Published Online:24 Nov 2005https://doi.org/10.1517/14622416.6.4.373
Abstract
Revolutionary new technologies, capable of transforming the economics of sequencing, are providing an unparalleled opportunity to analyze human genetic variation comprehensively at the whole-genome level within a realistic timeframe and at affordable costs. Current estimates suggest that it would cost somewhere in the region of US$30 million to sequence an entire human genome using Sanger-based sequencing, and on one machine it would take about 60 years. Solexa is widely regarded as a company with the necessary disruptive technology to be the first to achieve the ultimate goal of the so-called $1000 human genome – the conceptual cost-point needed for routine analysis of individual genomes. Solexa’s technology is based on completely novel sequencing chemistry capable of sequencing billions of individual DNA molecules simultaneously, a base at a time, to enable highly accurate, low cost analysis of an entire human genome in a single experiment. When applied over a large enough genomic region, these new approaches to resequencing will enable the simultaneous detection and typing of known, as well as unknown, polymorphisms, and will also offer information about patterns of linkage disequilibrium in the population being studied. Technological progress, leading to the advent of single-molecule-based approaches, is beginning to dramatically drive down costs and increase throughput to unprecedented levels, each being several orders of magnitude better than that which is currently available. A new sequencing paradigm based on single molecules will be faster, cheaper and more sensitive, and will permit routine analysis at the whole-genome level.
Keywords:
Papers of special note have been highlighted as either of interest (•) or of considerable interest (••) to readers.
Bibliography
- 1 Roses AD: Pharmacogenetics and future drug development and delivery. Lancet355, 1358–1361 (2000).
- 2 Bell JI: The double helix in clinical practice. Nature421, 414–416 (2003).
- 3 Botstein D, Risch N: Discovering genotypes underlying human phenotypes: past successes for Mendelian disease, future approaches for complex diseases. Nature Genet.33, 228–237 (2003).
- 4 Goldstein DB, Tate SK, Sisodiya SM: Pharmacogenetics goes genomic. Nature Rev. Genet.4, 937–947 (2003).
- 5 Zondervan KT, Cardon LR: The complex interplay among factors that influence allelic association. Nature Rev. Genet.5, 89–100 (2003).
- 6 Dahlman I, Eaves IA, Kosoy R et al.: Parameters for reliable results in genetic association studies in common disease. Nature Genet.30, 149–150 (2002).
- 7 Bennett ST, Lucassen AM, Gough SCL et al.: Susceptibility to human type 1 diabetes at IDDM2 is determined by tandem repeat variation at the insulin gene minisatellite locus. Nature Genet.9,284–292 (1995).
- 8 Ueda H, Howson JMM, Esposito L et al.: Association of the T-cell regulatory gene CTLA4 with susceptibility to autoimmune disease. Nature423, 506–511 (2003).
- 9 Ioannidis JPA, Ralston SH, Bennett ST et al.: Differential genetic effects of ESR1 polymorphisms on osteoporosis outcomes. JAMA292,2105–2114 (2004).
- 10 International Genome Sequencing Consortium: Initial sequencing and analysis of the human genome. Nature409, 860–921 (2001).
- 11 Venter JC, Adams MD, Myers EW et al.: The sequence of the human genome. Science291, 1304–1351 (2001).
- 12 Li WH, Sadler LA: Low nucleotide diversity in man. Genetics129, 513–523 (1991).
- 13 Wang DG, Fan JB, Siao CJ et al.: Large-scale identification, mapping, and genotyping of single nucleotide polymorphisms in the human genome. Science280, 1077–1082 (1998).
- 14 Cargill M, Altshuler D, Ireland J et al.: Characterization of single nucleotide polymorphisms in coding regions of human genes. Nature Genet.22, 231–238 (1991).
- 15 Halushka MK, Fan JB, Bentley K et al.: Patterns of single nucleotide polymorphisms in candidates genes for blood pressure homeostasis. Nature Genet.22, 239–247 (1999).
- 16 The International HapMap Consortium: The International HapMap Project. Nature426, 789–796 (2003).
- 17 Armour JA, Jeffreys AJ: Biology and applications of human minisatellites loci. Curr. Opin. Genet. Dev.6, 850–856 (1992).
- 18 Reed PW, Davies JL, Copeman JB et al.: Chromosome-specific microsatellite sets for fluorescence-based, semi-automated genome mapping. Nature Genet. 7, 390–395 (1994).
- 19 Kruglyak L, Nickerson DA: Variation is the spice of life. Nature Genet.27, 234–236 (2001).
- 20 Hinds DA, Stuve LL, Nilsen GB et al.: Whole-genome patterns of common DNA variation in three human populations. Science307, 1072–1079 (2005).
- 21 Johnson GCL, Esposito L, Barratt BJ et al.: Haplotype tagging for the identification of common disease genes. Nature Genet. 29, 233–237 (2001).
- 22 Salisbury BA, Pungliya M, Choi JY, Jiang R, Sun XJ, Stephens C: SNP and haplotype variation in the human genome. Mutat. Res.526, 53–61 (2003).
- 23 Sanger F: Determination of nucleotide sequences in DNA. Science214, 1205–1210 (1981).
- 24 Paegel BM, Blazej RG, Mathies RA: Microfluidic devices for DNA sequencing: sample preparation and electrophoretic analysis. Proc. Natl Acad. Sci. USA 100, 5926–5931 (2003).
- 25 Shendure J, Mitra RD, Varma C, Church GM: Advanced sequencing technologies: methods and goals. Nature Rev. Genet.5, 335–344 (2004).•• A thorough and balanced review of the various novel sequencing technologies in development, and the aspirations to reduce costs to the point at which genomes of individual humans could be sequenced as part of routine health care.
- 26 Zimmerman Z: The $1,000 Human Genome – Implications for Life Sciences, Healthcare and IT. IDC Publishers, Framingham, USA (2004).
- 27 Levine MJ et al: Zero-mode waveguides for single-molecule analysis at high concentrations. Science299, 682–686 (2003).
- 28 Tasara T, Angerer B, Damond M et al: Incorporation of reporter molecule-labeled nucleotides by DNA polymerases II. High-density labelling of natural DNA. Nucleic Acids Res.31(10), 2636–2646 (2003).
- 29 Brakmann S, Löbermann S: High-density labeling of DNA: preparation and characterization of the target material for single-molecule sequencing. Angew. Chem. Int. Ed.40(8), 1427–1429 (2001).
- 30 Deamer DW, Akeson M: Nanopores and nucleic acids: prospects for ultrarapid sequencing. Trends Biotechnol.4, 147–151 (2000).
- 31 Ashkenasy N, Sanchez-Quesada J, Bayley M, Ghadiri MR: Recognizing a single base in an individual DNA strand: a step toward DNA sequencing in nanopores. Angew. Chem. Int. Ed. Engl.44(9), 1401–1404 (2005).
- 32 Braslavsky I, Hebert B, Kartalov E, Quake SR: Sequence information can be obtained from single DNA molecules. Proc. Natl Acad. Sci. USA 100,3960–3964 (2003).•• The first study to demonstrate activity of DNA polymerase at the single-molecule level with single-base resolution and a high degree of parallelization, thus providing the foundation for a practical single-molecule sequencing technology.
- 33 Mitra RD, Church GM: In situ localized amplification and contact replication of many individual DNA molecules. Nucleic Acids Res.27, e34 (1999).
- 34 Mitra RD, Butty VL, Shendure J, Williams BR, Housman DE, Church GM: Digital genotyping and haplotyping with polymerase colonies. Proc. Natl Acad. Sci. USA 100, 5926–5931 (2003).
- 35 Adessi C, Matton G, Ayala G et al.: Solid phase DNA amplification: characterisation of primer attachment and amplification mechanisms. Nucleic Acids Res.15, e87 (2000).
- 36 Brenner S, Johnson M, Bridgham J et al.: In vitro cloning of complex mixtures of DNA on microbeads: Physical separation of differentially expressed cDNAs. Proc. Natl Acad. Sci. USA97, 1665–1670 (2000).
- 37 Leamon JH, Lee WL, Tartaro KR et al.: A massively parallel PicoTiterPlate™ based platform for discrete picoliter-scale polymerase chain reactions. Electrophoresis24, 3769–3777 (2003).
- 38 Brenner S, Johnson M, Bridgham J et al.: Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nature Biotechnol.6, 630–634 (2000). • The first commercially viable, multi-parallel, non-electrophoretic sequencing technology. A clever use of molecular biology for sequencing short reads of DNA.
- 39 Smit AFA: Interspersed repeats and other mementos of transposable elements in mammalian genomes. Curr. Opin. Genet. Dev. 9, 657–663 (1999).
- 101 www.illumina.com Illumina Inc., CA, USA.
- 102 www.perlegen.com Perlegen Sciences Inc., CA, USA.
- 103 www.solexa.com Solexa Ltd, Cambridge, UK & Solexa Inc., CA, USA.
- 104 www.nanofluidics.com Nanofluidics Inc., CA, USA.
- 105 www.helicosbio.com Helicos BioSciences Corporation, MA, USA.
- 106 www.solexa.com/news/2005/100305.htm Webpage reporting that Solexa completed first full genome sequence with cluster-SBS technology, 10th March 2005.
- 107 www.454.com 454 Life Sci. Corporation, CT, USA.
- 108 www.phrap.org Phil Green’s PHRAP web site.
- 109 www.ensembl.org Ensembl program team web site, European Bioinformatics Institute.
- 201 Jett JH, Keller RA, Martin JC et al.: Method for rapid base sequencing in DNA and RNA. WO8903432A1 (1989).
