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. 2018 Jan 1:2018:1-10.
doi: 10.1093/database/bay080.

SAGE: a comprehensive resource of genetic variants integrating South Asian whole genomes and exomes

Judith Mary Hariprakash  1 , Shamsudheen Karuthedath Vellarikkal  2 , Ankit Verma  2 , Anop Singh Ranawat  1 , Rijith Jayarajan  2 , Rowmika Ravi  2 , Anoop Kumar  2 , Vishal Dixit  2 , Ambily Sivadas  1 , Atul Kumar Kashyap  2 , Vigneshwar Senthivel  2 , Paras Sehgal  2 , Vijayalakshmi Mahadevan  3 , Vinod Scaria  1 , Sridhar Sivasubbu  2
Affiliations

SAGE: a comprehensive resource of genetic variants integrating South Asian whole genomes and exomes

Judith Mary Hariprakash et al. Database (Oxford). .

Abstract

South Asia is home to $\sim $20% of the world population and characterized by distinct ethnic, linguistic, cultural and genetic lineages. Only limited representative samples from the region have found its place in large population-scale international genome projects. The recent availability of genome scale data from multiple populations and datasets from South Asian countries in public domain motivated us to integrate the data into a comprehensive resource. In the present study, we have integrated a total of six datasets encompassing 1213 human exomes and genomes to create a compendium of 154 814 557 genetic variants and adding a total of 69 059 255 novel variants. The variants were systematically annotated using public resources and along with the allele frequencies are available as a browsable-online resource South Asian genomes and exomes. As a proof of principle application of the data and resource for genetic epidemiology, we have analyzed the pathogenic genetic variants causing retinitis pigmentosa. Our analysis reveals the genetic landscape of the disease and suggests subset of genetic variants to be highly prevalent in South Asia.

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Figures

Figure 1
Figure 1
Variant annotation. (a) Gene-based annotation: variant annotation revealing the position of the variants in the genomic region. (b) Functional consequences of the variant. (c) Filter-based annotation: clinical significance of variant based on ClinVar classification.
Figure 2
Figure 2
MDS analysis of SAGE: MDS analysis in three-dimensional model revealing the clustering of SAGs into a single cluster. Analysis of SAGE cluster reveals that the samples of SAGE group into a single unique cluster. SAGE cluster is far separated from other groups and as expected SSMP clustered with the other South East Asian cluster. AFR, African; AMR, American; EAS, East Asian; EUR, European; SAS, 1KGP South Asian.
Figure 3
Figure 3
Schematic representation of data integration, annotation and analysis pipeline.
Figure 4
Figure 4
Screenshot of SAGE summarizing the variant search page.
Figure 5
Figure 5
Screenshot of SAGE summarizing the results page.
Figure 6
Figure 6
MAF distribution of RP variants. AFR, African; AMR, American; EAS, East Asian; EUR, European; SAS, 1000K South Asian.
See this image and copyright information in PMC

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