The impact of next-generation sequencing on genomics

a.
COE for Neurosciences, Department of Anesthesiology, Texas Tech University Health Sciences Center El Paso, TX 79905, USA
b.
Department of Biomedical Sciences, Texas Tech University Health Sciences Center El Paso, TX 79905, USA
c.
Internal Medicine, Texas Tech University Health Sciences Center El Paso, TX 79905, USA
d.
College of Life Sciences, Beijing Normal University, Beijing 100875, China

More Information

Corresponding author: E-mail address: jun.zhang2000@gmail.com (Jun Zhang)

摘要

- /
- /
- /
- /
- /
Abstract: This article reviews basic concepts, general applications, and the potential impact of next-generation sequencing (NGS) technologies on genomics, with particular reference to currently available and possible future platforms and bioinformatics. NGS technologies have demonstrated the capacity to sequence DNA at unprecedented speed, thereby enabling previously unimaginable scientific achievements and novel biological applications. But, the massive data produced by NGS also presents a significant challenge for data storage, analyses, and management solutions. Advanced bioinformatic tools are essential for the successful application of NGS technology. As evidenced throughout this review, NGS technologies will have a striking impact on genomic research and the entire biological field. With its ability to tackle the unsolved challenges unconquered by previous genomic technologies, NGS is likely to unravel the complexity of the human genome in terms of genetic variations, some of which may be confined to susceptible loci for some common human conditions. The impact of NGS technologies on genomics will be far reaching and likely change the field for years to come.
- Next-generation sequencing /
- Genomics /
- Genetic variation /
- Polymorphism /
- Targeted sequence enrichment /
- Bioinformatics

HTML全文

参考文献(97)

[1]	Ahn, S.M., Kim, T.H., Lee, S. et al. The first Korean genome sequence and analysis: full genome sequencing for a socio-ethnic group Genome Res., 19 (2009),pp. 1622-1629
[2]	Ansorge, W.J. Next-generation DNA sequencing techniques Nat. Biotechnol., 25 (2009),pp. 195-203
[3]	Bainbridge, M.N., Wang, M., Burgess, D.L. et al. Whole exome capture in solution with 3 Gbp of data Genome Biol., 11 (2010),p. R62
[4]	Bau, S., Schracke, N., Kranzle, M. et al. Targeted next-generation sequencing by specific capture of multiple genomic loci using low-volume microfluidic DNA arrays Anal. Bioanal. Chem., 393 (2009),pp. 171-175
[5]	Bilguvar, K., Ozturk, A.K., Louvi, A. et al. Nature, 467 (2010),pp. 207-210
[6]	Branton, D., Deamer, D.W., Marziali, A. et al. The potential and challenges of nanopore sequencing Nat. Biotechnol., 26 (2008),pp. 1146-1153
[7]	Capriotti, E., Calabrese, R., Casadio, R. Predicting the insurgence of human genetic diseases associated to single point protein mutations with support vector machines and evolutionary information Bioinformatics, 22 (2006),pp. 2729-2734
[8]	Chaisson, M.J., Brinza, D., Pevzner, P.A. Genome Res., 19 (2009),pp. 336-346
[9]	Chistoserdova, L. Recent progress and new challenges in metagenomics for biotechnology Biotechnol. Lett., 32 (2010),pp. 1351-1359
[10]	Daly, A.K. Genome-wide association studies in pharmacogenomics Nat. Rev. Genet., 11 (2010),pp. 241-246
[11]	Daly, A.K. Pharmacogenetics and human genetic polymorphisms Biochem. J., 429 (2010),pp. 435-449
[12]	Editorial Gathering clouds and a sequencing storm: why cloud computing could broaden community access to next-generation sequencing Nat. Biotechnol., 28 (2010),p. 1
[13]	Flicek, P., Birney, E. Sense from sequence reads: methods for alignment and assembly Nat. Methods, 6 (2009),pp. S6-S12
[14]	Frazer, K.A., Murray, S.S., Schork, N.J. et al. Human genetic variation and its contribution to complex traits Nat. Rev. Genet., 10 (2009),pp. 241-251
[15]	Fuller, C.W., Middendorf, L.R., Benner, S.A. et al. The challenges of sequencing by synthesis Nat. Biotechnol., 27 (2009),pp. 1013-1023
[16]	Gnirke, A., Melnikov, A., Maguire, J. et al. Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing Nat. Biotechnol., 27 (2009),pp. 182-189
[17]	Gonzalez-Angulo, A.M., Hennessy, B.T., Mills, G.B. Future of personalized medicine in oncology: a systems biology approach J. Clin. Oncol., 28 (2010),pp. 2777-2783
[18]	Gupta, P.K. Single-molecule DNA sequencing technologies for future genomics research Trends Biotechnol., 26 (2008),pp. 602-611
[19]	Harismendy, O., Ng, P.C., Strausberg, R.L. et al. Evaluation of next generation sequencing platforms for population targeted sequencing studies Genome Biol., 10 (2009),p. R32
[20]	Holmes, M.V., Shah, T., Vickery, C. et al. Fulfilling the promise of personalized medicine? Systematic review and field synopsis of pharmacogenetic studies PLoS ONE, 4 (2009),p. e7960
[21]	Huang, W., Marth, G. EagleView: a genome assembly viewer for next-generation sequencing technologies Genome Res., 18 (2008),pp. 1538-1543
[22]	Igartua, C., Turner, E.H., Ng, S.B. et al. Targeted enrichment of specific regions in the human genome by array hybridization Curr. Protoc. Hum. Genet., 66 (2010),pp. 18.3.1-18.3.14
[23]	Iqbal, S.M., Akin, D., Bashir, R. Solid-state nanopore channels with DNA selectivity Nat. Nanotechnol., 2 (2007),pp. 243-248
[24]	Jiang, H., Wong, W.H. SeqMap: mapping massive amount of oligonucleotides to the genome Bioinformatics, 24 (2008),pp. 2395-2396
[25]	Kim, J.I., Ju, Y.S., Park, H. et al. A highly annotated whole-genome sequence of a Korean individual Nature, 460 (2009),pp. 1011-1015
[26]	Lander, E.S., Linton, L.M., Birren, B. et al. Initial sequencing and analysis of the human genome Nature, 409 (2001),pp. 860-921
[27]	Langmead, B., Schatz, M.C., Lin, J. et al. Searching for SNPs with cloud computing Genome Biol., 10 (2009),p. R134
[28]	Levin, J.Z., Berger, M.F., Adiconis, X. et al. Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts Genome Biol., 10 (2009),p. R115
[29]	Levy, S., Sutton, G., Ng, P.C. et al. The diploid genome sequence of an individual human PLoS Biol., 5 (2007),p. e254
[30]	Ley, T.J., Mardis, E.R., Ding, L. et al. DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome Nature, 456 (2008),pp. 66-72
[31]	Li, H., Homer, N. A survey of sequence alignment algorithms for next-generation sequencing Brief Bioinform., 11 (2010),pp. 473-483
[32]	Li, H., Ruan, J., Durbin, R. Mapping short DNA sequencing reads and calling variants using mapping quality scores Genome Res., 18 (2008),pp. 1851-1858
[33]	Li, R., Li, Y., Kristiansen, K. et al. SOAP: short oligonucleotide alignment program Bioinformatics, 24 (2008),pp. 713-714
[34]	Li, R., Li, Y., Fang, X. et al. SNP detection for massively parallel whole-genome resequencing Genome Res., 19 (2009),pp. 1124-1132
[35]	Li, R., Zhu, H., Ruan, J. et al. Genome Res., 20 (2010),pp. 265-272
[36]	Lunshof, J.E., Bobe, J., Aach, J. et al. Personal genomes in progress: from the human genome project to the personal genome project Dialogues Clin. Neurosci., 12 (2010),pp. 47-60
[37]	Manolio, T.A., Collins, F.S., Cox, N.J. et al. Finding the missing heritability of complex diseases Nature, 461 (2009),pp. 747-753
[38]	Manske, H.M., Kwiatkowski, D.P. LookSeq: a browser-based viewer for deep sequencing data Genome Res., 19 (2009),pp. 2125-2132
[39]	Mardis, E.R. Anticipating the 1,000 dollar genome Genome Biol., 7 (2006),p. 112
[40]	Mardis, E.R. The impact of next-generation sequencing technology on genetics Trends Genet., 24 (2008),pp. 133-141
[41]	Mardis, E.R. Next-generation DNA sequencing methods Annu. Rev. Genomics Hum. Genet., 9 (2008),pp. 387-402
[42]	Mardis, E.R. New strategies and emerging technologies for massively parallel sequencing: applications in medical research Genome Med., 1 (2009),p. 40
[43]	Margulies, M., Egholm, M., Altman, W.E. et al. Genome sequencing in microfabricated high-density picolitre reactors Nature, 437 (2005),pp. 376-380
[44]	McKusick, V.A., Ruddle, F.H. Toward a complete map of the human genome Genomics, 1 (1987),pp. 103-106
[45]	McPherson, J.D. Next-generation gap Nat. Methods, 6 (2009),pp. S2-S5
[46]	Medvedev, P., Stanciu, M., Brudno, M. Computational methods for discovering structural variation with next-generation sequencing Nat. Methods, 6 (2009),pp. S13-S20
[47]	Metzker, M.L. Sequencing technologies – the next generation Nat. Rev. Genet., 11 (2010),pp. 31-46
[48]	Mocali, S., Benedetti, A. Exploring research frontiers in microbiology: the challenge of metagenomics in soil microbiology Res. Microbiol., 161 (2010),pp. 497-505
[49]	Nakken, S., Alseth, I., Rognes, T. Computational prediction of the effects of non-synonymous single nucleotide polymorphisms in human DNA repair genes Neuroscience, 145 (2007),pp. 1273-1279
[50]	Ng, P.C., Henikoff, S. Predicting deleterious amino acid substitutions Genome Res., 11 (2001),pp. 863-874
[51]	Ng, P.C., Henikoff, S. Accounting for human polymorphisms predicted to affect protein function Genome Res., 12 (2002),pp. 436-446
[52]	Ng, P.C., Kirkness, E.F. Whole genome sequencing Methods Mol. Biol., 628 (2010),pp. 215-226
[53]	Ng, P.C., Murray, S.S., Levy, S. et al. An agenda for personalized medicine Nature, 461 (2009),pp. 724-726
[54]	Ng, S.B., Buckingham, K.J., Lee, C. et al. Exome sequencing identifies the cause of a mendelian disorder Nat. Genet., 42 (2010),pp. 30-35
[55]	Ng, S.B., Bigham, A.W., Buckingham, K.J. et al. Nat. Genet., 42 (2010),pp. 790-793
[56]	Ng, S.B., Turner, E.H., Robertson, P.D. et al. Targeted capture and massively parallel sequencing of 12 human exomes Nature, 461 (2009),pp. 272-276
[57]	Novelli, G., Predazzi, I.M., Mango, R. et al. Role of genomics in cardiovascular medicine World J. Cardiol., 2 (2010),pp. 428-436
[58]	Pettersson, E., Lundeberg, J., Ahmadian, A. Generations of sequencing technologies Genomics, 93 (2009),pp. 105-111
[59]	Pop, M., Salzberg, S.L. Bioinformatics challenges of new sequencing technology Trends Genet., 24 (2008),pp. 142-149
[60]	Pussegoda, K.A. Exome sequencing: locating causative genes in rare disorders Clin. Genet., 78 (2010),pp. 32-33
[61]	Ramensky, V., Bork, P., Sunyaev, S. Human non-synonymous SNPs: server and survey Nucleic Acids Res., 30 (2002),pp. 3894-3900
[62]	Rehman, A.U., Morell, R.J., Belyantseva, I.A. et al. Targeted capture and next-generation sequencing identifies C9orf75, encoding taperin, as the mutated gene in nonsyndromic deafness DFNB79 Am. J. Hum. Genet., 86 (2010),pp. 378-388
[63]	Rios, J., Stein, E., Shendure, J. et al. Identification by whole-genome resequencing of gene defect responsible for severe hypercholesterolemia Hum. Mol. Genet., 19 (2010),pp. 4313-4318
[64]	Schatz, M.C. CloudBurst: highly sensitive read mapping with MapReduce Bioinformatics, 25 (2009),pp. 1363-1369
[65]	Schork, N.J., Murray, S.S., Frazer, K.A. et al. Common vs. rare allele hypotheses for complex diseases Curr. Opin. Genet. Dev., 19 (2009),pp. 212-219
[66]	Schuster, S.C. Next-generation sequencing transforms today’s biology Nat. Methods, 5 (2008),pp. 16-18
[67]	Senapathy, P., Bhasi, A., Mattox, J. et al. Targeted genome-wide enrichment of functional regions PLoS ONE, 5 (2010),p. e11138
[68]	Shendure, J., Ji, H. Next-generation DNA sequencing Nat. Biotechnol., 26 (2008),pp. 1135-1145
[69]	Shendure, J., Porreca, G.J., Reppas, N.B. et al. Accurate multiplex polony sequencing of an evolved bacterial genome Science, 309 (2005),pp. 1728-1732
[70]	Singleton, A.B., Hardy, J., Traynor, B.J. et al. Towards a complete resolution of the genetic architecture of disease Trends Genet., 26 (2010),pp. 438-442
[71]	Stone, E.A., Sidow, A. Physicochemical constraint violation by missense substitutions mediates impairment of protein function and disease severity Genome Res., 15 (2005),pp. 978-986
[72]	Stratton, M. Genome resequencing and genetic variation Nat. Biotechnol., 26 (2008),pp. 65-66
[73]	Summerer, D., Schracke, N., Wu, H. et al. Targeted high throughput sequencing of a cancer-related exome subset by specific sequence capture with a fully automated microarray platform Genomics, 95 (2010),pp. 241-246
[74]	Summerer, D., Wu, H., Haase, B. et al. Microarray-based multicycle-enrichment of genomic subsets for targeted next-generation sequencing Genome Res., 19 (2009),pp. 1616-1621
[75]	Sunyaev, S., Ramensky, V., Koch, I. et al. Prediction of deleterious human alleles Hum. Mol. Genet., 10 (2001),pp. 591-597
[76]	Teer, J.K., Mullikin, J.C. Exome sequencing: the sweet spot before whole genomes Hum. Mol. Genet., 19 (2010),pp. R145-R151
[77]	Tewhey, R., Nakano, M., Wang, X. et al. Enrichment of sequencing targets from the human genome by solution hybridization Genome Biol., 10 (2009),p. R116
[78]	Thusberg, J., Vihinen, M. Pathogenic or not? And if so, then how? Studying the effects of missense mutations using bioinformatics methods Hum. Mutat., 30 (2009),pp. 703-714
[79]	Treffer, R., Deckert, V. Recent advances in single-molecule sequencing Curr. Opin. Biotechnol., 21 (2010),pp. 4-11
[80]	Tsuji, S. Genetics of neurodegenerative diseases: insights from high-throughput resequencing Hum. Mol. Genet., 19 (2010),pp. R65-R70
[81]	Tucker, T., Marra, M., Friedman, J.M. Massively parallel sequencing: the next big thing in genetic medicine Am. J. Hum. Genet., 85 (2009),pp. 142-154
[82]	van Oeveren, J., Janssen, A. Mining SNPs from DNA sequence data; computational approaches to SNP discovery and analysis Methods Mol. Biol., 578 (2009),pp. 73-91
[83]	Venter, J.C., Levy, S., Stockwell, T. et al. Massive parallelism, randomness and genomic advances Nat. Genet., 33 (2003),pp. 219-227
[84]	Venter, J.C., Adams, M.D., Myers, E.W. et al. The sequence of the human genome Science, 291 (2001),pp. 1304-1351
[85]	Voelkerding, K.V., Dames, S.A., Durtschi, J.D. Next-generation sequencing: from basic research to diagnostics Clin. Chem., 55 (2009),pp. 641-658
[86]	Volpi, L., Roversi, G., Colombo, E.A. et al. Targeted next-generation sequencing appoints c16orf57 as clericuzio-type poikiloderma with neutropenia gene Am. J. Hum. Genet., 86 (2010),pp. 72-76
[87]	von Bubnoff, A. Next-generation sequencing: the race is on Cell, 132 (2008),pp. 721-723
[88]	Walsh, T., Shahin, H., Elkan-Miller, T. et al. Whole exome sequencing and homozygosity mapping identify mutation in the cell polarity protein GPSM2 as the cause of nonsyndromic hearing loss DFNB82 Am. J. Hum. Genet., 87 (2010),pp. 90-94
[89]	Wang, J., Wang, W., Li, R. et al. The diploid genome sequence of an Asian individual Nature, 456 (2008),pp. 60-65
[90]	Wheeler, D.A., Srinivasan, M., Egholm, M. et al. The complete genome of an individual by massively parallel DNA sequencing Nature, 452 (2008),pp. 872-876
[91]	Wold, B., Myers, R.M. Sequence census methods for functional genomics Nat. Methods, 5 (2008),pp. 19-21
[92]	Wooley, J.C., Godzik, A., Friedberg, I. A primer on metagenomics PLoS Comput. Biol., 6 (2010),p. e1000667
[93]	Xu, M., Fujita, D., Hanagata, N. Perspectives and challenges of emerging single-molecule DNA sequencing technologies Small, 5 (2009),pp. 2638-2649
[94]	Yang, M.Q., Athey, B.D., Arabnia, H.R. et al. High-throughput next-generation sequencing technologies foster new cutting-edge computing techniques in bioinformatics BMC Genomics, 10 (2009),p. I1
[95]	Yngvadottir, B., Macarthur, D.G., Jin, H. et al. The promise and reality of personal genomics Genome Biol., 10 (2009),p. 237
[96]	Zhang, W., Dolan, M.E. Impact of the 1000 genomes project on the next wave of pharmacogenomic discovery Pharmacogenomics, 11 (2010),pp. 249-256
[97]	Zheng, J., Moorhead, M., Weng, L. et al. High-throughput, high-accuracy array-based resequencing Proc. Natl. Acad. Sci. USA, 106 (2009),pp. 6712-6717