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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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Citations
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Next-generation tag sequencing for cancer gene expression profilingPreprint
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BackgroundMinke whale genome and aquatic adaptation in cetaceans
Yim, H., Cho, Y. S., Guang, X., Kang, S. G., Jeong, J.-Y., Cha, S., Oh, H., Lee, J., Yang, E. C., Kwon, K. K., et al. (2013) · Nature Genetics · doi:10.1038/ng.2835 · Cited by 287
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MethodSelf-citationExome Sequencing Identifies WDR35 Variants Involved in Sensenbrenner Syndrome
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“However, although the secondgeneration technologies are comparatively very cheap, their application was mainly restricted to resequencing projects [4, 5] where a good reference sequence existed, due to the much shorter read length (30–400 bp) in comparison with Sanger sequencing (500–1000 bp).”
BackgroundSelf-citationGraphtyper enables population-scale genotyping using pangenome graphs
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Natural genetic variation caused by small insertions and deletions in the human genomePreprint
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“96 million INDELs (light blue, top) with Han Chinese (Wang et al. 2008) and Yoruban (Bentley et al.”
BackgroundInfluentialSebat, J., Levy, D. L., & McCarthy, S. E. (2009) · Trends in Genetics · doi:10.1016/j.tig.2009.10.004 · Cited by 260
Reis-Filho, J. S. (2009) · Breast Cancer Research · doi:10.1186/bcr2431 · Cited by 284
Building the sequence map of the human pan-genome
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Self-citationThe ClinSeq Project: Piloting large-scale genome sequencing for research in genomic medicinePreprint
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BackgroundLong-read sequencing and de novo assembly of a Chinese genome
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Self-citationAccurate whole-genome sequencing and haplotyping from 10 to 20 human cells
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MethodSelf-citationSOAP3: ultra-fast GPU-based parallel alignment tool for short reads
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Self-citationHaplotype-resolved genome sequencing of a Gujarati Indian individual
Kitzman, J. O., MacKenzie, A. P., Adey, A., Hiatt, J. B., Patwardhan, R. P., Sudmant, P. H., Ng, S. B. H., Alkan, C., Qiu, R., Eichler, E. E., et al. (2010) · Nature Biotechnology · doi:10.1038/nbt.1740 · Cited by 244
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Identification and correction of systematic error in high-throughput sequence dataPreprint
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“Although filters based on the depth of reads are frequently applied (mostly to screen for indels, copy number variants, or other structural variation) [7,8], most existing approaches will not identify systematic errors, or distinguish them from true SNPs.”
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“In fact, the detection of genome-wide SNPs in eukaryotes using high-throughput resequencing has been reported for the human, nematode, Arabidopsis, and rice genomes [18-21].”
BackgroundSimultaneous alignment of short reads against multiple genomes
Schneeberger, K., Hagmann, J., Ossowski, S., Warthmann, N., Gesing, S., Kohlbacher, O., & Weigel, D. (2009) · Genome biology · doi:10.1186/gb-2009-10-9-r98 · Cited by 238
“…thaliana (Arabidopsis) strains with Illumina reads [1,2] was recently complemented by genome sequences of several human individuals, generated with data derived from technologies from Illumina (San Diego, CA, USA), Applied Biosystems (Foster City, CA, USA), and Helicos (Cambridge, MA, USA) [3-10].”
MethodHigh genome heterozygosity and endemic genetic recombination in the wheat stripe rust fungus
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“…Tsudik Institute for Genomics and Bioinformatics Department of Computer Science {pfbaldi,rbaronio,edecrist,pgasti,gts}@uci.edu University of California, Irvine ABSTRACT Recent advances in DNA sequencing technologies have put ubiquitous availability of fully sequenced human genomes within reach.”
The genome of Mesobuthus martensii reveals a unique adaptation model of arthropods
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BackgroundRevisiting Mendelian disorders through exome sequencing
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“2010) and studies of human genetic variants (Bentley et al. 2008; Wheeler et al. 2008; Wang et al. 2008), research on Mendelian disorders will also benefit tremendously from de novo genome assembly when it becomes feasible with better assembly algorithms and longer sequence reads generated by third-generation sequenci…”
BackgroundDeep resequencing reveals excess rare recent variants consistent with explosive population growth
Coventry, A., Bull–Otterson, L., Liu, X., Clark, A. G., Maxwell, T. J., Crosby, J. R., Hixson, J. E., Rea, T. J., Muzny, D. M., Lewis, L. R., et al. (2010) · Nature Communications · doi:10.1038/ncomms1130 · Cited by 229
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“Between Cedric and Spirit we found 914,827 substitutions; a southern African Bushman (14) and a Japanese individual (15) contain 4,800,466 SNPs, compared with 3,256,979 for a Chinese individual (16) and the Japanese individual.”
BackgroundImpact of replication timing on non-CpG and CpG substitution rates in mammalian genomesPreprint
Chen, C.-L., Rappailles, A., Duquenne, L., Huvet, M., Guilbaud, G., Farinelli, L., Audit, B., d'Aubenton-Carafa, Y., Arnéodo, A., Hyrien, O., et al. (2010) · Genome Research · doi:10.1101/gr.098947.109 · Cited by 221
“SNP data from four fully sequenced individual genomes of C. Venter (Levy et al. 2007), J. Watson (Wheeler et al. 2008), an anonymous Asian male (YH) (Wang et al. 2008), and a male Yoruba from Ibadan (Bentley et al. 2008) were also used to evaluate the human diversity.”
BackgroundIs it time to change the reference genome?
Ballouz, S., Dobin, A., & Gillis, J. (2019) · Genome biology · doi:10.1186/s13059-019-1774-4 · Cited by 220
Trends in Next-Generation Sequencing and a New Era for Whole Genome Sequencing
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Accurate and comprehensive sequencing of personal genomes.Preprint
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Low-pass whole-genome sequencing in clinical cytogenetics: a validated approach
Dong, Z., Zhang, J., Hu, P., Chen, H., Xu, J., Tian, Q., Meng, L., Ye, Y., Wang, J., Zhang, M., et al. (2016) · Genetics in Medicine · doi:10.1038/gim.2015.199 · Cited by 210
Self-citationThe draft genome of the large yellow croaker reveals well-developed innate immunity
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“A total of 39 single cells were collected in our study, 29 from a lymphoblastoid cell line (YH cell line) established from the first Asian genome donor [23], the rest from a widely known gastric cancer cell line, BGC823.”
BackgroundMethodSelf-citationNucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library
Lam, H. Y. K., Mu, X. J., Stütz, A. M., Andrea Tanzer, A., Cayting, P. D., Snyder, M. P., Kim, P. M., Korbel, J. O., & Gerstein, M. (2009) · Nature Biotechnology · doi:10.1038/nbt.1600 · Cited by 193
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Self-citationThe impact of next-generation sequencing technologies on HLA research
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A statistical method for the detection of variants from next-generation resequencing of DNA pools
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“The Illumina allows multiplexed sequencing of eight samples per run (one each lane) and also sequencing of up to 96 samples using DNA preparation and sequencing costs, an alternate approach is to pool genomic DNA from multiple individuals and sequence the pooled samples (Sham et al. , 2002).”
Interpretation of Genomic Variants Using a Unified Biological Network Approach
Khurana, E., Fu, Y., Chen, J., & Gerstein, M. (2013) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002886 · Cited by 188
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“Owing to the relatively low cost of these methods, at least when compared with Sanger sequencing, an unprecedented amount of genome sequence data has been generated in the past few years, including high-coverage assemblies of individual genomes (84, 149, 185, 188).”
BackgroundDeep Whole-Genome Sequencing of 100 Southeast Asian Malays
Wong, L.-P., Ong, R. T., Poh, W.-T., Liu, X., Chen, P., Li, R., Lam, K., Pillai, N. E., Sim, K. S., Xu, H., et al. (2013) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2012.12.005 · Cited by 182
Self-citationGenes, mutations, and human inherited disease at the dawn of the age of personalized genomics
Cooper, D. N., Chen, J., Ball, E. V., Howells, K., Mort, M. E., Phillips, A. D., Chuzhanova, N. A., Krawczak, M., Kehrer‐Sawatzki, H., & Stenson, P. D. (2010) · Human Mutation · doi:10.1002/humu.21260 · Cited by 186
The clinical context of copy number variation in the human genome
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The pursuit of genome-wide association studies: where are we now?
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High-resolution human genome structure by single-molecule analysis
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“To estimate the accuracy of our method, we detected variants of 193 genes in YH DNA using our Targeted DNA-HiSeq technology and compared the results obtained with the results from whole-genome sequencing for the same 193 genes in the same DNA samples deposited in dbSNP (dbYH) [17].”
ResultSelf-citationA network medicine approach to human disease
Zanzoni, A., Soler‐López, M., & Aloy, P. (2009) · FEBS Letters · doi:10.1016/j.febslet.2009.03.001 · Cited by 172
“Nevertheless, given the recent improvements in genome sequencing techniques (e.g. [64,65]) it is likely that decoding an individual genome will be affordable in a few years, making personalized medicine a common practice.”
BackgroundWhole-genome haplotyping using long reads and statistical methods
Kuleshov, V., Xie, D., Chen, R., Pushkarev, D., Ma, Z., Blauwkamp, T. A., Kertesz, M., & Snyder, M. P. (2014) · Nature Biotechnology · doi:10.1038/nbt.2833 · Cited by 170
Copy number variation in the bovine genome
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“The latter identifies a more complete size and class ranges of structural variation [68-79].”
Archaic human ancestry in East Asia
Skoglund, P., & Jakobsson, M. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1108181108 · Cited by 170
Comprehensive comparison of three commercial human whole-exome capture platforms
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“The test DNA sample was from a cell line derived from the individual used in the YanHuang whole-genome sequencing analysis [26], allowing comparison with the existing high-coverage genome sequence.”
MethodInfluentialSelf-citationGao, Z., Zhao, S., He, W., Guo, L., Peng, Y., Wang, J., Guo, X., Zhang, X., Rao, Y., Zhang, C., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1306579110 · Cited by 161
“The trimming strategy for dealing with mismatches was as described previously (33).”
MethodSelf-citationCao, H., Hastie, A., Cao, D., Lam, E. T., Sun, Y., Huang, H., Lin, L., Lin, L., Andrews, W., Chan, S., et al. (2014) · GigaScience · doi:10.1186/2047-217x-3-34 · Cited by 156
“Here, we apply this rapid and highthroughput genome mapping method to discern genome wide SVs, as well as explore complex regions based on the YH (first Asian genome) [33] cell line.”
MethodSelf-citationEstimation of historical effective population size using linkage disequilibria with marker data
Corbin, L. J., LIU, A. Y. H., Bishop, S. C., & Woolliams, J. A. (2012) · Journal of Animal Breeding and Genetics · doi:10.1111/j.1439-0388.2012.01003.x · Cited by 161
Challenges of sequencing human genomes
Koboldt, D. C., Ding, L., Mardis, E. R., & Wilson, R. K. (2010) · Briefings in Bioinformatics · doi:10.1093/bib/bbq016 · Cited by 161
“87 81 YH (Asian) [8] Illumina 2 35 36 99.”
RazerS--fast read mapping with sensitivity control.Preprint
Weese, D., Emde, A., Rausch, T., Döring, A., & Reinert, K. (2009) · Genome Research · doi:10.1101/gr.088823.108 · Cited by 178
The Characterization of Twenty Sequenced Human Genomes
Pelak, K., Shianna, K. V., Ge, D., Maia, J. M., Zhu, M., Smith, J. P., Cirulli, E. T., Fellay, J., Dickson, S. P., Gumbs, C. E., et al. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1001111 · Cited by 159
Y Chromosomes of 40% Chinese Descend from Three Neolithic Super-Grandfathers
Yan, S. L., Wang, C., Zheng, H., Wang, W., Qin, Z., Wei, L., Wang, Y., Pan, X., Fu, W., He, Y., et al. (2014) · PLoS ONE · doi:10.1371/journal.pone.0105691 · Cited by 155
Self-citationAssessing structural variation in a personal genome—towards a human reference diploid genome
English, A. C., Salerno, W. J., Hampton, O. A., Gonzaga-Jauregui, C. G., Ambreth, S., Ritter, D., Beck, C. R., Davis, C., Dahdouli, M., Ma, S., et al. (2015) · BMC Genomics · doi:10.1186/s12864-015-1479-3 · Cited by 152
“Local hybrid assembly supported 7,708 loci, that is, at least 2 compares the size distributions of HS1011 deletions and insertions with those reported in other personal genomes [28,29].”
BackgroundSNP detection and genotyping from low-coverage sequencing data on multiple diploid samplesPreprint
Le, S. Q., & Durbin, R. M. (2010) · Genome Research · doi:10.1101/gr.113084.110 · Cited by 151
“Recent advances in sequencing technologies enable the sequencing of personal genomes to identify most genetic variations present in one sample (Venter et al. 2001; Levy et al. 2007; Wang et al. 2008; Wheeler et al. 2008; Kim et al. 2009).”
BackgroundSelf-citationMolecular genetic studies of complex phenotypes
Marian, A. J. (2011) · Translational research · doi:10.1016/j.trsl.2011.08.001 · Cited by 159
“Every genome contains about 4 million DSVs that collectively affect half of the genes in each genome and many are private (Table 1) (5-12).”
BackgroundThe next-generation sequencing technology and application
Zhou, X., Ren, L., Meng, Q., Li, Y., Yu, Y., & Yu, J. M. (2010) · Protein & Cell · doi:10.1007/s13238-010-0065-3 · Cited by 161
“The next four human genome sequences are from a Chinese (Wang et al., 2008), an African (Pushkarev et al., 2009), and two Korean individuals (Ahn et al., 2009; Kim et al., 2009); all were done using the Illumina Genome Analyzer and sequenced to around 20× haploid genome coverage with the exception of the African male’…”
BackgroundSelf-citationCharacterization of missing human genome sequences and copy-number polymorphic insertions
Kidd, J. M., Sampas, N., Antonacci, F., Graves, T., Fulton, R. S., Hayden, H. S., Alkan, C., Malig, M., Ventura, M., Giannuzzi, G., et al. (2010) · Nature Methods · doi:10.1038/nmeth.1451 · Cited by 150
Decelerated genome evolution in modern vertebrates revealed by analysis of multiple lancelet genomes
Huang, S., Chen, Z., Yan, X., Yu, T., Huang, G., Yan, Q., Pontarotti, P., Zhao, H., Li, J., Yang, P. S., et al. (2014) · Nature Communications · doi:10.1038/ncomms6896 · Cited by 156
“15).”
Self-citationUtilization of next-generation sequencing platforms in plant genomics and genetic variant discovery
Deschamps, S., & Campbell, M. A. (2009) · Molecular Breeding · doi:10.1007/s11032-009-9357-9 · Cited by 153
“…the alignment of short reads to a reference sequence (Barbazuk et al. 2007; Hillier et al. 2008; Ossowski et al. 2008; Van Tassel et al. 2008; Wang et al. 2008; Ahn et al. 2009; Amaral et al. 2009; Eck et al. 2009; Gore et al. 2009; Huang et al. 2009; Ramos et al. 2009), or the de novo…”
BackgroundMethodPervasive Multinucleotide Mutational Events in Eukaryotes
Schrider, D. R., Hourmozdi, J., & Hahn, M. W. (2011) · Current Biology · doi:10.1016/j.cub.2011.05.013 · Cited by 143
“Because the YH01 genome is based on Illumina short-read sequences, reads containing more than two differences from the reference genome were discarded during mapping [23].”
InfluentialIntegrated microfluidic systems for high-performance genetic analysis
Liu, P., & Mathies, R. A. (2009) · Trends in biotechnology · doi:10.1016/j.tibtech.2009.07.002 · Cited by 143
Nowrousian, M. (2010) · Eukaryotic Cell · doi:10.1128/ec.00123-10 · Cited by 145
Ju, Y. S., Kim, J., Kim, S., Hong, D., Park, H., Shin, J.-Y., Lee, S., Lee, W., Kim, S.-J., Yu, S.-B., et al. (2011) · Nature Genetics · doi:10.1038/ng.872 · Cited by 140
Salgado, D., Desvignes, J., Raï, G., Blanchard, A., Miltgen, M., Pinard, A., Lévy, N., Collod‐Béroud, G., & Béroud, C. (2016) · Human Mutation · doi:10.1002/humu.22965 · Cited by 150
“In addition, early whole genome sequencing (WGS) experiments have revealed that every human carries about 3 million single-nucleotide polymorphisms (SNP) [Levy et al., 2007; Wang et al., 2008; Wheeler etal.,2008;Pushkarevetal.,2009],thesedatabeingconsistentlycon-firmed.”
BackgroundPersonal genome sequencing: current approaches and challengesPreprint
Snyder, M. P., Du, J., & Gerstein, M. (2010) · Genes & Development · doi:10.1101/gad.1864110 · Cited by 145
“Fourteen genome sequences have been reported to date (Table 1; Levy et al. 2007; Bentley et al. 2008; Ley et al. 2008; Wang et al. 2008; Wheeler et al. 2008; Ahn et al. 2009; Drmanac et al. 2009; Kim et al. 2009; Mardis et al. 2009; McKernan et al. 2009; Pushkarev et al. 2009; Pleasance et al.…”
BackgroundMethodInfluentialCOPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly
Liu, B., Yuan, J., Yiu, S.-M., Li, Z., Xie, Y., Chen, Y., Shi, Y., Zhang, H., Li, Y., Lam, T.-W., et al. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts563 · Cited by 138
Self-citationTabor, H. K., Berkman, B. E., Hull, S. C., & Bamshad, M. J. (2011) · American Journal of Medical Genetics Part A · doi:10.1002/ajmg.a.34357 · Cited by 136
“…been reported, primarily as a consequence of testing different sequencing platforms, computational approaches, and analytical methods [Levy et al., 2007; Wang et al., 2008; Wheeler et al., 2008; Ashley et al., 2010; Li et al., 2010; Pelak et al., 2010;Roach et al., 2010; Schuster et al., 2010].”
BackgroundNext-Generation Sequencing and Large Genome Assemblies
Henson, J., Tischler, G., & Ning, Z. (2012) · Pharmacogenomics · doi:10.2217/pgs.12.72 · Cited by 146
Li, Y., Zheng, H., Luo, R., Wu, H., Zhu, H., Li, R., Cao, H., Wu, B., Huang, S., Shao, H., et al. (2011) · Nature Biotechnology · doi:10.1038/nbt.1904 · Cited by 133
Self-citationHuman inversions and their functional consequences
Puig, M., Casillas, S., Villatoro, S., & Cáceres, M. (2015) · Briefings in Functional Genomics · doi:10.1093/bfgp/elv020 · Cited by 133
“Second, paired-end sequencing and mapping (PEM) supposed a major breakthrough in the field, and most predicted inversions so far have been detected using this strategy [4, 5, 7, 11, 34–36].”
MethodCharacterizing natural variation using next-generation sequencing technologies
Gilad, Y., Pritchard, J. K., & Thornton, K. (2009) · Trends in Genetics · doi:10.1016/j.tig.2009.09.003 · Cited by 130
Methods for Genomic Partitioning
Turner, E. H., Ng, S. B. H., Nickerson, D. A., & Shendure, J. (2009) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-082908-150112 · Cited by 131
Studying the epigenome using next generation sequencing
Ku, C., Naidoo, N., Wu, M., & Soong, R. (2011) · Journal of Medical Genetics · doi:10.1136/jmedgenet-2011-100242 · Cited by 127
“51 This led to identi fi cation of 599 haploid differentially methylated regions covering 287 genes and demonstrated that allele speci fi c methylation is highly correlated with allele speci fi c expression.”
A beginners guide to SNP calling from high-throughput DNA-sequencing data
Altmann, A., Weber, P., Bader, D. M., Preuss, M. H., Binder, E. B., & Müller-Myhsok, B. (2012) · Human Genetics · doi:10.1007/s00439-012-1213-z · Cited by 138
3′-End Sequencing for Expression Quantification (3SEQ) from Archival Tumor Samples
Beck, A. H., Weng, Z., Witten, D., Zhu, S., Foley, J. W., Lacroute, P., Smith, C. L., Tibshirani, R. J., van de Rijn, M., Sidow, A., et al. (2010) · PLoS ONE · doi:10.1371/journal.pone.0008768 · Cited by 126
“to sequence human genomes [37,38], study the genome wide binding of transcription factors [39,40] and nucleosomes [41], characterize genome methylation patterns [42], and have been recently applied to the sequencing of transcriptomes (RNA-Seq) [35,36,43–45].”
MethodCoelacanth genomes reveal signatures for evolutionary transition from water to landPreprint
二階堂雅人, Noguchi, H., Nishihara, H., Toyoda, A., Suzuki, Y., Kajitani, R., Suzuki, Y., Okuno, M., 梶谷嶺, Ngatunga, B. P., et al. (2013) · Genome Research · doi:10.1101/gr.158105.113 · Cited by 125
“The lower heterozygosity rates in coelacanth individuals, as compared with those in human (0.069%; Wang et al. 2008) and gorilla (0.”
BackgroundInfluentialThe human Major Histocompatibility Complex as a paradigm in genomics research
Vandiedonck, C., & Knight, J. C. (2009) · Briefings in Functional Genomics and Proteomics · doi:10.1093/bfgp/elp010 · Cited by 125
“3), although some complete diploid sequences are now becoming available through re-sequencing [26–29].”
BackgroundDomestication Genomics: Evidence from Animals
Wang, G., Xie, H., Peng, M., Irwin, D. M., & Zhang, Y. (2013) · Annual Review of Animal Biosciences · doi:10.1146/annurev-animal-022513-114129 · Cited by 122
“At present, NGS technologies provide an alternative but effective way for whole-genome sequencing because of their improved sequencing throughput and reduced costs (25, 26).”
BackgroundTabor, H. K., Stock, J., Brazg, T., McMillin, M. J., Dent, K. M., Yu, J., Shendure, J., & Bamshad, M. J. (2012) · American Journal of Medical Genetics Part A · doi:10.1002/ajmg.a.35328 · Cited by 125
“…individuals have been reported, primarily as a consequence of testing different sequencing platforms, computational approaches, and analytical methods [Levy et al., 2007; Wang et al., 2008; Wheeler et al., 2008; Ashley et al., 2010; Pelak et al., 2010; Roach et al., 2010; Schuster et al., 2010].”
Sheridan, M. B., Kato, T., Haldeman‐Englert, C. R., Jalali, G. R., Milunsky, J. M., Zou, Y. S., Klaes, R., Gimelli, G., Gimelli, S., Gemmill, R. M., et al. (2010) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2010.07.002 · Cited by 117
Collins, S. C., Bray, S. M., Suhl, J. A., Cutler, D. J., Coffee, B. W., Zwick, M. E., & Warren, S. T. (2010) · American Journal of Medical Genetics Part A · doi:10.1002/ajmg.a.33626 · Cited by 126
The discovery of human genetic variations and their use as disease markers: past, present and future
Ku, C., Loy, E. Y., Salim, A., Yudi Pawitan, Y., & Chia, K. S. (2010) · Journal of Human Genetics · doi:10.1038/jhg.2010.55 · Cited by 119
Fujimoto, A., Nakagawa, H., Hosono, N., Nakano, K., Abe, T., Boroevich, K. A., Nagasaki, M., Yamaguchi, R., Shibuya, T., Kubo, M., et al. (2010) · Nature Genetics · doi:10.1038/ng.691 · Cited by 112
Liu, T., Zhu, S., Tang, Q., Chen, P., Yu, Y., & Tang, S. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-125 · Cited by 116
“Sequencer FLX Instrument, the ABI SOLiD System and the Illumina Genome Analyser, was a powerful tool and was untilized in many researching areas, including resequencing, micro-RNA expression profiling, DNA methylation, especially de novo transcriptome sequencing for non-model organisms [5-13].”
MethodRegions of homozygosity and their impact on complex diseases and traits
Ku, C., Naidoo, N., Teo, S. M., & Yudi Pawitan, Y. (2010) · Human Genetics · doi:10.1007/s00439-010-0920-6 · Cited by 114
“…been further corroborated with the Wndings from whole genome resequencing studies where several million single nucleotide polymorphisms (SNPs) and several hundred thousand indels and structural variants were identiWed (Wheeler et al. 2008; Bentley et al. 2008; Wang et al. 2008; Kim et al. 2009).”
Background
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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