Abstract
Innovative application of new technologies in research is one of the major factors driving advances in knowledge acquisition. In 1977, Maxam and Gilbert reported an approach in which terminally labeled DNA fragments were subjected to base-specific chemical cleavage and the reaction products were separated by gel electrophoresis (Maxam and Gilbert 1977). In an alternative approach, Sanger described the use of chain-terminating dideoxynucleotide analogs that caused base-specific termination of primed DNA synthesis (Sanger et al. 1977; Chap. 1). Improvements of the Sanger method led to utilization in the research community and eventually in the clinical diagnosis of many genetic disorders (http://www.ncbi.nlm.nih.gov/sites/GeneTests/). In a factory-based format, Sanger sequencing was the method of choice for the first human genome at an estimated cost of $2.7 billion (Fig. 1.1; Chap. 1). In 2008, by comparison, the genome of Dr. James Watson was sequenced over a 2-month period for less than $1 million (Wheeler et al. 2008). With the commercial availability of high-throughput massively parallel DNA sequencing platforms in the past few years, complete sequencing of the whole human genome can be done commercially today in 2–3 months at a cost below $10,000 (Bick and Dimmock 2011; Fig. 1.1). Since their introduction, next-generation sequencing (NGS) technologies have constantly improved and the costs have steadily decreased. A legitimate question therefore is what role targeted gene capture will play if whole-genome sequencing (WGS) can be done for about $1,000 in the future, with the ability to survey the human genome in an unbiased manner. This chapter describes NGS technologies and briefly explores how they have been translated into molecular diagnostics. The clinical applications of NGS will be covered in detail in Chaps. 4–8.
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References
1000 Genomes Project Consortium, Abecasis GR, Altshuler D et al (2010) A map of human genome variation from population-scale sequencing. Nature 467:1061–1073. doi:10.1038/nature09534
Abou Jamra R, Philippe O, Raas-Rothschild A et al (2011) Adaptor protein complex 4 deficiency causes severe autosomal-recessive intellectual disability, progressive spastic paraplegia, shy character, and short stature. Am J Hum Genet 88:788–795. doi:10.1016/j.ajhg.2011.04.019
Bao S, Jiang R, Kwan W et al (2011) Evaluation of next-generation sequencing software in mapping and assembly. J Hum Genet 56:406–414. doi:10.1038/jhg.2011.43
Barak T, Kwan KY, Louvi A et al (2011) Recessive LAMC3 mutations cause malformations of occipital cortical development. Nat Genet 43:590–594. doi:10.1038/ng.836
Bick D, Dimmock D (2011) Whole exome and whole genome sequencing. Curr Opin Pediatr 23:594–600. doi:10.1097/MOP.0b013e32834b20ec
Bilgüvar K, Oztürk AK, Louvi A et al (2010) Whole-exome sequencing identifies recessive WDR62 mutations in severe brain malformations. Nature 467:207–210. doi:10.1038/nature09327
Bolze A, Byun M, McDonald D et al (2010) Whole-exome-sequencing-based discovery of human FADD deficiency. Am J Hum Genet 87:873–881. doi:10.1016/j.ajhg.2010.10.028
Borgström E, Lundin S, Lundeberg J (2011) Large scale library generation for high throughput sequencing. PLoS One 6:e19119. doi:10.1371/journal.pone.0019119
Brkanac Z, Spencer D, Shendure J et al (2009) IFRD1 is a candidate gene for SMNA on chromosome 7q22-q23. Am J Hum Genet 84:692–697. doi:10.1016/j.ajhg.2009.04.008
Byun M, Abhyankar A, Lelarge V et al (2010) Whole-exome sequencing-based discovery of STIM1 deficiency in a child with fatal classic Kaposi sarcoma. J Exp Med 207:2307–2312. doi:10.1084/jem.20101597
Clark MJ, Chen R, Lam HYK et al (2011) Performance comparison of exome DNA sequencing technologies. Nat Biotechnol 29:908–914. doi:10.1038/nbt.1975
Eid J, Fehr A, Gray J et al (2009) Real-time DNA sequencing from single polymerase molecules. Science 323:133–138. doi:10.1126/science.1162986
Flusberg BA, Webster DR, Lee JH et al (2010) Direct detection of DNA methylation during single-molecule, real-time sequencing. Nat Methods 7:461–465. doi:10.1038/nmeth.1459
Huse SM, Huber JA, Morrison HG et al (2007) Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol 8:R143. doi:10.1186/gb-2007-8-7-r143
Kalay E, Yigit G, Aslan Y et al (2011) CEP152 is a genome maintenance protein disrupted in Seckel syndrome. Nat Genet 43:23–26. doi:10.1038/ng.725
Koboldt DC, Ding L, Mardis ER, Wilson RK (2010) Challenges of sequencing human genomes. Brief Bioinform 11:484–498. doi:10.1093/bib/bbq016
Krawitz PM, Schweiger MR, Rödelsperger C et al (2010) Identity-by-descent filtering of exome sequence data identifies PIGV mutations in hyperphosphatasia mental retardation syndrome. Nat Genet 42:827–829. doi:10.1038/ng.653
Kuhlenbäumer G, Hullmann J, Appenzeller S (2011) Novel genomic techniques open new avenues in the analysis of monogenic disorders. Hum Mutat 32:144–151. doi:10.1002/humu.21400
Ledergerber C, Dessimoz C (2011) Base-calling for next-generation sequencing platforms. Brief Bioinform 12:489–497. doi:10.1093/bib/bbq077
Lin X, Tang W, Ahmad S et al (2012) Applications of targeted gene capture and next-generation sequencing technologies in studies of human deafness and other genetic disabilities. Hear Res 288:67–76. doi:10.1016/j.heares.2012.01.004
Liu L, Li Y, Li S et al (2012) Comparison of next-generation sequencing systems. J Biomed Biotechnol 2012:251364. doi:10.1155/2012/251364
Mardis ER (2008) The impact of next-generation sequencing technology on genetics. Trends Genet 24:133–141. doi:10.1016/j.tig.2007.12.007
Margulies M, Egholm M, Altman WE et al (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376–380. doi:10.1038/nature03959
Maxam AM, Gilbert W (1977) A new method for sequencing DNA. Proc Natl Acad Sci U S A 74:560–564
Musunuru K, Pirruccello JP, Do R et al (2010) Exome sequencing, ANGPTL3 mutations, and familial combined hypolipidemia. N Engl J Med 363:2220–2227. doi:10.1056/NEJMoa1002926
Ng SB, Bigham AW, Buckingham KJ et al (2010a) Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome. Nat Genet 42:790–793. doi:10.1038/ng.646
Ng SB, Buckingham KJ, Lee C et al (2010b) Exome sequencing identifies the cause of a mendelian disorder. Nat Genet 42:30–35. doi:10.1038/ng.499
Nielsen R, Paul JS, Albrechtsen A, Song YS (2011) Genotype and SNP calling from next-generation sequencing data. Nat Rev Genet 12:443–451. doi:10.1038/nrg2986
Nikopoulos K, Gilissen C, Hoischen A et al (2010) Next-generation sequencing of a 40 Mb linkage interval reveals TSPAN12 mutations in patients with familial exudative vitreoretinopathy. Am J Hum Genet 86:240–247. doi:10.1016/j.ajhg.2009.12.016
Nothnagel M, Herrmann A, Wolf A et al (2011) Technology-specific error signatures in the 1000 Genomes Project data. Hum Genet 130:505–516. doi:10.1007/s00439-011-0971-3
Otto EA, Hurd TW, Airik R et al (2010) Candidate exome capture identifies mutation of SDCCAG8 as the cause of a retinal-renal ciliopathy. Nat Genet 42:840–850. doi:10.1038/ng.662
Pierce SB, Walsh T, Chisholm KM et al (2010) Mutations in the DBP-deficiency protein HSD17B4 cause ovarian dysgenesis, hearing loss, and ataxia of Perrault Syndrome. Am J Hum Genet 87:282–288. doi:10.1016/j.ajhg.2010.07.007
Puente XS, Quesada V, Osorio FG et al (2011) Exome sequencing and functional analysis identifies BANF1 mutation as the cause of a hereditary progeroid syndrome. Am J Hum Genet 88:650–656. doi:10.1016/j.ajhg.2011.04.010
Rehman AU, Morell RJ, Belyantseva IA et al (2010) Targeted capture and next-generation sequencing identifies C9orf75, encoding taperin, as the mutated gene in nonsyndromic deafness DFNB79. Am J Hum Genet 86:378–388. doi:10.1016/j.ajhg.2010.01.030
Rothberg JM, Hinz W, Rearick TM et al (2011) An integrated semiconductor device enabling non-optical genome sequencing. Nature 475:348–352. doi:10.1038/nature10242
Ruffalo M, LaFramboise T, Koyutürk M (2011) Comparative analysis of algorithms for next-generation sequencing read alignment. Bioinformatics (Oxf Engl) 27:2790–2796. doi:10.1093/bioinformatics/btr477
Ruparel H, Bi L, Li Z et al (2005) Design and synthesis of a 3’-O-allyl photocleavable fluorescent nucleotide as a reversible terminator for DNA sequencing by synthesis. Proc Natl Acad Sci U S A 102:5932–5937. doi:10.1073/pnas.0501962102
Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A 74:5463–5467
Shendure J, Porreca GJ, Reppas NB et al (2005) Accurate multiplex polony sequencing of an evolved bacterial genome. Science 309:1728–1732. doi:10.1126/science.1117389
Shoubridge C, Tarpey PS, Abidi F et al (2010) Mutations in the guanine nucleotide exchange factor gene IQSEC2 cause nonsyndromic intellectual disability. Nat Genet 42:486–488. doi:10.1038/ng.588
Simpson MA, Irving MD, Asilmaz E et al (2011) Mutations in NOTCH2 cause Hajdu-Cheney syndrome, a disorder of severe and progressive bone loss. Nat Genet 43:303–305. doi:10.1038/ng.779
Voelkerding KV, Dames SA, Durtschi JD (2009) Next-generation sequencing: from basic research to diagnostics. Clin Chem 55:641–658. doi:10.1373/clinchem.2008.112789
Volpi L, Roversi G, Colombo EA et al (2010) Targeted next-generation sequencing appoints c16orf57 as clericuzio-type poikiloderma with neutropenia gene. Am J Hum Genet 86:72–76. doi:10.1016/j.ajhg.2009.11.014
Walsh T, Shahin H, Elkan-Miller T et al (2010) 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 87:90–94. doi:10.1016/j.ajhg.2010.05.010
Wheeler DA, Srinivasan M, Egholm M et al (2008) The complete genome of an individual by massively parallel DNA sequencing. Nature 452:872–876. doi:10.1038/nature06884
Zheng J, Miller KK, Yang T et al (2011) Carcinoembryonic antigen-related cell adhesion molecule 16 interacts with alpha-tectorin and is mutated in autosomal dominant hearing loss (DFNA4). Proc Natl Acad Sci U S A 108:4218–4223. doi:10.1073/pnas.1005842108
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Valencia, C.A., Pervaiz, M.A., Husami, A., Qian, Y., Zhang, K. (2013). A Survey of Next-Generation–Sequencing Technologies. In: Next Generation Sequencing Technologies in Medical Genetics. SpringerBriefs in Genetics. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-9032-6_2
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