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The diploid genome sequence of an Asian individual
Open accessAbstract
Here we present the first diploid genome sequence of an Asian individual. The genome was sequenced to 36-fold average coverage using massively parallel sequencing technology. We aligned the short reads onto the NCBI human reference genome to 99.97% coverage, and guided by the reference genome, we used uniquely mapped reads to assemble a high-quality consensus sequence for 92% of the Asian individual’s genome. We identified approximately 3 million single-nucleotide polymorphisms (SNPs) inside this region, of which 13.6% were not in the dbSNP database. Genotyping analysis showed that SNP identification had high accuracy and consistency, indicating the high sequence quality of this assembly. We also carried out heterozygote phasing and haplotype prediction against HapMap CHB and JPT haplotypes (Chinese and Japanese, respectively), sequence comparison with the two available individual genomes (J. D. Watson and J. C. Venter), and structural variation identification. These variations were considered for their potential biological impact. Our sequence data and analyses demonstrate the potential usefulness of next-generation sequencing technologies for personal genomics. The power of the latest massively parallel synthetic DNA sequencing technologies is demonstrated in two major collaborations that shed light on the nature of genomic variation with ethnicity. The first describes the genomic characterization of an individual from the Yoruba ethnic group of west Africa. The second reports a personal genome of a Han Chinese, the group comprising 30% of the world's population. These new resources can now be used in conjunction with the Venter, Watson and NIH reference sequences. A separate study looked at genetic ethnicity on the continental scale, based on data from 1,387 individuals from more than 30 European countries. Overall there was little genetic variation between countries, but the differences that do exist correspond closely to the geographic map. Statistical analysis of the genome data places 50% of the individuals within 310 km of their reported origin. As well as its relevance for testing genetic ancestry, this work has implications for evaluating genome-wide association studies that link genes with diseases.
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“In contrast, Illumina transcriptome or genome sequencing was mainly limited to organisms with reference genomes available [14,51-53].”
From De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweetpotato (Ipomoea batatas) (2010) · cites this paper as [14]
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“High coverage 11,12 permitted the identification of 2.2 million heterozygous single-nucleotide variants (SNVs) within the sequenced individual (Supplementary Figs. 5 and 6 and Supplementary Tables 7 and 8).”
From The yak genome and adaptation to life at high altitude (2012) · cites this paper as [12]
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“The newly developed high throughput sequencing technology, i.e. Next Generation Sequencing (NGS), including the Roche/454 Genome Sequencer FLX Instrument, the ABI SOLiD System, and the Illumina Genome Analyser, is a powerful and cost-efficient tool for advanced research in many areas, including re-sequencing, microRNA expression profiling, DNA methylation, especially de novo transcriptome”
From De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweetpotato (Ipomoea batatas) (2010) · cites this paper as [14]
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Self-citationPaired-End Mapping Reveals Extensive Structural Variation in the Human Genome
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“This compares well against previous single individual genotyping efforts, which have seen concordance values for an individual of 86.4% and 99.6% (Wang et al. 2008; Wheeler et al. 2008).”
ResultInfluentialUltrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849
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SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler
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“We also used SOAPdenovo2 to reassemble and update the previously assembled YH Asian Genome [12].”
MethodSelf-citation
Metadata
- Authors
- Wang, J., Wang, W., Li, R., Li, Y., Tian, G., Goodman, L., Fan, W., Zhang, J., Li, J., Zhang, J., Guo, Y., Feng, B., Li, H., Lu, Y., Fang, X., Liang, H., Du, Z., Li, D., Zhao, Y., Hu, Y., Yang, Z., Zheng, H., Hellmann, I., Inouye, M., Pool, J., Yi, X., Zhao, J., Duan, J., Zhou, Y., Qin, J., Ma, L., Li, G., Yang, Z., Zhang, G., Yang, B., Yu, C., Liang, F., Li, W., Li, S., Li, D., Ni, P., Ruan, J., Li, Q., Zhu, H., Liu, D., Lu, Z., Li, N., Guo, G., Zhang, J., Ye, J., Fang, L., Hao, Q., Chen, Q., Liang, Y., Su, Y., san, A., Ping, C., Yang, S., Chen, F., Li, L., Zhou, K., Zheng, H., Ren, Y., Yang, L., Gao, Y., Yang, G., Li, Z., Feng, X., Kristiansen, K., Wong, G. K.-S., Nielsen, R., Durbin, R., Bolund, L., Zhang, X., Li, S., Yang, H., & Wang, J.
- Affiliations
- BGI Group (China) (CN)
- University of California, Berkeley (US)
- Wellcome Sanger Institute (GB)
- University of Southern Denmark (DK)
- Corresponding author
- Wang, Jun
- Wang, Jian
- ORCID
- Wang, Jun
- Wang, Wei
- Li, Ruiqiang
- Li, Yingrui
- Tian, Geng
- Goodman, Laurie
- Fan, Wei
- Zhang, Junqing
- Li, Jun
- Guo, Yiran
- Li, Heng
- Lu, Yao
- Fang, Xiaodong
- Liang, Huiqing
- Du, Zhenglin
- Li, Dong
- Zhao, Yiqing
- Hu, Yujie
- Yang, Zhenzhen
- Zheng, Hancheng
- Hellmann, Ines
- Inouye, Michael
- Pool, John
- Yi, Xin
- Zhao, Jing
- Duan, Jinjie
- Qin, Junjie
- Ma, Lijia
- Li, Guoqing
- Zhang, Guojie
- Yang, Bin
- Yu, Chang
- Li, Wenjie
- Li, Shaochuan
- Li, Dawei
- Ruan, Jue
- Li, Qibin
- Zhu, Hongmei
- Liu, Dongyuan
- Lu, Zhike
- Li, Ning
- Guo, Guangwu
- Zhang, Jianguo
- Ye, Jia
- Fang, Lin
- Hao, Qin
- Chen, Quan
- Liang, Yu
- Yang, Shuang
- Chen, Fang
- Li, Li
- Zheng, Hongkun
- Ren, Yuanyuan
- Yang, Ling
- Gao, Yang
- Yang, Guohua
- Li, Zhuo
- Feng, Xiaoli
- Kristiansen, Karsten
- Wong, Gane Ka-Shu
- Nielsen, Rasmus
- Durbin, Richard
- Bolund, Lars
- Zhang, Xiuqing
- Li, Songgang
- Yang, Huanming
- Wang, Jian
- Venue
- Nature
- Published
- 2008-11
- Volume
- 456
- Issue
- 7218
- Pages
- 60-65
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC2716080
- OpenAlex
- W2001725958
- Cited by
- 924
- References
- 23
- Citations by year
- 2026: 1 · 2025: 5 · 2024: 8 · 2023: 11 · 2022: 8 · 2021: 13 · 2020: 39 · 2019: 20 · 2018: 18 · 2017: 26 · 2016: 38 · 2015: 38 · 2014: 63 · 2013: 92 · 2012: 105
- FWCI
- 60.27
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Nature (publishedVersion, cc-by-nc-sa)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (submittedVersion)
- University of Southern Denmark Research Portal (University of Southern Denmark) (submittedVersion)
- Funders
- Wellcome Trust (077192)
- National Natural Science Foundation of China (30890032, 90608010, 30221004, 90612019, 90403130, 30725008, 30392130)
- Chinese Academy of Sciences (GJHZ0701-6, KSCX2-YWN-023)
- Lundbeckfonden
- Shenzhen University
- Beijing Municipal Science and Technology Commission (D07030200740000)
- H. Lundbeck A/S
- National High-tech Research and Development Program
- National Key Research and Development Program of China (2007CB815705, 2007CB815703, 2007CB815701)
- National Human Genome Research Institute (R01HG003229)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Keywords
- single nucleotide polymorphisms, structural variants, personal genomics, genetic ancestry, Han Chinese, Yoruba, HapMap, genome assembly, genome-wide association study
- MeSH terms
- Alleles, Animals, Pan troglodytes, Diploidy, Haplotypes, Humans, Phenotype, Sensitivity and Specificity, Genome, Human, Consensus Sequence, Sequence Alignment, Genetic Predisposition to Disease, Internet, Polymorphism, Single Nucleotide, Genomics, Databases, Genetic, Asian People
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