Genomics for Precision Medicine in Arab & Middle Eastern Populations
Precision Medicine is a new concept and an emerging model of healthcare where the genetic makeup and its interaction with the environment in incorporated towards enabling prevention, precise diagnosis and prognostication as well as precise treatment and management of a disease or condition.
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.
Collaborating on Genomics
We have been working over a decade with an extensive number of collaborators with interests spanning clinical genomics and basic sciences. Our relationships are built on mutual respect, trust and willingness to learn from each other and a common goal to advance genomics. This has impacted our research in a variety of ways, significantly improving our reach, outlook and applications. Our partners have also similarly been impacted through leveraging the support, knowledge base and network and see us as partners towards delivering world-class research and clinical services.
Why you should collaborate with us.
Our collaborators have access to a wide array of high-throughput genomics instrumentation to support their various needs, including genotyping and next generation sequencing.
Access and exposure to well-standardised data analysis pipelines customised to solve your needs and personalised to suit your specific requirements
Experience and knowledge base which has resulted in over 100 publications in peer reviewed journals, which comes a long way to showcase your research.
Proven track record in leveraging support to advance your science, through inputs, discussions which can enrich your scientific research, manuscripts as well as grant applications.
Disease Alleles in Arabs (DALIA) - a comprehensive resource of genetic variants associated with genetic diseases
The Arab world encompassing Middle East and North Africa is home to over 350 million people. This approximately represents over 5% of the world population and is characterized by significant ethnic, linguistic and genetic diversity, while encompassing similarities in language, traditions, cultural practices as well as geographic proximity. A number of diseases are quite prevalent in the Arab world. 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.
While a number of publications from this region have described genetic variants associated with diseases, many of these variants have not been adequately represented in global databases. The Disease Alleles in Arabs (dalia) is a unique venture to systematically characterize evidence from literature to build a comprehensive catalog of disease associated variants in the region.
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)
Genetic Landscape of Rare Autoinflammatory Disease Variants in Qatar and Middle Eastern Populations Through the Integration of Genomic Datasets
Rare monogenic autoinflammatory diseases are a group of recurrent inflammatory genetic disorders caused due to genetic variants in over 37 genes. While a number of these disorders have been identified and reported in Middle Eastern populations, the carrier frequency of these genetic variants in the Middle Eastern population is not known. The availability of whole-genome and exome datasets of over 1,000 individuals from Qatar persuaded us to explore the genetic epidemiology of rare autoinflammatory genetic variants. We have systematically analyzed genetic variants in genome-scale datasets from Qatar with a compendium of variants associated with autoinflammatory diseases. The variants were systematically reclassified according to the American College of Medical Genetics and Genomics guidelines for interpretation of variant pathogenicity. Our analysis identified seven pathogenic and likely pathogenic variants with significant differences in their allele frequencies compared to the global population. The cumulative carrier frequency of these variants was found to be 2.58%. Furthermore, our analysis revealed that five genes, implicated in rare autoinflammatory diseases, were under natural selection. To the best of our knowledge, this is the first and most comprehensive study on the population-scale analysis and genetic epidemiology of genetic variants that cause rare autoinflammatory disease in Middle Eastern populations.
Citation Sharma P, Jain A, Scaria VGenetic landscape of rare autoinflammatory disease variants in Qatar and Middle Eastern populations through the integration of genomic datasetsFront Genet . 2021 May 13;12:631340. doi: 10.3389/fgene.2021.631340.
Genetic epidemiology of Familial Mediterranean Fever through integrative analysis of whole genome and exome sequences from Middle East and North Africa
Familial Mediterranean fever (FMF), an autosomal recessive and rare autoinflammatory disease is caused by genetic mutations in the MEFV gene and is highly prevalent in the Mediterranean basin. Though the carrier frequency of specific disease variants in the MEFV gene has been reported from isolated studies, a comprehensive view of variants in the Mediterranean region has not been possible due to paucity of data. The recent availability of whole-genome and whole-exome datasets prompted us to study the genetic epidemiology of MEFV variants in the region. We assembled data from five datasets encompassing whole-genome and whole-exome datasets for 2115 individuals from multiple subpopulations in the region and also created a compendium for MEFV genetic variants, which were further systematically annotated as per the ACMG guidelines. Our analysis points to significant differences in allele frequencies in the subpopulations, and the carrier frequency for MEFV genetic variants in the population to be about 8%. The MEFV gene appears to be under natural selection from our analysis. To the best of our knowledge, this is the most comprehensive study and analysis of population epidemiology of MEFV gene variants in the Middle East and North African populations.
CitationKoshy R, Sivadas A, Scaria V.Genetic epidemiology of Familial Mediterranean Fever through integrative analysis of whole genome and exome sequences from Middle East and North AfricaClinical Genetics (2017) Accepted DOI: 10.1111/cge.13070
Genomic Education
2018
Workshop on Exome Sequence Analysis and Interpretation at the 7th International Genetic Disorders Conference, Dubai organized by UAE Genetic Diseases Association.
2022
Over 20 participants including clinicians and researchers were part of the Genomic Variant Analysis and Interpretation Course in 2022
Recent Publications
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) 16(1): e0244567. doi:10.1371/journal.pone.0244567
Sharma P, Jain A, Scaria VGenetic landscape of rare autoinflammatory disease variants in Qatar and Middle Eastern populations through the integration of genomic datasetsFront Genet . 2021 May 13;12:631340. doi: 10.3389/fgene.2021.631340.
Sivadas A, Scaria VPharmacogenomic survey of Qatari populations using whole genome and exome sequencesThe Pharmacogenomics Journal. (2018) Accepted
Jain, A, Gandhi S, Koshy R, Scaria V*Incidental and clinically actionable genetic variants in 1005 whole exomes and genomes from QatarMolecular Genetics and Genomics (2018) doi.org/10.1007/s0043
Jithesh PV, Scaria VFrom Genomes to Genomic Medicine- Enabling Personalised and Precision Medicine in the Middle EastPersonalized Medicine (2017) DOI: 10.2217/pme-2017-0048
Koshy R, Sivadas A, Scaria V.Genetic epidemiology of Familial Mediterranean Fever through integrative analysis of whole genome and exome sequences from Middle East and North AfricaClinical Genetics (2017) DOI: 10.1111/cge.13070
Koshy R, Ranawat A, Scaria V.al mena - a comprehensive resource of human genetic variants integrating genomes and exomes from Arab, Middle Eastern and North African populations.Journal of Human Genetics (2017) 62, 889–894; DOI:10.1038/jhg.2017.67
Scaria VEnabling Genomic Medicine in Qatar - from Genomes to Translational GenomicsResearch Reports, 1(1) Aug 28, 2017
Sandhya P, Vellarikkal SK, Nair A, Ravi R, Mathew J, Jayarajan R, Kumar A, Verma A, Sivadas A, Danda D, Sivasubbu S*, Scaria V*An Egyptian tale from India - application of whole-exome sequencing in diagnosis of atypical Familial Mediterranean FeverInt J Rheum Dis (2017) DOI: 10.1111/1756-185X.13042
Sivadas A, Sharma P, Scaria VLandscape of warfarin and clopidogrel pharmacogenetic variants in Qatari population from whole exome datasetsPharmacogenomics (2016) Accepted doi: 10.2217/pgs-2016-0130
New Resource:
A comprehensive characterization of blood group antigen variants in the Middle Eastern population genomes - Insights into genetic epidemiology
In communication (2023)