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Advanced sequencing technologies: methods and goals

Key Points

  • Several academic and commercial research groups are working to develop new ultra-low-cost sequencing (ULCS) technologies. These aim to reduce the cost of DNA sequencing by several orders of magnitude.

  • ULCS technology could potentially have an important impact on human health by enabling the sequencing of 'personal genomes' as a component of individualized health care.

  • Microelectrophoretic approaches borrow microfabrication techniques from the semiconductor industry to miniaturize and integrate the amplification, purification and electrophoretic sequencing of DNA.

  • Sequencing by hybridization involves highly parallel genomic resequencing. It is carried out by hybridizing target DNA to high-density microarrays that are designed to query the identity of individual bases.

  • Cyclic-array methods that operate on amplified templates include 'fluorescent in situ sequencing', Pyrosequencing and 'massively parallel signature sequencing'. Cyclic-array methods that aim to directly sequence single molecules are also under development.

  • Methods such as nanopore sequencing offer the prospect of non-cyclic, real-time, single-molecule sequencing.

  • The prospect of ULCS and personal genomes raises various important ethical, legal and social questions.


Nearly three decades have passed since the invention of electrophoretic methods for DNA sequencing. The exponential growth in the cost-effectiveness of sequencing has been driven by automation and by numerous creative refinements of Sanger sequencing, rather than through the invention of entirely new methods. Various novel sequencing technologies are being developed, each aspiring to reduce costs to the point at which the genomes of individual humans could be sequenced as part of routine health care. Here, we review these technologies, and discuss the potential impact of such a 'personal genome project' on both the research community and on society.

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Figure 1: Exponential growth in computing and sequencing.
Figure 2: Examples of microelectrophoretic sequencing and nanopore sequencing.
Figure 3: Examples of cyclic-array sequencing and sequencing by hybridization.


  1. Collins, F. S., Morgan, M. & Patrinos, A. The human genome project: lessons from large-scale biology. Science 300, 286–290 (2003). A retrospective analysis of the Human Genome Project that was written by the top-level management.

    Article  CAS  PubMed  Google Scholar 

  2. National Human Genome Research Institute. Revolutionary Genome Sequencing Technologies — The $1000 Genome [online], <> (2004).

  3. National Human Genome Research Institute. Near-term Technology Development for Genome Sequencing [online], <> (2004).

  4. Joneitz, E. Personal genomes. Technol. Rev. 104, 30 (2001).

    Google Scholar 

  5. Pray, L. A cheap personal genome? The Scientist [online], <> (2002).

    Google Scholar 

  6. Pennisi, E. Gene researchers hunt bargains, fixer-uppers. Science 298, 735–736 (2002).

    Article  CAS  PubMed  Google Scholar 

  7. Salisbury, M. W. Fourteen sequencing innovations that could change the way you work. Genome Technol. 35, 40–47 (2003).

    Google Scholar 

  8. Carroll, S. B. Genetics and the making of Homo sapiens. Nature 422, 840–857 (2003).

    Google Scholar 

  9. Ureta-Vidal, A., Ettwiller, L. & Birney, E. Comparative genomics: genome-wide analysis in metazoan eukaryotes. Nature Rev. Genet. 4, 251–62 (2003).

    Article  CAS  PubMed  Google Scholar 

  10. National Center for Biotechnology Information. GenBank Growth [online], <> (2003).

  11. National Center for Biotechnology Information. NCBI Taxonomy Browser [online], <> (2004).

  12. Integrated Genomics Inc. Genomes OnLine Database [online], <> (2004).

  13. Venter, J. C. et al. Environmental genome shotgun sequencing of the Sargasso Sea. Science 4 Mar 2004 (doi:10.1126/science.1093857).

  14. Gibbs, R. A. et al. The International HapMap Project. Nature 426, 789–796 (2003).

    Article  CAS  Google Scholar 

  15. Holtzman, N. A. & Marteau T. M. Will genetics revolutionize medicine? N. Engl. J. Med. 343, 141–144 (2000).

    Article  CAS  PubMed  Google Scholar 

  16. Vitkup, D., Sander, C. & Church, G. M. The amino-acid mutational spectrum of human genetic disease. Genome Biol. 4, R72 (2003).

    Article  PubMed  PubMed Central  Google Scholar 

  17. Farooqi, I. S. et al. Clinical spectrum of obesity and mutations in the melanocortin 4 receptor gene. N. Engl. J. Med. 348, 1085–1095 (2003).

    Article  CAS  PubMed  Google Scholar 

  18. Smirnova, I. et al. Assay of locus-specific genetic load implicates rare Toll-like receptor 4 mutations in meningococcal susceptibility. Proc. Natl Acad. Sci. USA 100, 6075–6080 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Kruglyak, L. Prospects for whole-genome linkage disequilibrium mapping of common disease genes. Nature Genet. 22, 139–144 (1999).

    Article  CAS  PubMed  Google Scholar 

  20. Merz J. F., McGee G. E. & Sankar P. 'Iceland Inc.'?: On the ethics of commercial population genomics. Soc. Sci. Med. 58, 1201–1209 (2004).

    Article  PubMed  Google Scholar 

  21. Rajagopalan, H., Nowak, M. A., Vogelstein, B. & Lengauer, C. The significance of unstable chromosomes in colorectal cancer. Nature Rev. Cancer 3, 695–701 (2003).

    Article  CAS  Google Scholar 

  22. Hanahan, D. & Weinberg, R. A. The hallmarks of cancer. Cell 10, 51–70 (2000).

    Google Scholar 

  23. Braich, R. S., Chelyapov, N., Johnson, C., Rothemund, P. W. & Adleman, L. Solution of a 20-variable 3-SAT problem on a DNA computer. Science 296, 499–450 (2002).

    Article  CAS  PubMed  Google Scholar 

  24. Reif, J. H. Computing: Successes and challenges. Science 296, 478–479 (2002).

    Article  CAS  PubMed  Google Scholar 

  25. Organisation for Economic Cooperation and Development (OECD). Health Data: Total Expenditure on Health, per capita US$ PPP [online], <> (2003).

  26. Keith, J. M. et al. Unlocking hidden genomic sequence. Nucleic Acids Res. 32, e35 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Emrich, C. A., Tian, H., Medintz, I. L. & Mathies, R. A. Microfabricated 384-lane capillary array electrophoresis bioanalyzer for ultrahigh-throughput genetic analysis. Anal. Chem. 74, 5076–5083 (2002).

    Article  CAS  PubMed  Google Scholar 

  28. Koutny, L. et al. Eight hundred-base sequencing in a microfabricated electrophoretic device. Anal. Chem. 72, 3388–3391 (2000).

    Article  CAS  PubMed  Google Scholar 

  29. Paegel, B. M., Blazej, R. G. & Mathies, R. A. Microfluidic devices for DNA sequencing: sample preparation and electrophoretic analysis. Curr. Opin. Biotechnol. 14, 42–50 (2003). A review from the Mathies group on the integration of sample preparation and microelectrophoretic sequencing within a single microfluidic device.

    Article  CAS  PubMed  Google Scholar 

  30. Drmanac, S. Accurate sequencing by hybridization for DNA diagnostics and individual genomics. Nature Biotechnol. 16, 54–58 (1998).

    Article  CAS  Google Scholar 

  31. Drmanac, R. et al. DNA sequencing by hybridization with arrays of samples or probes. Methods Mol. Biol. 170, 173–179 (2001).

    CAS  PubMed  Google Scholar 

  32. Lipshutz, R. J. et al. Using oligonucleotide probe arrays to access genetic diversity. Biotechniques 19, 442–447 (1995).

    CAS  PubMed  Google Scholar 

  33. Patil, N. et al. Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science 294, 1719–1723 (2001). Perlegen's discovery of SNPs and haplotypes on human chromosome 21 through sequencing by hybridization.

    Article  CAS  PubMed  Google Scholar 

  34. Kruglyak, L. & Nickerson, D. A. Variation is the spice of life. Nature Genet. 27, 234–236 (2001).

    Article  CAS  PubMed  Google Scholar 

  35. Reich, D. E., Gabriel, S. B. & Altshuler, D. Quality and completeness of SNP databases. Nature Genet. 33, 457–458 (2003).

    Article  CAS  PubMed  Google Scholar 

  36. Church, G. M. & Gilbert, W. Genomic sequencing. Proc. Natl Acad. Sci. USA 81, 1991–1995 (1984).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Nowak, R. Getting the bugs worked out. Science 267, 172–174 (1995).

    Article  CAS  PubMed  Google Scholar 

  38. Ronaghi, M. Pyrosequencing sheds light on DNA sequencing. Genome Res. 11, 3–11 (2001).

    Article  CAS  PubMed  Google Scholar 

  39. Gharizadeh, B., Nordstrom, T., Ahmadian, A., Ronaghi, M. & Nyren, P. Long-read Pyrosequencing using pure 2′-deoxyadenosine-5′-O′-(1-thiotriphosphate) Sp-isomer. Analyt. Biochem. 301, 82–90 (2002). Describes the relatively long reads (50–100 bases) obtained through improvements to the Pyrosequencing sequencing-by-synthesis method.

    Article  CAS  PubMed  Google Scholar 

  40. Mitra, R. D., Shendure, J., Olejnik, J., Olejnik, E. K. & Church, G. M. Fluorescent in situ sequencing on polymerase colonies. Analyt. Biochem. 320, 55–65 (2003). Introduces the cyclic-array sequencing-by-synthesis technology that is being developed in the Church and Mitra laboratories.

    Article  CAS  PubMed  Google Scholar 

  41. Brenner, S. et al. Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nature Biotechnol. 18, 630–634 (2000). Describes the 'massively parallel signature sequencing' (MPSS) technology that was developed by Lynx Therapeutics and involves cyclic-array sequencing by serial digestions, ligations and hybridizations.

    Article  CAS  Google Scholar 

  42. Leamon, J. H. et al. A massively parallel PicoTiterPlate based platform for discrete picoliter-scale polymerase chain reactions. Electrophoresis 24, 3769–2777 (2003).

    Article  CAS  PubMed  Google Scholar 

  43. Sarkis, G. et al. Sequence analysis of the pAdEasy-1 recombinant adenoviral construct using the 454 Life Sciences sequencing-by-synthesis method. NCBI AY370911, gi:34014919 (2003).

  44. Mitra, R. D. & Church, G. M. In situ localized amplification and contact replication of many individual DNA molecules. Nucleic Acids Res. 27, e34 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Mitra, R. D. et al. Digital genotyping and haplotyping with polymerase colonies. Proc. Natl Acad. Sci. USA 100, 5926–5931 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Dressman, D., Yan, H., Traverso, G., Kinzler, K. W. & Vogelstein, B. Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations. Proc. Natl Acad. Sci. USA 100, 8817–8822 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Metzker, M. L., et al. Termination of DNA synthesis by novel 3′-modified-deoxyribonucleoside 5—triphosphates. Nucleic Acids Res. 22, 4259–4267 (1994).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Welch, M. & Burgess, K. Synthesis of fluorescent, photolabile 3′-O-protected nucleoside triphosphates for the base addition sequencing scheme. Nucleosides Nucleotides 18, 197–199 (1999).

    Article  CAS  PubMed  Google Scholar 

  49. Hennig, C. AnyBase.nucleotides. GenoVoxx [online], <http://www.genovoxx.De> (2004).

  50. Braslavsky, I., Hebert, B., Kartalov, E. & Quake, S. R. Sequence information can be obtained from single DNA molecules. Proc. Natl Acad. Sci. USA 100, 3960–3964 (2003). A description of single-molecule cyclic-array sequencing.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Levene, M. J. et al. Zero-mode waveguides for single-molecule analysis at high concentrations. Science 299, 682–686 (2003). Describes the detection of single-nucleotide incorporation events in zeptolitre-scale observation volumes.

    Article  CAS  PubMed  Google Scholar 

  52. Dean, F. B. et al. Comprehensive human genome amplification using multiple displacement amplification. Proc. Natl Acad. Sci. USA 99, 5261–5266 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Nelson, J. R. et al. TempliPhi, phi29 DNA polymerase based rolling circle amplification of templates for DNA sequencing. Biotechniques (Suppl.), 44–47 (2002).

  54. Sorensen, K. J., Turteltaub, K., Vrankovich, G., Williams, J. & Christian, A. T. Whole-genome amplification of DNA from residual cells left by incidental contact. Anal. Biochem. 324, 312–314 (2004).

    Article  CAS  PubMed  Google Scholar 

  55. Rook, M. S., Delach, S. M., Deyneko, G., Worlock, A. & Wolfe, J. L. Whole genome amplification of DNA from laser capture-microdissected tissue for high-throughput single nucleotide polymorphism and short tandem repeat genotyping. Am. J. Pathol. 164, 23–33 (2003).

    Article  Google Scholar 

  56. Zhu, J., Shendure, J., Mitra, R. D. & Church, G. M. Single molecule profiling of alternative pre-mRNA splicing. Science 301, 836–838 (2003).

    Article  CAS  PubMed  Google Scholar 

  57. Deamer, D. W. & Branton, D. Characterization of nucleic acids by nanopore analysis. Acc. Chem. Res. 35, 817–825 (2002).

    Article  CAS  PubMed  Google Scholar 

  58. Li, J., Gershow, M., Stein, D., Brandin, E. & Golovchenko, J. A. DNA molecules and configurations in a solid-state nanopore microscope. Nature Mater. 2, 611–615 (2003).

    Article  CAS  Google Scholar 

  59. Deamer, D. W. & Akeson, M. Nanopores and nucleic acids: prospects for ultrarapid sequencing. Trends Biotechnol. 18, 147–151 (2000). A consideration of the successes and remaining challenges of nanopore sequencing.

    Article  CAS  PubMed  Google Scholar 

  60. Winters-Hilt, S. et al. Accurate classification of basepairs on termini of single DNA molecules. Biophys. J. 84, 967–976 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Hardin, S. H. Technologies at VisiGen. VisiGen Biotechnologies, Inc. [online], <> (2004).

  62. Williams, J. Heterogenous assay for pyrophosphate. US Patent 6,306,607 (2001).

  63. Robertson, J. A. The $1000 genome: ethical and legal issues in whole genome sequencing of individuals. Am. J. Bioeth. 3, W-IF1. (2003). A well-written overview of the ethical and legal implications of personal genomes.

  64. Cooper, D. N. et al. Statistics. Human Gene Mutation Database Cardiff (HGMD) [online], <> (2004).

  65. Oak Ridge National Laboratory. Genetics Privacy and Legislation. Human Genome Project Information [online], <> (2003).

  66. Gostin, L. O., Hodge, J. G. & Calvo, C. Genetics Policy & Law: A Report for Policymakers (National Council of State Legislators, Washington DC, 2001).

    Google Scholar 

  67. Biotechnological Process Patent Act. Pub. L. No. 104–41, 104th Cong., lst Sess. (1 Nov 1995).

  68. Venter, J. C. A part of the human genome sequence. Science 299, 1183–1184 (2003).

    Article  CAS  PubMed  Google Scholar 

  69. Witelson, S. F., Kigar, D. L. & Harvey, T. The exceptional brain of Albert Einstein. Lancet 19, 2149–2153 (1999).

    Article  Google Scholar 

  70. National Library of Medicine. The Visible Human Project [online], <> (2003).

  71. U.S. Government. US Federal Government announcement of first Federal E-Gov Health Information Exchange Standards. egov Press Releases [online], <> (2003).

  72. Nurses' Health Study at Brigham and Women's Hospital [online], <http://www.nurseshealthstudy.Org> (2003).

  73. Freimer, N. & Sabatti, C. The Human Phenome Project. Nature Genet. 3, 15–21 (2003).

    Article  CAS  Google Scholar 

  74. Shendure, J. S., Mitra, R. D., Varma, C. & Church, G. M. Personal Genome Project [online], <> (2004).

  75. Public Library of Science (PLoS) [online], <> (2004).

  76. SourceForge [online], <> (2004).

  77. The GNU Prjoect [online], <> (2004).

  78. Sanger, F., Nicklen, S. & Coulson, A. R. DNA sequencing with chain-terminating inhibitors. Proc. Natl Acad. Sci. USA 74, 5463–5467 (1977).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  79. Maxam, A. M. & Gilbert, W. A new method for sequencing DNA. Proc. Natl Acad. Sci. USA 74, 560–564 (1977).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Gilbert, W. DNA sequencing and gene structure. Science 214, 1305–1312 (1981).

    Article  CAS  PubMed  Google Scholar 

  81. Sanger, F. Sequences, sequences, and sequences. Annu. Rev. Biochem. 5, 1–28 (1988).

    Article  Google Scholar 

  82. Smith, L. M. et al. Fluorescence detection in automated DNA sequence analysis. Nature 321, 674–679 (1986).

    Article  CAS  PubMed  Google Scholar 

  83. Cook-Deegan, R. M. The Alta summit, December 1984. Genomics 5, 661–663 (1989).

    Article  CAS  PubMed  Google Scholar 

  84. Leder, P. Can the human genome project be saved from its critics ... and itself? Cell 63, 1–3 (1990).

    Article  CAS  PubMed  Google Scholar 

  85. Davis, B. D. The human genome and other initiatives. Science 249, 342–343 (1990).

    Article  CAS  PubMed  Google Scholar 

  86. Lander, E. S. et al. Initial sequencing and analysis of the human genome. Nature 409, 860–921 (2001).

    Article  CAS  PubMed  Google Scholar 

  87. Venter, J. C. et al. The sequence of the human genome. Science 291, 1304–1351 (2001).

    Article  CAS  PubMed  Google Scholar 

  88. Saha, S. et al. Using the transcriptome to annotate the genome. Nature Biotechnol. 20, 508–512 (2002).

    Article  CAS  Google Scholar 

  89. Reymond, A. et al. Human chromosome 21 gene expression atlas in the mouse. Nature 420, 582–586 (2002).

    Article  CAS  PubMed  Google Scholar 

  90. Hahn, W. C. & Weinberg, R. A. Mechanisms of disease: rules for making human tumor cells. N. Engl. J. Med. 34, 1593–1603 (2002).

    Article  Google Scholar 

  91. Paulson, T. G., Galipeau, P. C. & Reid, B. J. Loss of heterozygosity analysis using whole genome amplification, cell sorting, and fluorescence-based PCR. Genome Res. 9, 482–491 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  92. Golub, T. R. et al. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 286, 531–537 (1999).

    Article  CAS  PubMed  Google Scholar 

  93. Ramaswamy, S. et al. A molecular signature of metastasis in primary solid tumors. Nature Genet. 33, 49–54 (2003).

    Article  CAS  PubMed  Google Scholar 

  94. Weber, G., Shendure, J., Tanenbaum, D. M., Church, G. M., & Meyerson, M. Microbial sequence identification by computational subtraction of the human transcriptome. Nature Genet. 30, 141–142 (2002).

    Article  CAS  PubMed  Google Scholar 

  95. Stenger, D. A., Andreadis, J. D., Vora, G. J. & Pancrazio, J. J. Potential applications of DNA microarrays in biodefense-related diagnostics. Curr. Opin. Biotechnol. 13, 208–212 (2002).

    Article  CAS  PubMed  Google Scholar 

  96. Boffelli, D. et al. Phylogenetic shadowing of primate sequences to find functional regions of the human genome. Science 299, 1391–1394 (2003).

    Article  CAS  PubMed  Google Scholar 

  97. Roberts, G. C. & Smith, C. W. Alternative splicing: combinatorial output from the genome. Curr. Opin. Chem. Biol. 6, 375–383 (2002).

    Article  CAS  PubMed  Google Scholar 

  98. Robyr, D. et al. Microarray deacetylation maps determine genome-wide functions for yeast histone deacetylases. Cell 109, 437–446 (2002).

    Article  CAS  PubMed  Google Scholar 

  99. Yatabe, Y., Tavare, S. & Shibata, D. Investigating stem cells in human colon by using methylation patterns. Proc. Natl Acad. Sci. USA 9, 10839–10844 (2001).

    Article  Google Scholar 

  100. Dymecki, S. M., Rodriguez, C. I. & Awatramani, R. B. Switching on lineage tracers using site-specific recombination. Methods Mol. Biol. 18, 309–334 (2002).

    Google Scholar 

  101. Lenski, R. E., Winkworth, C. L. & Riley, M. A. Rates of DNA sequence evolution in experimental populations of Escherichia coli during 20,000 generations. J. Mol. Evol. 56, 498–508 (2003).

    Article  CAS  PubMed  Google Scholar 

  102. Cooper, T. F., Rozen, D. E. & Lenski, R. E. Parallel changes in gene expression after 20,000 generations of evolution in Escherichia coli. Proc. Natl Acad. Sci. USA 100, 1072–1077 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  103. Gillespie, D. E. et al. Isolation of antibiotics turbomycin a and B from a metagenomic library of soil microbial DNA. Appl. Environ. Microbiol. 68, 4301–4306 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  104. Badarinarayana, V. et al. Selection analyses of insertional mutants using subgenic-resolution arrays. Nature Biotechnol. 1, 1060–1065 (2001).

    Article  CAS  Google Scholar 

  105. Sassetti, C. M., Boyd D. H. & Rubin E. J. Genes required for mycobacterial growth defined by high density mutagenesis. Mol. Microbiol. 48, 77–84 (2003).

    Article  CAS  PubMed  Google Scholar 

  106. Cerchia, L., Hamm, J., Libri, D., Tavitian, B. & de Franciscis, V. Nucleic acid aptamers in cancer medicine. FEBS Lett. 528, 12–16 (2002).

    Article  CAS  PubMed  Google Scholar 

  107. Cutler, D. J. et al. High-throughput variation detection and genotyping using microarrays. Genome Res. 11, 1913–1925 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  108. Kurzweil, R. The 21st century: a confluence of accelerating revolutions. [online], <> (2001).

  109. Zakon, R. F. Hobbes' Internet Timeline [online], <> (2004).

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The authors thank members of the polony community and C. Hennig for sharing unpublished work, T. Wu and G. Porreca for helpful discussions, and R. Shendure and K. McKernan for critical reading of the manuscript.

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sickle-cell anaemia


International HapMap Project

Personal Genome Project

Revolutionary Genome Sequencing Technologies — The $1000 Genome



A commitment that was made in Bermuda (February 1996) by an international assortment of genome-research sponsors to the principles of public sharing and the rapid release of human genome sequence information.


(SNPs). Those single-nucleotide substitutions that occur with an allelic frequency of more than 1% in a given population.


A technique that involves the use of combinations of 'common' DNA polymorphisms to find blocks of association with phenotypic traits.


Describes situations in which a similar phenotype can result from various genetic defects.


A discipline that embraces the emerging ability to design, synthesize and evolve new genomes or biomimetic systems.


The annotation of functional elements in a genome through bioinformatic comparisons to the genomes of one or more related species.


The evolution of a protein (or organism) in the laboratory through rounds of mutation and selection for a particular activity or trait.


A cyclical, polymerase-driven sequencing method in which nucleotides are modified with fluorescent labels that can be chemically removed at each step.


The heritable component of variation among individuals with respect to drug response or adverse reaction.


(Chain termination or dideoxy method). A technique that uses an enzymatic procedure to synthesize DNA chains of varying length in four different reactions, stopping the DNA replication at positions that are occupied by one of the four bases, and then determining the resulting fragment lengths to decipher the sequence.


A colony of PCR amplicons that is derived from a single molecule of nucleic acid, amplified in situ in an acrylamide gel.


A type of restriction endonuclease that is characterized by an asymmetric recognition site and cleavage at a fixed distance outside the recognition site.


The actual nucleotide sequence that is generated by a sequencing instrument. This contrasts with the finished sequence, which is produced by obtaining the consensus sequence of many overlapping raw reads.


(FRET). A phenomenon by which excitation is transferred from a donor fluorescent molecule to an acceptor fluorescent molecule; the interaction is distance-dependent and can be used to probe molecular interactions at distances below the limit of optical resolution.


A nanostructure device with physical properties that markedly limit the effective volume of observation.


The progressive loss of synchronization between templates within features as a consequence of the failure to achieve 100% extension at each extension cycle.


A technique for achieving whole-genome amplification that uses a strand-displacing polymerase to catalyse the isothermal (that is, at a constant temperature) amplification of DNA.


(WGA). The in vitro amplification of a full genome sequence, ideally with even representation of the genome in the amplified product. Techniques for achieving WGA include PCR primed with random or degenerate oligonucleotides, or multiple-displacement amplification.


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Shendure, J., Mitra, R., Varma, C. et al. Advanced sequencing technologies: methods and goals. Nat Rev Genet 5, 335–344 (2004).

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