Large-Scale Whole-Genome Sequencing of Three Diverse Asian Populations in Singapore

Wu, Degang; Dou, Jun; Chai, Xiaoran; Bellis, Claire; Wilm, Andreas; Shih, Chih Chuan; Soon, Wendy Wei Jia; Bertin, Nicolas; Lin, Clarabelle Bitong; Khor, Chiea Chuen; DeGiorgio, Michael; Cheng, Shanshan; Bao, Li; Karnani, Neerja; Hwang, William Ying Khee; Dávila, Sonia; Tan, Patrick; Shabbir, Asim; Moh, Angela; Tan, Eng‐King; Foo, Jia Nee; Goh, Liuh Ling; Leong, Khai Pang; Foo, Roger; Lam, Carolyn S.P.; Richards, A. Mark; Cheng, Ching-Yu; Aung, Tin; Wong, Tien Yin; Ng, Huck Hui; Li, Jianjun; Wang, Chaolong

doi:10.1016/j.cell.2019.09.019

Cited by 142 publications

(137 citation statements)

References 101 publications

Supporting

Mentioning

123

Contrasting

Order By: Relevance

“…In the period from 1 million years ago to ~ 6 thousand years ago (kya), the Han Chinese size histories of four regions experienced almost identical dynamics. From 200 kya to ~10 kya, the effective population size experienced a steep decline and then grew rapidly, with the lowest point reached at ~60 kya, which was indicative of a bottleneck, consistent with previous demographic history studies 11,25,29 . Around 6 kya, the size histories of the Han Chinese from the Lingnan began to deviate from the other three regions, potentially re ecting the existence of a population substructure within the Lingnan Han Chinese (Fig.3d).…”

Section: Populationsupporting

confidence: 88%

“…The sex estimation and con rmation were analyzed by the ratio of sequencing depths aligned to the X chromosome and autosomes 11 . The inferred sex was consistent with the self-reported sex for each sample.…”

Section: Sample Ltrationsmentioning

confidence: 99%

“…Recently, some studies have sequenced and analyzed the Asian populations including Japanese 9 and Korean 10 . The Singapore SG10K pilot project reported 4,810 whole-genome sequenced samples, including 903 Malays, 1,127 Indians and 2,780 Chinese 11 , and the pilot study of the GenomeAsia 100K…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Genomic analyses of 10,376 individuals provides comprehensive map of genetic variations, structure and reference haplotypes for Chinese population

Zheng

Cong

Bai

et al. 2021

Preprint

View full text Add to dashboard Cite

Here, we initiated the Westlake BioBank for Chinese (WBBC) pilot project with 4,535 whole-genome sequencing individuals and 5,481 high-density genotyping individuals. We identified 80.99 million SNPs and INDELs, of which 38.6% are novel. The genetic evidence of Chinese population structure supported the corresponding geographical boundaries of the Qinling-Huaihe Line and Nanling Mountains. The genetic architecture within North Han was more homogeneous than South Han, and the history of effective population size of Lingnan began to deviate from the other three regions from 6 thousand years ago. In addition, we identified a novel locus (SNX29) under selection pressure and confirmed several loci associated with alcohol metabolism and histocompatibility systems. We observed significant selection of genes on epidermal cell differentiation and skin development only in southern Chinese. Finally, the WBBC haplotype panel, which is a population-specific reference panel, yielded substantial improvement of imputation performance in Chinese population for low-frequency and rare variants compared to 1KG Project, and merging EAS individuals to increase the haplotype size of WBBC could improve the performance across all MAF bins. We provided an online imputation server (https://wbbc.westlake.edu.cn/) which could result in higher imputation accuracy compared to the existing panels, especially for lower frequency variants.

show abstract

Section: Populationsupporting

confidence: 88%

Section: Sample Ltrationsmentioning

confidence: 99%

See 1 more Smart Citation

Genomic analyses of 10,376 individuals provides comprehensive map of genetic variations, structure and reference haplotypes for Chinese population

Zheng

Cong

Bai

et al. 2021

Preprint

View full text Add to dashboard Cite

show abstract

“…SNPs (Huang et al, 2009;Wu et al, 2019), a total of 5,679 individuals were included and 2,600 SNPs were masked for the next evaluation.…”

Section: Reference Panel Evaluation For Imputation In the Chinese Popmentioning

confidence: 99%

Genomic analyses of 10,376 individuals provides comprehensive map of genetic variations, structure and reference haplotypes for Chinese population

Cong

Bai

et al. 2021

Preprint

View full text Add to dashboard Cite

Here, we initiated the Westlake BioBank for Chinese (WBBC) pilot project with 4,535 whole-genome sequencing individuals and 5,481 high-density genotyping individuals. We identified 80.99 million SNPs and INDELs, of which 38.6% are novel. The genetic evidence of Chinese population structure supported the corresponding geographical boundaries of the Qinling-Huaihe Line and Nanling Mountains. The genetic architecture within North Han was more homogeneous than South Han, and the history of effective population size of Lingnan began to deviate from the other three regions from 6 thousand years ago. In addition, we identified a novel locus (SNX29) under selection pressure and confirmed several loci associated with alcohol metabolism and histocompatibility systems. We observed significant selection of genes on epidermal cell differentiation and skin development only in southern Chinese. Finally, we provided an online imputation server (https://wbbc.westlake.edu.cn/) which could result in higher imputation accuracy compared to the existing panels, especially for lower frequency variants.

show abstract

“…Following the successful initiative of the 1000 genomes project [1], several large-scale genome 44 and exome sequencing projects have been conducted, either as international collaboration 45 efforts such as ExACT [2], gnomAD [3], or for a specific country or population [4][5][6][7][8]. Those 46 projects have provided comprehensive profiles of human genetic variation in some populations, 47 paving the way for unprecedented advance in treatment of common genetic diseases.…”

mentioning

confidence: 99%

Genetic profiling of Vietnamese population from large-scale genomic analysis of non-invasive prenatal testing data

Tran

Nguyen

et al. 2019

Preprint

View full text Add to dashboard Cite

24The under-representation of several ethnic groups in existing genetic databases and studies 25 have undermined our understanding of the genetic variations and associated traits or diseases 26 in many populations. Cost and technology limitations remain the challenges in performing large-27 scale genome sequencing projects in many developing countries, including Vietnam. As one of 28 the most rapidly adopted genetic tests, non-invasive prenatal testing (NIPT) data offers an 29 alternative untapped resource for genetic studies. Here we performed a large-scale genomic 30 analysis of 2,683 pregnant Vietnamese women using their NIPT data and identified a 31 comprehensive set of 8,054,515 single-nucleotide polymorphisms, among which 8.2% were 32 new to the Vietnamese population. Our study also revealed 24,487 disease-associated genetic 33 variants and their allele frequency distribution, especially 5 pathogenic variants for prevalent 34 genetic disorders in Vietnam. We also observed major discrepancies in the allele frequency 35 distribution of disease-associated genetic variants between the Vietnamese and other 36 populations, thus highlighting a need for genome-wide association studies dedicated to the 37 Vietnamese population. The resulted database of Vietnamese genetic variants, their allele 38 frequency distribution, and their associated diseases presents a valuable resource for future 39 genetic studies. 40

show abstract

Large-Scale Whole-Genome Sequencing of Three Diverse Asian Populations in Singapore

Cited by 142 publications

References 101 publications

Genomic analyses of 10,376 individuals provides comprehensive map of genetic variations, structure and reference haplotypes for Chinese population

Genomic analyses of 10,376 individuals provides comprehensive map of genetic variations, structure and reference haplotypes for Chinese population

Genomic analyses of 10,376 individuals provides comprehensive map of genetic variations, structure and reference haplotypes for Chinese population

Genetic profiling of Vietnamese population from large-scale genomic analysis of non-invasive prenatal testing data

Contact Info

Product

Resources

About