IndiGenomes


35178516	*An Alu* insertion map of the Indian population: identification and analysis in 1021 genomes of the IndiGen project.** [PMID: 35178516] Prakrithi P, Singhal K, Sharma D, Jain A, Bhoyar RC, Imran M, Senthilvel V, Divakar MK, Mishra A, Scaria V, Sivasubbu S, Mukerji M. Abstract Actively retrotransposing primate-specific Alu repeats display insertion-deletion (InDel) polymorphism through their insertion at new loci. In the global datasets, Indian populations remain under-represented and so do their Alu InDels. Here, we report the genomic landscape of Alu InDels from the recently released 1021 Indian Genomes (IndiGen) (available at https://clingen.igib.res.in/indigen). We identified 9239 polymorphic Alu insertions that include private (3831), rare (3974) and common (1434) insertions with an average of 770 insertions per individual. We achieved an 89% PCR validation of the predicted genotypes in 94 samples tested. About 60% of identified InDels are unique to IndiGen when compared to other global datasets; 23% of sites were shared with both SGDP and HGSVC; among these, 58% (1289 sites) were common polymorphisms in IndiGen. The insertions not only show a bias for genic regions, with a preference for introns but also for the associated genes showing enrichment for processes like cell morphogenesis and neurogenesis (P-value < 0.05). Approximately, 60% of InDels mapped to genes present in the OMIM database. Finally, we show that 558 InDels can serve as ancestry informative markers to segregate global populations. This study provides a valuable resource for baseline Alu InDels that would be useful in population genomics. NAR Genom Bioinform. 2022:4(1) \| 1 Citations (from Europe PMC, 2025-03-22)
33095885	IndiGenomes: a comprehensive resource of genetic variants from over 1000 Indian genomes. [PMID: 33095885] Jain A, Bhoyar RC, Pandhare K, Mishra A, Sharma D, Imran M, Senthivel V, Divakar MK, Rophina M, Jolly B, Batra A, Sharma S, Siwach S, Jadhao AG, Palande NV, Jha GN, Ashrafi N, Mishra PK, A K V, Jain S, Dash D, Kumar NS, Vanlallawma A, Sarma RJ, Chhakchhuak L, Kalyanaraman S, Mahadevan R, Kandasamy S, B M P, Rajagopal RE, J ER, P ND, Bajaj A, Gupta V, Mathew S, Goswami S, Mangla M, Prakash S, Joshi K, S S, Gajjar D, Soraisham R, Yadav R, Devi YS, Gupta A, Mukerji M, Ramalingam S, B K B, Scaria V, Sivasubbu S. Abstract With the advent of next-generation sequencing, large-scale initiatives for mining whole genomes and exomes have been employed to better understand global or population-level genetic architecture. India encompasses more than 17% of the world population with extensive genetic diversity, but is under-represented in the global sequencing datasets. This gave us the impetus to perform and analyze the whole genome sequencing of 1029 healthy Indian individuals under the pilot phase of the 'IndiGen' program. We generated a compendium of 55,898,122 single allelic genetic variants from geographically distinct Indian genomes and calculated the allele frequency, allele count, allele number, along with the number of heterozygous or homozygous individuals. In the present study, these variants were systematically annotated using publicly available population databases and can be accessed through a browsable online database named as 'IndiGenomes' http://clingen.igib.res.in/indigen/. The IndiGenomes database will help clinicians and researchers in exploring the genetic component underlying medical conditions. Till date, this is the most comprehensive genetic variant resource for the Indian population and is made freely available for academic utility. The resource has also been accessed extensively by the worldwide community since it's launch. Nucleic Acids Res. 2021:49(D1) \| 47 Citations (from Europe PMC, 2025-03-22)

An Alu insertion map of the Indian population: identification and analysis in 1021 genomes of the IndiGen project. [PMID: 35178516]

Prakrithi P, Singhal K, Sharma D, Jain A, Bhoyar RC, Imran M, Senthilvel V, Divakar MK, Mishra A, Scaria V, Sivasubbu S, Mukerji M.

Abstract

Actively retrotransposing primate-specific Alu repeats display insertion-deletion (InDel) polymorphism through their insertion at new loci. In the global datasets, Indian populations remain under-represented and so do their Alu InDels. Here, we report the genomic landscape of Alu InDels from the recently released 1021 Indian Genomes (IndiGen) (available at https://clingen.igib.res.in/indigen). We identified 9239 polymorphic Alu insertions that include private (3831), rare (3974) and common (1434) insertions with an average of 770 insertions per individual. We achieved an 89% PCR validation of the predicted genotypes in 94 samples tested. About 60% of identified InDels are unique to IndiGen when compared to other global datasets; 23% of sites were shared with both SGDP and HGSVC; among these, 58% (1289 sites) were common polymorphisms in IndiGen. The insertions not only show a bias for genic regions, with a preference for introns but also for the associated genes showing enrichment for processes like cell morphogenesis and neurogenesis (P-value < 0.05). Approximately, 60% of InDels mapped to genes present in the OMIM database. Finally, we show that 558 InDels can serve as ancestry informative markers to segregate global populations. This study provides a valuable resource for baseline Alu InDels that would be useful in population genomics.

NAR Genom Bioinform. 2022:4(1) | 1 Citations (from Europe PMC, 2025-03-22)

IndiGenomes: a comprehensive resource of genetic variants from over 1000 Indian genomes. [PMID: 33095885]

Jain A, Bhoyar RC, Pandhare K, Mishra A, Sharma D, Imran M, Senthivel V, Divakar MK, Rophina M, Jolly B, Batra A, Sharma S, Siwach S, Jadhao AG, Palande NV, Jha GN, Ashrafi N, Mishra PK, A K V, Jain S, Dash D, Kumar NS, Vanlallawma A, Sarma RJ, Chhakchhuak L, Kalyanaraman S, Mahadevan R, Kandasamy S, B M P, Rajagopal RE, J ER, P ND, Bajaj A, Gupta V, Mathew S, Goswami S, Mangla M, Prakash S, Joshi K, S S, Gajjar D, Soraisham R, Yadav R, Devi YS, Gupta A, Mukerji M, Ramalingam S, B K B, Scaria V, Sivasubbu S.

Abstract

With the advent of next-generation sequencing, large-scale initiatives for mining whole genomes and exomes have been employed to better understand global or population-level genetic architecture. India encompasses more than 17% of the world population with extensive genetic diversity, but is under-represented in the global sequencing datasets. This gave us the impetus to perform and analyze the whole genome sequencing of 1029 healthy Indian individuals under the pilot phase of the 'IndiGen' program. We generated a compendium of 55,898,122 single allelic genetic variants from geographically distinct Indian genomes and calculated the allele frequency, allele count, allele number, along with the number of heterozygous or homozygous individuals. In the present study, these variants were systematically annotated using publicly available population databases and can be accessed through a browsable online database named as 'IndiGenomes' http://clingen.igib.res.in/indigen/. The IndiGenomes database will help clinicians and researchers in exploring the genetic component underlying medical conditions. Till date, this is the most comprehensive genetic variant resource for the Indian population and is made freely available for academic utility. The resource has also been accessed extensively by the worldwide community since it's launch.

Nucleic Acids Res. 2021:49(D1) | 47 Citations (from Europe PMC, 2025-03-22)

URL:	https://clingen.igib.res.in/indigen
Full name:
Description:	The database contains information on variant allele frequency, allele number, allele count, number of heterozygous and homozygous individuals recorded in this study. This will help clinicians and researchers in querying variants for various medical applications and will enable them to differentiate the pathogenic variants from the benign ones in the context of Indian population.
Year founded:	2021
Last update:	2022
Version:	1.0
Accessibility:	Accessible
Country/Region:	India

Data type:	DNA
Data object:	Animal
Database category:	Genotype phenotype and variation
Major species:	Homo sapiens
Keywords:	whole genome sequencing

University/Institution:	CSIR-Institute of Genomics and Integrative Biology
Address:	Mathura Road
City:	New Delhi
Province/State:
Country/Region:	India
Contact name (PI/Team):	Sridhar Sivasubbu
Contact email (PI/Helpdesk):	sridhar@igib.in

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