Author
Listed:
- Lai-Ping Wong
- Jason Kuan-Han Lai
- Woei-Yuh Saw
- Rick Twee-Hee Ong
- Anthony Youzhi Cheng
- Nisha Esakimuthu Pillai
- Xuanyao Liu
- Wenting Xu
- Peng Chen
- Jia-Nee Foo
- Linda Wei-Lin Tan
- Seok-Hwee Koo
- Richie Soong
- Markus Rene Wenk
- Wei-Yen Lim
- Chiea-Chuen Khor
- Peter Little
- Kee-Seng Chia
- Yik-Ying Teo
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.Author Summary: Indians of South Asia has long been a population of interest to a wide audience, due to its unique diversity. 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. Indeed, among Asians in our population panel, SSIP was most diverse, followed by the Malays in Singapore (SSMP). Their diversity is further observed in the population's chromosome Y haplogroup and mitochondria haplogroup profiles; individuals with European-dominant haplogroups had greater proportion of European admixture. Among variants (single nucleotide polymorphism and small insertions/deletions) discovered in SSIP, 21.69% were novel with respect to previous sequencing projects. In addition, some 14 loss-of-function variants (LOFs) were associated to cancer, Type II diabetes, and cholesterol levels. Finally, D statistic test with ancient hominids concurred that there was gene flow to East Asians compared to South Asians.
Suggested Citation
Lai-Ping Wong & Jason Kuan-Han Lai & Woei-Yuh Saw & Rick Twee-Hee Ong & Anthony Youzhi Cheng & Nisha Esakimuthu Pillai & Xuanyao Liu & Wenting Xu & Peng Chen & Jia-Nee Foo & Linda Wei-Lin Tan & Seok-H, 2014.
"Insights into the Genetic Structure and Diversity of 38 South Asian Indians from Deep Whole-Genome Sequencing,"
PLOS Genetics, Public Library of Science, vol. 10(5), pages 1-15, May.
Handle:
RePEc:plo:pgen00:1004377
DOI: 10.1371/journal.pgen.1004377
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References listed on IDEAS
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"Genetic history of an archaic hominin group from Denisova Cave in Siberia,"
Nature, Nature, vol. 468(7327), pages 1053-1060, December.
- Andreas Keller & Angela Graefen & Markus Ball & Mark Matzas & Valesca Boisguerin & Frank Maixner & Petra Leidinger & Christina Backes & Rabab Khairat & Michael Forster & Björn Stade & Andre Franke & J, 2012.
"New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing,"
Nature Communications, Nature, vol. 3(1), pages 1-9, January.
Full references (including those not matched with items on IDEAS)
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