AbbreviationCSIR-IGIB
Established1977
TypeGovernment organization
PurposeTo translate concepts developed in basic biological research to commercially viable technologies for health care
Location
  • Sukhdev Vihar, Mathura Road,
    Delhi-110 025.
Director
Anurag Agrawal
Parent organization
Council of Scientific and Industrial Research
Websitewww.igib.res.in
CSIR-IGIB South Campus

The institute was founded in 1977 as the Center for Biochemical Technology with a primary focus on biochemical research, but has since shifted its research focus to integrative biology.

Location

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The Institute has two campuses in Delhi. The North Campus is the older of the two campuses and is in the campus of Delhi University, on Mall Road opposite to Jubilee Hall. The new campus is in South Delhi, on Mathura Road at Sukhdev Vihar.

History

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IGIB was established in 1977 as the Center for Biochemical Technology (CBT). The Functional Genomics Unit was established in 1998 with the focus shifting from chemical to genomics research. The institute was renamed "Institute of Genomics and Integrative Biology" in 2002.

Achievements

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In 2009, a team at the institute sequenced the genome of the wild-type zebrafish, with about 1.7 billion base pairs. This made the fish, which is native to the Himalayan region, the first vertebrate to have its whole genome sequenced in India, as previously Indian scientists had only sequenced bacteria and plant genomes.[2][3]

In December 2009, scientists at IGIB performed the first re-sequencing of a human genome in India.[4][5][6] The Institute also collaborated on decoding the first Sri Lankan [7][8] genome and Malaysian genome.[9] The Institute is also a member of the Open Personal Genomics Consortium.[10]

COVID-19 pandemic

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The institute plays a leading role in the understanding of new variants of SARS-CoV-2 in India[11][12] and across the world.[13] The institute also maintains a number of informatics resources which are key to identification and characterization of emerging variants of SARS-CoV-2.[14][15]

Researchers at the institute reported the first high-throughput[16] next-generation sequencing based approach for detection and genetic epidemiology of SARS-CoV-2.[17] This approach has been extensively used to understand the genetic epidemiology of SARS-CoV-2 in the state of Kerala,[18] which has significantly influenced policy and preparedness[19] in the state to curb the spread of the epidemic as well as implementation of evidence based policies.[20]

The institute has been instrumental in creating the concept of MegaLabs for COVID-19 testing and genomic surveillance[21] which also provided the genetic epidemiology of states including Kerala,[22] Andhra Pradesh[23] and Maharashtra.[24]

Researchers at the institute also reported the first cases of COVID-19 reinfection in the country[25] apart from identifying a novel clade of SARS-CoV-2 in India named I/A3i.[26] Researchers at the institute also discovered an emerging lineage with N440K mutation in spike protein associated with immune escape.[27][28] A comprehensive suite for computational resources to understand the genomes and genetic epidemiology of SARS-CoV-2 has been maintained.[15] One of the first genetically characterized cases of COVID-19 vaccine breakthrough infections was reported by the institute.[29]

Researchers at the institute have been instrumental in the development of COVIDSure[30] an Reverse transcription polymerase chain reaction based kit for diagnosis of COVID-19 and now widely used in India and marketed by Trivitron Healthcare.[31]

Researchers at CSIR-IGIB also developed the test called FELUDA based on CRISPR gene editing which is highly efficient and fast to combat the testing capacity of the country and has been approved by Drugs Controller General of India. The test has been licensed to Tata Group for commercial production.[32]

The institute has also been playing a leading role in the national COVID-19 genomics consortium[33] and maintains the informatics resources and dashboards.[14]

Genomics of rare genetic diseases

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The institute has initiated a unique programme to use cutting-edge genomic technologies to understand Rare genetic diseases in India and pioneering the application of genomics for Precision Medicine in clinics. One of the programmes which has been initiated on this front is Genomics for Understanding Rare Disease, India Alliance Network (GUaRDIAN).[34] GUaRDIAN is a large-scale collaborative network of clinicians from around India trying to use genomics in clinical practice, with the focused aim to understand genetic structure of rare genetic diseases in India.[35]

The consortium aims at using cutting-edge genomics technology to enable identification of genetic variations in diseases and enable clinicians arrive at precise diagnosis for rare genetic disease. Apart from working closely with clinicians, the consortium aims to foster education, awareness and the widespread adoption of genomic technology in clinical settings, in addition to creating and disseminating the highest standards of genomic data generation and interpretation in India.[36]

In the few years, it has been able to work closely with clinicians in the network to be able to offer proof of principles for the application of Genomics for Precision Medicine.[37][38][39] A comprehensive programme for patient referral is also functional.[40]

IndiGen Programme for Public Health

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The IndiGen programme on Public Health Genomics[41] aims to undertake whole genome sequencing  of 1000 Indian individuals representing diverse ethnic groups from India. The data generated as part of IndiGen would provide the baseline for allele frequencies of genetic variants for genetic epidemiology and aid policy decisions. The frequencies of clinically relevant genetic variants would form the template for enabling diagnostic approaches for prevalent genetic diseases and also for optimising therapies through pharmacogenomics. A comprehensive resource providing searchable access to the data is also made available.[42]

Extension Centers (Branches)

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The main IGIB campus is located at Mall Road, New Delhi near Delhi University North Campus. IGIB's alliance with the Biotech/Pharmaceuticals has led to its growth and setting up of two extension centers - one at South Delhi (IGIB Annex at TCGA, Okhla) and the other at Western Delhi at Naraina.

International Meetings

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IGIB was a co-host of the 13th meeting of the Human Genome Organization (HUGO) in 2008, held at Hyderabad International Convention Centre.[43]

See also

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References

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  1. ^ Council of Scientific and Industrial Research India Website Archived 2015-09-27 at the Wayback Machine.
  2. ^ Zebrafish Genome Webpage Archived 19 July 2018 at the Wayback Machine 'Institute of Genomics and Integrative Biology' (IGIB)
  3. ^ Decoding the Genome Mystery Indian Express, 5 July 2009.
  4. ^ Indian Scientists decode human genome Indian Express, 10 December 2009 [dead link‍]
  5. ^ * Patowary A, Purkanti R, Singh M, Chauhan RK, Bhartiya D, Dwivedi OP, et al. (July 2012). "Systematic analysis and functional annotation of variations in the genome of an Indian individual". Human Mutation. 33 (7): 1133–40. doi:10.1002/humu.22091. PMID 22461382. S2CID 11466942. [1]
  6. ^ Compilation of news articles and Press releases on Indian Genome, 10 December 2009
  7. ^ "Sri Lankan genome". Archived from the original on 18 February 2013. Retrieved 17 January 2013.
  8. ^ Dissanayake VH, Samarakoon PS, Scaria V, Patowary A, Sivasubbu S, Gokhale RS, et al. (2012). "The Sri Lankan Personal Genome Project: an overview". Sri Lanka Journal of Biomedical Informatics. 1 (2): 4–8. [2] Archived 5 April 2013 at the Wayback Machine
  9. ^ "Wedding Day Ancilleries".[permanent dead link‍]
  10. ^ "OpenPGx Consortium". Archived from the original on 18 December 2017. Retrieved 7 November 2018.
  11. ^ Dandekar, Vikas. "Genome meets GitHub: Using tech tools, India's virus hunters track a shape-shifting killer". The Economic Times. Retrieved 14 August 2021.
  12. ^ "How one of India's premier research institutes is tracking new SARS-COV2 variants". The Indian Express. 3 August 2021. Retrieved 14 August 2021.
  13. ^ "Meet the people who warn the world about new covid variants". MIT Technology Review. Retrieved 14 August 2021.
  14. ^ a b "COVID-19 Genomic Surveillance". clingen.igib.res.in. Retrieved 14 August 2021.
  15. ^ a b "Genetic epidemiology of novel and emerging pathogens in India". clingen.igib.res.in. Retrieved 30 October 2020.
  16. ^ "Plans afoot to set up megalabs in four states to strengthen surveillance". Hindustan Times. 24 September 2020. Retrieved 30 October 2020.
  17. ^ Bhoyar, Rahul C.; Jain, Abhinav; Sehgal, Paras; Divakar, Mohit Kumar; Sharma, Disha; Imran, Mohamed; Jolly, Bani; Ranjan, Gyan; Rophina, Mercy; Sharma, Sumit; Siwach, Sanjay (10 August 2020). "High throughput detection and genetic epidemiology of SARS-CoV-2 using COVIDSeq next generation sequencing". bioRxiv: 2020.08.10.242677. doi:10.1101/2020.08.10.242677. S2CID 221141897.
  18. ^ Maya, C. (12 September 2020). "Inter-State travel brought coronavirus strains to Kerala: study". The Hindu. ISSN 0971-751X. Retrieved 30 October 2020.
  19. ^ Bhagat, Shalini Venugopal (23 May 2021). "As India Stumbles, One State Charts Its Own Covid Course". The New York Times. ISSN 0362-4331. Retrieved 28 May 2021.
  20. ^ "Pinarayi pushes for double masking; more curbs planned in Kerala". The Indian Express. 1 May 2021. Retrieved 28 May 2021.
  21. ^ Koshy, Jacob (12 August 2020). "Coronavirus | CSIR moots 'mega labs' to boost COVID-19 testing". The Hindu. ISSN 0971-751X. Retrieved 14 August 2021.
  22. ^ Radhakrishnan, Chandni; Divakar, Mohit Kumar; Jain, Abhinav; Viswanathan, Prasanth; Bhoyar, Rahul C.; Jolly, Bani; Imran, Mohamed; Sharma, Disha; Rophina, Mercy; Ranjan, Gyan; Sehgal, Paras (2021). "Initial Insights Into the Genetic Epidemiology of SARS-CoV-2 Isolates From Kerala Suggest Local Spread From Limited Introductions". Frontiers in Genetics. 12: 630542. doi:10.3389/fgene.2021.630542. ISSN 1664-8021. PMC 8010186. PMID 33815467.
  23. ^ Rani, Pallavali Roja; Imran, Mohamed; Lakshmi, J. Vijaya; Jolly, Bani; Afsar, S.; Jain, Abhinav; Divakar, Mohit Kumar; Suresh, Panyam; Sharma, Disha; Rajesh, Nambi; Bhoyar, Rahul C. (3 August 2021). "Insights from genomes and genetic epidemiology of SARS-CoV-2 isolates from the state of Andhra Pradesh". Epidemiology & Infection. 149: e181. doi:10.1017/S0950268821001424. ISSN 0950-2688. PMC 8367868.
  24. ^ "Maharashtra approaches IGIB to perform genome sequencing of coronavirus samples". The Indian Express. 3 May 2021. Retrieved 14 August 2021.
  25. ^ Gupta, Vivek; Bhoyar, Rahul C.; Jain, Abhinav; Srivastava, Saurabh; Upadhayay, Rashmi; Imran, Mohamed; Jolly, Bani; Divakar, Mohit Kumar; Sharma, Disha; Sehgal, Paras; Ranjan, Gyan (2020). "Asymptomatic Reinfection in 2 Healthcare Workers From India With Genetically Distinct Severe Acute Respiratory Syndrome Coronavirus 2". Clinical Infectious Diseases. 73 (9): e2823–e2825. doi:10.1093/cid/ciaa1451. PMC 7543380. PMID 32964927.
  26. ^ Banu, Sofia; Jolly, Bani; Mukherjee, Payel; Singh, Priya; Khan, Shagufta; Zaveri, Lamuk; Shambhavi, Sakshi; Gaur, Namami; Reddy, Shashikala; Kaveri, K.; Srinivasan, Sivasubramanian (2020). "A distinct phylogenetic cluster of Indian SARS-CoV-2 isolates". Open Forum Infectious Diseases. 7 (11): ofaa434. doi:10.1093/ofid/ofaa434. PMC 7543508. PMID 33200080.
  27. ^ "Indian Covid-19 mutation 'N440k' found in one-third of Andhra Pradesh's coronavirus genomes". Deccan Herald. 27 December 2020. Retrieved 28 December 2020.
  28. ^ Jolly, Bani; Rophina, Mercy; Shamnath, Afra; Imran, Mohammed; Bhoyar, Rahul C.; Divakar, Mohit Kumar; Rani, Pallavi Roja; Ranjan, Gyan; Sehgal, Paras; Chandrasekhar, Pulala; Afsar, S. (26 December 2020). "Genetic epidemiology of variants associated with immune escape from global SARS-CoV-2 genomes". bioRxiv: 2020.12.24.424332. doi:10.1101/2020.12.24.424332. S2CID 229935726.
  29. ^ J, Beena Philomina; Jolly, Bani; John, Neethu; Bhoyar, Rahul C.; Majeed, Nisha; Senthivel, Vigneshwar; P, Fairoz C.; Rophina, Mercy; Vasudevan, Bindhu; Imran, Mohamed; Viswanathan, Prasanth (24 May 2021). "Genomic survey of SARS-CoV-2 vaccine breakthrough infections in healthcare workers from Kerala, India". Journal of Infection. 83 (2): 237–279. doi:10.1016/j.jinf.2021.05.018. ISSN 0163-4453. PMC 8143909. PMID 34044037.
  30. ^ "CSIR Technologies for COVID-19 Mitigation" (PDF). Council of Scientific and Industrial Research. 14 August 2021.
  31. ^ "COVIDsure Multiplex Realtime RT-PCR Kit | qualitative RT-PCR assay for COVID-19". www.trivitron.com. Retrieved 14 August 2021.
  32. ^ Rajalakshmi, Niranjana (28 October 2020). "Explained: How Does India's Feluda COVID-19 Test Work?". The Wire Science. Retrieved 30 October 2020.
  33. ^ "INSACOG | Department of Biotechnology". Government of India Ministry of Science & Technology. Retrieved 28 September 2021.
  34. ^ "Genomics for Understanding Rare Diseases India Alliance Network (GUaRDIAN)". Archived from the original on 16 May 2021. Retrieved 17 September 2015.
  35. ^ Sivasubbu S, Scaria V, et al. (GUaRDIAN Consortium) (September 2019). "Genomics of rare genetic diseases-experiences from India". Human Genomics. 14 (1): 52. doi:10.1186/s40246-019-0215-5. PMC 6760067. PMID 31554517.
  36. ^ Scaria V, Sivasubbu S (2015). Exome Sequence Analysis and Interpretation - Handbook for Clinicians (First ed.). The Readers Paradise. ISBN 978-93-82110-58-3.
  37. ^ Gupta A, Sharma YK, Vellarikkal SK, Jayarajan R, Dixit V, Verma A, et al. (April 2016). "Whole-exome sequencing solves diagnostic dilemma in a rare case of sporadic acrokeratosis verruciformis". Journal of the European Academy of Dermatology and Venereology. 30 (4): 695–7. doi:10.1111/jdv.12983. PMID 25622760. S2CID 35181817.
  38. ^ Gupta A, Sharma Y, Deo K, Vellarikkal S, Jayarajan R, Dixit V, et al. (2015). "Case Report: Whole exome sequencing helps in accurate molecular diagnosis in siblings with a rare co-occurrence of paternally inherited 22q12 duplication and autosomal recessive non-syndromic ichthyosis". F1000Research. 4: 446. doi:10.12688/f1000research.6779.1. PMC 4648218. PMID 26594337.
  39. ^ Vellarikkal SK, Patowary A, Singh M, Kumari R, Faruq M, Master DC, et al. (2014). "Exome sequencing reveals a novel mutation, p.L325H, in the KRT5 gene associated with autosomal dominant Epidermolysis Bullosa Simplex Koebner type in a large family from western India". Human Genome Variation. 1 (1): 14007. doi:10.1038/hgv.2014.7. PMC 4785511. PMID 27081501.
  40. ^ Patient Referral Page Genomics for Understanding Rare Diseases India Alliance Network (GUaRDIAN)
  41. ^ "Genomics for Public Health". sites.google.com. Retrieved 3 September 2019.
  42. ^ Jain, Abhinav; Bhoyar, Rahul C.; Pandhare, Kavita; Mishra, Anushree; Sharma, Disha; Imran, Mohamed; Senthivel, Vigneshwar; Divakar, Mohit Kumar; Rophina, Mercy; Jolly, Bani; Batra, Arushi (2020). "IndiGenomes: a comprehensive resource of genetic variants from over 1000 Indian genomes". Nucleic Acids Research. 49 (D1): D1225–D1232. doi:10.1093/nar/gkaa923. PMC 7778947. PMID 33095885.
  43. ^ HGM-2008 website Archived 2 October 2016 at the Wayback Machine.
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