Emerging DNA sequencing technologies for human genomic medicine.

The completion of draft sequences of the human genome represented a remarkable achievement for automated DNA sequencing based on Sanger technology. However, the future requires substantial leaps in sequencing technology such that whole genome sequencing will become a standard component of biomedical research and patient care. In this review we describe current advances that are in early stages of development, but that point toward technology that will enable the onset of genomic medicine encompasses strategies for preventative medicine and intervention based on complete knowledge of an individual's genome.

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

[2]  G. Church,et al.  Polony Multiplex Analysis of Gene Expression (PMAGE) in Mouse Hypertrophic Cardiomyopathy , 2007, Science.

[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]  J. V. Moran,et al.  Initial sequencing and analysis of the human genome. , 2001, Nature.

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

[7]  Stanley Fields,et al.  Site-Seeing by Sequencing , 2007, Science.

[8]  D. Dressman,et al.  Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations , 2003, Proceedings of the National Academy of Sciences of the United States of America.

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

[10]  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.

[11]  Peng Wang,et al.  Regulation of Cdx2 expression by promoter methylation, and effects of Cdx2 transfection on morphology and gene expression of human esophageal epithelial cells. , 2006, Carcinogenesis.

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

[13]  Jay Shendure,et al.  Fluorescent in situ sequencing on polymerase colonies. , 2003, Analytical biochemistry.

[14]  Richard A Mathies,et al.  Microfabricated bioprocessor for integrated nanoliter-scale Sanger DNA sequencing. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[15]  J. Gillespie,et al.  Identification of a unique epigenetic sub‐microenvironment in prostate cancer , 2007, The Journal of pathology.

[16]  Neil Hall,et al.  Advanced sequencing technologies and their wider impact in microbiology , 2007, Journal of Experimental Biology.

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

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

[19]  Le Kang,et al.  LocustDB: a relational database for the transcriptome and biology of the migratory locust (Locusta migratoria) , 2006, BMC Genomics.

[20]  K. Hopkins,et al.  Rapid detection of gyrA and parC mutations in quinolone-resistant Salmonella enterica using Pyrosequencing technology. , 2007, Journal of microbiological methods.

[21]  G. Church,et al.  Quantitative monitoring by polymerase colony assay of known mutations resistant to ABL kinase inhibitors , 2008, Oncogene.

[22]  J. Hoheisel,et al.  Monitoring methylation changes in cancer. , 2007, Advances in biochemical engineering/biotechnology.

[23]  Y. Goekoop-Ruiterman,et al.  Exploratory analysis of four polymorphisms in human GGH and FPGS genes and their effect in methotrexate-treated rheumatoid arthritis patients. , 2007, Pharmacogenomics.

[24]  I. Gut,et al.  Expressional and Epigenetic Alterations of Placental Serine Protease Inhibitors: SERPINA3 Is a Potential Marker of Preeclampsia , 2007, Hypertension.

[25]  Lloyd M. Smith,et al.  Fluorescence detection in automated DNA sequence analysis , 1986, Nature.

[26]  C. Kai,et al.  CAGE: cap analysis of gene expression , 2006, Nature Methods.

[27]  J. M. Prober,et al.  A system for rapid DNA sequencing with fluorescent chain-terminating dideoxynucleotides. , 1987, Science.

[28]  Michael Q. Zhang,et al.  Using quality scores and longer reads improves accuracy of Solexa read mapping , 2008, BMC Bioinformatics.

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

[30]  Steven J. M. Jones,et al.  BMC Genomics BioMed Central Methodology article , 2006 .

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

[32]  M. Hudson,et al.  Global repeat discovery and estimation of genomic copy number in a large, complex genome using a high-throughput 454 sequence survey , 2007, BMC Genomics.

[33]  D. Deamer,et al.  Nanopores and nucleic acids: prospects for ultrarapid sequencing. , 2000, Trends in biotechnology.

[34]  M Ronaghi,et al.  Analyses of secondary structures in DNA by pyrosequencing. , 1999, Analytical biochemistry.

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

[36]  L. Hou,et al.  Changes in DNA methylation patterns in subjects exposed to low-dose benzene. , 2007, Cancer research.

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

[38]  W. Lichtenegger,et al.  Polymorphism of IL-1α, IL-1β and IL-10 in patients with advanced ovarian cancer: Results of a prospective study with 147 patients , 2007 .

[39]  J. Barnwell,et al.  Pyrosequencing, a High-Throughput Method for Detecting Single Nucleotide Polymorphisms in the Dihydrofolate Reductase and Dihydropteroate Synthetase Genes of Plasmodium falciparum , 2006, Journal of Clinical Microbiology.

[40]  A. Kerlavage,et al.  Complementary DNA sequencing: expressed sequence tags and human genome project , 1991, Science.

[41]  C. Heiner,et al.  Rapid and reliable fluorescent cycle sequencing of double-stranded templates. , 1992, DNA sequence : the journal of DNA sequencing and mapping.

[42]  B. Evengård,et al.  Rapid genotyping of Toxoplasma gondii by pyrosequencing. , 2007, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

[43]  C. Heiner,et al.  New energy transfer dyes for DNA sequencing. , 1997, Nucleic acids research.

[44]  A B Chetverin,et al.  Cloning of RNA molecules in vitro. , 1993, Nucleic acids research.

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

[46]  Jay Shendure,et al.  Long-range polony haplotyping of individual human chromosome molecules , 2006, Nature Genetics.

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

[48]  Eugene W. Myers,et al.  A whole-genome assembly of Drosophila. , 2000, Science.

[49]  Jun Yao,et al.  SAGE and related approaches for cancer target identification. , 2006, Drug discovery today.

[50]  D. Bentley,et al.  Whole-genome re-sequencing. , 2006, Current opinion in genetics & development.

[51]  M. Ronaghi,et al.  PCR-introduced loop structure as primer in DNA sequencing. , 1998, BioTechniques.

[52]  Zhaohui S. Qin,et al.  A second generation human haplotype map of over 3.1 million SNPs , 2007, Nature.

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

[54]  D. Barker,et al.  Implementation of a capillary array electrophoresis instrument. , 1996, Journal of capillary electrophoresis.

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

[56]  Thomas LaFramboise,et al.  Sensitive mutation detection in heterogeneous cancer specimens by massively parallel picoliter reactor sequencing , 2006, Nature Medicine.

[57]  R A Mathies,et al.  Fluorescence energy transfer dye-labeled primers for DNA sequencing and analysis. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[58]  B. Haas,et al.  Sequencing Medicago truncatula expressed sequenced tags using 454 Life Sciences technology , 2006, BMC Genomics.

[59]  Stanley Fields Molecular biology. Site-seeing by sequencing. , 2007, Science.

[60]  E. D. Hyman A new method of sequencing DNA. , 1988, Analytical biochemistry.

[61]  W. Gilbert,et al.  A new method for sequencing DNA. , 1977, Proceedings of the National Academy of Sciences of the United States of America.

[62]  A. Rich,et al.  The rise of single-molecule DNA biochemistry. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[63]  Kenta Nakai,et al.  DBTSS: database of transcription start sites, progress report 2008 , 2007, Nucleic Acids Res..

[64]  Christoph Heller,et al.  A fully automated multicapillary electrophoresis device for DNA analysis , 1999 .

[65]  G. Heinze,et al.  Vascular Endothelial Growth Factor Gene Polymorphisms Are Associated with Prognosis in Ovarian Cancer , 2007, Clinical Cancer Research.

[66]  J. Lupski,et al.  The complete genome of an individual by massively parallel DNA sequencing , 2008, Nature.

[67]  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.

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

[69]  D. Barker,et al.  DNA sequencing by capillary electrophoresis with a hydroxyethylcellulose sieving buffer. , 1996, Applied and theoretical electrophoresis : the official journal of the International Electrophoresis Society.

[70]  S. Turner,et al.  Zero-Mode Waveguides for Single-Molecule Analysis at High Concentrations , 2003, Science.

[71]  Harald Seitz,et al.  Analytics of protein-DNA interactions , 2006 .