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Deep whole-genome sequencing of 100 southeast Asian Malays.

Publication ,  Journal Article
Wong, L-P; Ong, RT-H; Poh, W-T; Liu, X; Chen, P; Li, R; Lam, KK-Y; Pillai, NE; Sim, K-S; Xu, H; Sim, N-L; Teo, S-M; Foo, J-N; Tan, LW-L ...
Published in: Am J Hum Genet
January 10, 2013

Whole-genome sequencing across multiple samples in a population provides an unprecedented opportunity for comprehensively characterizing the polymorphic variants in the population. Although the 1000 Genomes Project (1KGP) has offered brief insights into the value of population-level sequencing, the low coverage has compromised the ability to confidently detect rare and low-frequency variants. In addition, the composition of populations in the 1KGP is not complete, despite the fact that the study design has been extended to more than 2,500 samples from more than 20 population groups. The Malays are one of the Austronesian groups predominantly present in Southeast Asia and Oceania, and the Singapore Sequencing Malay Project (SSMP) aims to perform deep whole-genome sequencing of 100 healthy Malays. By sequencing at a minimum of 30× coverage, we have illustrated the higher sensitivity at detecting low-frequency and rare variants and the ability to investigate the presence of hotspots of functional mutations. Compared to the low-pass sequencing in the 1KGP, the deeper coverage allows more functional variants to be identified for each person. A comparison of the fidelity of genotype imputation of Malays indicated that a population-specific reference panel, such as the SSMP, outperforms a cosmopolitan panel with larger number of individuals for common SNPs. For lower-frequency (<5%) markers, a larger number of individuals might have to be whole-genome sequenced so that the accuracy currently afforded by the 1KGP can be achieved. The SSMP data are expected to be the benchmark for evaluating the value of deep population-level sequencing versus low-pass sequencing, especially in populations that are poorly represented in population-genetics studies.

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Published In

Am J Hum Genet

DOI

EISSN

1537-6605

Publication Date

January 10, 2013

Volume

92

Issue

1

Start / End Page

52 / 66

Location

United States

Related Subject Headings

  • Singapore
  • Population Groups
  • Polymorphism, Single Nucleotide
  • Malaysia
  • Humans
  • High-Throughput Nucleotide Sequencing
  • Genome, Human
  • Genetics, Population
  • Genetics & Heredity
  • Genetic Variation
 

Citation

APA
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ICMJE
MLA
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Wong, L.-P., Ong, R.-H., Poh, W.-T., Liu, X., Chen, P., Li, R., … Teo, Y.-Y. (2013). Deep whole-genome sequencing of 100 southeast Asian Malays. Am J Hum Genet, 92(1), 52–66. https://doi.org/10.1016/j.ajhg.2012.12.005
Wong, Lai-Ping, Rick Twee-Hee Ong, Wan-Ting Poh, Xuanyao Liu, Peng Chen, Ruoying Li, Kevin Koi-Yau Lam, et al. “Deep whole-genome sequencing of 100 southeast Asian Malays.Am J Hum Genet 92, no. 1 (January 10, 2013): 52–66. https://doi.org/10.1016/j.ajhg.2012.12.005.
Wong L-P, Ong RT-H, Poh W-T, Liu X, Chen P, Li R, et al. Deep whole-genome sequencing of 100 southeast Asian Malays. Am J Hum Genet. 2013 Jan 10;92(1):52–66.
Wong, Lai-Ping, et al. “Deep whole-genome sequencing of 100 southeast Asian Malays.Am J Hum Genet, vol. 92, no. 1, Jan. 2013, pp. 52–66. Pubmed, doi:10.1016/j.ajhg.2012.12.005.
Wong L-P, Ong RT-H, Poh W-T, Liu X, Chen P, Li R, Lam KK-Y, Pillai NE, Sim K-S, Xu H, Sim N-L, Teo S-M, Foo J-N, Tan LW-L, Lim Y, Koo S-H, Gan LS-H, Cheng C-Y, Wee S, Yap EP-H, Ng PC, Lim W-Y, Soong R, Wenk MR, Aung T, Wong T-Y, Khor C-C, Little P, Chia K-S, Teo Y-Y. Deep whole-genome sequencing of 100 southeast Asian Malays. Am J Hum Genet. 2013 Jan 10;92(1):52–66.
Journal cover image

Published In

Am J Hum Genet

DOI

EISSN

1537-6605

Publication Date

January 10, 2013

Volume

92

Issue

1

Start / End Page

52 / 66

Location

United States

Related Subject Headings

  • Singapore
  • Population Groups
  • Polymorphism, Single Nucleotide
  • Malaysia
  • Humans
  • High-Throughput Nucleotide Sequencing
  • Genome, Human
  • Genetics, Population
  • Genetics & Heredity
  • Genetic Variation