Genomics & Genome Informatics touching lives
We are a group of passionate researchers at the CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB) working towards using advanced Genomics and Data Analytics to understand biology and impact lives around us.
Pathogen Genomics
The recent declaration of COVID-19 as a global pandemic by the World Health Organisation has prompted us to venure into research in this area as well as make the relevant Data, Research and Resources at the Vinod Scaria Lab at CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB) in an open format to ensure that they are widely accessible as well as relevant. The programme would embrace the concepts of open-source and open access.
Learn more at Open COVID-19
COVID-19 and Research on Epidemic Preparedness
COVID-19 Data Open To All
It was as early as January 2020 when Vinod Scaria and his team at Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology (CSIR-IGIB) knew that the SARS-CoV-2 virus was weeks from hitting India. They had to understand the novel Coronavirus better and fast if diagnostics had to keep pace with the spread. But with the nationwide lockdown, their Delhi lab was shuttered. Of the team of 12, a handful were allowed to work from office. The rest had to manage from home with no infrastructure available to them.
Read more at https://www.mid-day.com/sunday-mid-day/article/covid-19-data-open-to-all-23153687
Genetic Epidemiology of Novel and Emerging Pathogens in India
GENEPI is a collaborative programme to use high-throughput genomics approaches to understand the genetic makeup and genetic epidemiology of novel and emerging pathogens in India.
GENEPI Resources for Pathogen Genomics
KAISER is a citizen science initiative relying on open science to be able to prepare, understand and respond to epidemics.
This initiative also endeavours to build the much required skill base, resources, data and technologies to be able to help and cater to similar requirements nationally and globally.
Recent Publications
Complete list of Publications are available here
Sehgal P, Mathew S, Sivadas A, Ray A, Tanwar J, Vishwakarma S, Ranjan G, Shamsudheen KV, Bhoyar RC, Pateria A, Leonard E, Lalwani M, Vats A, Pappuru RR, Tyagi M, Jakati S, Sengupta S, B K B, Chakrabarti S, Kaur I, Motiani RK, Scaria V, Sivasubbu S. LncRNA VEAL2 regulates PRKCB2 to modulate endothelial permeability in diabetic retinopathy. EMBO J. 2021 Jun 28:e107134. doi: 10.15252/embj.2020107134.
Mittal G, Anu RI, Vatsyayan A, Pandhare K, Scaria VMUSTARD - a comprehensive resource of Mutation Specific Therapies in Cancer Database (Oxford) 2021 Accepted
Sahana S, Sivadas A, Mangla M,et al, Pharmacogenomic landscape of COVID-19 therapies from Indian population genomes. Pharmacogenomics. 2021 Jun 18. doi: 10.2217/pgs-2021-0028. Epub ahead of print. PMID: 34142560.
Cotsapas C, Saarela J, Farmer JR, Scaria V, Abraham RS. Do monogenic inborn errors of immunity cause susceptibility to severe COVID-19? J Clin Invest. 2021 Jun 1:149459. doi: 10.1172/JCI149459 .
Sharma P, Jain A and Scaria V*Genetic landscape of rare autoinflammatory disease variants in Qatar and Middle Eastern populations through the integration of whole-genome and exome datasetsFront. Genet.(2021) Accepted
Ranjan G, Sehgal P, Sharma D, Scaria V, Sivasubbu SFunctional long non-coding and circular RNAs in zebrafishBriefings in Functional Genomics, elab014, https://doi.org/10.1093/bfgp/elab014
Jain, A, Sharma D, Bajaj, A, Gupta V, Scaria VFounder variants and population genomes—Toward precision medicineAdvances in Genetics (Academic Press) (2021) Accepted
Vatsyayan V, 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 VDALIA- a comprehensive resource of Disease Alleles in Arab populationPLoS ONE (2021)
Jain A, Bhoyar RC,Pandhare K, Mishra A, Sharma D,Imran M, Senthivel V,Divakar1 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, Senthil Kumar N, Vanlallawma A, Sarma RJ, Chhakchhuak L, Kalyanaraman S,Mahadevan R, Kandasamy S, Pabitha BM, Rajagopal RE, Ramya E, Nirmala Devi P, Bajaj A, Gupta V, Mathew S,Goswami SG, Mangla M, Prakash S, Joshi K, Meyakumla, Sreedevi S, Gajjar D, Ronibala Soraisham, Yadav R, Silla Devi Y, Gupta A, Mukerji M, Ramalingam S, Binukumar BK, Scaria V,Sivasubbu SIndiGenomes: a comprehensive resource of genetic variants from over 1000 Indian genomesNucleic Acids Research (2020) doi: 10.1093/nar/gkaa923
Mahadevan R, Bhoyar RC, Viswanathan N, Rajagopal RE, Essaki B, Suroliya V, Chelladurai R, Sankaralingam S, Shanmugam G, Vayanakkan S, Shamim U, Mathur A, Jain A, Imran M, Faruq M, Scaria V, Sivasubbu S, Kalyanaraman SGenomic analysis of patients in a South Indian Community with autosomal dominant cortical tremor, myoclonus and epilepsy suggests a founder repeat expansion mutation in the SAMD12 geneBrain Communications (2021) fcaa214, https://doi.org/10.1093/braincomms/fcaa214
Jalali S, Singh A, Scaria V and Maiti SGenome-wide computational analysis and validation of potential long noncoding RNA mediated DNA-DNA:RNA triplexes in the human genomeMethods in Molecular Biology (2021) 2254:61-71. doi: 10.1007/978-1-0716-1158-6_5.
Jain A, Rophina M, Mahajan S, Krishnan BB, Sharma M, Mandal S, Fernandez T, Sultanji S, Mathew S, Sivasubbu S, Scaria V Analysis of the potential impact of genomic variants in global SARS-CoV-2 genomes on molecular diagnostic assays International Journal of Infectious Diseases (2021) https://doi.org/10.1016/j.ijid.2020.10.086 [COVID-19]
The Wire 23/06/2020
Recent Preprints on COVID-19 Research
Rophina, M., Pandhare, K., Mangla, M., Shamnath, A., Jolly, B., Sethi, M., & Scaria, V. FaviCoV -a comprehensive manually curated resource for functional genetic variants in SARS-CoV-2.OSF Preprints (2020, November 17). https://doi.org/10.31219/osf.io/wp5tx [Preprint]
Jolly B, Rophina M, Shamnath A, Imran M, Bhoyar RC, Divakar M, Rani PR, Ranjan G, Sehgal P, Chandrasekhar P, Afsar S, Vijaya Lakshmi J, Surekha A, Sivasubbu S, Scaria VGenetic epidemiology of variants associated with immune escape from global SARS-CoV-2 genomesbioRxiv 2020.12.24.424332; doi: https://doi.org/10.1101/2020.12.24.424332 [Preprint]
Rophina M, Pandhare K, Shamnath A, et al. ESC - a comprehensive resource for SARS-CoV-2 immune escape variants. bioRxiv; 2021. DOI: 10.1101/2021.02.18.431922.
Bhoyar, Rahul C., et al. An Amplicon-based Approach for Sequencing of Sars-cov-2 Using Covidseq Assay on Illumina Miseq Sequencing Platforms.OSF Preprints, 10 May 2021. Web.
Singh, U. B., Rophina, M., Chaudhry, R., Senthivel, V., Bala, K., Bhoyar, R. C.et alGenomic analysis of symptomatic SARS-CoV-2 vaccine breakthrough infections from a tertiary care centre in India. OSF Preprints (2021) https://doi.org/10.31219/osf.io/fgd4x
Complete list of COVID-19 Publications are available at Publications page
Research in News
OPEN MINDS 2020: MIND OVER MATTER
COVID-19 Response: Young Scientists Are Among India’s Unsung Heroes
Genome sequencing by CSIR to help in Precision Medicine in India
Genome sequencing to map population diversity
5-year-old ‘butterfly’ boy at PGI for treatment
Interpretation of a malady: how scientists zeroed in on one family's rare and crippling disease
