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. 2019 Mar;26(3):225-234.
doi: 10.1089/cmb.2018.0199. Epub 2019 Jan 7.

INDEX-db: The Indian Exome Reference Database (Phase I)

Husayn Ahmed P  1   2 , Vidhya V  3 , Ravi Prabhakar More  1 , Biju Viswanath  4 , Sanjeev Jain  4 , Mahendra S Rao  3 , Odity Mukherjee; ADBS Consortium
Collaborators, Affiliations

INDEX-db: The Indian Exome Reference Database (Phase I)

Husayn Ahmed P et al. J Comput Biol. 2019 Mar.

Abstract

Deep sequencing-based genetic mapping has greatly enhanced the ability to catalog variants with plausible disease association. Confirming how these identified variants contribute to specific disease conditions, across human populations, poses the next challenge. Differential selection pressure may impact the frequency of genetic variations, and thus detection of association with disease conditions, across populations. To understand genotype to phenotype correlations, it thus becomes important to first understand the spectrum of genetic variation within a population by creating a reference map. In this study, we report the development of phase I of a new database of genetic variations called INDian EXome database (INDEX-db), from the Indian population, with an aim to establish a centralized database of integrated information. This could be useful for researchers involved in studying disease mechanisms at clinical, genetic, and cellular levels.

Keywords: Indian population; genetic variations catalogue; population-specific database; whole exome sequencing.

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Conflict of interest statement

The authors declare that no competing financial interests exist.

Figures

<b>FIG. 1.</b>
FIG. 1.
The workflow of development of phase I of INDEX-db. The steps involved in development of INDEX-db. The tools used in every step are mentioned in brackets.
<b>FIG. 2.</b>
FIG. 2.
INDEX-db web implementation. (A) A screenshot of the INDEX-db home page. (B) A screenshot of results of a gene query in the database. The result includes the list of variants in the gene, their frequency in the INDEX database, and other associated information. The link to visualize the gene and genetic variations in the genome browser is generated and provided in the query result page. (C) A screenshot of the INDEX genome browser, with tracks of SNPs, indels, CNVs, and LD blocks. CNV, copy number variation; LD, linkage disequilibrium; SNP, single-nucleotide polymorphism.
<b>FIG. 3.</b>
FIG. 3.
Variant profile. The distribution of coding and noncoding variants, the nonsynonymous-to-synonymous ratio, and the percentage coverage of sequencing at 20 × of 31 individuals cataloged in INDEX-db. The number of SNPs and CNVs detected in every individual. ncRNA, noncoding RNA; NS, nonsynonymous; S, synonymous; UTR, untranslated region.
<b>FIG. 4.</b>
FIG. 4.
INDEX-db genetic catalog. (A) Comparison of INDEX-db with other public databases. (B) The circos plot showing the copy number variation events cataloged in INDEX-db. Duplication and deletion events have been colored green and red, respectively. (C) Mean length of linkage disequilibrium blocks identified in autosomes.
See this image and copyright information in PMC

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