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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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“Short insertions and deletions (InDels) and Structural Variants (SVs) Short insertions and deletions are the second most abundant type of genetic variation in the whole genome (Wang et al. 2008).”
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“The Yan Huang genome sample [26] was utilized as reference material to assess the sequencing depth needed for detecting variants of target regions.”
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“Recently, next generation sequencing techniques have been applied to characterize the intestinal microbiota of humans [3-5] as well as a number of mammalian species [6-10].”
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BackgroundInfluentialHigh resolution discovery and confirmation of copy number variants in 90 Yoruba Nigerians
Matsuzaki, H., Wang, P., Hu, J., Rava, R., & Fu, G. K. (2009) · Genome biology · doi:10.1186/gb-2009-10-11-r125 · Cited by 59
Evaluation of a target region capture sequencing platform using monogenic diabetes as a study-model
Gao, R., Liu, Y., Gjesing, A. P., Hollensted, M., Wan, X., He, S., Pedersen, O. B., Yi, X., Wang, J., & Hansen, T. F. (2014) · BMC Genetics · doi:10.1186/1471-2156-15-13 · Cited by 59
“The purified PCR products containing 3 ug DNA were hybridized to the GenCap ™ probe (in solution) at 65°C for 22 hours using a PCR machine.”
InfluentialSelf-citationRainbow: a tool for large-scale whole-genome sequencing data analysis using cloud computing
Zhao, S., Prenger, K., Smith, L., Messina, T., Fan, H., Jaeger, E., & Stephens, S. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-425 · Cited by 57
“High-throughput next-generation sequencing (NGS) technologies from Illumina (San Diego, CA, USA), Life Technology (Carlsbad, CA, USA), and Roche/454 (Branford, CT, USA) have evolved rapidly and are reshaping the scope of genomics research [1-3].”
BackgroundUse of Genetics in the Clinical Evaluation of Cardiomyopathy
Judge, D. P. (2009) · JAMA · doi:10.1001/jama.2009.1787 · Cited by 56
“More recently, 2 articles in Nature reported full genome sequencing of the third and fourth individuals by this same techinque.(30,43) The cost for each of these was estimated to be less than $500 000.”
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“However, the number of indels reported by various studies ranges considerably: from 135 262 indels of size 1–3 bp reported in the Han Chinese genome (17), to ∼400 000 indels reported in a Yoruban genome NA18507 (18); for a comprehensive review, see (14).”
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“Already, complete genomes from many individual humans have been sequenced, and projects are underway to expand that number to over a thousand genomes in the near future (Levy et al. 2007; Bentley et al. 2008; Wang et al. 2008; Wheeler et al. 2008).”
BackgroundGenomics of medulloblastoma: from Giemsa-banding to next-generation sequencing in 20 years
Northcott, P. A., Rutka, J. T., & Taylor, M. D. (2009) · Neurosurgical FOCUS · doi:10.3171/2009.10.focus09218 · Cited by 54
Sry, more than testis determination?
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“Advances in sequencing technology and computational methods are resulting in increasingly cost-effective, high-throughput sequencing, making the sequencing of genomes from individuals possible [3, 12, 14, 20, 24, 25].”
BackgroundConceptual approaches for lncRNA drug discovery and future strategies
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“This has also been supplemented by initiatives of sequencing multiple individuals and populations such as the Korean [9], Chinese [10], Sri Lankan [11,12], Indian [13], and other genome projects.”
MethodDoes massively parallel DNA resequencing signify the end of histopathology as we know it?
Aparicio, S. A. J. R., & Huntsman, D. D. (2009) · The Journal of Pathology · doi:10.1002/path.2636 · Cited by 55
MacConaill, L. E., Hummelen, P. V., Meyerson, M. M., & Hahn, W. C. (2011) · Cancer Discovery · doi:10.1158/2159-8290.cd-11-0110 · Cited by 57
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Self-citationMobile element biology: new possibilities with high-throughput sequencing
Xing, J., Witherspoon, D. J., & Jorde, L. B. (2013) · Trends in Genetics · doi:10.1016/j.tig.2012.12.002 · Cited by 54
Accurate Distinction of Pathogenic from Benign CNVs in Mental Retardation
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“The benefits of such methods will increase with advancements in microarray technology, which already identifies many thousands of such structural variants per individual [50–53], and in whole genome resequencing technology,.”
MethodDNA copy number, including telomeres and mitochondria, assayed using next-generation sequencing
Castle, J. C., Biery, M. C., Bouzek, H. K., Xie, T., Chen, R., Misura, K. M. S., Jackson, S., Armour, C. D., Johnson, J. M., Rohl, C. A., et al. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-244 · Cited by 52
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“00069) [54] and bald eagle”
Exome versus transcriptome sequencing in identifying coding region variants
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Microarray-based multicycle-enrichment of genomic subsets for targeted next-generation sequencingPreprint
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“Another study detected approximately 150,000 indels with a size of 1 – 3 bp (Wang et al., 2008).”
BackgroundOTG-snpcaller: An Optimized Pipeline Based on TMAP and GATK for SNP Calling from Ion Torrent Data
Zhu, P., He, L., Li, Y., Huang, W., Xi, F., Lin, L., Zhi, Q., Zhang, W., Tang, Y. T., Geng, C., et al. (2014) · PLoS ONE · doi:10.1371/journal.pone.0097507 · Cited by 51
“First, we filtered the YH-WGS SNPs within the exon target region.”
MethodInfluentialSelf-citationData structures and compression algorithms for high-throughput sequencing technologies
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“Take for example the Yan Huang genome [5] we used for Dataset 3; the total amount of read data generated by the project is almost 120 GB.”
BackgroundMethodSequencing and analysis of an Irish human genome
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Massively Parallel Sequencing Approaches for Characterization of Structural Variation
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“Massively parallel sequencing has since been employed to systematically characterize large-scale variation in individual (2, 6, 8, 13) and cancer (14–17) genomes.”
MethodRosenfeld, J., Malhotra, A. K., & Lencz, T. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq408 · Cited by 51
“The Chinese genome data was obtained from (10) as raw FASTQ sequencing reads and only those paired ended reads that were 35 bp in length were used in the analysis.”
MethodInfluentialnpInv: accurate detection and genotyping of inversions using long read sub-alignment
Shao, H., Ganesamoorthy, D., Duarte, T., Cao, M. D., Hoggart, C., & Coin, L. (2018) · BMC Bioinformatics · doi:10.1186/s12859-018-2252-9 · Cited by 49
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“Finally, recently resequenced genomes revealed that current single nucleotide polymorphism (SNP) databases are still far from being complete [24–29].”
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“Although the question of what constitutes sufficient coverage for detecting the presence of inserts is debatable, many publications have suggested that the higher the sequencing depth is, the better it is for achieving precise molecular characterization of GM events [27, 28].”
BackgroundUltraaccurate genome sequencing and haplotyping of single human cells
Chu, W. K., Edge, P., Lee, H. S., Bansal, V., Bafna, V., Huang, X. C., & Zhang, K. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1707609114 · Cited by 48
Identification of Characteristic Genomic Markers in Human Hepatoma HuH-7 and Huh7.5.1-8 Cell Lines
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“Previous studies found that (1) the gene expression of SPP1 in liver tissue was increased according to the progress of hepatitis C45, (2) SPP1 enhanced autophagy in human hepatocellular carcinoma cells46, and (3) SPP1 interacted with HCV proteins and helped replicate and assemble HCV47.”
Galante, P. A. F., Parmigiani, R. B., Zhao, Q., Caballero, O. L., de Souza, J. E., Navarro, F. C. P., Gerber, A. L., Nicolás, M., Salim, A. C. M., Silva, A. P. M., et al. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr221 · Cited by 54
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BackgroundWang, M., Zhao, X., Takemoto, K., Xu, H., Li, Y., Akutsu, T., & Song, J. (2012) · PLoS ONE · doi:10.1371/journal.pone.0043847 · Cited by 49
“It is estimated that there are 3 , 5 million SAVs in an individual according to the recent sequencing of the whole human genome [2,3,4,5].”
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Efficient study design for next generation sequencing
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BackgroundThe promise and reality of personal genomics
Yngvadóttir, B., MacArthur, D. G., Jin, H., & Tyler‐Smith, C. (2009) · Genome biology · doi:10.1186/gb-2009-10-9-237 · Cited by 45
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BackgroundGenetics and Genomics of Single-Gene Cardiovascular Diseases
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“The Illumina sequencing technology is the next generation sequencing (NGS) which is a powerful tool utilized in many researching areas, including re-sequencing, micro-RNA expression profiling, DNA methylation, de novo transcriptome sequencing and whole sequencing [15-21], especially in the analysis of whole-genome exp…”
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Self-citationPlanning the Human Variome Project: The Spain report
Kaput, J., Cotton, R. G. H., Hardman, L., Watson, M. S., Aqeel, A. I. A., Al-Aama, J. Y., Al‐Mulla, F., Alonso, S., Aretz, S., Auerbach, A. D., et al. (2009) · Human Mutation · doi:10.1002/humu.20972 · Cited by 48
“, 2008) and Han Chinese (Wang et al., 2008) genomes, along with gene specific re-sequencing efforts (see Introduction), suggest that a large number of SNPs and other sequence variation exists in the human population.”
Li, D., Guo, Y., Shao, H., Tellier, L. C. A. M., Wang, J., Xiang, Z., & Xia, Q. (2010) · BMC Evolutionary Biology · doi:10.1186/1471-2148-10-81 · Cited by 47
“8 × 10 [37] in our mt and nuclear genomes, respectively, provides an interesting contrast to that of the silkworm.”
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“Applications vary from genome re-sequencing [2-4] to transcriptome analysis [5-7], metagenomics projects [8-10], and sequencing of ancient genomes [11-16].”
BackgroundNo Evidence of Increased Mutation Rates at Microsatellite Loci in Offspring of A-Bomb Survivors
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“of European, African and Asian descent, including famous personalities such as James Watson, Craig Ventor, and Stephen Quake [5–13].”
BackgroundGenomic approaches with natural fish populations
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“Importantly, significant Antarctic specific gene duplications occurred for 118 genes, many corresponding to the upregulated genes identified in silico (Chen et al., 2008).”
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“Recently, highthroughput DNA sequencing technology has begun to have a major impact on this field and is shedding light on genomic sequence variations between human individuals [7–10].”
BackgroundNext-generation sequencing to identify genetic causes of cardiomyopathies
Norton, N., Li, D., & Hershberger, R. E. (2012) · Current Opinion in Cardiology · doi:10.1097/hco.0b013e328352207e · Cited by 45
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“…carried out the genetic investigations [185] in 2003 the sequencing of the human genome [186], in 2008 the high throughput NGS methods [187–189], in the 10s of the new millennium the advent of single cell analysis techniques [112], in 2014 the innovative gene editing technology CRSPR/CAS9…”
MethodCridland, J. M., & Thornton, K. (2010) · Genome Biology and Evolution · doi:10.1093/gbe/evq001 · Cited by 43
“Key words: Drosophila, structural variation, mutation, polymorphism, high-throughput sequencing.”
The YH database: the first Asian diploid genome database
Li, G., Ma, L., Song, C., Yang, Z., Wang, X., Huang, H., Li, Y., Li, R., Zhang, X., Yang, H., et al. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn966 · Cited by 42
“SNPs and indels have been submitted to NCBI dbSNP and will be available in dbSNP version 130 (1).”
BackgroundMethodInfluentialSelf-citationChen, S., Ge, H., Wang, X., Pan, X., Yao, X., Li, X., Zhang, C., Chen, F., Jiang, F., Li, P., et al. (2013) · Genome Medicine · doi:10.1186/gm422 · Cited by 42
“Moreover, the fetal haplotype information is especially useful in detecting some haplotype-related diseases, such as systemic lupus erythematosus [18], as well as personal genomic analyses in the future [19,20].”
BackgroundSelf-citationBeal, M. A., Glenn, T. C., & Somers, C. M. (2011) · Mutation Research/Reviews in Mutation Research · doi:10.1016/j.mrrev.2011.11.002 · Cited by 41
Gonzalez-Beltran, A. N., Li, P., Zhao, J., Ávila-García, M. S., Roos, M., Thompson, M., van der Horst, E., Kaliyaperumal, R., Luo, R., Lee, T., et al. (2015) · PLoS ONE · doi:10.1371/journal.pone.0127612 · Cited by 45
“As [20] accounts for refinements to the first published diploid genome sequence of an Asian individual (referred to here as Chinese Han genome or YH genome) [25, 33] with new reads generated on the newer Illumina platform, the assay template “genome sequencing using nucleotide sequencing” was chosen from the various w…”
BackgroundMethodSelf-citationChallenges in Medical Applications of Whole Exome/Genome Sequencing Discoveries
Marian, A. J. (2012) · Trends in Cardiovascular Medicine · doi:10.1016/j.tcm.2012.08.001 · Cited by 42
“In addition, each genome/exome contains about 10,000 non–synonymous variants (nsSNVs) that – by definition – affect the amino acid sequence in the encoded proteins and hence, might exert biological effects (Levy et al., 2007; Ng et al., 2008; Wang et al., 2008; Wheeler et al., 2008).”
BackgroundInfluentialSeqGene: a comprehensive software solution for mining exome- and transcriptome- sequencing data
Deng, X. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-267 · Cited by 41
“Detecting genomic variants (such as SNPs, indels and structural variants) via whole-genome sequencing, RNASeq and exome-Seq is an essential approach to understanding the association of genotypic difference to phenotypic consequences with the eventual goal of personalized genomics for medical purposes [1,12-15].”
BackgroundCharacterizing sensitivity and coverage of clinical WGS as a diagnostic test for genetic disorders
Sun, Y., Liu, F., Fan, C., Wang, Y., Song, L., Fang, Z., Han, R., Wang, Z., Wang, X., Yang, Z., et al. (2021) · BMC Medical Genomics · doi:10.1186/s12920-021-00948-5 · Cited by 42
“The 171 alleles validated by the Illumina 1M BeadChip were considered as “true-positive” calls 172 for YH [30].”
Self-citationPurdy, K. J., Hurd, P. J., Moya‐Laraño, J., Trimmer, M., Oakley, B. B., & Woodward, G. (2010) · Advances in ecological research/Advances in Ecological Research · doi:10.1016/b978-0-12-385005-8.00003-4 · Cited by 42
“, 2008), including humans (Ahn et al., 2009; Bentley et al., 2008; Kim et al., 2009; Wang et al., 2008).”
Next-generation sequencing of vertebrate experimental organisms
Turner, D., Keane, T., Sudbery, I. M., & Adams, D. J. (2009) · Mammalian Genome · doi:10.1007/s00335-009-9187-4 · Cited by 41
“…an endeavour has already commenced, first with the publication of the complete genomes of four individuals (Bentley et al. 2008; Levy et al. 2007; Wang et al. 2008; Wheeler et al. 2008), and now with the 1000 genomes project (www.1000genomes.org), which is using next-generation sequencing to…”
BackgroundMethodInfluentialDames, S. A., Durtschi, J., Geiersbach, K. B., Stephens, J., & Voelkerding, K. V. (2010) · PubMed Central · Cited by 39
Sequencing of Chloroplast Genome Using Whole Cellular DNA and Solexa Sequencing Technology
Wu, J., Liu, B., Cheng, F., Ramchiary, N., Choi, S. R., Lim, Y. P., & Wang, X. (2012) · Frontiers in Plant Science · doi:10.3389/fpls.2012.00243 · Cited by 39
“The nucleotide sequence was determined according to the Solexa sequencing method (Wang et al., 2008).”
MethodNext-generation sequencing applied to molecular diagnostics
Natrajan, R., & Reis-Filho, J. S. (2011) · Expert Review of Molecular Diagnostics · doi:10.1586/erm.11.18 · Cited by 41
Genome sequence and global sequence variation map with 5.5 million SNPs in Chinese rhesus macaque
Fang, X., Zhang, Y., Zhang, R., Yang, L., Li, M., Ye, K., Guo, X., Wang, J., & Su, B. (2011) · Genome biology · doi:10.1186/gb-2011-12-7-r63 · Cited by 39
“8%) were deletions since deletions are easier to detect, consistent with previous reports [20,21,23].”
MethodResultSelf-citationERGC: an efficient referential genome compression algorithm
Saha, S., & Rajasekaran, S. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv399 · Cited by 39
“Some notable algorithms such as Pavlichin et al. (2013), Deorowicz et al.”
MethodNGS catalog: A database of next generation sequencing studies in humans
Xia, J., Wang, Q., Jia, P., Wang, B., Pao, W. J., & Zhao, Z. (2012) · Human Mutation · doi:10.1002/humu.22096 · Cited by 39
Recent Advances in Understanding the Role of Nutrition in Human Genome Evolution
Ye, K., & Gu, Z. (2011) · Advances in Nutrition · doi:10.3945/an.111.001024 · Cited by 40
High-speed and high-ratio referential genome compression
Liu, Y., Peng, H., Wong, L., & Li, J. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx412 · Cited by 41
Self-citationHodoğlugil, U., Williamson, D. W., & Mahley, R. W. (2009) · Journal of Lipid Research · doi:10.1194/jlr.p001578 · Cited by 40
Tanisawa, K., Miyamoto‐Mikami, E., Fuku, N., Honda, Y., Honda, S., Ohsawa, I., Ito, M., Endo, S., Ihara, K., Ohno, K., et al. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-248 · Cited by 38
“Recent advances in next-generation sequencing technologies have made it possible to rapidly determine the DNA sequence of the whole genome of individual humans [12,13].”
BackgroundSequencing nucleic acids: from chemistry to medicine
Balasubramanian, S. (2011) · Chemical Communications · doi:10.1039/c1cc11078k · Cited by 39
Human genome at ten: The sequence explosion
(2010) · Nature · doi:10.1038/464670a · Cited by 40
Reference-Free Validation of Short Read Data
Schröder, J., Bailey, J., Conway, T., & Zobel, J. (2010) · PLoS ONE · doi:10.1371/journal.pone.0012681 · Cited by 39
“Practical experience demonstrates that short read data is feasible for the common tasks of re-sequencing or assembly [5,6].”
BackgroundAguado, C., Gayà‐Vidal, M., Villatoro, S., Oliva, M., Izquierdo, D., Giner-Delgado, C., Montalvo, V. E. O., García‐González, J., Martinez‐Fundichely, A., Capilla, L., et al. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004208 · Cited by 37
“With the development of sequencing techniques, it has been possible to identify inversions at a genome-wide level by sequence comparison [18,27,28] or paired-end sequencing and mapping (PEM) [20,23,25,29–32].”
Paving the Way to Personalized Genomic Medicine: Steps to Successful Implementation
Fackler, J., & McGuire, A. L. (2009) · Current pharmacogenomics and personalized medicine (Online)/Current pharmacogenomics and personalized medicine · doi:10.2174/187569209788653998 · Cited by 38
Reduced Representation Methods for Subgenomic Enrichment and Next-Generation Sequencing
Good, J. M. (2011) · Methods in molecular biology · doi:10.1007/978-1-61779-228-1_5 · Cited by 39
Moore, B., Hu, H., Singleton, M., Vega, F. M. D. L., Reese, M. G., & Yandell, M. D. (2011) · Genetics in Medicine · doi:10.1097/gim.0b013e31820ed321 · Cited by 37
Genome-wide association study of serious blistering skin rash caused by drugs
Shen, Y., Nicoletti, P., Floratos, A., Pirmohamed, M., Molokhia, M., Geppetti, P., Benemei, S., Giomi, B., Schena, D., Vultaggio, A., et al. (2011) · The Pharmacogenomics Journal · doi:10.1038/tpj.2010.84 · Cited by 37
Population Demographic History Can Cause the Appearance of Recombination Hotspots
Johnston, H. R., & Cutler, D. J. (2012) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2012.03.011 · Cited by 37
THE REFERENCE HUMAN GENOME DEMONSTRATES HIGH RISK OF TYPE 1 DIABETES AND OTHER DISORDERS
Chen, R., & Butte, A. J. (2010) · WORLD SCIENTIFIC eBooks · doi:10.1142/9789814335058_0025 · Cited by 35
Updating the Y-chromosomal phylogenetic tree for forensic applications based on whole genome SNPs
Geystelen, A. V., Decorte, R., & Larmuseau, M. (2013) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2013.03.010 · Cited by 36
Azam, S., Thakur, V., Ruperao, P., Shah, T. M., Balaji, J., Amindala, B., Farmer, A. D., Studholme, D. J., May, G. D., Edwards, D., et al. (2012) · American Journal of Botany · doi:10.3732/ajb.1100419 · Cited by 36
“…of reference genome sequences for human and several animal and plant species has triggered whole genome resequencing of genotypes of such species by using NGS technologies ( Bentley, 2006 ; Hillier et al., 2008 ; Hudson, 2008 ; Wang et al., 2008 ; Wheeler et al., 2008 ; Ahn et al., 2009 ).”
BackgroundExperimental Therapies in Hypertrophic Cardiomyopathy
Marian, A. J. (2009) · Journal of Cardiovascular Translational Research · doi:10.1007/s12265-009-9132-7 · Cited by 36
“The recent sequencing of individuals genomes clearly illustrates the presence of three to four million DNA sequence variants including several thousand insertions/deletions and copy number variants in each individual’s genome [5, 29, 35, 112, 113].”
Lucas‐Lledó, J. I., & Cáceres, M. (2013) · PLoS ONE · doi:10.1371/journal.pone.0061292 · Cited by 35
“, [11,12,27]; but see [10]) that are not suited to detect inversions between inverted repeats (Figure 5).”
BackgroundA new strategy for genome assembly using short sequence reads and reduced representation librariesPreprint
Young, A. L., Abaan, H. Ö., Zerbino, D. R., Mullikin, J. C., Birney, E., & Margulies, E. H. (2010) · Genome Research · doi:10.1101/gr.097956.109 · Cited by 37
“…current mammalian genomic analyses utilizing short-read sequencing technology either use alignments of individual reads against a reference genome (Ley et al. 2008; Wang et al. 2008) or require elaborate parallelization schemes across a large compute farm (Simpson et al. 2009) for assembly.”
BackgroundSequencing Your Genome: What Does it Mean?
Marian, A. J. (2014) · Methodist DeBakey Cardiovascular Journal · doi:10.14797/mdcj-10-1-3 · Cited by 38
“Common diseases such as coronary artery disease and hypertension are caused, at the genetic level, by combination of common and rare variants.”
Tucker, T., Montpetit, A., Chai, D., Chan, S. Y., Chénier, S., Coe, B. P., Delaney, A. D., Eydoux, P., Lam, W. L., Langlois, S., et al. (2011) · BMC Medical Genomics · doi:10.1186/1755-8794-4-25 · Cited by 37
“In fact, CNVs are the greatest source of genetic variation in normal people; the mean number of apparently benign CNVs observed ranges from 10’s1000’s per person, depending on the technology used [5-9].”
BackgroundCoGI: Towards Compressing Genomes as an Image
Xie, X., Zhou, S., & Guan, J. (2015) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2015.2430331 · Cited by 35
Genetic variations as cancer prognostic markers: review and update
Savas, S., & Liu, G. (2009) · Human Mutation · doi:10.1002/humu.21078 · Cited by 35
“One such application is the sequencing of the complete individual genome, as exemplified by the genome sequences of the three individuals published recently [Wang et al., 2008; Wheeler et al., 2008; Levy et al., 2007].”
BackgroundConsensus Rules in Variant Detection from Next-Generation Sequencing Data
Jia, P., Li, F., Xia, J., Chen, H., Ji, H., Pao, W. J., & Zhao, Z. (2012) · PLoS ONE · doi:10.1371/journal.pone.0038470 · Cited by 38
“Based on several recently sequenced individual genomes [10,11,12], a pattern has been recognized that, in general, approximately 3–4 million SNVs are expected to be found in a human genome by WGS when compared to the reference genome [13], and ,20,000 SNVs are to be found in a human exome by WES [14].”
BackgroundSequencing and analysis of a South Asian-Indian personal genome
Gupta, R. K., Ratan, A., Rajesh, C., Chen, R., Kim, H. L., Burhans, R. C., Miller, W., Santhosh, S., Davuluri, R. V., Butte, A. J., et al. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-440 · Cited by 34
“Genomes of individuals representing the Yoruba West-African, Han Chinese, South Korean, Khoisan and Bantu of Africa, Japanese, and Australian aborigines have also been published [14-19].”
BackgroundMendelian Randomization Studies Promise to Shorten the Journey to FDA Approval
Roberts, R. (2018) · JACC Basic to Translational Science · doi:10.1016/j.jacbts.2018.08.001 · Cited by 31
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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