Wold, B. & Myers, R. M. Sequence census methods for functional genomics. Nature Methods5, 19–21 (2008). CASPubMed Google Scholar
Wang, Z., Gerstein, M. & Snyder, M. RNA-Seq: a revolutionary tool for transcriptomics. Nature Rev. Genet.10, 57–63 (2009). The Review provides a comprehensive overview of recent advances and challenges in techniques that are used in transcriptome profiling methods that use NGS technologies (RNA–seq).
Branton, D. et al. The potential and challenges of nanopore sequencing. Nature Biotech.26, 1146–1153 (2008). An excellent review of the current state of nanopore sequencing that highlights recent accomplishments and remaining challenges in the field. CAS Google Scholar
Fan, J.-B., Chee, M. S. & Gunderson, K. L. Highly parallel genomic assays. Nature Rev. Genet.7, 632–644 (2006). CASPubMed Google Scholar
Pop, M. & Salzberg, S. L. Bioinformatics challenges of new sequencing technology. Trends Genet.24, 142–149 (2008). CASPubMedPubMed 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. USA100, 8817–8822 (2003). CASPubMedPubMed Central Google Scholar
Fedurco, M., Romieu, A., Williams, S., Lawrence, I. & Turcatti, G. BTA, a novel reagent for DNA attachment on glass and efficient generation of solid-phase amplified DNA colonies. Nucleic Acids Res.34, e22 (2006). PubMedPubMed Central Google Scholar
Shendure, J. et al. Accurate multiplex polony sequencing of an evolved bacterial genome. Science309, 1728–1732 (2005). This paper describes the development of the non-cleavable SBL method and shows its feasibility by sequencing theE. coligenome. The prototype described led to the development of the Polonator instrument. CASPubMed Google Scholar
Kim, J. B. et al. Polony multiplex analysis of gene expression (PMAGE) in mouse hypertrophic cardiomyopathy. Science316, 1481–1484 (2007). CASPubMed Google Scholar
Leamon, J. H. A massively parallel PicoTiterPlate based platform for discrete picoliter-scale polymerase chain reactions. Electrophoresis24, 3769–3777 (2003). CASPubMed Google Scholar
Harris, T. D. et al. Single-molecule DNA sequencing of a viral genome. Science320, 106–109 (2008). Developers from Helicos BioSciences and colleagues describe the development of the first single-molecule sequencing method using reversible terminators and demonstrate the technology by sequencing the M13 genome. CASPubMed Google Scholar
Eid, J. et al. Real-time DNA sequencing from single polymerase molecules. Science323, 133–138 (2009). The authors describe the development of a real-time sequencing method using their ZMW detection system and demonstrate its feasibility by sequencing synthetic templates. CASPubMed Google Scholar
Hardin, S., Gao, X., Briggs, J., Willson, R. & Tu, S.-C. Methods for real-time single molecule sequence determination. US Patent 7,329,492 (2000). Google Scholar
Williams, J. G. K. System and methods for nucleic acid sequencing of single molecules by polymerase synthesis. US Patent 6,255,083 (1998). Google Scholar
Erlich, Y., Mitra, P. P., delaBastide, M., McCombie, W. R. & Hannon, G. J. Alta-Cyclic: a self-optimizing base caller for next-generation sequencing. Nature Methods5, 679–682 (2008). CASPubMedPubMed Central Google Scholar
Metzker, M. L. et al. Termination of DNA synthesis by novel 3′-modified deoxyribonucleoside triphosphates. Nucleic Acids Res.22, 4259–4267 (1994). CASPubMedPubMed Central Google Scholar
Canard, B. & Sarfati, R. DNA polymerase fluorescent substrates with reversible 3′-tags. Gene148, 1–6 (1994). CASPubMed Google Scholar
Ju, J. et al. Four-color DNA sequencing by synthesis using cleavable fluorescent nucleotide reversible terminators. Proc. Natl. Acad. Sci. USA103, 19635–19640 (2006). CASPubMedPubMed Central Google Scholar
Guo, J. et al. Four-color DNA sequencing with 3′-_O_-modified nucleotide reversible terminators and chemically cleavable fluorescent dideoxynucleotides. Proc. Natl Acad. Sci. USA105, 9145–9150 (2008). CASPubMedPubMed Central Google Scholar
Bentley, D. R. et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature456, 53–59 (2008). Developers from Illumina/Solexa and colleagues report details on their reversible terminator platform and demonstrate the technology by sequencing a flow-sorted X chromosome and the genome from a Yoruban male. CASPubMedPubMed Central Google Scholar
Dohm, J. C., Lottaz, C., Borodina, T. & Himmelbauer, H. Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res.36, e105 (2008). PubMedPubMed Central Google Scholar
Hillier, L. W. et al. Whole-genome sequencing and variant discovery in C. elegans. Nature Methods5, 183–188 (2008). CASPubMed Google Scholar
Harismendy, O. et al. Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biol.10, R32 (2009). PubMedPubMed Central Google Scholar
Li, H., Ruan, J. & Durbin, R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res.18, 1851–1858 (2008). CASPubMedPubMed Central Google Scholar
Frazer, K. A., Murray, S. S., Schork, N. J. & Topol, E. J. Human genetic variation and its contribution to complex traits. Nature Rev. Genet.10, 241–251 (2009). CASPubMed Google Scholar
Ley, T. J. et al. DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature456, 66–72 (2008). CASPubMedPubMed Central Google Scholar
Sarin, S., Prabhu, S., O'Meara, M. M., Pe'er, I. & Hobert, O. Caenorhabditis elegans mutant allele identification by whole-genome sequencing. Nature Methods5, 865–867 (2008). CASPubMedPubMed Central Google Scholar
Wu, W. et al. Termination of DNA synthesis by N _6_-alkylated, not 3′-_O_-alkylated, photocleavable 2′-deoxyadenosine triphosphates. Nucleic Acid Res.35, 6339–6349 (2007). CASPubMedPubMed Central Google Scholar
Wu, W., Litosh, V. A., Stupi, B. P. & Metzker, M. L. Photocleavable labeled nucleotides and nucleosides and methods for their use in DNA sequencing. US Patent Application 11/567,189 (2009). Google Scholar
Bowers, J. et al. Virtual terminator nucleotides for next-generation DNA sequencing. Nature Methods6, 593–595 (2009). CASPubMedPubMed Central Google Scholar
Braslavsky, I., Hebert, B., Kartalov, E. & Quake, S. R. Sequence information can be obtained from single DNA molecules. Proc. Natl. Acad. Sci. USA100, 3960–3964 (2003). CASPubMedPubMed Central Google Scholar
Tomkinson, A. E., Vijayakumar, S., Pascal, J. M. & Ellenberger, T. DNA ligases: structure, reaction mechanism, and function. Chem. Rev.106, 687–699 (2006). CASPubMed Google Scholar
Landegren, U., Kaiser, R., Sanders, J. & Hood, L. A ligase-mediated gene detection technique. Science241, 1077–1080 (1988). CASPubMed Google Scholar
Valouev, A. et al. A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Res.18, 1051–1063 (2008). This paper describes Life/APG's SBL method, which uses cleavable two-base-encoded probes on the SOLiD platform. The authors demonstrate the technology through the application of genome-wide nucleosome mapping inC. elegans . CASPubMedPubMed Central Google Scholar
Shen, Y., Sarin, S., Liu, Y., Hobert, O. & Pe'er, I. Comparing platforms for C. elegans mutant identification using high-throughput whole-genome sequencing. PLoS ONE3, e4012 (2008). PubMedPubMed Central Google Scholar
Ronaghi, M., Uhlén, M. & Nyrén, P. A sequencing method based on real-time pyrophosphate. Science281, 363–365 (1998). CASPubMed Google Scholar
Ronaghi, M., Karamohamed, S., Pettersson, B., Uhlén, M. & Nyrén, P. Real-time DNA sequencing using detection of pyrophosphate release. Anal. Biochem.242, 84–89 (1996). CASPubMed Google Scholar
Margulies, M. et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature437, 376–380 (2005). The authors describe the development of the first NGS technology using the pyrosequencing method and demonstrate its feasibility through the sequencing andde novoassembly of theMycoplasma genitaliumgenome. CASPubMedPubMed Central Google Scholar
Metzker, M. L. Sequencing in real time. Nature Biotech.27, 150–151 (2009). CAS Google Scholar
Levene, M. J. et al. Zero-mode waveguides for single-molecule analysis at high concentrations. Science299, 682–686 (2003). CASPubMed Google Scholar
Trapnell, C. & Salzberg, S. L. How to map billions of short reads onto genomes. Nature Biotech.27, 455–457 (2009). CAS Google Scholar
Chaisson, M. J., Brinza, D. & Pevzner, P. A. De novo fragment assembly with short mate-paired reads: does the read length matter? Genome Res.19, 336–346 (2009). CASPubMedPubMed Central Google Scholar
Hofreuter, D. et al. Unique features of a highly pathogenic Campylobacter jejuni strain. Infect. Immun.74, 4694–4707 (2006). CASPubMedPubMed Central Google Scholar
Holt, K. E. et al. High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi. Nature Genet.40, 987–993 (2008). CASPubMed Google Scholar
Srivatsan, A. et al. High-precision, whole-genome sequencing of laboratory strains facilitates genetic studies. PLoS Genet.4, e1000139 (2008). PubMedPubMed Central Google Scholar
Suchland, R. J. et al. Identification of concomitant infection with Chlamydia trachomatis IncA-negative mutant and wild-type strains by genomic, transcriptional, and biological characterizations. Infect. Immun.76, 5438–5446 (2008). CASPubMedPubMed Central Google Scholar
Nusbaum, C. et al. Sensitive, specific polymorphism discovery in bacteria using massively parallel sequencing. Nature Methods6, 67–69 (2009). CASPubMed Google Scholar
Moran, N. A., McLaughlin, H. J. & Sorek, R. The dynamics and time scale of ongoing genomic erosion in symbiotic bacteria. Science323, 379–382 (2009). CASPubMed Google Scholar
Ossowski, S. et al. Sequencing of natural strains of Arabidopsis thaliana with short reads. Genome Res.18, 2024–2033 (2008). CASPubMedPubMed Central Google Scholar
Korbel, J. O. et al. Paired-end mapping reveals extensive structural variation in the human genome. Science318, 420–426 (2007). CASPubMedPubMed Central Google Scholar
Kidd, J. M. et al. Mapping and sequencing of structural variation from eight human genomes. Nature453, 56–64 (2008). CASPubMedPubMed Central Google Scholar
Warren, R. L., Sutton, G. G., Jones, S. J. M. & Holt, R. A. Assembling millions of short DNA sequences using SSAKE. Bioinformatics23, 500–501 (2007). CASPubMed Google Scholar
Chaisson, M. J. & Pevzner, P. A. Short read fragment assembly of bacterial genomes. Genome Res.18, 324–330 (2008). CASPubMedPubMed Central Google Scholar
Hernandez, D., François, P., Farinelli, L., Østerås, M. & Schrenzel, J. De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer. Genome Res.18, 802–809 (2008). CASPubMedPubMed Central Google Scholar
Zerbino, D. R. & Birney, E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res.18, 821–829 (2008). CASPubMedPubMed Central Google Scholar
Aury, J.-M. et al. High quality draft sequences for prokaryotic genomes using a mix of new sequencing technologies. BMC Genomics9, 603 (2008). PubMedPubMed Central Google Scholar
Reinhardt, J. A. et al. De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae. Genome Res.19, 294–305 (2009). CASPubMedPubMed Central Google Scholar
Schloss, J. A. How to get genomes at one ten-thousandth the cost. Nature Biotech.26, 1113–1115 (2008). CAS Google Scholar
Wang, L. & Weinshilboum, R. M. Pharmacogenomics: candidate gene identification, functional validation and mechanisms. Hum. Mol. Genet.17, R174–R179 (2008). CASPubMedPubMed Central Google Scholar
Haaland, W. C. et al. A–β– subtype of ketosis-prone diabetes is not predominantly a monogenic diabetic syndrome. Diabetes Care32, 873–877 (2009). CASPubMedPubMed Central Google Scholar
Tewhey, R. et al. Microdroplet-based PCR enrichment for large-scale targeted sequencing. Nature Biotech.27, 1025–1031 (2009). CAS Google Scholar
Singh-Gasson, S. et al. Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array. Nature Biotech.17, 974–978 (1999). CAS Google Scholar
Albert, T. J. et al. Direct selection of human genomic loci by microarray hybridization. Nature Methods4, 903–905 (2007). CASPubMed Google Scholar
Hodges, E. et al. Genome-wide in situ exon capture for selective resequencing. Nature Genet.39, 1522–1527 (2007). CASPubMed Google Scholar
Okou, D. T. et al. Microarray-based genomic selection for high-throughput resequencing. Nature Methods4, 907–909 (2007). CASPubMed Google Scholar
Porreca, G. J. et al. Multiplex amplification of large sets of human exons. Nature Methods4, 931–936 (2007). CASPubMed Google Scholar
Krishnakumar, S. et al. A comprehensive assay for targeted multiplex amplification of human DNA sequences. Proc. Natl Acad. Sci. USA105, 9296–9301 (2008). CASPubMedPubMed Central Google Scholar
Turner, E. H., Lee, C., Ng, S. B., Nickerson, D. A. & Shendure, J. Massively parallel exon capture and library-free resequencing across 16 genomes. Nature Methods6, 315–316 (2009). CASPubMedPubMed Central Google Scholar
Gnirke, A. et al. Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nature Biotech.27, 182–189 (2009). CAS Google Scholar
Olson, M. Enrichment of super-sized resequencing targets from the human genome. Nature Methods4, 891–892 (2007). CASPubMed Google Scholar
Garber, K. Fixing the front end. Nature Biotech.26, 1101–1104 (2008). CAS Google Scholar
Petrosino, J. F., Highlander, S., Luna, R. A., Gibbs, R. A. & Versalovic, J. Metagenomic pyrosequencing and microbial identification. Clin. Chem.55, 856–866 (2009). These authors describe the current state of metagenomics research and highlight the use of the Roche/454 platform for microbial identification through16S ribosomal DNA phylogenetic analysis; other NGS platforms may be better suited for gene discovery efforts (seeTable 2). CASPubMedPubMed Central Google Scholar
Lipson, D. et al. Quantification of the yeast transcriptome by single-molecule sequencing. Nature Biotech.27, 652–658 (2009). CAS Google Scholar
Park, P. J. ChIP–seq: advantages and challenges of a maturing technology. Nature Rev. Genet.10, 669–680 (2009). The article provides a comprehensive review of recent technological advances and challenges in genome-wide profiling of DNA-binding proteins, histone modifications and nucleosomes using NGS technologies (ChIP–seq). CASPubMed Google Scholar
Wheeler, D. A. et al. The complete genome of an individual by massively parallel DNA sequencing. Nature452, 872–876 (2008). CASPubMed Google Scholar
Iafrate, A. J. et al. Detection of large-scale variation in the human genome. Nature Genet.36, 949–951 (2004). CASPubMed Google Scholar
Sebat, J. et al. Large-scale copy number polymorphism in the human genome. Science305, 525–528 (2004). CASPubMed Google Scholar
Tuzun, E. et al. Fine-scale structural variation of the human genome. Nature Genet.37, 727–732 (2005). CASPubMed Google Scholar
Stranger, B. E. et al. Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science315, 848–853 (2007). CASPubMedPubMed Central Google Scholar
Ahn, S. M. et al. The first Korean genome sequence and analysis: full genome sequencing for a socio-ethnic group. Genome Res.19, 1622–1629 (2009). CASPubMedPubMed Central Google Scholar
McKernan, K. J. et al. Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Res.19, 1527–1541 (2009). CASPubMedPubMed Central Google Scholar
Pushkarev, D., Neff, N. F. & Quake, S. R. Single-molecule sequencing of an individual human genome. Nature Biotech.27, 847–850 (2009). CAS Google Scholar
Mardis, E. R. et al. Recurring mutations found by sequencing an acute myeloid leukemia genome. N. Engl. J. Med.361, 1058–1066 (2009). CASPubMedPubMed Central Google Scholar
Lupski, J. R. et al. Complete genome sequencing identifies recessive alleles in SH3TC2 causing a CMT1 neuropathy. N. Engl. J. Med. (in the press).
Collins, F. S. & Barker, A. D. Mapping the cancer genome. Sci. Am.296, 50–57 (2007). CASPubMed Google Scholar
Drmanac, R. et al. Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Science 5 Nov 2009 (doi:10.1126/science.1181498). PubMed Google Scholar
Sanderson, K. Personal genomes: standard and pores. Nature456, 23–25 (2008). CASPubMed Google Scholar
Green, R. E. et al. Analysis of one million base pairs of Neanderthal DNA. Nature444, 330–336 (2006). CASPubMed Google Scholar
Briggs, A. W. et al. Targeted retrieval and analysis of five Neandertal mtDNA genomes. Science325, 318–321 (2009). CASPubMed Google Scholar
Ponting, C. P., Oliver, P. L. & Reik, W. Evolution and functions of long noncoding RNAs. Cell136, 629–641 (2009). CASPubMed Google Scholar
Barnes, C., Balasubramanian, S., Liu, X., Swerdlow, H. & Milton, J. Labelled nucleotides. US Patent 7,057,026 (2002). Google Scholar
Mitra, R. D., Shendure, J., Olejnik, J., Edyta-Krzymanska-Olejnik & Church, G. M. Fluorescent in situ sequencing on polymerase colonies. Anal. Biochem.320, 55–65 (2003). CASPubMed Google Scholar
Turcatti, G., Romieu, A., Fedurco, M. & Tairi, A.-P. A new class of cleavable fluorescent nucleotides: synthesis and optimization as reversible terminators for DNA sequencing by synthesis. Nucleic Acids Res.36, e25 (2008). PubMedPubMed Central Google Scholar
Yarbrough, L. R., Schlageck, J. G. & Baughman, M. Synthesis and properties of fluorescent nucleotide substrates for DNA-dependent RNA polymerases. J. Biol. Chem.254, 12069–12073 (1979). CASPubMed Google Scholar
Kumar, S. et al. Terminal phosphate labeled nucleotides: synthesis, applications, and linker effect on incorporation by DNA polymerases. Nucleosides Nucleotides Nucleic Acids24, 401–408 (2005). CASPubMed Google Scholar
McKernan, K., Blanchard, A., Kotler, L. & Costa, G. Reagents, methods, and libraries for bead-based sequencing. US Patent Application 11/345,979 (2005). Google Scholar
Macevicz, S. C. DNA sequencing by parallel oligonucleotide extensions. US Patent 5,969,119 (1995). Google Scholar
Mir, K. U., Qi, H., Salata, O. & Scozzafava, G. Sequencing by cyclic ligation and cleavage (CycLiC) directly on a microarray captured template. Nucleic Acids Res.37, e5 (2009). PubMed Google Scholar