Publications

Sivadas A, Sharma P, Scaria V
Landscape of warfarin and clopidogrel pharmacogenetic variants in Qatari population from whole exome datasets
Pharmacogenomics (2016) Accepted

Sivadas A, Salleh MZ, Teh LK, Scaria V*
Genetic epidemiology of pharmacogenetic variants in South East Asian Malays using whole genome sequences
The Pharmacogenomics Journal (2016) Accepted

Giri AK, Khan NM, Grover S, Kaur I, Basu A, Tandon N, Scaria V, Consortium IGI, INDICO*, Kukreti R, Brahmachari SK, Bharadwaj D
Genetic epidemiology of pharmacogenetic variations in CYP2C9, CYP4F2 and VKORC1 genes associated with Warfarin dosage in Indian population
Current Genetic Medicine Reports (2014) Accepted

Giri AK, Khan NM, Narayanan D, INDICO, Basu A, Tandon N, Scaria V*, Bharadwaj D*
Pharmacogenetic landscape of Clopidogrel in North Indians suggest distinct inter-population differences in allele frequencies
Pharmacogenomics (2014) Accepted

Salleh MZ*, Teh LK, Lee LS, Ismet RI, Patowary A, Joshi K, Pasha A, Ahmed AZ, Janor MH, Hamzah AS, Adam I, Yusoff K, Hoh BP, Hatta FM, Ismail MI, Scaria V*, Sivasubbu S*
Systematic Pharmacogenomics analysis of a Malay whole genome : Proof of concept for Personalised Medicine.
PLoS ONE (2013) Aug 23;8(8):e71554.

Pasha A and Scaria V
Pharmacogenomics in the era of personal genomics: a quick guide to online resources and tools
Omics for Personalised Medicine [Edited by Barh D, Dhawan D, and Ganguly NK] Springer 2013

Patowary A,Purkanti R, Singh M, Chauhan RK, Bhartiya D, Dwivedi OP, Chauhan G, Bharadwaj D, Sivasubbu S,Scaria V
Systematic analysis and functional annotation of variations in the genome of an Indian individual
Hum. Mutat., 33: 1133–1140.

Kandoi G, Nanda, A, Scaria V*, Sivasubbu S*
A case of pharmacogenomics in management of cardiac arrhythmias
Indian Pacing and Electrophysiology J (2012) 2012;12(2):54-64

Landscape of warfarin and clopidogrel pharmacogenetic variants in Qatari population from whole exome datasets

posted Apr 23, 2017, 2:44 AM by Vinod Scaria


Pharmacogenetic landscapes of commonly used antiplatelet drugs, warfarin and clopidogrel have been studied in-depth in many countries. However, there is a paucity of data to understand their patterns in the Arab populations.We analyzed the whole exome sequencing datasets of 100 Qatar individuals available in public domain with this perspective. Results: We characterized the allelic distribution of variants routinely tested for warfarin and clopidogrel. We additionally evaluated the population stratification and its effect on allele frequency distribution. Our analysis points to ethnic differences in the frequency distribution even for the small population studied.This is one of the first and most comprehensive pharmacogenetic maps of variants associated with warfarin and clopidogrel for an Arab population, which can help tailor the drug dosage to the population.

Sivadas A, Sharma P, Scaria V
Landscape of warfarin and clopidogrel pharmacogenetic variants in Qatari population from whole exome datasets
Pharmacogenomics (2016) Accepted
DOI: 10.2217/pgs-2016-0130

Genetic epidemiology of pharmacogenetic variants in South East Asian Malays using whole genome sequences

posted Sep 30, 2016, 8:23 AM by Vinod Scaria   [ updated Oct 4, 2016, 5:26 AM ]


Expanding the scope of pharmacogenomic research by including multiple global populations is integral to building robust evidence for its clinical translation. Deep whole-genome sequencing of diverse ethnic populations provides a unique opportunity to study rare and common pharmacogenomic markers that often vary in frequency across populations. In this study, we aim to build a diverse map of pharmacogenetic variants in South East Asian (SEA) Malay population using deep whole-genome sequences of 100 healthy SEA Malay individuals. We investigated the allelic diversity of potentially deleterious pharmacogenomic variants in SEA Malay population. Our analysis revealed 227 common and 466 rare potentially functional single nucleotide variants (SNVs) in 437 pharmacogenomic genes involved in drug metabolism, transport and target genes, including 74 novel variants. This study has created one of the most comprehensive maps of pharmacogenetic markers in any population from whole genomes and will hugely benefit pharmacogenomic investigations and drug dosage recommendations in SEA Malays.

Sivadas A, Salleh MZ, Teh LK, Scaria V*
Genetic epidemiology of pharmacogenetic variants in South East Asian Malays using whole genome sequences
The Pharmacogenomics Journal (2016) doi:10.1038/tpj.2016.39

Pharmacogenomics for Precision Medicine in the era of collaborative co-creation and crowdsourcing

posted Sep 30, 2016, 8:05 AM by Vinod Scaria   [ updated Apr 22, 2017, 7:13 AM ]

The whole gamut of new technologies in the past decade has revolutionized DNA sequencing, making it cheaper, efficient, and scalable. The consequent big-data in genomics have posed new challenges and opportunities. The transformation of internet as a fabric that intertwines multiple technological and social layers and the rise of platforms that can organize and integrate massively parallel human activities have transformed the workplaces in many industries and offers a new opportunity in the area of genomics. In this short review, we discuss the state-of-the art of crowdsourcing in genomics research with special focus on pharmacogenomics. We discuss the field, starting with an overview of technology and the major challenges. We also discuss a number of ongoing crowdsourcing approaches in the area of pharmacogenomics and personal genomics. We conclude with deliberating on the issues in genomics and how crowdsourcing could offer a plausible alternative to conventional approaches in genomics.

Hasija Y, Khan JA, Scaria V*
Pharmacogenomics for Precision Medicine in the era of collaborative co-creation and crowdsourcing
Curr Genet Med Rep (2014) 2: 182. doi:10.1007/s40142-014-0041-y

Pharmacogenetic landscape of Clopidogrel in North Indians suggest distinct inter-population differences in allele frequencies

posted Sep 30, 2016, 8:03 AM by Vinod Scaria   [ updated Apr 22, 2017, 7:13 AM ]

Clopidogrel, a widely used antiplatelet drug, exhibits high interindividual variability; more than 80% of which could be explained by genetic polymorphisms. We built an allele frequency map of variants affecting clopidogrel response in north Indians. We mined a cross-sectional population-scale genome-wide dataset of 2128 Indo-Europeans residing in north India for presence of variants associated with pharmacogenetics of clopidogrel. Our analysis reveals significant differences in population-scale allele frequencies between Indians and the global population. Indians had a higher allele frequency for variants in the CYP2C9*2, CYP2C9*3 and P2RY1 genes whereas lower frequency for the ABCB1, CYP1A2, CYP2C19*2C, CYP3A5 and PON1 genes compared with the global population. Furthermore, from our study we proposed a model to explain the higher prevalence of clopidogrel metabolizers in north Indians. This is the largest population-scale genetic epidemiology study that provides a high-resolution map of variants associated with clopidogrel response that could be potentially valuable to clinicians to rationally plan appropriate dosage for therapy in resource poor conditions based on population level allele frequencies.


Giri AK, Khan NM, Narayanan D, INDICO, Basu A, Tandon N, Scaria V*, Bharadwaj D*
Pharmacogenetic landscape of Clopidogrel in North Indians suggest distinct inter-population differences in allele frequencies
Pharmacogenomics (2014) 15 (5). pp. 643-653.

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