The new paradigm of flow cell sequencing.

DNA sequencing is in a period of rapid change, in which capillary sequencing is no longer the technology of choice for most ultra-high-throughput applications. A new generation of instruments that utilize primed synthesis in flow cells to obtain, simultaneously, the sequence of millions of different DNA templates has changed the field. We compare and contrast these new sequencing platforms in terms of stage of development, instrument configuration, template format, sequencing chemistry, throughput capability, operating cost, data handling issues, and error models. While these platforms outperform capillary instruments in terms of bases per day and cost per base, the short length of sequence reads obtained from most instruments and the limited number of samples that can be run simultaneously imposes some practical constraints on sequencing applications. However, recently developed methods for paired-end sequencing and for array-based direct selection of desired templates from complex mixtures extend the utility of these platforms for genome analysis. Given the ever increasing demand for DNA sequence information, we can expect continuous improvement of this new generation of instruments and their eventual replacement by even more powerful technology.

[1]  M. Uhlén,et al.  Solid phase DNA minisequencing by an enzymatic luminometric inorganic pyrophosphate detection assay. , 1993, Analytical biochemistry.

[2]  D. Mccormick.  Sequence the Human Genome , 1986, Bio/Technology.

[3]  Vincent J. Magrini,et al.  Extending assembly of short DNA sequences to handle error , 2007, Bioinform..

[4]  Susan M. Huse,et al.  Accuracy and quality of massively parallel DNA pyrosequencing , 2007, Genome Biology.

[5]  Philip M. Kim,et al.  Paired-End Mapping Reveals Extensive Structural Variation in the Human Genome , 2007, Science.

[6]  M. Ronaghi,et al.  Real-time DNA sequencing using detection of pyrophosphate release. , 1996, Analytical biochemistry.

[7]  B. Pearson,et al.  The Complete Genome Sequence of Campylobacter jejuni Strain 81116 (NCTC11828) , 2007, Journal of bacteriology.

[8]  James R. Knight,et al.  Genome sequencing in microfabricated high-density picolitre reactors , 2005, Nature.

[9]  S. Quake,et al.  Sequence information can be obtained from single DNA molecules , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[10]  Z. Xuan,et al.  Genome-wide in situ exon capture for selective resequencing , 2007, Nature Genetics.

[11]  L. Du,et al.  Unique Features of a Highly Pathogenic Campylobacter jejuni Strain , 2007, Infection and Immunity.

[12]  C. Nusbaum,et al.  Quality scores and SNP detection in sequencing-by-synthesis systems. , 2008, Genome research.

[13]  T. Mikkelsen,et al.  Genome-wide maps of chromatin state in pluripotent and lineage-committed cells , 2007, Nature.

[14]  F. Sanger,et al.  DNA sequencing with chain-terminating inhibitors. , 1977, Proceedings of the National Academy of Sciences of the United States of America.

[15]  E. Southern,et al.  Fidelity of DNA ligation: a novel experimental approach based on the polymerisation of libraries of oligonucleotides. , 1998, Nucleic acids research.

[16]  M. Ronaghi,et al.  A Sequencing Method Based on Real-Time Pyrophosphate , 1998, Science.

[17]  Timothy B. Stockwell,et al.  The Sequence of the Human Genome , 2001, Science.

[18]  W. Gilbert,et al.  The nucleotide sequence of the lac operator. , 1973, Proceedings of the National Academy of Sciences of the United States of America.

[19]  Evan Powell,et al.  Comparative Genomic Analyses of Seventeen Streptococcus pneumoniae Strains: Insights into the Pneumococcal Supragenome , 2007, Journal of bacteriology.

[20]  K. Novak.  The complete genome sequence… , 1998, Nature Medicine.

[21]  Timothy B. Stockwell,et al.  The Diploid Genome Sequence of an Individual Human , 2007, PLoS biology.

[22]  Erika Check Hayden,et al.  Genomics sizes up , 2008, Nature.

[23]  David Hernández,et al.  De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer. , 2008, Genome research.

[24]  Juliane C. Dohm,et al.  SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing. , 2007, Genome research.

[25]  C. T. Farley,et al.  Accurate Multiplex Polony Sequencing of an Evolved Bacterial Genome , 2008 .

[26]  William H. Majoros,et al.  A Comparison of Whole-Genome Shotgun-Derived Mouse Chromosome 16 and the Human Genome , 2002, Science.

[27]  F. Barany,et al.  Cloning, overexpression and nucleotide sequence of a thermostable DNA ligase-encoding gene. , 1991, Gene.

[28]  Hanlee P. Ji,et al.  Multigene amplification and massively parallel sequencing for cancer mutation discovery , 2007, Proceedings of the National Academy of Sciences.

[29]  Ronald W. Davis,et al.  Multiplexed genotyping with sequence-tagged molecular inversion probes , 2003, Nature Biotechnology.

[30]  A. Halpern,et al.  A Sanger/pyrosequencing hybrid approach for the generation of high-quality draft assemblies of marine microbial genomes. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[31]  P. Green,et al.  Base-calling of automated sequencer traces using phred. I. Accuracy assessment. , 1998, Genome research.

[32]  Jay Shendure,et al.  Multiplex amplification of large sets of human exons , 2007, Nature Methods.

[33]  P Green,et al.  Base-calling of automated sequencer traces using phred. II. Error probabilities. , 1998, Genome research.

[34]  E. Birney,et al.  Patterns of somatic mutation in human cancer genomes , 2007, Nature.

[35]  Ewan Birney,et al.  Automated generation of heuristics for biological sequence comparison , 2005, BMC Bioinformatics.

[36]  Ryan D. Hernandez,et al.  Natural selection on protein-coding genes in the human genome , 2005, Nature.

[37]  J. Roach,et al.  Pairwise end sequencing: a unified approach to genomic mapping and sequencing. , 1995, Genomics.

[38]  A. Mortazavi,et al.  Genome-Wide Mapping of in Vivo Protein-DNA Interactions , 2007, Science.

[39]  René L. Warren,et al.  Assembling millions of short DNA sequences using SSAKE , 2006, Bioinform..

[40]  G. Weinstock,et al.  Direct selection of human genomic loci by microarray hybridization , 2007, Nature Methods.

[41]  Jian Wang,et al.  The Genome Sequence of the Malaria Mosquito Anopheles gambiae , 2002, Science.

[42]  Dustin E. Schones,et al.  High-Resolution Profiling of Histone Methylations in the Human Genome , 2007, Cell.

[43]  Allen D. Delaney,et al.  Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing , 2007, Nature Methods.

[44]  Lisa M. D'Souza,et al.  Genome sequence of the Brown Norway rat yields insights into mammalian evolution , 2004, Nature.

[45]  Serafim Batzoglou,et al.  Toward an Individual Approach to Methadone Therapy of Heroin Addicts , 2006, PLoS Medicine.

[46]  C. Nusbaum,et al.  ALLPATHS: de novo assembly of whole-genome shotgun microreads. , 2008, Genome research.

[47]  F. Sanger,et al.  A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. , 1975, Journal of molecular biology.

[48]  Mark Gerstein,et al.  New insights into Acinetobacter baumannii pathogenesis revealed by high-density pyrosequencing and transposon mutagenesis. , 2007, Genes & development.