Abstract
South Asia possesses a significant amount of genetic diversity due to considerable intergroup differences in culture and language. There have been numerous reports on the genetic structure of Asian Indians, although these have mostly relied on genotyping microarrays or targeted sequencing of the mitochondria and Y chromosomes. Asian Indians in Singapore are primarily descendants of immigrants from Dravidian-language–speaking states in south India, and 38 individuals from the general population underwent deep whole-genome sequencing with a target coverage of 30X as part of the Singapore Sequencing Indian Project (SSIP). The genetic structure and diversity of these samples were compared against samples from the Singapore Sequencing Malay Project and populations in Phase 1 of the 1,000 Genomes Project (1 KGP). SSIP samples exhibited greater intra-population genetic diversity and possessed higher heterozygous-to-homozygous genotype ratio than other Asian populations. When compared against a panel of well-defined Asian Indians, the genetic makeup of the SSIP samples was closely related to South Indians. However, even though the SSIP samples clustered distinctly from the Europeans in the global population structure analysis with autosomal SNPs, eight samples were assigned to mitochondrial haplogroups that were predominantly present in Europeans and possessed higher European admixture than the remaining samples. An analysis of the relative relatedness between SSIP with two archaic hominins (Denisovan, Neanderthal) identified higher ancient admixture in East Asian populations than in SSIP. The data resource for these samples is publicly available and is expected to serve as a valuable complement to the South Asian samples in Phase 3 of 1 KGP.
Highlights
Next-generation sequencing (NGS) technologies have enabled an entire genome to be sequenced in a cost-effective manner [1], and this has allowed multiple individuals from a population to be surveyed in order to catalogue genetic variants that are present in the population
We have deep-sequenced 38 individuals of Indian descent residing in Singapore (SSIP) in an effort to illustrate their diversity from a whole-genome standpoint
Among variants discovered in Singapore Sequencing Indian Project (SSIP), 21.69% were novel with respect to previous sequencing projects
Summary
Next-generation sequencing (NGS) technologies have enabled an entire genome to be sequenced in a cost-effective manner [1], and this has allowed multiple individuals from a population to be surveyed in order to catalogue genetic variants that are present in the population. By adopting an unbiased approach to survey the whole genome, NGS presents a more comprehensive catalogue of different classes of genetic variants with a single assay: from changes that affect only a single base in the genome (single nucleotide polymorphisms, SNPs), to small-size additions and omissions (insertion-deletions, indels); and to larger contiguous changes in the genome that affect either the number of copies of a stretch of genome or differences in the genomic structure (structural variants, SVs). While the 1 KGP adopted the approach of sequencing multiple individuals at a lower sequence depth of 2-6X, a recently concluded project in Southeast Asia sequenced 100 Austronesian Malays
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