An Alu insertion map of the Indian population: identification and analysis in 1021 genomes of the IndiGen project

Actively retrotransposing primate-specific Alu repeats display insertion-deletion (InDel) polymorphism through their insertion at new loci. In the global datasets, Indian populations remain underrepresented 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 (Pvalue < 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.

Automated summary

This study reports the genomic landscape of Alu InDels in Indian populations, revealing a high frequency of polymorphic Alu insertions that are preferentially located in genic regions and associated with cell morphogenesis and neurogenesis processes. Some insertions correspond to genes present in the OMIM database. Additionally, a subset of these insertions can be used as ancestry informative markers for segregating global populations.