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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]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
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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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MethodSelf-citationSequencing technologies and genome sequencing
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“Since then, several additional diploid human genomes have been sequenced with NGS utilizing a variety of related techniques to rapidly sequence genomes with varying degrees of coverage (Ley et al., 2008; Wang et al., 2008; Ahn et al., 2009; Kim et al., 2009; Yngvadottir et al., 2009; Metzker, 2010).”
BackgroundSelf-citationSHRiMP: Accurate Mapping of Short Color-space Reads
Rumble, S. M., Lacroute, P., Dalca, A. V., Fiume, M., Sidow, A., & Brudno, M. (2009) · PLoS Comput. Biol. · doi:10.1371/journal.pcbi.1000386 · Cited by 639
Applications of New Sequencing Technologies for Transcriptome Analysis
Morozova, O., Hirst, M., & Marra, M. A. (2009) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-082908-145957 · Cited by 590
McKernan, K. J., Peckham, H. E., Costa, G. L., McLaughlin, S. F., Fu, Y., Tsung, E. F., Clouser, C. R., Duncan, C., Ichikawa, J. K., Lee, C. C., et al. (2009) · Genome Research · doi:10.1101/gr.091868.109 · Cited by 535
“Due to the error correcting qualities of the color space reads, we only need to see each allele twice to call a variant in contrast to other methods that require 3 and 4 alleles (Bentley et al 2008; Wang et al 2008).”
BackgroundMethodResultInfluentialSelf-citationShen, Z., Xiao, Y., Kang, L., Ma, W., Shi, L., Zhang, L., Zhou, Z., Yang, J., Zhong, J., Yang, D., et al. (2020) · Clinical Infectious Diseases · doi:10.1093/cid/ciaa203 · Cited by 513
“gov/pub/ agarwala/bmtagger) [14], and ribosomal reads removal with SortMeRNA software (version 2.”
MethodSelf-citationComprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome
Peng, Z., Cheng, Y., Tan, B. C., Kang, L., Tian, Z., Zhu, Y., Zhang, W., Liang, Y., Hu, X., Tan, X., et al. (2012) · Nature Biotechnology · doi:10.1038/nbt.2122 · Cited by 506
Self-citationAssembly of large genomes using second-generation sequencingPreprint
Schatz, M. C., Delcher, A. L., & Salzberg, S. L. (2010) · Genome Research · doi:10.1101/gr.101360.109 · Cited by 518
Complete Khoisan and Bantu genomes from southern Africa
Schuster, S. C., Miller, W., Ratan, A., Tomsho, L. P., Giardine, B. M., Kasson, L. R., Harris, R. S., Petersen, D. C., Zhao, F., Qi, J., et al. (2010) · Nature · doi:10.1038/nature08795 · Cited by 502
“7).”
The 1001 Genomes Project for Arabidopsis thaliana
Weigel, D., & Mott, R. (2009) · Genome biology · doi:10.1186/gb-2009-10-5-107 · Cited by 507
“Indeed, a 1000 Genomes Project for humans was announced in January 2008 [33], and the first results of this initiative are very encouraging [34,35].”
BackgroundChen, W., Lin, Y., Xiong, Z., Wei, W., Wang, N., Tan, G., Guo, S., He, J., Chen, Y., Zhang, Q., et al. (2011) · Nature Genetics · doi:10.1038/ng.1008 · Cited by 498
Self-citationSearching for SNPs with cloud computing
Langmead, B., Schatz, M. C., Lin, J., Pop, M., & Salzberg, S. L. (2009) · Genome biology · doi:10.1186/gb-2009-10-11-r134 · Cited by 490
“To demonstrate performance on real-world data, we used Crossbow to align and call SNPs from the set of 2.7 billion reads and paired-end reads sequenced from a Han Chinese male by Wang et al [5].”
BackgroundMethodInfluentialLaFramboise, T. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp552 · Cited by 467
“For example, a large study recently used billions of paired end reads (81) to detect thousands of CNVs in a single individual, most of which would have been missed by SNP arrays.”
BackgroundHuman Genome Sequencing in Health and Disease
Gonzaga-Jauregui, C. G., Lupski, J. R., & Gibbs, R. A. (2011) · Annual Review of Medicine · doi:10.1146/annurev-med-051010-162644 · Cited by 491
Genome-wide patterns of genetic variation among elite maize inbred lines
Lai, J., Li, R., Xu, X., Jin, W., Xu, M., Zhao, H., Xiang, Z., Song, W., Ying, K., Zhang, M., et al. (2010) · Nature Genetics · doi:10.1038/ng.684 · Cited by 473
Self-citationMicrodroplet-based PCR enrichment for large-scale targeted sequencing
Tewhey, R., Warner, J. B., Nakano, M., Libby, B., Medkova, M., David, P. H., Kotsopoulos, S. K., Samuels, M. L., Hutchison, J. B., Larson, J. W., et al. (2009) · Nature Biotechnology · doi:10.1038/nbt.1583 · Cited by 454
“Of the 22 loci discordant with HapMap, the errors fell into three classes: (1) nine are homozygous reference genotypes with a HapMap homozygous alternate, (2) five are heterozygous genotypes with a HapMap homozygous reference and (3) eight are homozygous reference with a HapMap heterozygous genotype (Supplementary Tab…”
Klambauer, G., Schwarzbauer, K., Mayr, A., Clevert, D.-A., Mitterecker, A., Bodenhofer, U., & Hochreiter, S. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks003 · Cited by 454
“MOFDOC (‘MOdel Free Depth Of Coverage’) belongs to class (a) and has been used by Alkan et al. (6), Campbell et al. (9), Wang et al. (10), Bentley et al. (11) and Wheeler et al. (12) for NGS copy number detection and earlier by Bailey et al. (13) for whole-genome shotgun sequencing.”
MethodMugsy: Fast multiple alignment of closely related whole genomes
Angiuoli, S. V., & Salzberg, S. L. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btq665 · Cited by 444
Wang, Z., Fang, B., Chen, J., Zhang, X., Luo, Z., Huang, L., Chen, X., & Li, Y. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-726 · Cited by 433
“In contrast, Illumina transcriptome or genome sequencing was mainly limited to organisms with reference genomes available [14,51-53].”
BackgroundMethodSelf-citationSingle-molecule sequencing of an individual human genome
Pushkarev, D., Neff, N. F., & Quake, S. R. (2009) · Nature Biotechnology · doi:10.1038/nbt.1561 · Cited by 450
Copy number variants, diseases and gene expression
Henrichsen, C. N., Chaignat, E., & Reymond, A. (2009) · Human Molecular Genetics · doi:10.1093/hmg/ddp011 · Cited by 442
SOAP3-dp: Fast, Accurate and Sensitive GPU-Based Short Read Aligner
Luo, R., Wong, T. K. F., Zhu, J.-Q., Liu, C.-M., Zhu, X., Wu, E., Lee, L., Lin, H., Zhu, W., Cheung, D. W.-L., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0065632 · Cited by 424
“In particular, 41-‐fold of 100bp (PE100) and 77-‐fold of 150bp 14 (PE150) Illumina paired-‐end reads of YH[16] samples have been generated 15 (Supplementary Table 1) for the testing for variant calling.”
Self-citationSingle-Cell Whole-Genome Amplification and Sequencing: Methodology and Applications
Huang, L., Ma, F., Chapman, A. R., Lü, S., & Xie, X. S. (2015) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-090413-025352 · Cited by 427
“Advances in next-generation DNA sequencing technologies have enabled individual human genomes to be sequenced at affordable costs (4, 43, 69, 72).”
BackgroundGenotype to Phenotype: A Complex Problem
Dowell, R. D., Ryan, O., Jansen, A., Cheung, D., Agarwala, S., Danford, T., Bernstein, D. A., Rolfe, P. A., Heisler, L. E., Chin, B., et al. (2010) · Science · doi:10.1126/science.1189015 · Cited by 396
Personalized Medicine: Progress and Promise
Chan, I. S., & Ginsburg, G. S. (2011) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-082410-101446 · Cited by 409
Genome assembly reborn: recent computational challenges
Pop, M. (2009) · Briefings in Bioinformatics · doi:10.1093/bib/bbp026 · Cited by 396
“Since the introduction of the chain termination sequencing method by Frederick Sanger in 1977 [1], the genomes of more than 800 bacteria and 100 eukaryotes have been sequenced, including the genomes of several human individuals [2–4].”
MethodMassively Parallel Sequencing: The Next Big Thing in Genetic Medicine
Tucker, T., Marra, M. A., & Friedman, J. M. (2009) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2009.06.022 · Cited by 393
Complete Resequencing of 40 Genomes Reveals Domestication Events and Genes in Silkworm ( Bombyx )
Xia, Q., Guo, Y., Zhang, Z., Li, D., Xuan, Z., Li, Z., Dai, F., Li, Y., Cheng, D., Li, R., et al. (2009) · Science · doi:10.1126/science.1176620 · Cited by 381
Self-citationLandscape of Next-Generation Sequencing Technologies
Niedringhaus, T. P., Milanova, D., Kerby, M. B., Snyder, M. P., & Barron, A. E. (2011) · Analytical Chemistry · doi:10.1021/ac2010857 · Cited by 399
Validating, augmenting and refining genome-wide association signals
Ioannidis, J. P. A., Thomas, G. D., & Daly, M. J. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2544 · Cited by 382
Clan Genomics and the Complex Architecture of Human Disease
Lupski, J. R., Belmont, J. W., Boerwinkle, E., & Gibbs, R. A. (2011) · Cell · doi:10.1016/j.cell.2011.09.008 · Cited by 375
“Remarkably, from the small number determined and publicly available to date, it is apparent that even more genetic variation exists between individuals than was previously expected (Ahn et al., 2009; Bentley et al., 2008; Kim et al., 2009; Levy et al., 2007; Lupski et al., 2010; Schuster et al., 2010; Wang et al., 200…”
BackgroundHuman Copy Number Variation and Complex Genetic Disease
Girirajan, S., Campbell, C. D., & Eichler, E. E. (2011) · Annual Review of Genetics · doi:10.1146/annurev-genet-102209-163544 · Cited by 378
“However, recent work has led to the identification of insertions of sequences not in the reference genome assembly (56, 68, 128).”
Towards a comprehensive structural variation map of an individual human genome
Pang, A. W., MacDonald, J. R., Pinto, D., Wei, J., Rafiq, M. A., Conrad, D. F., Park, H., Hurles, M. E., Lee, C., Venter, J. C., et al. (2010) · Genome Biology · doi:10.1186/gb-2010-11-5-r52 · Cited by 335
“Similar numbers of SNPs, but significantly less SVs (ranging from approximately 137,000 to approximately 400,000) are reported in other individual genome sequencing projects [2-4,6-8,11].”
InfluentialWhole-genome molecular haplotyping of single cells
Fan, H. C., Wang, J., Potanina, A., & Quake, S. R. (2010) · Nature Biotechnology · doi:10.1038/nbt.1739 · Cited by 368
Self-citationNext generation disparities in human genomics: concerns and remedies
Need, A. C., & Goldstein, D. B. (2009) · Trends in Genetics · doi:10.1016/j.tig.2009.09.012 · Cited by 398
Small insertions and deletions (INDELs) in human genomes
Mullaney, J. M., Mills, R. E., Pittard, W. S., & Devine, S. E. (2010) · Human Molecular Genetics · doi:10.1093/hmg/ddq400 · Cited by 383
A highly annotated whole-genome sequence of a Korean individual
Kim, J.-I., Ju, Y. S., Park, H., Kim, S., Lee, S., Yi, J.-H., Mudge, J., Miller, N. A., Hong, D., Bell, C. J., et al. (2009) · Nature · doi:10.1038/nature08211 · Cited by 330
Kim, M. Y., Lee, S., Van, K., Kim, T. P., Jeong, S., Choi, I., Kim, D.-S., Lee, Y., Park, D., Ma, J., et al. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1009526107 · Cited by 341
The first Korean genome sequence and analysis: Full genome sequencing for a socio-ethnic groupPreprint
Ahn, S., Kim, T. P., Lee, S., Kim, D., Ghang, H., Kim, D., Kim, B.-C., Kim, S.-Y., Kim, W.-Y., Kim, C., et al. (2009) · Genome Research · doi:10.1101/gr.092197.109 · Cited by 326
“Although the first Asian genome based on the genome sequencing of a Han Chinese was recently reported (Wang et al. 2008), various SNP studies have shown that ethnic groups in Asia, including the Chinese, the Japanese, and the Korean, have genetically diverged relatively recently (Karafet et al.”
BackgroundInfluentialMazet, O., Rodríguez, W., Grusea, S., Boitard, S., & Chikhi, L. (2015) · Heredity · doi:10.1038/hdy.2015.104 · Cited by 338
The DNA Methylome of Human Peripheral Blood Mononuclear Cells
Li, Y., Zhu, J., Tian, G., Li, N., Li, Q., Ye, M., Zheng, H., Yu, J., Wu, H., Sun, J., et al. (2010) · PLoS Biology · doi:10.1371/journal.pbio.1000533 · Cited by 321
“Integration of our methylome data with the YH haploid genome sequences [11] enabled us to determine ASM for 1.”
BackgroundMethodInfluentialSelf-citationA reference human genome dataset of the BGISEQ-500 sequencer
Huang, J., Liang, X., Xuan, Y., Geng, C., Li, Y., Lu, H., Qu, S., Mei, X., Chen, H., Yu, T., et al. (2017) · GigaScience · doi:10.1093/gigascience/gix024 · Cited by 313
“With the large amount of data and well-developed analysis tools, second-generation sequencing data can be used to effectively and accurately identify genomic variations [2].”
Self-citationMobile elements create structural variation: Analysis of a complete human genomePreprint
Xing, J., Zhang, Y., Han, K., Salem, A. H., Sen, S. K., Huff, C., Zhou, Q., Kirkness, E. F., Levy, S., Batzer, M. A., et al. (2009) · Genome Research · doi:10.1101/gr.091827.109 · Cited by 326
“First, the HuRef genome was sequenced by the traditional Sanger sequencing method, while other currently available individual genomes are sequenced using secondgeneration sequencing techniques (Bentley et al. 2008; Wang et al. 2008; Wheeler et al. 2008).”
MethodRecent de novo origin of human protein-coding genes
Knowles, D. G., & McLysaght, A. (2009) · Genome Research · doi:10.1101/gr.095026.109 · Cited by 291
“In addition to the standard human genome sequence, several individual genomes have been completely sequenced (Levy et al. 2007; Wang et al. 2008; Wheeler et al. 2008).”
BackgroundU87MG Decoded: The Genomic Sequence of a Cytogenetically Aberrant Human Cancer Cell Line
Clark, M. J., Homer, N., O’Connor, B. D., Chen, Z., Eskin, A., Lee, H., Merriman, B., & Nelson, S. F. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1000832 · Cited by 321
“We compared the SNVs discovered in U87MG to two of these published genomes: the James D. Watson genome [12] and the first Asian genome (YanHuang) [14].”
BackgroundMethodInfluential
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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