Advanced sequencing technologies: methods and goals (original) (raw)

• 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
• National Human Genome Research Institute. Revolutionary Genome Sequencing Technologies — The $1000 Genome [online], <http://grants1.nih.gov/grants/guide/rfa-files/RFA-HG-04-003.html> (2004).
• National Human Genome Research Institute. Near-term Technology Development for Genome Sequencing [online], <http://grants.nih.gov/grants/guide/rfa-files/RFA-HG-04-002.html> (2004).
• Joneitz, E. Personal genomes. Technol. Rev. 104, 30 (2001).
  Google Scholar
• Pray, L. A cheap personal genome? The Scientist [online], <http://www.biomedcentral.com/news/20021004/04> (2002).
  Google Scholar
• Pennisi, E. Gene researchers hunt bargains, fixer-uppers. Science 298, 735–736 (2002).
  Article CAS PubMed Google Scholar
• Salisbury, M. W. Fourteen sequencing innovations that could change the way you work. Genome Technol. 35, 40–47 (2003).
  Google Scholar
• Carroll, S. B. Genetics and the making of Homo sapiens. Nature 422, 840–857 (2003).
  Google Scholar
• 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
• National Center for Biotechnology Information. GenBank Growth [online], <http://www.ncbi.nlm.nih.gov/Genbank/genbankstats.html> (2003).
• National Center for Biotechnology Information. NCBI Taxonomy Browser [online], <http://www.ncbi.nlm.nih.gov/Taxonomy/txstat.cgi?uncultured=hide&unspecified=hide&m=0> (2004).
• Integrated Genomics Inc. Genomes OnLine Database [online], <http://wit.integratedgenomics.com/GOLD> (2004).
• Venter, J. C. et al. Environmental genome shotgun sequencing of the Sargasso Sea. Science 4 Mar 2004 (doi:10.1126/science.1093857).
• Gibbs, R. A. et al. The International HapMap Project. Nature 426, 789–796 (2003).
  Article CAS Google Scholar
• Holtzman, N. A. & Marteau T. M. Will genetics revolutionize medicine? N. Engl. J. Med. 343, 141–144 (2000).
  Article CAS PubMed Google Scholar
• 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
• 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
• 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
• Kruglyak, L. Prospects for whole-genome linkage disequilibrium mapping of common disease genes. Nature Genet. 22, 139–144 (1999).
  Article CAS PubMed Google Scholar
• 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
• 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
• Hanahan, D. & Weinberg, R. A. The hallmarks of cancer. Cell 10, 51–70 (2000).
  Google Scholar
• 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
• Reif, J. H. Computing: Successes and challenges. Science 296, 478–479 (2002).
  Article CAS PubMed Google Scholar
• Organisation for Economic Cooperation and Development (OECD). Health Data: Total Expenditure on Health, per capita US$ PPP [online], <http://www.oecd.org/dataoecd/1/33/2957315.xls> (2003).
• Keith, J. M. et al. Unlocking hidden genomic sequence. Nucleic Acids Res. 32, e35 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• 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
• Koutny, L. et al. Eight hundred-base sequencing in a microfabricated electrophoretic device. Anal. Chem. 72, 3388–3391 (2000).
  Article CAS PubMed Google Scholar
• 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
• Drmanac, S. Accurate sequencing by hybridization for DNA diagnostics and individual genomics. Nature Biotechnol. 16, 54–58 (1998).
  Article CAS Google Scholar
• 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
• Lipshutz, R. J. et al. Using oligonucleotide probe arrays to access genetic diversity. Biotechniques 19, 442–447 (1995).
  CAS PubMed Google Scholar
• 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
• Kruglyak, L. & Nickerson, D. A. Variation is the spice of life. Nature Genet. 27, 234–236 (2001).
  Article CAS PubMed Google Scholar
• 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
• Church, G. M. & Gilbert, W. Genomic sequencing. Proc. Natl Acad. Sci. USA 81, 1991–1995 (1984).
  Article CAS PubMed PubMed Central Google Scholar
• Nowak, R. Getting the bugs worked out. Science 267, 172–174 (1995).
  Article CAS PubMed Google Scholar
• Ronaghi, M. Pyrosequencing sheds light on DNA sequencing. Genome Res. 11, 3–11 (2001).
  Article CAS PubMed Google Scholar
• 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
• 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
• 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
• 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
• 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).
• 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
• 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
• 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
• 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
• 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
• Hennig, C. AnyBase.nucleotides. GenoVoxx [online], <http://www.genovoxx.De> (2004).
• 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
• 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
• 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
• Nelson, J. R. et al. TempliPhi, phi29 DNA polymerase based rolling circle amplification of templates for DNA sequencing. Biotechniques (Suppl.), 44–47 (2002).
• 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
• 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
• 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
• Deamer, D. W. & Branton, D. Characterization of nucleic acids by nanopore analysis. Acc. Chem. Res. 35, 817–825 (2002).
  Article CAS PubMed Google Scholar
• 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
• 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
• 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
• Hardin, S. H. Technologies at VisiGen. VisiGen Biotechnologies, Inc. [online], <http://www.visigenbio.com/tech.html> (2004).
• Williams, J. Heterogenous assay for pyrophosphate. US Patent 6,306,607 (2001).
• 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.
• Cooper, D. N. et al. Statistics. Human Gene Mutation Database Cardiff (HGMD) [online], <http://archive.uwcm.ac.uk/uwcm/mg/docs/hahaha.Html> (2004).
• Oak Ridge National Laboratory. Genetics Privacy and Legislation. Human Genome Project Information [online], <http://www.ornl.gov/TechResources/Human_Genome/elsi/legislat.Html> (2003).
• 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
• Biotechnological Process Patent Act. Pub. L. No. 104–41, 104th Cong., lst Sess. (1 Nov 1995).
• Venter, J. C. A part of the human genome sequence. Science 299, 1183–1184 (2003).
  Article CAS PubMed Google Scholar
• Witelson, S. F., Kigar, D. L. & Harvey, T. The exceptional brain of Albert Einstein. Lancet 19, 2149–2153 (1999).
  Article Google Scholar
• National Library of Medicine. The Visible Human Project [online], <http://www.nlm.nih.gov/research/visible/visible_human.Html> (2003).
• U.S. Government. US Federal Government announcement of first Federal E-Gov Health Information Exchange Standards. egov Press Releases [online], <http://www.whitehouse.gov/omb/egov/press/chi_march.Htm> (2003).
• Nurses' Health Study at Brigham and Women's Hospital [online], <http://www.nurseshealthstudy.Org> (2003).
• Freimer, N. & Sabatti, C. The Human Phenome Project. Nature Genet. 3, 15–21 (2003).
  Article CAS Google Scholar
• Shendure, J. S., Mitra, R. D., Varma, C. & Church, G. M. Personal Genome Project [online], <http://arep.med.harvard.edu/PGP> (2004).
• Public Library of Science (PLoS) [online], <http://www.plos.org/cgi-bin/plosSigned.pl> (2004).
• SourceForge [online], <http://sourceforge.net> (2004).
• The GNU Prjoect [online], <http://www.gnu.org> (2004).
• 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
• 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
• Gilbert, W. DNA sequencing and gene structure. Science 214, 1305–1312 (1981).
  Article CAS PubMed Google Scholar
• Sanger, F. Sequences, sequences, and sequences. Annu. Rev. Biochem. 5, 1–28 (1988).
  Article Google Scholar
• Smith, L. M. et al. Fluorescence detection in automated DNA sequence analysis. Nature 321, 674–679 (1986).
  Article CAS PubMed Google Scholar
• Cook-Deegan, R. M. The Alta summit, December 1984. Genomics 5, 661–663 (1989).
  Article CAS PubMed Google Scholar
• Leder, P. Can the human genome project be saved from its critics ... and itself? Cell 63, 1–3 (1990).
  Article CAS PubMed Google Scholar
• Davis, B. D. The human genome and other initiatives. Science 249, 342–343 (1990).
  Article CAS PubMed Google Scholar
• Lander, E. S. et al. Initial sequencing and analysis of the human genome. Nature 409, 860–921 (2001).
  Article CAS PubMed Google Scholar
• Venter, J. C. et al. The sequence of the human genome. Science 291, 1304–1351 (2001).
  Article CAS PubMed Google Scholar
• Saha, S. et al. Using the transcriptome to annotate the genome. Nature Biotechnol. 20, 508–512 (2002).
  Article CAS Google Scholar
• Reymond, A. et al. Human chromosome 21 gene expression atlas in the mouse. Nature 420, 582–586 (2002).
  Article CAS PubMed Google Scholar
• 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
• 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
• 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
• Ramaswamy, S. et al. A molecular signature of metastasis in primary solid tumors. Nature Genet. 33, 49–54 (2003).
  Article CAS PubMed Google Scholar
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• Badarinarayana, V. et al. Selection analyses of insertional mutants using subgenic-resolution arrays. Nature Biotechnol. 1, 1060–1065 (2001).
  Article CAS Google Scholar
• 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
• 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
• 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
• Kurzweil, R. The 21st century: a confluence of accelerating revolutions. KurzweilAI.net [online], <http://www.kurzweilai.net/meme/frame.html?main=/articles/art0184.html> (2001).
• Zakon, R. F. Hobbes' Internet Timeline [online], <http://www.zakon.org/robert/internet/timeline> (2004).