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.
Genomics of Rare Genetic Diseases
Genomics for Understanding Rare Diseases India Alliance Network (GUaRDIAN) is a consortium of over 280 clinicians and researchers from over 60 medical and research centers making it one of the largest clinical genomics research networks in India
Omics for Precise Therapeutic Interventions Minimising Adverse Events (OPTIMA) is a research collaboration aimed at pioneering Precision Medicine in India through enabling genomic understanding of sub-optimal therapeutic response
Genetic Epidemiology & Population Genomes
IndiGen programme aims to undertake whole genome sequencing of thousands of individuals representing diverse ethnic groups from India. The objective is to enable genetic epidemiology and develop public health technologies applications using population genome data
A number of diseases are quite prevalent in the Arab world which spans Middle East and North Africa. A large part of this is attributed to the widespread practice and norm of consanguinity in the region. Understanding the genetic characteristics of many such diseases would provide the much necessary knowledge to build an effective healthcare system where early screening, early diagnosis and effective management can significantly reduce the morbidity and mortality due to such diseases.
It is estimated that there are between 370 and 500 million Indigenous Peoples worldwide, in over 90 countries. While the indigenous peoples account for about 5% of the global population, encompass a significant and uncovered human genetic diversity. A number of disease genes and traits in these populations also suggest a founder effect, with significant impact on the precision health of the people. Genomic studies in indigenous populations could significantly augment our understanding of genetic diseases and traits and contribute to the well-being of the populations through targeted and accessible genetic diagnosis and precision medicine.
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
A unique partnership between the Department of Health & Family Welfare, Government of Kerala, National health Mission Kerala, CSIR Institute of Genomics & Integrative Biology (CSIR-IGIB) and various clinical and public health centers in Kerala aimed at providing insights into the genetic epidemiology of COVID-19 in Kerala.
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.
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.
Shankar AJ, Jadhao S, Hoy W, McMorran B, Fotte S, Patel H, Scaria V, Nagaraj SH, Pharmacogenomic analysis of a genetically distinct Indigenous populationThe Pharmacogenomics Journal (Accepted 2021)
Rophina M, Pandhare K, Shamnath A, Imran M, Jolly B and Scaria VESC - a comprehensive resource for SARS-CoV-2 immune escape variants. Nucleic Acids Research (2021) Accepted
Gupta A; Bhoyar RC; Mirza S; Jolly B; Senthivel V; Shamnath A; Divakar MK; Imran M; Gupta V; Agrawal SJ; Mukhida S; Sivasubbu S; Scaria VSARS-CoV-2 vaccine breakthrough infection following a previous infection in a healthcare workerJournal of Infection (2021) Accepted
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
Roja Rani P, Imran M, Vijaya Lakshmi J, Jolly B, Afsar S, Jain A, Divakar MK, Suresh P, Sharma D, Rajesh N, Bhoyar RC, Ankaiah D, Shanthi Kumari S, Ranjan G, Anitha Lavanya V, Rophina M, Umadevi S, Sehgal P, Renuka Devi A, Surekha A, Chandra Sekhar P, Hymavathy R, Vanaja PR, Scaria V, Sivasubbu S. Insights from Genomes and Genetic Epidemiology of SARS-CoV-2 isolates from the state of Andhra Pradesh. Epidemiology and Infection. 2021;:1–11.
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)
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
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]
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